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A

a - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
a - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
a - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
a - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
a - Variable in class org.jmol.dssx.Bridge
 
a - Variable in class org.jmol.jvxl.readers.MapFileReader
 
a - Variable in class org.jmol.minimize.forcefield.Calculation
 
a - Variable in class org.jmol.render.SticksRenderer
 
a - Variable in class org.jmol.util.SimpleUnitCell
 
A0 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
a1 - Variable in class org.jmol.g3d.HermiteRenderer
 
a1 - Variable in class org.jmol.util.Modulation
 
a2 - Variable in class org.jmol.g3d.HermiteRenderer
 
a2 - Variable in class org.jmol.util.Modulation
 
A4_BNDK - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
A4_CHRG - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
A4_SB - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
A4_SBDEF - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
A4_VDW - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
a_ - Variable in class org.jmol.util.SimpleUnitCell
 
aa - Variable in class org.jmol.renderbio.BioShapeRenderer
 
aaPlus - Static variable in class org.jmol.modelsetbio.Resolver
 
aaRet - Variable in class org.jmol.modelset.AtomCollection
 
aaSp2 - Static variable in class org.jmol.modelsetbio.Resolver
 
aaStep - Variable in class org.jmol.thread.MoveToThread
 
aaStepCenter - Variable in class org.jmol.navigate.Navigator
 
aaStepCenter - Variable in class org.jmol.thread.MoveToThread
 
aaStepNavCenter - Variable in class org.jmol.thread.MoveToThread
 
aaT - Variable in class org.jmol.render.MeasuresRenderer
 
aaTest1 - Variable in class org.jmol.viewer.TransformManager
 
aatoken - Variable in class org.jmol.script.ScriptContext
 
aatoken - Variable in class org.jmol.script.ScriptEval
 
aatoken - Variable in class org.jmol.script.ScriptFunction
 
aatokenCompiled - Variable in class org.jmol.script.ScriptCompiler
 
aaTotal - Variable in class org.jmol.thread.MoveToThread
 
ab - Variable in class org.jmol.popup.AwtSwingComponent
 
abc - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
ABI_IJ - Static variable in class org.jmol.minimize.forcefield.ForceField
 
ABI_JK - Static variable in class org.jmol.minimize.forcefield.ForceField
 
abinitContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
AbinitReader - Class in org.jmol.adapter.readers.xtal
 
AbinitReader() - Constructor for class org.jmol.adapter.readers.xtal.AbinitReader
 
abNo - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
aboutAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
AboutAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
 
AboutDialog - Class in org.openscience.jmol.app.jmolpanel
 
AboutDialog(JFrame, JmolViewer) - Constructor for class org.openscience.jmol.app.jmolpanel.AboutDialog
 
aboutURL - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
abs - Static variable in class org.jmol.script.T
 
absolute - Static variable in class org.jmol.script.T
 
ABSOLUTE_MIN_MESH_SIZE - Static variable in class org.jmol.renderbio.BioShapeRenderer
 
absoluteButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
abYes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
ac - Variable in class org.jmol.adapter.readers.cif.CifReader
 
ac - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
ac - Variable in class org.jmol.adapter.readers.more.MdTopReader
 
ac - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
ac - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
ac - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
ac - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
ac - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
ac - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
ac - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
 
ac - Variable in class org.jmol.adapter.readers.simple.AmpacReader
 
ac - Variable in class org.jmol.adapter.readers.simple.CubeReader
 
ac - Variable in class org.jmol.adapter.readers.simple.InputReader
 
ac - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
ac - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
ac - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
ac - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
ac - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
ac - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
ac - Variable in class org.jmol.adapter.smarter.AtomIterator
 
ac - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
ac - Variable in class org.jmol.atomdata.AtomData
 
ac - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
ac - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
ac - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
ac - Variable in class org.jmol.minimize.forcefield.Calculations
 
ac - Variable in class org.jmol.minimize.Minimizer
 
ac - Variable in class org.jmol.modelset.AtomCollection
 
ac - Variable in class org.jmol.modelset.Model
 
ac - Variable in class org.jmol.popup.JmolGenericPopup
 
ac - Variable in class org.jmol.shape.AtomShape
 
ac - Variable in class org.jmol.shapesurface.Contact
 
ac - Variable in class org.jmol.smiles.SmilesGenerator
 
ac - Variable in class org.jmol.util.JmolMolecule
 
ac0 - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
accept(File, String) - Method in class org.jmol.console.JmolConsole.FileChecker
 
accept(File) - Method in class org.jmol.dialog.Dialog.TypeFilter
 
access - Variable in class org.jmol.viewer.Viewer
 
ACCESS() - Constructor for enum org.jmol.viewer.Viewer.ACCESS
 
acdAssignments - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
acdMolFile - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
acm - Variable in class org.jmol.viewer.Viewer
 
acos - Static variable in class org.jmol.script.T
 
acr - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
action - Variable in class org.jmol.viewer.Gesture
 
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
 
action - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
 
ACTION_assignNew - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_center - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_clickFrank - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_connectAtoms - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_count - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_deleteAtom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_deleteBond - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_depth - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragAtom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragDrawObject - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragDrawPoint - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragLabel - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragMinimize - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragMinimizeMolecule - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragSelected - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_dragZ - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_multiTouchSimulation - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_navTranslate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickAtom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickIsosurface - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickLabel - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickMeasure - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickNavigate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_pickPoint - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_popupMenu - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_reset - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateBranch - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateSelected - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateZ - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_rotateZorZoom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_select - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectAndDrag - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectAndNot - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectNone - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectOr - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectToggle - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_selectToggleExtended - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_setMeasure - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_slab - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_slabAndDepth - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_slideZoom - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_spinDrawObjectCCW - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_spinDrawObjectCW - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_stopMotion - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_swipe - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_translate - Static variable in class org.jmol.viewer.ActionManager
 
ACTION_wheelZoom - Static variable in class org.jmol.viewer.ActionManager
 
ActionChangedListener(AbstractButton) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
 
actionInfo - Static variable in class org.jmol.viewer.ActionManager
 
actionManager - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
actionManager - Variable in class org.jmol.thread.HoverWatcherThread
 
ActionManager - Class in org.jmol.viewer
 
ActionManager() - Constructor for class org.jmol.viewer.ActionManager
 
ActionManagerMT - Class in org.jmol.multitouch
 
ActionManagerMT() - Constructor for class org.jmol.multitouch.ActionManagerMT
 
actionNames - Static variable in class org.jmol.viewer.ActionManager
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.AppletConsole
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.JmolConsole
 
actionPerformed(ActionEvent) - Method in class org.jmol.console.ScriptEditor
 
actionPerformed(ActionEvent) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
actionPerformed(ActionEvent) - Method in class org.jmol.popup.JSSwingPopupHelper
 
actionPerformed(ActionEvent) - Method in class org.openscience.chimetojmol.ChimePanel
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AboutAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NBOAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.Test
 
actionPerformed(ActionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
actionRotateBond(int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
actionStates - Variable in class org.jmol.viewer.Viewer
 
actionStatesRedo - Variable in class org.jmol.viewer.Viewer
 
activate() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
active - Variable in class org.jmol.dialog.FilePreview
 
active_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
actualID - Variable in class org.jmol.shapesurface.Isosurface
 
adapter - Variable in class org.jmol.multitouch.ActionManagerMT
 
adapterModelCount - Variable in class org.jmol.modelset.ModelLoader
 
adapterTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
 
add(Container, JmolAbstractButton) - Method in class org.jmol.console.AppletConsole
 
add(Map<String, Object>, NucleicMonomer, NucleicMonomer) - Static method in class org.jmol.modelsetbio.BasePair
 
add(SC) - Method in class org.jmol.popup.AwtSwingComponent
 
add - Static variable in class org.jmol.script.T
 
add(int, int, int, long) - Method in class org.jmol.viewer.Gesture
 
ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JC
 
addActionListener(Object) - Method in class org.jmol.popup.AwtSwingComponent
 
addAllLists(Lst<SV>, Lst<SV>) - Method in class org.jmol.scriptext.MathExt
 
addAllTriangles() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
addArray(Map<String, Object>, String, float[]) - Method in class org.jmol.dssx.AnnotationParser
 
addAssembly() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
addAtom(Lst<Object>, int, int, Lst<Object>, Lst<Object>, BS, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
addAtom(Atom) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
addAtom() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
addAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtom(boolean, BS, int, Object, int, String, int, float, Lst<Object>, float, float, P3, boolean, int, int, String, V3, char, float) - Method in class org.jmol.modelset.ModelLoader
 
addAtom(int, Group, int, String, String, int, int, int, P3, float, V3, int, float, float, float, Lst<Object>, boolean, byte, BS) - Method in class org.jmol.modelset.ModelSet
 
addAtom() - Method in class org.jmol.smiles.SmilesSearch
 
addAtomModulation(String, char, char, double[], String, double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
Create a list of modulations for each atom type (atom name).
addAtomOr() - Method in class org.jmol.smiles.SmilesAtom
 
addAtomProp(int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
addAtoms(BS) - Method in interface org.jmol.api.AtomIndexIterator
 
addAtoms(BS) - Method in class org.jmol.modelset.AtomIteratorWithinModel
turns this into a SPHERICAL iterator for "within Distance" measures
addAtoms(int) - Method in class org.jmol.modelset.Group
 
addAtomWithMappedName(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtomWithMappedSerialNumber(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addAtomXYZSymName(String[], int, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addAttr() - Method in class org.jmol.export._MayaExporter
 
addAttrib(Lst<String[]>, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
addAxis(int, V3) - Method in class org.jmol.symmetry.PointGroup
 
addBasePair(BasePair) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
addBinding(String, Object) - Method in class org.jmol.viewer.binding.Binding
 
addBioMoleculeOperation(M4, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
addBioMoleculeOperation(M4, boolean) - Method in class org.jmol.symmetry.Symmetry
 
addBioPolymer(BioPolymer) - Method in class org.jmol.modelsetbio.BioModel
 
addBond(Bond) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addBond(MinBond, int) - Method in class org.jmol.minimize.MinAtom
 
addBond(SmilesBond) - Method in class org.jmol.smiles.SmilesAtom
Add a bond to the atom.
addBondOr() - Method in class org.jmol.smiles.SmilesBond
 
addBonds(Lst<Bond>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
addBonds(String, int) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
addBondToAtom(Atom, Bond) - Method in class org.jmol.modelset.BondCollection
 
addBoundBoxPoint(T3) - Method in class org.jmol.util.BoxInfo
 
addBracketedBioName(SB, Node, String) - Method in class org.jmol.smiles.SmilesGenerator
 
addBridge(Bridge, Map<int[][], Boolean>) - Method in class org.jmol.dssx.Bridge
 
addBs(SB, String, BS) - Method in class org.jmol.viewer.StateCreator
 
addBundle(Viewer, String, String) - Method in class org.jmol.i18n.GT
 
addBundles(Viewer, String, String, String, String) - Method in class org.jmol.i18n.GT
 
addButton(JmolAbstractButton, String) - Method in class org.jmol.console.GenericConsole
 
addButton(JPanel, String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
addCellType(String, String, boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
 
addCGO(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
addColix(short, boolean) - Method in class org.jmol.export._IdtfExporter
 
addColix(int) - Method in class org.jmol.shapecgo.CGOMesh
 
addColor(Integer, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
 
addColors(Lst<Object>, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Add new colors from the main "colors" map object.
addColorToMap(Map<String, BS>, String, BS) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
adds a set of specifically-colored vertices to the map, ensuring that no vertex is in two maps.
addCommand(String) - Method in class org.jmol.util.CommandHistory
Adds any number of lines to the command history
addCommand(String) - Method in class org.jmol.viewer.Viewer
Adds one or more commands to the command history
addCommandLine(String) - Method in class org.jmol.util.CommandHistory
Adds a single line to the bottom of the list, resets list position.
addCompare(T, T) - Method in class org.jmol.script.ScriptTokenParser
 
addConnect() - Method in class org.jmol.export._MayaExporter
 
addConnection(int[]) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
addConsoleListener(Object) - Method in interface org.jmol.api.JmolAbstractButton
 
addConsoleListener(Object) - Method in class org.jmol.console.JmolButton
 
addConsoleListener(Object) - Method in class org.jmol.console.JmolLabel
 
addConsoleListener(Object) - Method in class org.jmol.console.JmolToggleButton
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBox
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJCheckBoxMenuItem
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenu
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJMenuItem
 
addConsoleListener(Object) - Method in class org.jmol.console.KeyJRadioButtonMenuItem
 
addConstraint(Object[]) - Method in class org.jmol.minimize.Minimizer
 
addContextVariable(Map<String, SV>, String) - Static method in class org.jmol.script.ScriptCompiler
 
addContourPoints(Lst<Object>, BS, int, SB, T3[], float[], int, int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
addContourVertex(P3, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
addCount - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
addData10F() - Method in class org.jmol.quantum.MOCalculation
 
addData5D() - Method in class org.jmol.quantum.MOCalculation
 
addData6D() - Method in class org.jmol.quantum.MOCalculation
 
addData7F() - Method in class org.jmol.quantum.MOCalculation
 
addDataP() - Method in class org.jmol.quantum.MOCalculation
 
addDataS() - Method in class org.jmol.quantum.MOCalculation
 
addDataSP() - Method in class org.jmol.quantum.MOCalculation
 
addDirectory(String, String) - Static method in class org.jmol.viewer.FileManager
 
addDisplayedBackbone(int, boolean) - Method in class org.jmol.modelset.Atom
 
addDisplayedBond(int, boolean) - Method in class org.jmol.modelset.Atom
 
addedData - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addedDataKey - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addEdge(int, int, int) - Method in class org.jmol.util.MeshCapper
Input method from MeshSlicer.
addEdgeData(float) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
addFace(IsoSolventReader.Face) - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
addFile(String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
Adds this file to the history.
addFloat(Map<String, Object>, String, int) - Method in class org.jmol.dssx.AnnotationParser
 
addForce(V3d, int, double) - Method in class org.jmol.minimize.forcefield.Calculations
 
addForces(Calculation, int) - Method in class org.jmol.minimize.forcefield.Calculations
 
addFunction(JmolScriptFunction) - Method in class org.jmol.viewer.Viewer
 
addFunctions(SB, Map<String, JmolScriptFunction>, String, boolean, boolean) - Method in class org.jmol.viewer.StateCreator
 
addGroup(Lst<Object>, String, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Create a hierarchical list of named groups as generally seen on the PyMOL app's right-hand object menu.
addGroup(Chain, Group) - Method in class org.jmol.modelset.ModelLoader
 
addGroup3Name(String) - Static method in class org.jmol.modelsetbio.Resolver
These can overrun 3 characters; that is not significant.
addGroupAtoms(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
addHbond(Monomer, Monomer, int, int, Map<String, Boolean>) - Method in class org.jmol.dssx.DSSP
 
addHBond(Atom, Atom, int, float) - Method in class org.jmol.modelset.BondCollection
 
addHelpItems(JMenu, String, String) - Method in class org.jmol.console.AppletConsole
 
addHelpMenuBar(JMenuBar) - Method in class org.jmol.console.AppletConsole
 
addHelpMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addHetero(String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
addHistoryWindowInfo(String, Component, Point) - Method in interface org.jmol.api.JmolAppAPI
 
addHistoryWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.JmolApp
 
addHydrogenBond(Lst<Bond>, Atom, Atom) - Static method in class org.jmol.modelsetbio.NucleicPolymer
 
addHydrogens - Variable in class org.jmol.jvxl.readers.Parameters
 
addHydrogens(Lst<Atom>, P3[]) - Method in class org.jmol.modelset.ModelSet
these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEW
addHydrogens() - Method in class org.jmol.modelsetbio.Resolver
 
addhydrogens - Static variable in class org.jmol.script.T
 
addHydrogens(BS, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
addHydrogensInline(BS, Lst<Atom>, P3[]) - Method in interface org.jmol.api.JmolScriptManager
 
addHydrogensInline(BS, Lst<Atom>, P3[]) - Method in class org.jmol.script.ScriptManager
 
addHydrogensInline(BS, Lst<Atom>, P3[]) - Method in class org.jmol.viewer.Viewer
 
addImplicitHydrogenAtoms(JmolAdapter, int, int) - Method in interface org.jmol.api.JmolBioResolver
 
addImplicitHydrogenAtoms(JmolAdapter, int, int) - Method in class org.jmol.modelsetbio.Resolver
 
addIncompleteFaces(BS) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
addIndex - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
addInfo(SB, String[], String, String) - Method in class org.jmol.viewer.binding.Binding
 
addInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
addIntersectionVertex(T3, float, int, int, Map<String, Integer>, int, int) - Method in class org.jmol.util.MeshSlicer
 
addIsosurface(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
addItemListener(Object) - Method in class org.jmol.popup.AwtSwingComponent
 
addItems(String[][]) - Method in class org.jmol.popup.PopupResource
 
addItemText(SB, char, int, String, String, String, String) - Static method in class org.jmol.popup.GenericSwingPopup
 
addJmolFiles(String) - Method in class org.openscience.chimetojmol.ChimePanel
 
addJmolObject(int, BS, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
addJmolScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addKeyBuffer(char) - Method in class org.jmol.awt.Mouse
 
addKeyBuffer(char) - Method in class org.jmol.awtjs2d.Mouse
 
addKeys(SB, String, Map<String, SV>, String, boolean, boolean, int, boolean) - Static method in class org.jmol.script.SV
 
addLabel(int, int, int, Lst<Object>, String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
addLadder(Map<int[][], Boolean>) - Method in class org.jmol.dssx.Bridge
 
addLatticeVector(Lst<float[]>, String) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
addLatticeVector(Lst<float[]>, String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
addLatticeVectors() - Method in class org.jmol.adapter.readers.cif.CifReader
 
addLatticeVectors(Lst<float[]>) - Method in interface org.jmol.api.SymmetryInterface
 
addLatticeVectors(Lst<float[]>) - Method in class org.jmol.symmetry.SpaceGroup
 
addLatticeVectors(Lst<float[]>) - Method in class org.jmol.symmetry.Symmetry
 
addList(PyMOLGroup) - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
addListener(JmolSelectionListener) - Method in class org.jmol.viewer.SelectionManager
 
addMacrosMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addMeasurements(MeasurementData[], int, Lst<Object>, BS, int, Lst<Object>, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
addMenuItem(SC, String) - Method in class org.jmol.popup.GenericSwingPopup
 
addMenuItems(String, String, SC, PopupResource) - Method in class org.jmol.popup.GenericSwingPopup
 
addMesh(int, Lst<Object>, String, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
addMesh(String, MeshSurface, M4, M4, short, int[], BS) - Method in class org.jmol.export._ObjExporter
Adds a new mesh using the given data (faces, vertices, and normals) and colix after transforming it via the given affine transform matrix.
addMeshData(String, int, int, int, int, SB, SB, SB, SB, SB, SB) - Method in class org.jmol.export._IdtfExporter
 
addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Contact
 
addMeshInfo(IsosurfaceMesh, Map<String, Object>) - Method in class org.jmol.shapesurface.Isosurface
 
addMessage(String) - Method in class org.jmol.dssx.AnnotationParser
 
addMo(String, int, float, float) - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
addMod(String, String, double[]) - Method in class org.jmol.adapter.readers.cif.MSCifRdr
 
addMOData(int, Lst<String>[], Map<String, Object>[]) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
addModulation(Map<String, double[]>, String, double[], int) - Method in class org.jmol.adapter.readers.cif.MSRdr
Types include O (occupation) D (displacement) U (anisotropy) M (magnetic moment) _coefs_ indicates this is a wave description
addModulation(Map<String, double[]>, String, double[], int) - Method in interface org.jmol.adapter.smarter.MSInterface
 
addMolAtom(int, int, String, int, float, float, float) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
addMolBond(String, String, int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
addMolecule(JmolMolecule[], int, Node[], int, BS, int, int, BS) - Static method in class org.jmol.util.JmolMolecule
 
addMolFile(SB, BS, BS, boolean, boolean, Quat) - Method in class org.jmol.viewer.PropertyManager
 
addMolSS(String, STR) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Secondary structure definition.
addMolStructures() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
addMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
Note that this method does not check to see that there are no overlapping protein structures.
addMore() - Method in class org.jmol.adapter.readers.cif.CifReader
 
addMouseListener(Object) - Method in class org.jmol.popup.AwtSwingComponent
 
addName(String) - Method in class org.jmol.script.ContextToken
 
addNeighboringVertexes(short[], short, short) - Static method in class org.jmol.util.Geodesic
 
addNested(String) - Method in class org.jmol.smiles.SmilesSearch
 
addNewAtom() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBond(int, int, int) - Method in class org.jmol.adapter.readers.cif.CifReader
add the bond and mark it for molecular processing
addNewBond(String, String, int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
addNewBondFromNames(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBondWithOrder(int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNewBondWithOrderA(Atom, Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addNextToken() - Method in class org.jmol.script.ScriptTokenParser
 
addNextTokenIf(int) - Method in class org.jmol.script.ScriptTokenParser
 
addNormal(V3, V3, float) - Static method in class org.jmol.smiles.SmilesAromatic
 
addNormalMenuBar(JMenuBar) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
addNormix(int) - Method in class org.jmol.shapecgo.CGOMesh
 
addNumber(int, int, Object) - Method in class org.jmol.script.ScriptCompiler
 
addObject(JmolObject) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
addOp(String, Matrix, Matrix, Matrix) - Method in interface org.jmol.api.SymmetryInterface
 
addOp(T) - Method in class org.jmol.script.ScriptMathProcessor
addOp The primary driver of the Reverse Polish Notation evaluation engine.
addOp(SymmetryOperation, String, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
addOp(String, Matrix, Matrix, Matrix) - Method in class org.jmol.symmetry.Symmetry
 
addOpAllowMath(T, boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
addOperation(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
addPeakData(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
addPeakData(String) - Method in interface org.jmol.api.JmolJDXMOLReader
 
addPixel(int, int, int) - Method in class org.jmol.g3d.Pixelator
 
addPixel(int, int, int) - Method in class org.jmol.g3d.PixelatorScreened
 
addPixel(int, int, int) - Method in class org.jmol.g3d.PixelatorShaded
 
addPixel(int, int, int) - Method in class org.jmol.g3d.PixelatorT
 
addPngFileBytes(String, byte[], int, Hashtable<Object, String>, boolean, String, int, Lst<Object>) - Method in class org.jmol.viewer.OutputManager
 
addPoint(int, Point3fi, boolean) - Method in class org.jmol.modelset.MeasurementPending
 
addPoint(T3, int) - Method in class org.jmol.shapespecial.Draw
 
addPoint(int) - Method in class org.jmol.smiles.SmilesMeasure
 
addPoint(T3, T3, T3, float) - Static method in class org.jmol.util.BoxInfo
 
addPoint(int, int) - Method in class org.jmol.util.MeshCapper
The MeshSlicer class manages all introduction of vertices; we must pass on to it the subset of vertices from the original Jmol isosurface being capped.
addPointXYZ(float, float, float, P3, P3, float) - Static method in class org.jmol.util.BoxInfo
 
addPolygon(int[], BS) - Method in class org.jmol.util.MeshSurface
 
addPolygonC(int[], int, BS, boolean) - Method in class org.jmol.util.MeshSurface
 
addPolygonV3(int, int, int, int, int, int, BS) - Method in class org.jmol.util.MeshSurface
 
addPrimitive() - Method in class org.jmol.smiles.SmilesAtom
 
addPrimitive() - Method in class org.jmol.smiles.SmilesBond
 
addPrimitiveLatticeVector(int, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addProcess(String, ScriptContext) - Method in interface org.jmol.api.JmolParallelProcessor
 
addProcess(Lst<T[]>, int, int) - Method in class org.jmol.script.ScriptEval
 
addProcess(String, ScriptContext) - Method in class org.jmol.script.ScriptParallelProcessor
 
addProperties(Properties) - Method in class org.openscience.jmol.app.HistoryFile
Adds the given properties to the history.
addProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
Adds the given property to the history.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
 
addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
 
addRenderer(int) - Method in interface org.jmol.api.JmolRendererInterface
 
addRenderer(int) - Method in class org.jmol.export.Export3D
 
addRenderer(int) - Method in class org.jmol.g3d.Graphics3D
allows core JavaScript loading to not involve these classes
addRenderer(int) - Method in class org.jmol.util.GData
 
addRequiredFile(String) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
addRequiredFile(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
addRequiredFile(String) - Method in class org.jmol.shapesurface.Isosurface
 
addResidueHydrogenBond(Atom, Atom, int, int, float, Lst<Bond>) - Method in class org.jmol.modelsetbio.AminoPolymer
 
ADDRESS_BITS_PER_WORD - Static variable in class org.jmol.java.BS
 
addRotatedTensor(Atom, Tensor, int, boolean, SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
addScr(String, String, String, boolean) - Method in class org.jmol.script.ScriptManager
 
addScript(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
addScript(String, boolean) - Method in class org.jmol.script.ScriptManager
 
addSecondaryStructure(STR, String, int, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
 
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
 
addSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
 
addSetting(int, int, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
addShader(String, short) - Method in class org.jmol.export._IdtfExporter
 
addShapeProperty(Lst<Object[]>, String, Object) - Method in class org.jmol.scriptext.IsoExt
 
addSinCos(int, String, String, boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
Add x, y, and z modulations as [ csin, ccos, 0 ] or, possibly Legendre [ coef, order, 0 ]
addSites(Map<String, Map<String, Object>>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addSiteScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addSlabInfo(Object[]) - Method in class org.jmol.jvxl.readers.Parameters
 
addSlater(int, int, int, int, int, double, float) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
addSlater(SlaterData, int) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
 
addSpaceGroupOperation(String, boolean) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
addSpaceGroupOperation(String, int) - Method in interface org.jmol.api.SymmetryInterface
 
addSpaceGroupOperation(String, int) - Method in class org.jmol.symmetry.Symmetry
 
addStateScript(String, BS, BS, BS, String, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
addStateScript(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
addStereoCheck(int, Node[], int, String) - Method in class org.jmol.smiles.SmilesGenerator
checks a group and either adds a new group to the growing check string or returns null
addString(Atom, int, String, String) - Method in class org.jmol.shape.Labels
 
addStructure(Structure) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addStructure(STR, String, int, int, int, int, int, int, int, int, BS) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addStructureProtected(STR, String, int, int, int, int) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addStructuresFromTags(STR[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
addSubstituteTokenIf(int, T) - Method in class org.jmol.script.ScriptTokenParser
 
addSubsystem(String, Matrix) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
addSubsystem(String, Matrix) - Method in interface org.jmol.adapter.smarter.MSInterface
 
addSymmetry(String, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
addSymmetrySM(String, M4) - Method in class org.jmol.symmetry.SpaceGroup
 
addTensor(Tensor, String, boolean) - Method in class org.jmol.adapter.smarter.Atom
 
addTensor(Tensor, String) - Method in class org.jmol.modelset.AtomCollection
 
addTexture(short, String) - Method in class org.jmol.export._ObjExporter
Adds a texture to the .mtl file if it is a new texture.
addTickInfo(SB, TickInfo, boolean) - Static method in class org.jmol.viewer.StateCreator
 
addTo(T3, float) - Method in interface org.jmol.api.JmolModulationSet
 
addTo(T3, float) - Method in class org.jmol.util.ModulationSet
 
addToBonds(Bond, Bond[]) - Method in class org.jmol.modelset.BondCollection
 
addToken(String, T) - Static method in class org.jmol.script.T
 
addTokenToPostfix(int, Object) - Method in class org.jmol.script.ScriptTokenParser
 
addTokenToPostfixInt(int, int, Object) - Method in class org.jmol.script.ScriptTokenParser
 
addTokenToPostfixToken(T) - Method in class org.jmol.script.ScriptTokenParser
 
addTokenToPrefix(T) - Method in class org.jmol.script.ScriptCompiler
 
addToMeasurement(int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
 
addToMessages(String) - Method in class org.jmol.dssx.AnnotationParser
 
addTriangle(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
addTriangle(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
addTriangle(MeshCapper.CapVertex, MeshCapper.CapVertex, MeshCapper.CapVertex, String) - Method in class org.jmol.util.MeshCapper
Add the triangle and remove v1 from the chain.
addTriangle(int, int, int) - Method in class org.jmol.util.MeshSlicer
from MeshCapper
addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
 
addTriangle(int, int, int, int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
addTriangleCheck(int, int, int, int, int, boolean, int) - Method in class org.jmol.shapesurface.Isosurface
 
addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
 
addTuple(int, P3) - Method in class org.jmol.bspt.Bspf
 
addTuple(P3) - Method in class org.jmol.bspt.Bspt
Iterate through all of your data points, calling addTuple
addTuple(int, P3) - Method in class org.jmol.bspt.Element
 
addTuple(int, P3) - Method in class org.jmol.bspt.Leaf
 
addTuple(int, P3) - Method in class org.jmol.bspt.Node
 
addType(int, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
sets an auxiliaryInfo string to "HNMR 13CNMR" or "IR" or "MS"
addTypeStr(String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
addUnitCellOffset(P3) - Method in class org.jmol.viewer.Viewer
 
addUStr(Atom, String, float) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
addUTens(String, float) - Method in class org.jmol.util.ModulationSet
 
addV(T3, boolean) - Method in class org.jmol.util.MeshSurface
 
addValue(Map<String, Object>, String, String, Object) - Method in class org.jmol.applet.Jmol
 
addValuesSquared(float) - Method in class org.jmol.quantum.MOCalculation
 
addVariable(String, boolean) - Method in class org.jmol.script.ScriptFunction
 
addVC(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
addVCVal(T3, float, boolean) - Method in class org.jmol.util.MeshSurface
 
addVertex(int, int, int, int, float) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
addVertexCopy(T3, float, int, boolean) - Method in interface org.jmol.jvxl.api.VertexDataServer
addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.data.MeshData
 
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
addVertexCopy(T3, float, int, boolean) - Method in class org.jmol.shapesurface.Isosurface
 
addVertexCopy(T3, float, int, boolean, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
addVibrations - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
addVibrationVector(int, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addVibrationVectorWithSymmetry(int, float, float, float, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
addWidget(int) - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
addWindowBorder(String, Point) - Method in class org.openscience.jmol.app.HistoryFile
Adds the window border to the history.
addWindowInfo(String, Component, Point) - Method in class org.openscience.jmol.app.HistoryFile
Adds the window informations to the history.
addWindowListener() - Method in class org.jmol.console.JmolConsole
 
addWindowPosition(String, Point) - Method in class org.openscience.jmol.app.HistoryFile
Adds the window position to the history.
addWindowSize(String, Dimension) - Method in class org.openscience.jmol.app.HistoryFile
Adds the window size to the history.
addWindowVisibility(String, boolean) - Method in class org.openscience.jmol.app.HistoryFile
Adds the window visibility to the history.
addX(SV) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAD(double[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAF(float[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAFF(float[][]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAI(int[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAII(int[][]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAS(String[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXAV(SV[]) - Method in class org.jmol.script.ScriptMathProcessor
 
addXBool(boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
addXBs(BS) - Method in class org.jmol.script.ScriptMathProcessor
 
addXCopy(SV) - Method in class org.jmol.script.ScriptMathProcessor
 
addXFloat(float) - Method in class org.jmol.script.ScriptMathProcessor
 
addXInt(int) - Method in class org.jmol.script.ScriptMathProcessor
 
addXList(Lst<?>) - Method in class org.jmol.script.ScriptMathProcessor
 
addXM3(M3) - Method in class org.jmol.script.ScriptMathProcessor
 
addXM4(M4) - Method in class org.jmol.script.ScriptMathProcessor
 
addXMap(Map<String, ?>) - Method in class org.jmol.script.ScriptMathProcessor
 
addXNum(T) - Method in class org.jmol.script.ScriptMathProcessor
 
addXObj(Object) - Method in class org.jmol.script.ScriptMathProcessor
 
addXPt(P3) - Method in class org.jmol.script.ScriptMathProcessor
 
addXPt4(P4) - Method in class org.jmol.script.ScriptMathProcessor
 
addXStr(String) - Method in class org.jmol.script.ScriptMathProcessor
 
addZoomTranslationNavigationText(SB) - Method in class org.jmol.viewer.TransformManager
 
adfContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
AdfReader - Class in org.jmol.adapter.readers.quantum
TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.
AdfReader() - Constructor for class org.jmol.adapter.readers.quantum.AdfReader
 
AdfReader.SymmetryData - Class in org.jmol.adapter.readers.quantum
 
adjust - Static variable in class org.jmol.script.T
 
adjustAtomArrays(int[], int, int) - Method in class org.jmol.modelset.ModelSet
 
adjustCartoonSeamNormals(int, int) - Method in class org.jmol.renderbio.BioShapeRenderer
Matches normals for adjacent mesh sections to create a seamless overall mesh.
adjustForWindow - Variable in class org.jmol.modelset.Object2d
 
adjustM40Occupancies() - Method in class org.jmol.adapter.readers.xtal.JanaReader
M40 occupancies are divided by the site multiplicity; here we factor that back in.
aDOMNode - Variable in class org.jmol.io.DOMReader
 
ADP_FACTOR - Static variable in class org.jmol.util.Tensor
 
ADP_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
adpmax - Static variable in class org.jmol.script.T
 
adpmin - Static variable in class org.jmol.script.T
 
adpMode - Variable in class org.jmol.atomdata.AtomData
 
after(String, String) - Method in class org.jmol.dssx.AnnotationParser
 
afterMath - Variable in class org.jmol.script.ScriptCompiler
 
afterWhite - Variable in class org.jmol.script.ScriptCompiler
 
AimsReader - Class in org.jmol.adapter.readers.xtal
FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).
AimsReader() - Constructor for class org.jmol.adapter.readers.xtal.AimsReader
 
AlchemyReader - Class in org.jmol.adapter.readers.simple
TRIPOS simple Alchemy reader.
AlchemyReader() - Constructor for class org.jmol.adapter.readers.simple.AlchemyReader
 
align - Variable in class org.jmol.modelset.Object2d
 
align - Static variable in class org.jmol.script.T
 
align1 - Variable in class org.jmol.shapespecial.Polyhedra
 
align2 - Variable in class org.jmol.shapespecial.Polyhedra
 
ALIGN_CENTER - Static variable in class org.jmol.viewer.JC
 
ALIGN_LEFT - Static variable in class org.jmol.viewer.JC
 
ALIGN_NONE - Static variable in class org.jmol.viewer.JC
 
ALIGN_RIGHT - Static variable in class org.jmol.viewer.JC
 
alignLeft - Variable in class org.jmol.modelset.LabelToken
 
alignment_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
alignZX(P3, P3, P3) - Method in class org.jmol.navigate.Navigator
brings pt0-pt1 vector to [0 0 -1], then rotates about [0 0 1] until ptVectorWing is in xz plane
all - Static variable in class org.jmol.script.T
 
ALL_BUTTONS - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
all_states - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
allCarbohydrates - Static variable in class org.jmol.modelsetbio.Resolver
this form is used for counting groups in ModelSet GLX added for 13.1.16
allconnected - Static variable in class org.jmol.script.T
 
allfloat - Static variable in class org.jmol.script.T
 
allFractionalRelative - Variable in class org.jmol.symmetry.UnitCell
 
allFramesCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
allInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
allocateArray(JmolMolecule[], int) - Static method in class org.jmol.util.JmolMolecule
 
allocateBioPolymer(Group[], int, boolean) - Static method in class org.jmol.modelsetbio.Resolver
 
allocateBuffers(int, int, boolean, boolean) - Method in class org.jmol.g3d.Platform3D
 
allocateColix(int, boolean) - Static method in class org.jmol.util.C
 
allocateCubeIterator() - Method in class org.jmol.bspt.Bspt
 
allocateOffscreenImage(int, int) - Method in class org.jmol.g3d.Platform3D
 
allocateRgbImage(int, int, int[], int, boolean) - Static method in class org.jmol.awt.Image
 
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awt.Platform
 
allocateRgbImage(int, int, int[], int, boolean) - Static method in class org.jmol.awtjs.Image
 
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awtjs.Platform
 
allocateRgbImage(int, int, int[], int, boolean, Object) - Static method in class org.jmol.awtjs2d.Image
 
allocateRgbImage(int, int, int[], int, boolean, boolean) - Method in class org.jmol.awtjs2d.Platform
 
allocateTBuffers(boolean) - Method in class org.jmol.g3d.Platform3D
 
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.api.JmolViewer
This is the older main access point for creating an application or applet vwr.
allocateViewer(Object, JmolAdapter) - Static method in class org.jmol.api.JmolViewer
a simpler option
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener) - Static method in class org.jmol.api.JmolViewer
legacy only
allocateViewer(Object, JmolAdapter, String, URL, URL, String, JmolStatusListener, GenericPlatform) - Static method in class org.jmol.viewer.Viewer
old way...
allocDipole(String, String) - Method in class org.jmol.shapespecial.Dipoles
 
allocDotsConvexMaps(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
allocMesh(String, Mesh) - Method in class org.jmol.shape.MeshCollection
 
allocMesh(String, Mesh) - Method in class org.jmol.shapecgo.CGO
 
allocMesh(String, Mesh) - Method in class org.jmol.shapespecial.Draw
 
allocMesh(String, Mesh) - Method in class org.jmol.shapesurface.Isosurface
 
allocRaster(boolean, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
 
allocTempEnum(int) - Method in class org.jmol.util.TempArray
 
allocTempEnum(int) - Method in class org.jmol.viewer.Viewer
 
allocTempPoints(int) - Method in class org.jmol.util.TempArray
 
allocTempPoints(int) - Method in class org.jmol.viewer.Viewer
 
allocTempScreens(int) - Method in class org.jmol.util.TempArray
 
allocTempScreens(int) - Method in class org.jmol.viewer.Viewer
 
allocVertexColixes() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
allow2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
allowArrayDotNotation - Variable in class org.jmol.viewer.Viewer
 
allowAtomName(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
allowCapture() - Method in class org.jmol.viewer.Viewer
 
allowDebug - Static variable in class org.jmol.i18n.GT
 
allowedQuaternionFrames - Static variable in class org.jmol.viewer.JC
 
allowembeddedscripts - Static variable in class org.jmol.script.T
 
allowEmbeddedScripts - Variable in class org.jmol.viewer.GlobalSettings
 
allowEmbeddedScripts() - Method in class org.jmol.viewer.Viewer
 
allowgestures - Static variable in class org.jmol.script.T
 
allowGestures - Variable in class org.jmol.viewer.GlobalSettings
 
allowJSEval - Variable in class org.jmol.applet.Jmol
 
allowJSThreads - Variable in class org.jmol.script.ScriptContext
 
allowJSThreads - Variable in class org.jmol.script.ScriptEval
 
allowkeystrokes - Static variable in class org.jmol.script.T
 
allowKeyStrokes - Variable in class org.jmol.viewer.GlobalSettings
 
allowMapData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
allowMesh - Variable in class org.jmol.shapesurface.Isosurface
 
allowMissingEnd - Variable in class org.jmol.script.ScriptCompiler
 
allowmodelkit - Static variable in class org.jmol.script.T
 
allowModelkit - Variable in class org.jmol.viewer.GlobalSettings
 
allowmoveatoms - Static variable in class org.jmol.script.T
 
allowMoveAtoms - Variable in class org.jmol.viewer.GlobalSettings
 
allowMultiple - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
allowmultitouch - Static variable in class org.jmol.script.T
 
allowMultiTouch - Variable in class org.jmol.viewer.GlobalSettings
 
allowNegative - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
allowNoOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
allowPDBFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
allowrotateselected - Static variable in class org.jmol.script.T
 
allowRotateSelected - Variable in class org.jmol.viewer.GlobalSettings
 
allowRotations - Variable in class org.jmol.adapter.readers.cif.CifReader
 
allowScripting - Variable in class org.jmol.viewer.Viewer
 
allowSigma - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
allowSignedFeatures - Variable in class org.jmol.popup.GenericSwingPopup
 
allowSmilesUnbracketed(String) - Static method in class org.jmol.smiles.SmilesAtom
 
allowSpecAtom() - Method in class org.jmol.modelset.ModelSet
 
allowStatusReporting - Variable in class org.jmol.viewer.StatusManager
 
allowSurface - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
allowUnderflow - Variable in class org.jmol.script.ScriptMathProcessor
 
allowVolumeRender - Variable in class org.jmol.jvxl.data.JvxlData
 
allowVolumeRender - Variable in class org.jmol.jvxl.readers.Parameters
 
allPositive - Variable in class org.jmol.symmetry.HallRotationTerm
 
allSelectedWidgets() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
allStates - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
allTypes - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
almost180 - Static variable in class org.jmol.modelset.AtomCollection
 
alpha - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
alpha - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
alpha - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
alpha - Variable in class org.jmol.jvxl.readers.MapFileReader
 
ALPHA - Static variable in class org.jmol.shapecgo.CGOMesh
 
alpha - Variable in class org.jmol.util.SimpleUnitCell
 
ALPHA_CARBON_VISIBILITY_FLAG - Static variable in class org.jmol.viewer.JC
 
ALPHA_SHIFT - Static variable in class org.jmol.util.C
 
ALPHA_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
 
alphaBeta - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
AlphaMonomer - Class in org.jmol.modelsetbio
 
AlphaMonomer() - Constructor for class org.jmol.modelsetbio.AlphaMonomer
 
alphaOffsets - Static variable in class org.jmol.modelsetbio.AlphaMonomer
 
alphaOffsets - Static variable in class org.jmol.modelsetbio.CarbohydrateMonomer
 
AlphaPolymer - Class in org.jmol.modelsetbio
 
AlphaPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.AlphaPolymer
 
AlphaPolymer.Code - Enum in org.jmol.modelsetbio
 
alphas - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
ALT - Static variable in class org.jmol.util.ColorEncoder
 
ALT - Static variable in class org.jmol.viewer.binding.Binding
 
ALT_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
altArgbsCpk - Variable in class org.jmol.viewer.ColorManager
 
altArgbsCpk - Static variable in class org.jmol.viewer.JC
 
altElementCounts - Variable in class org.jmol.util.JmolMolecule
 
altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
 
altElementMax - Static variable in class org.jmol.util.Elements
length of the altElementSymbols, altElementNames, altElementNumbers arrays
altElementMax - Variable in class org.jmol.util.JmolMolecule
 
altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
 
altElementNames - Static variable in class org.jmol.util.Elements
 
altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
 
altElementNumbers - Static variable in class org.jmol.util.Elements
 
altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
 
altElementSymbols - Static variable in class org.jmol.util.Elements
 
altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
 
altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
 
altLoc - Variable in class org.jmol.adapter.smarter.Atom
 
altloc - Variable in class org.jmol.modelset.Atom
 
altloc - Static variable in class org.jmol.script.T
 
altlocs - Variable in class org.jmol.popup.JmolGenericPopup
 
altNames - Variable in class org.jmol.adapter.readers.pdb.P2nReader
 
altType - Variable in class org.jmol.util.Tensor
 
altVertices - Variable in class org.jmol.util.MeshSurface
 
am - Variable in class org.jmol.modelset.ModelSet
 
am - Variable in class org.jmol.thread.AnimationThread
 
am - Variable in class org.jmol.viewer.Viewer
 
ambient - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ambient_occlusion_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ambient_occlusion_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ambient_occlusion_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ambientFraction - Variable in class org.jmol.util.Shader
 
ambientocclusion - Static variable in class org.jmol.script.T
 
ambientOcclusion - Variable in class org.jmol.util.GData
 
ambientpercent - Static variable in class org.jmol.script.T
 
ambientPercent - Variable in class org.jmol.util.Shader
 
ambiguityType - Variable in class org.jmol.symmetry.SpaceGroup
 
ambiguousNames - Static variable in class org.jmol.symmetry.SpaceGroup
 
amino - Static variable in class org.jmol.script.T
 
AMINO - Static variable in class org.jmol.util.ColorEncoder
 
AminoMonomer - Class in org.jmol.modelsetbio
 
AminoMonomer() - Constructor for class org.jmol.modelsetbio.AminoMonomer
 
AminoPolymer - Class in org.jmol.modelsetbio
 
AminoPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.AminoPolymer
 
ampacContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
AmpacReader - Class in org.jmol.adapter.readers.simple
A reader for AMPAC output.
AmpacReader() - Constructor for class org.jmol.adapter.readers.simple.AmpacReader
 
AMPLITUDE_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for vibration scale.
AMPLITUDE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Precision of the vibration scale slider
AMPLITUDE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Initial value of vibration scale.
amplitudeSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
anaglyph_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
anaglyphChannelBytes - Variable in class org.jmol.g3d.Graphics3D
 
anaglyphLength - Variable in class org.jmol.g3d.Graphics3D
 
and(BS) - Method in class org.jmol.java.BS
Performs a logical AND of this target bit set with the argument bit set.
andBitSet(BS) - Method in class org.jmol.shapespecial.Polyhedra
 
andequals - Static variable in class org.jmol.script.T
 
andNot(BS) - Method in class org.jmol.java.BS
Clears all of the bits in this BitSet whose corresponding bit is set in the specified BitSet.
andNot(BS, BS) - Static method in class org.jmol.util.BSUtil
 
angle - Static variable in class org.jmol.script.T
 
angle - Variable in class org.jmol.thread.SpinThread
 
angle_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
angle_label_position - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
angle_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
angleCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
angleCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
angleCount - Variable in class org.jmol.minimize.forcefield.Calculations
 
anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
anglefromZ - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
angleUnits - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
angleUnitsList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
angleUnitsPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
angleXY - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
angleXY - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
angleXYSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
angleZSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
angMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
angstroms - Static variable in class org.jmol.script.T
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.Parameters
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JC
 
angstromsToPixels(float) - Method in class org.jmol.viewer.TransformManager
 
angularPart(double, double, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
animation - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
animation - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
animation - Static variable in class org.jmol.script.T
 
animation(boolean) - Method in class org.jmol.viewer.AnimationManager
 
animation_duration - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
animationDirection - Variable in class org.jmol.viewer.AnimationManager
 
animationfps - Static variable in class org.jmol.script.T
 
animationFps - Variable in class org.jmol.viewer.AnimationManager
 
animationFps - Variable in class org.jmol.viewer.GlobalSettings
 
animationFrames - Variable in class org.jmol.viewer.AnimationManager
 
AnimationManager - Class in org.jmol.viewer
 
AnimationManager(Viewer) - Constructor for class org.jmol.viewer.AnimationManager
 
animationmode - Static variable in class org.jmol.script.T
 
animationOn - Variable in class org.jmol.viewer.AnimationManager
 
animationPaused - Variable in class org.jmol.viewer.AnimationManager
 
animationReplayMode - Variable in class org.jmol.viewer.AnimationManager
 
animationStep - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
AnimationThread - Class in org.jmol.thread
 
AnimationThread() - Constructor for class org.jmol.thread.AnimationThread
 
animationThread - Variable in class org.jmol.viewer.AnimationManager
 
AnimationWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
 
AnimButton(ImageIcon, String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
animThread - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
anionLookupTable - Static variable in class org.jmol.util.Elements
 
aniosU - Variable in class org.jmol.jvxl.readers.Parameters
 
ANISO_B11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_B12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_B13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_B22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_B23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_B33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_BETA_11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_BETA_12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_BETA_13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_BETA_22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_BETA_23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_BETA_33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_LABEL - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_MMCIF_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_MMCIF_U11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_MMCIF_U12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_MMCIF_U13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_MMCIF_U22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_MMCIF_U23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_MMCIF_U33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_U11 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_U12 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_U13 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_U22 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_U23 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ANISO_U33 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
anisoB - Variable in class org.jmol.jvxl.readers.Parameters
 
anisoBorU - Variable in class org.jmol.adapter.smarter.Atom
 
anisotropy - Variable in class org.jmol.jvxl.readers.Parameters
 
anisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
anisotropy - Static variable in class org.jmol.script.T
 
anisotropy() - Method in class org.jmol.util.Tensor
anisotropy = directed distance from (center of two closest) to (the furthest)
anisou() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
Annotation - Class in org.jmol.modelsetbio
 
Annotation() - Constructor for class org.jmol.modelsetbio.Annotation
 
AnnotationParser - Class in org.jmol.dssx
A parser for output from 3DNA web service.
AnnotationParser() - Constructor for class org.jmol.dssx.AnnotationParser
 
annotationParser - Variable in class org.jmol.viewer.Viewer
 
antialias - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
antialias - Variable in class org.jmol.render.MeshRenderer
 
antialias - Variable in class org.jmol.viewer.TransformManager
 
antialias2 - Variable in class org.jmol.g3d.Graphics3D
 
antiAliasCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
antialiasdisplay - Static variable in class org.jmol.script.T
 
antialiasDisplay - Variable in class org.jmol.viewer.GlobalSettings
 
antialiased - Variable in class org.jmol.viewer.Viewer
 
antialiasEnabled - Variable in class org.jmol.util.GData
 
antialiasimages - Static variable in class org.jmol.script.T
 
antialiasImages - Variable in class org.jmol.viewer.GlobalSettings
 
antialiasThisFrame - Variable in class org.jmol.util.GData
 
antialiastranslucent - Static variable in class org.jmol.script.T
 
antialiasTranslucent - Variable in class org.jmol.viewer.GlobalSettings
 
ANUM - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
AO_TYPES - Static variable in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
aobuf - Variable in class org.jmol.g3d.Graphics3D
 
aoMax - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
aoMax2 - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
aPar - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
 
ApbsReader - Class in org.jmol.jvxl.readers
 
ApbsReader() - Constructor for class org.jmol.jvxl.readers.ApbsReader
 
aperatureAngle - Variable in class org.jmol.export.___Exporter
 
aperatureAngle - Variable in class org.jmol.viewer.TransformManager
 
apiPlatform - Variable in class org.jmol.api.JmolViewer
 
apiPlatform - Variable in class org.jmol.g3d.Platform3D
 
apiPlatform - Variable in class org.jmol.util.GData
 
apm - Variable in class org.jmol.viewer.ActionManager
picking modes set picking....
apolymer - Variable in class org.jmol.modelsetbio.ProteinStructure
 
app(SB, String) - Method in class org.jmol.viewer.GlobalSettings
 
app(SB, String) - Method in class org.jmol.viewer.StateCreator
 
appCheckItem(String, SC) - Method in class org.jmol.popup.GenericSwingPopup
 
appCheckItem(String, SC) - Method in class org.jmol.popup.JmolGenericPopup
 
appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.GenericSwingPopup
 
appCheckSpecialMenu(String, SC, String) - Method in class org.jmol.popup.JmolGenericPopup
 
AppCloser() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
 
appConsole - Variable in class org.jmol.viewer.Viewer
 
AppConsole - Class in org.openscience.jmol.app.jmolpanel.console
 
AppConsole() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
AppConsole(JmolViewer, Container, String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole
general entry point
AppConsole.ConsoleDocument - Class in org.openscience.jmol.app.jmolpanel.console
 
AppConsole.ConsoleTextPane - Class in org.openscience.jmol.app.jmolpanel.console
 
AppConsole.ExecuteCommandThread - Class in org.openscience.jmol.app.jmolpanel.console
 
APPEND - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
append(String) - Method in class org.jmol.console.AppletConsole.GenericTextPane
 
append(String) - Method in interface org.jmol.console.GenericTextArea
 
append - Variable in class org.jmol.dialog.FilePreview
 
append - Static variable in class org.jmol.script.T
 
appendAtomSetCollection(int, AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Appends an AtomSetCollection
appendAtomSetCollectionList(Lst<?>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
appendAtomTokenValue(Viewer, Atom, LabelToken, SB, int[], P3) - Static method in class org.jmol.modelset.LabelToken
 
appendCmd(SB, String) - Static method in class org.jmol.shape.Shape
 
appendContourTriangleIntersection(int, float, float, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
appends an integer (3, 5, or 6) representing two sides of a triangle ABC -- AB/BC(3), AB/CA(5), or BC/CA(6) -- along with two fractions along the edges for the intersection point base-90-encoded.
appendedData - Variable in class org.jmol.adapter.readers.cif.CifReader
 
appendEncodedBitSetTag(SB, String, BS, int, Object[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
appendFontCmd(SB) - Method in class org.jmol.modelset.Text
 
appendLoadNote(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
appendLoadStates(SB) - Method in class org.jmol.viewer.StateCreator
 
appendLogData(String) - Method in class org.jmol.minimize.forcefield.Calculations
 
appendNew - Variable in class org.jmol.modelset.ModelLoader
 
appendnew - Static variable in class org.jmol.script.T
 
appendNew - Variable in class org.jmol.viewer.GlobalSettings
 
appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
appendNewline() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
APPENDS - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
appendTickInfo(String, SB, TickInfo) - Method in class org.jmol.viewer.StateCreator
 
appendUunitCellInfo(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
appendXmlColorData(SB, String, boolean, boolean, float, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
appendXmlEdgeData(SB, JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
appendXmlTriangleData(SB, int[][], int, BS, int[], boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
encode triangle data -- [ia ib ic] [ia ib ic] [ia ib ic] ...
appendXmlVertexData(SB, JvxlData, int[], T3[], float[], int, String, int, BS, int[], boolean, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
encode the vertex data.
appendXmlVertexOnlyData(SB, JvxlData, MeshData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
appFixLabel(String) - Method in class org.jmol.popup.GenericSwingPopup
 
appFixLabel(String) - Method in class org.jmol.popup.JmolGenericPopup
 
appFixScript(String, String) - Method in class org.jmol.popup.GenericSwingPopup
 
appFixScript(String, String) - Method in class org.jmol.popup.JmolGenericPopup
 
appGetBooleanProperty(String) - Method in class org.jmol.popup.GenericSwingPopup
 
appGetBooleanProperty(String) - Method in class org.jmol.popup.JmolGenericPopup
 
appGetMenuAsString(String) - Method in class org.jmol.popup.GenericSwingPopup
 
appGetMenuAsString(String) - Method in class org.jmol.popup.JmolGenericPopup
 
appIsSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.GenericSwingPopup
 
appIsSpecialCheckBox(SC, String, String, boolean) - Method in class org.jmol.popup.JmolGenericPopup
 
applet - Variable in class org.jmol.applet.Jmol
 
applet - Variable in class org.jmol.applet.TickerThread
 
applet - Variable in class org.jmol.applet.WrappedAppletLoader
 
appletCodeBase - Static variable in class org.jmol.viewer.Viewer
 
AppletConsole - Class in org.jmol.console
 
AppletConsole() - Constructor for class org.jmol.console.AppletConsole
 
AppletConsole - Class in org.jmol.consolejs
An interface to Jmol.Console.
AppletConsole() - Constructor for class org.jmol.consolejs.AppletConsole
 
AppletConsole.ControlEnterTextArea - Class in org.jmol.console
 
AppletConsole.GenericTextPane - Class in org.jmol.console
 
appletContext - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
appletDocumentBase - Static variable in class org.jmol.viewer.Viewer
 
appletDocumentBaseURL - Variable in class org.jmol.viewer.FileManager
 
appletIdiomaBase - Static variable in class org.jmol.viewer.Viewer
 
appletInfoDivs - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
appletName - Variable in class org.jmol.viewer.Viewer
 
appletObject - Variable in class org.jmol.util.GenericApplet
 
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.ScriptButtons
 
appletParamPanel() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
appletPath - Variable in class org.openscience.jmol.app.webexport.Test
 
appletproxy - Static variable in class org.jmol.script.T
 
appletProxy - Variable in class org.jmol.viewer.FileManager
 
appletProxy - Variable in class org.jmol.viewer.GlobalSettings
 
appletSizeSpinnerH - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
appletSizeSpinnerP - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
appletSizeSpinnerW - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
AppletWrapper - Class in org.jmol.applet
 
AppletWrapper(String, int, String[]) - Constructor for class org.jmol.applet.AppletWrapper
 
appletWrapper - Variable in class org.jmol.applet.ClassPreloader
 
ApplicationCloser() - Constructor for class org.openscience.chimetojmol.ChimeToJmol.ApplicationCloser
 
apply(ModulationSet, double[][]) - Method in class org.jmol.util.Modulation
 
apply() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
applyAllSymmetry(MSInterface, BS) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
applyAnaglygh(STER, int[]) - Method in class org.jmol.g3d.Graphics3D
 
applyAnaglygh(STER, int[]) - Method in class org.jmol.util.GData
 
applyBlueAnaglyph() - Method in class org.jmol.g3d.Graphics3D
 
applyButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
applyColorScale() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
applyCustomAnaglyph(int[]) - Method in class org.jmol.g3d.Graphics3D
 
applyCyanAnaglyph() - Method in class org.jmol.g3d.Graphics3D
 
applyEmpiricalRules(MinObject, double[], int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
applyGreenAnaglyph() - Method in class org.jmol.g3d.Graphics3D
 
applyLeftMouse(int) - Static method in class org.jmol.awt.Mouse
 
applyLeftMouse(int) - Static method in class org.jmol.awtjs2d.Mouse
 
applyPerspective(T3, T3) - Method in class org.jmol.viewer.TransformManager
adjusts the temporary point for perspective and offsets
applyRotation(M3, boolean, BS, V3, boolean, M4) - Method in class org.jmol.viewer.TransformManager
 
applyStereochemistry() - Method in class org.jmol.modelset.ModelLoader
 
applySymmetry - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
applySymmetry() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.cif.CifReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
applySymmetryAndSetTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
applySymmetryBio(Map<String, Object>, float[], boolean, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
applySymmetryFromReader(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
applySymmetryLattice(MSInterface, String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
applySymmetryToBonds - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
applysymmetrytobonds - Static variable in class org.jmol.script.T
 
applySymmetryToBonds - Variable in class org.jmol.viewer.GlobalSettings
 
applySymTrajASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
appRestorePopupMenu() - Method in class org.jmol.popup.GenericSwingPopup
 
appRestorePopupMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
approx(T3) - Static method in class org.jmol.symmetry.SymmetryDesc
 
approx0(T3) - Static method in class org.jmol.symmetry.SymmetryDesc
 
approxF(float) - Static method in class org.jmol.symmetry.SymmetryOperation
 
approxInt(float) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
appRunScript(String) - Method in class org.jmol.popup.GenericSwingPopup
 
appRunScript(String) - Method in class org.jmol.popup.JmolGenericPopup
 
appUpdateForShow() - Method in class org.jmol.popup.GenericSwingPopup
 
appUpdateForShow() - Method in class org.jmol.popup.JmolGenericPopup
 
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.GenericSwingPopup
 
appUpdateSpecialCheckBoxValue(SC, String, boolean) - Method in class org.jmol.popup.JmolGenericPopup
(1) setOption --> set setOption true or set setOption false
arc - Static variable in class org.jmol.script.T
 
area - Static variable in class org.jmol.script.T
 
areAxesTainted() - Method in class org.jmol.viewer.Viewer
 
areEqual(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
areEqual(SV, SV) - Static method in class org.jmol.script.SV
For legacy reasons, "x" == "X" but see isLike()
areEqual(String, String) - Method in class org.jmol.smiles.SmilesMatcher
 
areEqual(String, SmilesSearch) - Method in class org.jmol.smiles.SmilesMatcher
for JUnit test, mainly
areEqual(BS, BS) - Static method in class org.jmol.util.BSUtil
 
argb - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
argb - Variable in class org.jmol.g3d.TextString
 
argbCurrent - Variable in class org.jmol.util.GData
 
argbEndcap - Variable in class org.jmol.g3d.CylinderRenderer
 
argbNoisyDn - Variable in class org.jmol.util.GData
 
argbNoisyUp - Variable in class org.jmol.util.GData
 
argbs - Static variable in class org.jmol.util.C
 
argbsAmino - Static variable in class org.jmol.modelsetbio.Resolver
 
argbsAmino - Variable in class org.jmol.util.ColorEncoder
 
argbsChainAtom - Static variable in class org.jmol.modelsetbio.Resolver
some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
argbsChainAtom - Static variable in class org.jmol.util.ColorEncoder
 
argbsChainHetero - Static variable in class org.jmol.modelsetbio.Resolver
 
argbsChainHetero - Static variable in class org.jmol.util.ColorEncoder
 
argbsCpk - Static variable in enum org.jmol.c.PAL
Default table of CPK atom colors.
argbsCpk - Variable in class org.jmol.util.ColorEncoder
 
argbsCpk - Variable in class org.jmol.viewer.ColorManager
 
argbsCpkRasmol - Static variable in enum org.jmol.c.PAL
 
argbsFormalCharge - Static variable in class org.jmol.viewer.JC
 
argbsGreyscale - Static variable in class org.jmol.util.C
 
argbsHbondType - Static variable in class org.jmol.util.Edge
 
argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JC
 
argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JC
 
argbsRoygb - Variable in class org.jmol.util.ColorEncoder
 
argbsRoygbScale - Static variable in class org.jmol.viewer.JC
 
argbsRwb - Variable in class org.jmol.util.ColorEncoder
 
argbsRwbScale - Static variable in class org.jmol.viewer.JC
 
argbsShapely - Static variable in class org.jmol.modelsetbio.Resolver
 
argbsShapely - Variable in class org.jmol.util.ColorEncoder
 
arom - Variable in class org.jmol.minimize.forcefield.AtomType
 
aromatic - Static variable in class org.jmol.script.T
 
aromaticAmbiguous - Variable in class org.jmol.smiles.SmilesAtom
 
aromaticDouble - Variable in class org.jmol.smiles.SmilesSearch
 
array - Static variable in class org.jmol.script.T
 
arrayListHandler - Variable in class org.openscience.jmol.app.webexport.Test
 
ArrayListTransferable(Lst<String>) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
ArrayListTransferHandler - Class in org.openscience.jmol.app.webexport
 
ArrayListTransferHandler(WebPanel) - Constructor for class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
ArrayListTransferHandler.ArrayListTransferable - Class in org.openscience.jmol.app.webexport
 
arrayPt - Variable in class org.jmol.script.SV.Sort
 
arrow - Static variable in class org.jmol.script.T
 
arrowHeadBase - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
arrowHeadFaces - Static variable in class org.jmol.renderbio.RocketRenderer
 
arrowHeadOffset - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
arrowHeadOffset - Static variable in class org.jmol.renderspecial.VectorsRenderer
 
arrowHeadTip - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
arrowHeadWidthFactor - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
as - Static variable in class org.jmol.script.T
 
asBitSet - Variable in class org.jmol.script.ScriptMathProcessor
 
asBoolean() - Method in class org.jmol.script.SV
 
asc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
asc - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
ASCENDER - Static variable in class org.jmol.util.MeshCapper
 
ascent - Variable in class org.jmol.g3d.TextRenderer
 
ascent - Variable in class org.jmol.modelset.Text
 
ascent - Variable in class org.jmol.render.LabelsRenderer
 
asFloat() - Method in class org.jmol.script.SV
 
ashades - Variable in class org.jmol.util.Shader
 
ashadesGreyscale - Variable in class org.jmol.util.Shader
 
asHTML(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
ASimpleJvxlWriter - Class in org.openscience.jvxl.simplewriter
 
ASimpleJvxlWriter() - Constructor for class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
asInt() - Method in class org.jmol.script.SV
 
asLineOnly - Variable in class org.jmol.render.FontLineShapeRenderer
 
aspectRatio - Variable in class org.jmol.renderbio.BioShapeRenderer
 
asResidues - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
 
assem - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
ASSEM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
ASSEM_LIST - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
ASSEM_OPERS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
assemblyFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
assemblyIdAtoms - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
assign - Static variable in class org.jmol.script.T
 
assign() - Method in class org.jmol.scriptext.CmdExt
 
assignAromaticBondsBs(boolean, BS) - Method in class org.jmol.modelset.BondCollection
algorithm discussed above.
assignAromaticDouble(Bond) - Method in class org.jmol.modelset.BondCollection
try to assign AROMATICDOUBLE to this bond.
assignAromaticDoubleForAtom(Atom) - Method in class org.jmol.modelset.BondCollection
N atoms with 3 bonds cannot also have a double bond; other atoms need one and only one double bond; the rest must be single bonds.
assignAromaticNandO(BS) - Method in class org.jmol.modelset.BondCollection
 
assignAromaticSingle(Bond) - Method in class org.jmol.modelset.BondCollection
try to assign AROMATICSINGLE to this bond.
assignAromaticSingleForAtom(Atom, int) - Method in class org.jmol.modelset.BondCollection
N atoms with 3 bonds cannot also have a double bond; other atoms needs all single bonds, because the bond leading up to it is double.
assignAromaticSingleHetero(Atom) - Method in class org.jmol.modelset.BondCollection
 
assignAtom(int, String, boolean) - Method in class org.jmol.modelset.ModelSet
 
assignAtom(int, P3, String) - Method in class org.jmol.scriptext.CmdExt
 
assignBond(int, char) - Method in class org.jmol.scriptext.CmdExt
 
assignConnect(int, int) - Method in class org.jmol.scriptext.CmdExt
 
assignLeft - Variable in class org.jmol.script.ScriptMathProcessor
 
assignNew(int, int) - Method in class org.jmol.viewer.ActionManager
 
assignPDBH(String, String) - Method in class org.jmol.dssx.AnnotationParser
 
assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in interface org.jmol.api.MepCalculationInterface
 
assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MepCalculation
 
assignPotentials(Atom[], float[], BS, BS, BS, String) - Method in class org.jmol.quantum.MlpCalculation
 
assignValueFromGapColorForKin(String) - Method in class org.jmol.jvxl.readers.KinemageReader
C++ code gives these as " value > x.x ? "xxxxx", etc.
assocCutoff - Variable in class org.jmol.jvxl.readers.Parameters
 
assocCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
assocGridPointMap - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
assocGridPointNormals - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
associatedAtoms - Variable in class org.jmol.modelset.BondSet
 
associateNormals - Variable in class org.jmol.shapesurface.Isosurface
 
asString() - Method in class org.jmol.script.SV
 
assumeAtomRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
astrType - Static variable in class org.jmol.script.T
 
asVector - Variable in class org.jmol.script.ScriptMathProcessor
 
asVector - Variable in class org.jmol.smiles.SmilesSearch
 
ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
asymMatrix - Variable in class org.jmol.util.Tensor
 
asymmetry() - Method in class org.jmol.util.Tensor
asymmetry = deviation from a symmetric tensor
async - Static variable in class org.jmol.script.T
 
async - Variable in class org.jmol.viewer.Viewer
 
async_builds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
at - Variable in class org.jmol.modelset.AtomCollection
 
ati_bugs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
atModel - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
atokenInfix - Variable in class org.jmol.script.ScriptTokenParser
 
atom() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
atom - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
atom() - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
Atom - Class in org.jmol.adapter.smarter
 
Atom() - Constructor for class org.jmol.adapter.smarter.Atom
 
atom - Variable in class org.jmol.adapter.smarter.AtomIterator
 
atom - Variable in class org.jmol.minimize.MinAtom
 
Atom - Class in org.jmol.modelset
 
Atom() - Constructor for class org.jmol.modelset.Atom
 
atom - Variable in class org.jmol.quantum.QMAtom
 
atom - Variable in class org.jmol.render.LabelsRenderer
 
atom1 - Variable in class org.jmol.modelset.Bond
 
atom1 - Variable in class org.jmol.smiles.SmilesBond
 
atom2 - Variable in class org.jmol.modelset.Bond
 
atom2 - Variable in class org.jmol.smiles.SmilesBond
 
ATOM_COUNT_MAX - Static variable in class org.jmol.symmetry.PointGroup
 
ATOM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ATOM_INFRAME - Static variable in class org.jmol.viewer.JC
 
ATOM_INFRAME_NOTHIDDEN - Static variable in class org.jmol.viewer.JC
 
atom_name_wildcard - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ATOM_NOFLAGS - Static variable in class org.jmol.viewer.JC
 
ATOM_NOTHIDDEN - Static variable in class org.jmol.viewer.JC
 
ATOM_SHAPE_VIS_MASK - Static variable in class org.jmol.viewer.JC
 
atom_type_format - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ATOM_TYPE_OXIDATION_NUMBER - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ATOM_TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
ATOM_VISIBLE - Static variable in class org.jmol.viewer.JC
 
ATOM_VISSET - Static variable in class org.jmol.viewer.JC
 
atomA - Variable in class org.jmol.render.FontLineShapeRenderer
 
atomArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
atomB - Variable in class org.jmol.render.FontLineShapeRenderer
 
atomCenterOrCoordinateParameter(int) - Method in class org.jmol.script.ScriptParam
 
atomCharges - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
AtomCollection - Class in org.jmol.modelset
 
AtomCollection() - Constructor for class org.jmol.modelset.AtomCollection
 
AtomCollection.AtomSorter - Class in org.jmol.modelset
 
atomColorList - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
atomCoordAngstroms - Variable in class org.jmol.quantum.MepCalculation
 
atomCount - Variable in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
AtomData - Class in org.jmol.atomdata
 
AtomData() - Constructor for class org.jmol.atomdata.AtomData
 
atomData - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
atomData - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
AtomDataReader - Class in org.jmol.jvxl.readers
 
AtomDataReader() - Constructor for class org.jmol.jvxl.readers.AtomDataReader
 
AtomDataServer - Interface in org.jmol.atomdata
 
atomDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
atomEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
 
atomExpression(T[], int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptExpr
 
atomExpression(T[], int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptParam
 
atomExpression - Static variable in class org.jmol.viewer.PropertyManager
 
atomExpressionAt(int) - Method in class org.jmol.script.ScriptExpr
 
atomExpressionAt(int) - Method in class org.jmol.script.ScriptParam
 
atomExpressionAt(int) - Method in class org.jmol.scriptext.CmdExt
 
atomExpressionCommand - Static variable in class org.jmol.script.T
 
atomFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
atomFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
atomFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
atomFormats - Variable in class org.jmol.shape.Hover
 
atomFrag - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
ATOMIC_ORBITAL_ZERO_CUT_OFF - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
atomicAndIsotopeNumber - Variable in class org.jmol.modelset.Atom
 
atomicMass - Variable in class org.jmol.smiles.SmilesAtom
 
atomicMass - Static variable in class org.jmol.util.Elements
 
atomicNumber - Variable in class org.jmol.atomdata.AtomData
 
atomicNumbers - Variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
atomicorbital - Static variable in class org.jmol.script.T
 
atomID - Variable in class org.jmol.modelset.Atom
 
atomid - Static variable in class org.jmol.script.T
 
ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JC
 
ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JC
 
ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JC
 
ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C2_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C4 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C5 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C5_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_C5M - Static variable in class org.jmol.viewer.JC
 
ATOMID_C6 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C7 - Static variable in class org.jmol.viewer.JC
 
ATOMID_C8 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JC
 
ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JC
 
ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JC
 
ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JC
 
ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_MAX - Static variable in class org.jmol.modelsetbio.Resolver
 
ATOMID_N1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N3 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N4 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N6 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N7 - Static variable in class org.jmol.viewer.JC
 
ATOMID_N9 - Static variable in class org.jmol.viewer.JC
 
ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JC
 
ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JC
 
ATOMID_O1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_O1P - Static variable in class org.jmol.viewer.JC
 
ATOMID_O2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_O2P - Static variable in class org.jmol.viewer.JC
 
ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_O4 - Static variable in class org.jmol.viewer.JC
 
ATOMID_O4_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JC
 
ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JC
 
ATOMID_O6 - Static variable in class org.jmol.viewer.JC
 
ATOMID_OP1 - Static variable in class org.jmol.viewer.JC
 
ATOMID_OP2 - Static variable in class org.jmol.viewer.JC
 
ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JC
 
ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JC
 
ATOMID_S4 - Static variable in class org.jmol.viewer.JC
 
ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JC
 
atomIdNames - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
atomIndex - Variable in class org.jmol.adapter.readers.simple.HyperChemReader
 
atomIndex - Variable in class org.jmol.atomdata.AtomData
 
atomIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
atomIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
atomIndex - Variable in class org.jmol.quantum.QuantumCalculation
 
atomindex - Static variable in class org.jmol.script.T
 
atomIndex - Variable in class org.jmol.shape.Hover
 
atomIndex - Variable in class org.jmol.shape.Mesh
 
atomIndex - Variable in class org.jmol.shapesurface.Isosurface
 
atomIndex1 - Variable in class org.jmol.adapter.smarter.Bond
 
atomIndex1 - Variable in class org.jmol.shapespecial.Dipoles
 
atomIndex1 - Variable in class org.jmol.util.Tensor
 
atomIndex1 - Variable in class org.jmol.viewer.Connection
 
atomIndex2 - Variable in class org.jmol.adapter.smarter.Bond
 
atomIndex2 - Variable in class org.jmol.shapespecial.Dipoles
 
atomIndex2 - Variable in class org.jmol.util.Tensor
 
atomIndex2 - Variable in class org.jmol.viewer.Connection
 
AtomIndexIterator - Interface in org.jmol.api
note: YOU MUST RELEASE THE ITERATOR
atomIndexLast - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
AtomIterator - Class in org.jmol.adapter.smarter
 
AtomIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.AtomIterator
 
AtomIteratorWithinModel - Class in org.jmol.modelset
 
AtomIteratorWithinModel() - Constructor for class org.jmol.modelset.AtomIteratorWithinModel
 
AtomIteratorWithinModelSet - Class in org.jmol.modelset
 
AtomIteratorWithinModelSet(BS) - Constructor for class org.jmol.modelset.AtomIteratorWithinModelSet
 
atomLabels - Variable in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
atomLabels - Variable in class org.jmol.shape.Labels
 
atomList - Variable in class org.jmol.util.JmolMolecule
 
atomMap - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
 
atomMap - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
atomMap - Variable in class org.jmol.adapter.readers.simple.InputReader
 
atomMap - Variable in class org.jmol.minimize.Minimizer
 
atomMolecule - Variable in class org.jmol.atomdata.AtomData
 
atomName - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
atomName - Variable in class org.jmol.adapter.smarter.Atom
 
atomname - Static variable in class org.jmol.script.T
 
atomName - Variable in class org.jmol.smiles.SmilesAtom
 
atomName1 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
atomName2 - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
atomNames - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
atomNames - Variable in class org.jmol.adapter.readers.quantum.PsiReader
 
atomNames - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
atomNames - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
atomNames - Variable in class org.jmol.modelset.AtomCollection
 
atomNo - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomno - Static variable in class org.jmol.script.T
 
atomOrPointPicked(int, Point3fi) - Method in class org.jmol.viewer.ActionManager
 
atomPicked(int) - Method in interface org.jmol.api.JmolJSpecView
 
atomPicked(int) - Method in class org.jmol.jsv.JSpecView
 
atompicking - Static variable in class org.jmol.script.T
 
atomPicking - Variable in class org.jmol.viewer.GlobalSettings
 
atomPositions - Variable in class org.jmol.adapter.readers.simple.AmpacReader
 
atomProp - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomproperty - Static variable in class org.jmol.script.T
 
atomPropertyFloat(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
atomPropertyInt(int) - Method in class org.jmol.modelset.Atom
called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()
AtomPropertyMapper - Class in org.jmol.jvxl.readers
maps property data
AtomPropertyMapper() - Constructor for class org.jmol.jvxl.readers.AtomPropertyMapper
 
atomPropertyString(Viewer, int) - Method in class org.jmol.modelset.Atom
 
atomPropertyTuple(Viewer, int, P3) - Method in class org.jmol.modelset.Atom
 
atomPt - Variable in class org.jmol.render.LabelsRenderer
 
atomPts - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
atomRadius - Variable in class org.jmol.adapter.readers.cif.CifReader
 
atomRadius - Variable in class org.jmol.atomdata.AtomData
 
atomRadius - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomRadiusData - Variable in class org.jmol.jvxl.readers.Parameters
 
atoms - Variable in class org.jmol.adapter.readers.cif.CifReader
 
atoms - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
atoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
atoms - Variable in class org.jmol.adapter.smarter.AtomIterator
 
atoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atoms - Variable in class org.jmol.minimize.Minimizer
 
atoms - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
atoms - Variable in class org.jmol.modelset.MeasurementData
 
atoms - Static variable in class org.jmol.script.T
 
atoms - Variable in class org.jmol.shape.AtomShape
 
atoms - Variable in class org.jmol.shapebio.BioShapeCollection
 
atoms - Variable in class org.jmol.shapespecial.Dipole
 
atoms - Variable in class org.jmol.shapesurface.Contact
 
atoms - Variable in class org.jmol.smiles.SmilesGenerator
 
atoms - Variable in class org.jmol.symmetry.PointGroup
 
atomSeqIDs - Variable in class org.jmol.modelset.AtomCollection
 
atomSerial - Variable in class org.jmol.adapter.smarter.Atom
 
atomSerials - Variable in class org.jmol.modelset.AtomCollection
 
AtomSet(int, String) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
 
atomSetAtomCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetAtomIndexes - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetAuxiliaryInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetBondCounts - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetChooser - Class in org.openscience.jmol.app.jmolpanel
A JFrame that allows for choosing an Atomset to view.
AtomSetChooser(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
atomSetChooser - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
AtomSetChooser.AtomSet - Class in org.openscience.jmol.app.jmolpanel
Objects in the AtomSetChooser tree
atomsetchooserAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
AtomSetChooserAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.AtomSetChooserAction
 
AtomSetCollection - Class in org.jmol.adapter.smarter
 
AtomSetCollection(String, AtomSetCollectionReader, AtomSetCollection[], Lst<?>) - Constructor for class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetCollection - Variable in class org.jmol.io.DOMReader
 
atomSetCollection - Variable in class org.jmol.io.FileReader
 
atomSetCollection - Variable in class org.jmol.io.FilesReader
 
AtomSetCollectionReader - Class in org.jmol.adapter.smarter
 
AtomSetCollectionReader() - Constructor for class org.jmol.adapter.smarter.AtomSetCollectionReader
 
atomSetCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetIndex - Variable in class org.jmol.adapter.smarter.Atom
 
atomSetIndex - Variable in class org.jmol.adapter.smarter.AtomSetObject
 
atomSetIndex - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
The index of that AtomSet
atomSetInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSetName - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
The name of the AtomSet
atomSetNumbers - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
AtomSetObject - Class in org.jmol.adapter.smarter
 
AtomSetObject() - Constructor for class org.jmol.adapter.smarter.AtomSetObject
 
AtomShape - Class in org.jmol.shape
 
AtomShape() - Constructor for class org.jmol.shape.AtomShape
 
atomSite - Variable in class org.jmol.adapter.smarter.Atom
 
atomSite - Variable in class org.jmol.modelset.Atom
 
atomSite - Variable in class org.jmol.smiles.SmilesAtom
 
atomsOr - Variable in class org.jmol.smiles.SmilesAtom
 
AtomSorter() - Constructor for class org.jmol.modelset.AtomCollection.AtomSorter
 
atomStartEnd - Variable in class org.jmol.adapter.smarter.Structure
 
atomSym - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
atomSymbolicMap - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
atomSymmetry - Variable in class org.jmol.modelset.Atom
 
atomSyms - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
atomTensorList - Variable in class org.jmol.modelset.AtomCollection
 
atomTensors - Variable in class org.jmol.modelset.AtomCollection
 
atomTest - Variable in class org.jmol.symmetry.SymmetryOperation
 
AtomType - Class in org.jmol.minimize.forcefield
 
AtomType(int, int, int, float, int, String, String) - Constructor for class org.jmol.minimize.forcefield.AtomType
 
atomtype - Static variable in class org.jmol.script.T
 
atomType - Variable in class org.jmol.smiles.SmilesAtom
 
atomTypeFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
atomTypeLen - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
atomTypePt0 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
atomTypes - Variable in class org.jmol.adapter.readers.cif.CifReader
 
atomTypes - Variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
atomTypes - Variable in class org.jmol.adapter.readers.more.MdTopReader
 
atomTypes - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
atomTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
atomTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
atomTypes - Variable in class org.jmol.modelset.AtomCollection
 
atomtypes - Static variable in class org.jmol.script.T
 
atomTypes - Variable in class org.jmol.viewer.GlobalSettings
 
atomX - Variable in class org.jmol.modelset.Object2d
 
atomx - Static variable in class org.jmol.script.T
 
atomXyz - Variable in class org.jmol.atomdata.AtomData
 
atomXyz - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
atomY - Variable in class org.jmol.modelset.Object2d
 
atomy - Static variable in class org.jmol.script.T
 
atomZ - Variable in class org.jmol.modelset.Object2d
 
atomz - Static variable in class org.jmol.script.T
 
attArgs - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
attEcho - Variable in class org.jmol.console.ScriptEditor
 
attEcho - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
attError - Variable in class org.jmol.console.ScriptEditor
 
attError - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
attHighlight - Variable in class org.jmol.console.ScriptEditor
 
attPrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
attribs - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
atts - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
attStatus - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
attUserInput - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
auditBlockCode - Variable in class org.jmol.adapter.readers.cif.CifReader
 
augmentGroup3List(SC, String, boolean) - Method in class org.jmol.popup.JmolGenericPopup
 
AUTH_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
AUTH_ATOM - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
AUTH_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
auto - Static variable in class org.jmol.script.T
 
auto_classify_atoms - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_color_next - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_copy_images - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_defer_atom_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_defer_builds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_dss - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_hide_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_indicate_flags - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_number_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_remove_hydrogens - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_rename_duplicate_objects - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_sculpt - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_show_lines - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_show_nonbonded - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_show_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_show_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
auto_zoom - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
autoAnimationDelay - Variable in class org.openscience.jmol.app.JmolApp
 
autoBond(BS, BS, BS, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
autobond - Static variable in class org.jmol.script.T
 
autoBond - Variable in class org.jmol.viewer.GlobalSettings
 
autoBond - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
autoBond_Pre_11_9_24(BS, BS, BS, BS, short) - Method in class org.jmol.modelset.ModelSet
 
autoBondBs4(BS, BS, BS, BS, short, boolean) - Method in class org.jmol.modelset.ModelSet
 
autoBondCheck(Atom, Atom, int, short, BS) - Method in class org.jmol.modelset.ModelSet
 
autoCalculate(int) - Method in class org.jmol.viewer.Viewer
 
autoclose_dialogs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
autoExit - Variable in class org.jmol.viewer.Viewer
 
autofps - Static variable in class org.jmol.script.T
 
autoFps - Variable in class org.jmol.viewer.GlobalSettings
 
autoHbond(BS, BS, boolean) - Method in class org.jmol.modelset.ModelSet
a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.
autoHbond(BS, BS, boolean) - Method in class org.jmol.viewer.Viewer
 
autoScaleOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
auxiliaryInfo - Variable in class org.jmol.modelset.Model
 
average - Static variable in class org.jmol.script.T
 
averageAtomPoint - Variable in class org.jmol.modelset.AtomCollection
 
AviCreator - Class in org.jmol.image
 
AviCreator() - Constructor for class org.jmol.image.AviCreator
 
AwtClipboard - Class in org.jmol.awt
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
AwtClipboard(Object) - Constructor for class org.jmol.awt.AwtClipboard
 
AwtColor - Class in org.jmol.awt
 
AwtColor(int) - Constructor for class org.jmol.awt.AwtColor
 
AwtColor(int, int, int) - Constructor for class org.jmol.awt.AwtColor
 
AwtColor(int, int, int, int) - Constructor for class org.jmol.awt.AwtColor
 
AwtFile - Class in org.jmol.awt
a subclass of File allowing extension to JavaScript private to org.jmol.awt
AwtFile(String) - Constructor for class org.jmol.awt.AwtFile
 
AwtFont - Class in org.jmol.awt
methods required by Jmol that access java.awt.Font private to org.jmol.awt
AwtFont() - Constructor for class org.jmol.awt.AwtFont
 
AwtG2D - Class in org.jmol.awt
generic 2D drawing methods -- AWT version
AwtG2D() - Constructor for class org.jmol.awt.AwtG2D
 
AwtSwingComponent - Class in org.jmol.popup
A javax.swing implementation of SwingComponent that mirrors javajs.swing for compatibility with compilation with java2script.
AwtSwingComponent() - Constructor for class org.jmol.popup.AwtSwingComponent
 
AwtSwingPopupHelper - Class in org.jmol.popup
all popup-related awt/swing class references are in this file.
AwtSwingPopupHelper(GenericMenuInterface) - Constructor for class org.jmol.popup.AwtSwingPopupHelper
 
ax - Variable in class org.jmol.g3d.TriangleRenderer
 
axE - Variable in class org.jmol.g3d.TriangleRenderer
 
axes - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
axes - Static variable in class org.jmol.script.T
 
Axes - Class in org.jmol.shape
 
Axes() - Constructor for class org.jmol.shape.Axes
 
axes - Variable in class org.jmol.shapespecial.DrawMesh
 
axes - Variable in class org.jmol.symmetry.PointGroup
 
AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
axesAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
axesAreTainted - Variable in class org.jmol.viewer.Viewer
 
axescolor - Static variable in class org.jmol.script.T
 
axesLengths - Variable in class org.jmol.util.ModulationSet
 
axesMaxN - Static variable in class org.jmol.symmetry.PointGroup
 
axesmode - Static variable in class org.jmol.script.T
 
axesMode - Variable in class org.jmol.viewer.GlobalSettings
 
axesmolecular - Static variable in class org.jmol.script.T
 
axesorientationrasmol - Static variable in class org.jmol.script.T
 
axesOrientationRasmol - Variable in class org.jmol.viewer.GlobalSettings
 
axesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
AxesRenderer - Class in org.jmol.render
 
AxesRenderer() - Constructor for class org.jmol.render.AxesRenderer
 
axesscale - Static variable in class org.jmol.script.T
 
axesScale - Variable in class org.jmol.viewer.GlobalSettings
 
axesTypes - Static variable in class org.jmol.render.AxesRenderer
 
axesunitcell - Static variable in class org.jmol.script.T
 
axeswindow - Static variable in class org.jmol.script.T
 
axis - Variable in class org.jmol.navigate.Navigator
 
axis - Static variable in class org.jmol.script.T
 
axis - Variable in class org.jmol.shapespecial.DrawMesh
 
axis - Variable in class org.jmol.util.Modulation
 
axis1color - Static variable in class org.jmol.script.T
 
axis2color - Static variable in class org.jmol.script.T
 
axis3color - Static variable in class org.jmol.script.T
 
axisA - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisangle - Static variable in class org.jmol.script.T
 
axisangleT - Variable in class org.jmol.viewer.TransformManager
 
axisB - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisChoice - Variable in class org.jmol.symmetry.SpaceGroup
 
axisLabels - Static variable in class org.jmol.render.AxesRenderer
 
axisNX - Static variable in class org.jmol.viewer.JC
 
axisNY - Static variable in class org.jmol.viewer.JC
 
axisNZ - Static variable in class org.jmol.viewer.JC
 
axisPoints - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
axisPoints - Variable in class org.jmol.shape.Axes
 
axisType - Variable in class org.jmol.shape.Axes
 
axisType - Variable in class org.jmol.symmetry.HallRotationTerm
 
axisUnitVector - Variable in class org.jmol.modelsetbio.ProteinStructure
 
axisX - Static variable in class org.jmol.viewer.JC
 
axisXY - Variable in class org.jmol.shape.Axes
 
axisY - Static variable in class org.jmol.viewer.JC
 
axisZ - Static variable in class org.jmol.viewer.JC
 
axW - Variable in class org.jmol.g3d.TriangleRenderer
 
ay - Variable in class org.jmol.g3d.TriangleRenderer
 
az - Variable in class org.jmol.g3d.TriangleRenderer
 
azE - Variable in class org.jmol.g3d.TriangleRenderer
 
azW - Variable in class org.jmol.g3d.TriangleRenderer
 

B

b - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
b - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
b - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
b - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
b - Variable in class org.jmol.dssx.Bridge
 
b - Variable in class org.jmol.jvxl.readers.MapFileReader
 
b - Variable in class org.jmol.minimize.forcefield.Calculation
 
b - Variable in class org.jmol.render.SticksRenderer
 
b - Variable in class org.jmol.util.Rgb16
 
b - Variable in class org.jmol.util.SimpleUnitCell
 
b - Variable in class org.jmol.viewer.ActionManager
 
b1 - Variable in class org.jmol.g3d.HermiteRenderer
 
b2 - Variable in class org.jmol.g3d.HermiteRenderer
 
b8 - Static variable in class org.jmol.jvxl.readers.MrcBinaryReader
 
b_ - Variable in class org.jmol.util.SimpleUnitCell
 
B_ISO - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
babel - Static variable in class org.jmol.script.T
 
babel21 - Static variable in class org.jmol.script.T
 
back - Static variable in class org.jmol.script.T
 
backbone - Static variable in class org.jmol.script.T
 
Backbone - Class in org.jmol.shapebio
 
Backbone() - Constructor for class org.jmol.shapebio.Backbone
 
backbonePt - Variable in class org.jmol.renderbio.NucleicRenderer
 
BackboneRenderer - Class in org.jmol.renderbio
 
BackboneRenderer() - Constructor for class org.jmol.renderbio.BackboneRenderer
 
backboneScreen - Variable in class org.jmol.renderbio.NucleicRenderer
 
backbonesteps - Static variable in class org.jmol.script.T
 
backboneSteps - Variable in class org.jmol.viewer.GlobalSettings
 
backface_cull - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
background - Static variable in class org.jmol.script.T
 
backgroundColix - Variable in class org.jmol.export.___Exporter
 
backgroundColix - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
backgroundcolor - Static variable in class org.jmol.script.T
 
BackgroundColorWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
 
backgroundImage - Variable in class org.jmol.util.GData
 
backgroundImageFileName - Variable in class org.jmol.viewer.GlobalSettings
 
backgroundmodel - Static variable in class org.jmol.script.T
 
backgroundModelIndex - Variable in class org.jmol.viewer.AnimationManager
 
backgroundTransparent - Static variable in class org.jmol.g3d.Platform3D
 
backlit - Static variable in class org.jmol.script.T
 
bad() - Method in class org.jmol.script.ScriptError
 
balls - Static variable in class org.jmol.script.T
 
Balls - Class in org.jmol.shape
 
Balls() - Constructor for class org.jmol.shape.Balls
 
BallsRenderer - Class in org.jmol.render
 
BallsRenderer() - Constructor for class org.jmol.render.BallsRenderer
 
bannerFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
BannerFrame - Class in org.openscience.jmol.app.jsonkiosk
A simple class that throws up a white rectangle that has a single centered label.
BannerFrame(int, int) - Constructor for class org.openscience.jmol.app.jsonkiosk.BannerFrame
 
bannerLabel - Variable in class org.openscience.jmol.app.jsonkiosk.BannerFrame
 
barb - Static variable in class org.jmol.script.T
 
barray - Static variable in class org.jmol.script.T
 
baseAtomIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
baseAtomIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
baseAtomIndex - Variable in class org.jmol.modelset.ModelLoader
 
baseBondIndex - Variable in class org.jmol.modelsetbio.Resolver
 
baseCenter - Variable in class org.jmol.modelsetbio.NucleicMonomer
 
baseColor - Variable in class org.jmol.jvxl.data.JvxlData
 
baseFont3d - Variable in class org.jmol.shape.Frank
 
baseGroupIndex - Variable in class org.jmol.modelset.ModelLoader
 
baseModel - Variable in class org.jmol.jsv.JDXMOLParser
 
basemodel - Static variable in class org.jmol.script.T
 
baseModelCount - Variable in class org.jmol.modelset.ModelLoader
 
baseModelIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
baseModelIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
baseModelIndex - Variable in class org.jmol.modelset.ModelLoader
 
BasePair - Class in org.jmol.modelsetbio
 
BasePair() - Constructor for class org.jmol.modelsetbio.BasePair
 
basepair - Static variable in class org.jmol.script.T
 
basePairs - Variable in class org.jmol.dssx.AnnotationParser
 
basePt - Variable in class org.jmol.renderbio.NucleicRenderer
 
baseScreen - Variable in class org.jmol.renderbio.NucleicRenderer
 
baseStrandOffset - Variable in class org.jmol.renderbio.StrandsRenderer
 
baseSymmetry - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
baseSymmetryAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
baseTrajectoryCount - Variable in class org.jmol.modelset.ModelLoader
 
baseUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
BASIS_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
basisBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
BasisFunctionReader - Class in org.jmol.adapter.readers.quantum
 
BasisFunctionReader() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
BasisFunctionReader.MOEnergySorter - Class in org.jmol.adapter.readers.quantum
 
basisFunctions - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
batch_prefix - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
Bbcage - Class in org.jmol.shape
 
Bbcage() - Constructor for class org.jmol.shape.Bbcage
 
BbcageRenderer - Class in org.jmol.render
 
BbcageRenderer() - Constructor for class org.jmol.render.BbcageRenderer
 
bbcageTickEdges - Static variable in class org.jmol.util.BoxInfo
 
bbCenter - Variable in class org.jmol.util.BoxInfo
 
bbCorner0 - Variable in class org.jmol.util.BoxInfo
 
bbCorner1 - Variable in class org.jmol.util.BoxInfo
 
bboxAtoms - Variable in class org.jmol.modelset.ModelSet
 
bboxModels - Variable in class org.jmol.modelset.ModelSet
 
bButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
bbVector - Variable in class org.jmol.util.BoxInfo
 
bbVertices - Variable in class org.jmol.util.BoxInfo
 
bdSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
beenSliced - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
BEG_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
BEG_INS_CODE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
BEG_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
BEGIN - Static variable in class org.jmol.shapecgo.CGOMesh
 
beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
 
beginRendering(M3, boolean, boolean, boolean) - Method in class org.jmol.util.GData
 
beginRendering(boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
best - Static variable in class org.jmol.script.T
 
beta - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
beta - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
beta - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
beta - Variable in class org.jmol.jvxl.readers.MapFileReader
 
beta - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
beta - Variable in class org.jmol.util.SimpleUnitCell
 
betas - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
bfactor - Variable in class org.jmol.adapter.smarter.Atom
 
bfactor100Hi - Variable in class org.jmol.modelset.AtomCollection
 
bfactor100Lo - Variable in class org.jmol.modelset.AtomCollection
 
bfactor100s - Variable in class org.jmol.modelset.AtomCollection
 
bfactorMax - Variable in class org.jmol.shapebio.BioShape
 
bfactorMin - Variable in class org.jmol.shapebio.BioShape
 
BFXN_ANGL - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
bg_gradient - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
bg_image_filename - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
bg_image_linear - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
bg_image_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
bg_image_tilesize - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
bg_rgb - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
bg_rgb_bottom - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
bg_rgb_top - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
bgargb - Variable in class org.jmol.g3d.TextString
 
bgcolix - Variable in class org.jmol.modelset.Object2d
 
bgcolix - Variable in class org.jmol.render.LabelsRenderer
 
bgcolixes - Variable in class org.jmol.shape.Labels
 
bgcolor - Variable in class org.jmol.applet.AppletWrapper
 
bgcolor - Variable in class org.jmol.util.GData
 
bgColor - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
bGlobals - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
bgRgb - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bgRGB - Variable in class org.jmol.g3d.PixelatorShaded
 
BGYOR - Static variable in class org.jmol.util.ColorEncoder
 
bilbaoContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
BilbaoReader - Class in org.jmol.adapter.readers.xtal
Bilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML.
BilbaoReader() - Constructor for class org.jmol.adapter.readers.xtal.BilbaoReader
 
bin - Static variable in class org.jmol.script.T
 
binary - Static variable in class org.jmol.script.T
 
BinaryDcdReader - Class in org.jmol.adapter.readers.more
DCD binary trajectory file reader.
BinaryDcdReader() - Constructor for class org.jmol.adapter.readers.more.BinaryDcdReader
 
binaryDoc - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
binaryDoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
binarydoc - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
binaryOp(T, SV, SV) - Method in class org.jmol.script.ScriptMathProcessor
 
bind - Static variable in class org.jmol.script.T
 
bind(String, String) - Method in class org.jmol.viewer.ActionManager
 
bindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
 
bindAction(String, String) - Method in class org.jmol.viewer.Viewer
 
Binding - Class in org.jmol.viewer.binding
 
Binding() - Constructor for class org.jmol.viewer.binding.Binding
 
bindings - Variable in class org.jmol.viewer.binding.Binding
 
bindName(int, String) - Method in class org.jmol.viewer.binding.Binding
 
BINFLOAT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
BINGET - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
BININT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
BININT1 - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
BININT2 - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
BINPUT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
BINSTRING - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
BINUNICODE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
bioAtoms - Variable in class org.jmol.smiles.SmilesSearch
 
bioModel - Variable in class org.jmol.modelset.ModelSet
 
BioModel - Class in org.jmol.modelsetbio
 
BioModel(ModelSet, int, int, String, Properties, Map<String, Object>) - Constructor for class org.jmol.modelsetbio.BioModel
 
biomtChainAtomCounts - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
BioPolymer - Class in org.jmol.modelsetbio
 
BioPolymer() - Constructor for class org.jmol.modelsetbio.BioPolymer
 
bioPolymer - Variable in class org.jmol.modelsetbio.Monomer
 
bioPolymer - Variable in class org.jmol.shapebio.BioShape
 
bioPolymerCount - Variable in class org.jmol.dssx.DSSP
 
bioPolymerCount - Variable in class org.jmol.modelsetbio.BioModel
 
bioPolymerIndexInModel - Variable in class org.jmol.modelsetbio.BioPolymer
 
bioPolymers - Variable in class org.jmol.dssx.DSSP
 
bioPolymers - Variable in class org.jmol.modelsetbio.BioModel
 
BioShape - Class in org.jmol.shapebio
 
BioShape(BioShapeCollection, int, BioPolymer) - Constructor for class org.jmol.shapebio.BioShape
 
BioShapeCollection - Class in org.jmol.shapebio
Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape for each BioPolymer in the model set.
BioShapeCollection() - Constructor for class org.jmol.shapebio.BioShapeCollection
 
BioShapeRenderer - Class in org.jmol.renderbio
 
BioShapeRenderer() - Constructor for class org.jmol.renderbio.BioShapeRenderer
 
bioShapes - Variable in class org.jmol.shapebio.BioShapeCollection
 
biosymmetry - Variable in class org.jmol.modelset.Model
 
biosymmetryCount - Variable in class org.jmol.modelset.Model
 
bioType - Variable in class org.jmol.smiles.SmilesAtom
 
bioType - Variable in class org.jmol.smiles.SmilesParser
 
BIRTH - Static variable in class org.jmol.multitouch.ActionManagerMT
 
BITS_PER_WORD - Static variable in class org.jmol.java.BS
 
bitset - Static variable in class org.jmol.script.T
 
bitSetForModelFileNumber(int) - Method in class org.jmol.script.ScriptExpr
 
BLACK - Static variable in class org.jmol.util.C
 
BLOCK_ATOMS - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
 
BLOCK_CALC - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
 
BLOCK_MAGRES - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
 
BLOCK_NEW - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
 
BLOCK_NONE - Static variable in class org.jmol.adapter.readers.xtal.MagresReader
 
blockCubeData - Variable in class org.jmol.jvxl.readers.Parameters
 
blockdata - Static variable in class org.jmol.script.T
 
BLUE - Static variable in class org.jmol.util.C
 
bnd(int, int) - Method in class org.jmol.viewer.ActionManager
 
BNode - Interface in org.jmol.util
 
bo - Variable in class org.jmol.modelset.BondCollection
 
bohr_per_angstrom - Static variable in class org.jmol.quantum.QuantumCalculation
 
BOND - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
Bond - Class in org.jmol.adapter.smarter
 
Bond(int, int, int) - Constructor for class org.jmol.adapter.smarter.Bond
 
bond - Variable in class org.jmol.adapter.smarter.BondIterator
 
Bond - Class in org.jmol.modelset
 
Bond(Atom, Atom, int, short, short) - Constructor for class org.jmol.modelset.Bond
 
bond - Variable in class org.jmol.render.SticksRenderer
 
bond - Variable in class org.jmol.shapespecial.Dipole
 
BOND_AROMATIC - Static variable in class org.jmol.util.Edge
 
BOND_AROMATIC_DOUBLE - Static variable in class org.jmol.util.Edge
 
BOND_AROMATIC_MASK - Static variable in class org.jmol.util.Edge
 
BOND_AROMATIC_SINGLE - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_DOUBLE - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_MASK - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_QUADRUPLE - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_SINGLE - Static variable in class org.jmol.util.Edge
 
BOND_COVALENT_TRIPLE - Static variable in class org.jmol.util.Edge
 
BOND_GROWTH_INCREMENT - Static variable in class org.jmol.modelset.BondCollection
 
BOND_H_CALC - Static variable in class org.jmol.util.Edge
 
BOND_H_CALC_MASK - Static variable in class org.jmol.util.Edge
 
BOND_H_MINUS_3 - Static variable in class org.jmol.util.Edge
 
BOND_H_MINUS_4 - Static variable in class org.jmol.util.Edge
 
BOND_H_NUCLEOTIDE - Static variable in class org.jmol.util.Edge
 
BOND_H_PLUS_2 - Static variable in class org.jmol.util.Edge
 
BOND_H_PLUS_3 - Static variable in class org.jmol.util.Edge
 
BOND_H_PLUS_4 - Static variable in class org.jmol.util.Edge
 
BOND_H_PLUS_5 - Static variable in class org.jmol.util.Edge
 
BOND_H_REGULAR - Static variable in class org.jmol.util.Edge
 
BOND_HBOND_SHIFT - Static variable in class org.jmol.util.Edge
 
BOND_HYDROGEN_MASK - Static variable in class org.jmol.util.Edge
 
BOND_NEW - Static variable in class org.jmol.util.Edge
 
BOND_ORDER_ANY - Static variable in class org.jmol.util.Edge
 
BOND_ORDER_NULL - Static variable in class org.jmol.util.Edge
 
BOND_ORDER_UNSPECIFIED - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL01 - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL12 - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL23 - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL32 - Static variable in class org.jmol.util.Edge
 
BOND_PARTIAL_MASK - Static variable in class org.jmol.util.Edge
 
BOND_PYMOL_MULT - Static variable in class org.jmol.util.Edge
 
BOND_PYMOL_SINGLE - Static variable in class org.jmol.util.Edge
 
BOND_STEREO_FAR - Static variable in class org.jmol.util.Edge
 
BOND_STEREO_MASK - Static variable in class org.jmol.util.Edge
Extended Bond Definition Types
BOND_STEREO_NEAR - Static variable in class org.jmol.util.Edge
 
BOND_STRUT - Static variable in class org.jmol.util.Edge
 
BOND_SULFUR_MASK - Static variable in class org.jmol.util.Edge
 
bondArray - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
bondAtoms(Atom, Atom, int, short, BS, float, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
 
bondAtoms(Object, Object, short) - Method in class org.jmol.modelset.ModelLoader
 
bondCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
bondCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
BondCollection - Class in org.jmol.modelset
 
BondCollection() - Constructor for class org.jmol.modelset.BondCollection
 
bondCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
bondCount - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
 
bondCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
bondCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bondCount - Variable in class org.jmol.adapter.smarter.BondIterator
 
bondCount - Variable in class org.jmol.minimize.forcefield.Calculations
 
bondCount - Variable in class org.jmol.minimize.Minimizer
 
bondCount - Variable in class org.jmol.modelset.BondCollection
 
bondCount - Variable in class org.jmol.modelset.BondIteratorSelected
 
bondCount - Variable in class org.jmol.modelset.Model
 
bondcount - Static variable in class org.jmol.script.T
 
bondCount - Variable in class org.jmol.smiles.SmilesAtom
 
bondCount - Variable in class org.jmol.viewer.Connections
 
bondCount0 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
bondData - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
bondData - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
bondedAtoms - Variable in class org.jmol.minimize.MinAtom
 
bondedOnly - Variable in class org.jmol.shapespecial.Polyhedra
 
bondFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
bondFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
bondIndex0 - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bonding_vdw_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
bondingRadii - Variable in class org.jmol.modelset.AtomCollection
 
bondingradius - Static variable in class org.jmol.script.T
 
bondingversion - Static variable in class org.jmol.script.T
 
bondingVersion - Static variable in class org.jmol.util.Elements
 
bondingVersion - Variable in class org.jmol.viewer.GlobalSettings
 
bondingVersion - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
BondIterator - Class in org.jmol.adapter.smarter
 
BondIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.BondIterator
 
BondIterator - Interface in org.jmol.modelset
 
BondIteratorSelected - Class in org.jmol.modelset
 
BondIteratorSelected(Bond[], int, int, BS, boolean) - Constructor for class org.jmol.modelset.BondIteratorSelected
 
bondmode - Static variable in class org.jmol.script.T
 
bondmodeor - Static variable in class org.jmol.script.T
 
bondModeOr - Variable in class org.jmol.viewer.GlobalSettings
 
bondMutually(Atom, Atom, int, short, float) - Method in class org.jmol.modelset.BondCollection
 
bondOrder - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
bondOrder - Variable in class org.jmol.render.SticksRenderer
 
bondorder - Static variable in class org.jmol.script.T
 
bondPicked(int) - Method in class org.jmol.viewer.ActionManager
 
bondpicking - Static variable in class org.jmol.script.T
 
bondPicking - Variable in class org.jmol.viewer.GlobalSettings
 
bondPickingMode - Variable in class org.jmol.viewer.ActionManager
 
bondradiusmilliangstroms - Static variable in class org.jmol.script.T
 
bondRadiusMilliAngstroms - Variable in class org.jmol.viewer.GlobalSettings
 
bonds - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bonds - Variable in class org.jmol.adapter.smarter.BondIterator
 
bonds - Variable in class org.jmol.minimize.MinAtom
 
bonds - Variable in class org.jmol.minimize.Minimizer
 
bonds - Variable in class org.jmol.modelset.Atom
MAY BE NULL
bonds - Variable in class org.jmol.modelset.BondIteratorSelected
 
bonds - Static variable in class org.jmol.script.T
 
bonds - Variable in class org.jmol.smiles.SmilesAtom
 
bondsBackbone - Variable in class org.jmol.render.SticksRenderer
 
bondSelectionModeOr - Variable in class org.jmol.modelset.BondIteratorSelected
 
BondSet - Class in org.jmol.modelset
 
BondSet() - Constructor for class org.jmol.modelset.BondSet
 
bondset - Static variable in class org.jmol.script.T
 
bondsOr - Variable in class org.jmol.smiles.SmilesBond
 
BondSorter() - Constructor for class org.jmol.modelsetbio.Resolver.BondSorter
 
bondtolerance - Static variable in class org.jmol.script.T
 
bondTolerance - Variable in class org.jmol.viewer.GlobalSettings
 
bondTolerance - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
bondType - Variable in class org.jmol.modelset.BondIteratorSelected
 
bondTypes - Variable in class org.jmol.adapter.readers.cif.CifReader
 
booleanparam - Static variable in class org.jmol.script.T
 
booleanSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bOptions - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
border - Variable in class org.openscience.jmol.app.JmolApp
 
border - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
BORDERCOLOR - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
 
BORDERSIZE - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
 
bottom - Static variable in class org.jmol.script.T
 
bottomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
boundaryPlaneCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
boundbox - Static variable in class org.jmol.script.T
 
boundBox - Variable in class org.jmol.shapespecial.Draw
 
boundboxAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
boundBoxCenter - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
boundboxcolor - Static variable in class org.jmol.script.T
 
boundBoxNegCorner - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
boundBoxPosCorner - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
boundingBox - Variable in class org.jmol.jvxl.data.JvxlData
 
boundingBox - Variable in class org.jmol.jvxl.readers.Parameters
 
boundingBox - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
Box(String) - Static method in class org.jmol.popup.MainPopupResourceBundle
 
boxFaces - Static variable in class org.jmol.renderbio.RocketRenderer
 
boxHeight - Variable in class org.jmol.modelset.Object2d
 
boxInfo - Variable in class org.jmol.modelset.ModelSet
 
BoxInfo - Class in org.jmol.util
 
BoxInfo() - Constructor for class org.jmol.util.BoxInfo
 
boxVec - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
boxWidth - Variable in class org.jmol.modelset.Object2d
 
boxX - Variable in class org.jmol.modelset.Object2d
 
boxXY - Variable in class org.jmol.modelset.Object2d
 
boxXY - Variable in class org.jmol.render.LabelsRenderer
 
boxY - Variable in class org.jmol.modelset.Object2d
 
boxYoff2 - Variable in class org.jmol.modelset.Text
 
bps - Variable in class org.jmol.modelsetbio.NucleicMonomer
 
br - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
br - Variable in class org.jmol.jvxl.readers.XmlReader
 
braceCount - Variable in class org.jmol.script.ScriptCompiler
 
braceCount - Variable in class org.jmol.script.ScriptMathProcessor
 
braceCount - Variable in class org.jmol.smiles.SmilesParser
 
bracketCount - Variable in class org.jmol.script.ScriptCompiler
 
branch - Static variable in class org.jmol.script.T
 
branchLevel - Variable in class org.jmol.smiles.SmilesParser
 
breakAt(int) - Method in class org.jmol.script.ScriptEval
 
breakcmd - Static variable in class org.jmol.script.T
 
breakOutAtomTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
breakOutBondTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
breakOutTokens(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
brickLayer - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
brickLayerByteCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
brickLayerVoxelCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
brickRowByteCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
Bridge - Class in org.jmol.dssx
A class for cataloging ladder bridges in a DSSP calculation
Bridge(Atom, Atom, Map<int[][], Boolean>) - Constructor for class org.jmol.dssx.Bridge
 
bridgesA - Variable in class org.jmol.dssx.DSSP
 
bridgesP - Variable in class org.jmol.dssx.DSSP
 
brillouin - Static variable in class org.jmol.script.T
 
browseButton - Variable in class org.openscience.chimetojmol.ChimePanel
 
BS - Class in org.jmol.java
a fast 64-bit BitSet optimized as 32-bit in Java2Script -- about 25 times faster than java.util.BitSet in JavaScript.
BS() - Constructor for class org.jmol.java.BS
Creates a new bit set.
bs - Variable in class org.jmol.jvxl.data.MeshData.SSet
 
bs14 - Variable in class org.jmol.minimize.MinAtom
 
bsA() - Method in class org.jmol.viewer.Viewer
 
bsAdded - Variable in class org.jmol.modelset.Group
 
bsAddedHydrogens - Variable in class org.jmol.modelsetbio.Resolver
 
bsAddedMask - Variable in class org.jmol.modelsetbio.Resolver
 
bsAll - Variable in class org.jmol.modelset.ModelSet
 
bsAllModels - Variable in class org.jmol.shapespecial.Draw
 
bsAnions - Static variable in class org.jmol.util.Elements
 
bsAromatic - Variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
bsAromatic - Variable in class org.jmol.modelset.BondCollection
 
bsAromatic - Variable in class org.jmol.smiles.SmilesGenerator
 
bsAromatic - Variable in class org.jmol.smiles.SmilesSearch
 
bsAromatic5 - Variable in class org.jmol.smiles.SmilesSearch
 
bsAromatic6 - Variable in class org.jmol.smiles.SmilesSearch
 
bsAromaticDouble - Variable in class org.jmol.modelset.BondCollection
 
bsAromaticSingle - Variable in class org.jmol.modelset.BondCollection
 
bsAssigned - Variable in class org.jmol.modelsetbio.Resolver
 
bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
bsAtomMinMax - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
bsAtomOK - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
bsAtoms - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
bsAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
bsAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsAtoms - Variable in class org.jmol.adapter.smarter.AtomIterator
 
bsAtoms - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bsAtoms - Variable in class org.jmol.adapter.smarter.BondIterator
 
bsAtoms - Variable in class org.jmol.minimize.Minimizer
 
bsAtoms - Variable in class org.jmol.modelset.Model
 
bsAtoms - Variable in class org.jmol.symmetry.PointGroup
 
bsAtoms - Variable in class org.jmol.thread.SpinThread
 
bsAtoms1 - Variable in class org.jmol.modelset.StateScript
 
bsAtoms2 - Variable in class org.jmol.modelset.StateScript
 
bsAtomsDeleted - Variable in class org.jmol.modelset.Model
 
bsAtomsForHs - Variable in class org.jmol.modelsetbio.Resolver
 
bsBackbone - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
 
bsBad - Variable in class org.jmol.dssx.DSSP
 
bsBadIndex - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
bsBgColixSet - Variable in class org.jmol.shape.Labels
 
bsBonds - Variable in class org.jmol.modelset.StateScript
 
bsBondsDn - Variable in class org.jmol.smiles.SmilesGenerator
 
bsBondsUp - Variable in class org.jmol.smiles.SmilesGenerator
 
bsBranches - Variable in class org.jmol.thread.SpinThread
 
bsBytesExcluded - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
bsCartoon - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsCarve - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsCations - Static variable in class org.jmol.util.Elements
 
bsCheck - Variable in class org.jmol.smiles.SmilesSearch
 
bsClickable - Variable in class org.jmol.modelset.AtomCollection
 
bsColixSet - Variable in class org.jmol.shape.Shape
 
bsConnected - Variable in class org.jmol.adapter.readers.cif.CifReader
 
bsDeleted - Variable in class org.jmol.viewer.SelectionManager
 
bsDisplay - Variable in class org.jmol.shape.MeshCollection
 
bsDisplay - Variable in class org.jmol.util.MeshSurface
 
bsDisplay - Variable in class org.jmol.viewer.AnimationManager
 
bsExclude - Variable in class org.jmol.adapter.readers.cif.CifReader
 
bsExcluded - Variable in class org.jmol.jvxl.readers.Parameters
 
bsExcluded - Variable in class org.jmol.quantum.QuantumCalculation
 
bsExcludedPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsExcludedTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsExcludedVertices - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
bsFixed - Variable in class org.jmol.minimize.forcefield.ForceField
 
bsFixed - Variable in class org.jmol.minimize.Minimizer
 
bsFixed - Variable in class org.jmol.viewer.SelectionManager
 
bsFixedDefault - Variable in class org.jmol.minimize.Minimizer
 
bsFontSet - Variable in class org.jmol.shape.Labels
 
bsForPass2 - Variable in class org.jmol.render.SticksRenderer
 
bsFound - Variable in class org.jmol.smiles.SmilesSearch
 
bsFrameOffsets - Variable in class org.jmol.viewer.Viewer
 
bsFree - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
bsHandles - Variable in class org.jmol.renderspecial.DrawRenderer
 
bsHidden - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsHidden - Variable in class org.jmol.modelset.AtomCollection
 
bsHidden - Variable in class org.jmol.viewer.SelectionManager
 
bsHighlight - Variable in class org.jmol.shape.Halos
 
bsHydrogen - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsIgnore - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
bsIgnore - Variable in class org.jmol.jvxl.readers.Parameters
 
bsIgnore - Variable in class org.jmol.shapespecial.Dots
 
bsIgnored - Variable in class org.jmol.atomdata.AtomData
 
bsIncludingH - Variable in class org.jmol.smiles.SmilesGenerator
 
bsLabeled - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsLineBonds - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsLocale - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
bsMeshesVisible - Variable in class org.jmol.shapespecial.DrawMesh
 
bsMinFixed - Variable in class org.jmol.minimize.Minimizer
 
bsModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
bsModels - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
 
bsModelsDefined - Variable in class org.jmol.adapter.smarter.StructureIterator
 
bsModulated - Variable in class org.jmol.modelset.AtomCollection
 
bsMolecule - Variable in class org.jmol.adapter.readers.cif.CifReader
 
bsMolecule - Variable in class org.jmol.shapespecial.Dipole
 
bsMolecules - Variable in class org.jmol.atomdata.AtomData
 
bsMyIgnored - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsMySelected - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
bsMySelected - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsNearby - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsNonbonded - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsNoSurface - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsNucleic - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsOK - Variable in class org.jmol.quantum.NciCalculation
 
bsOn - Variable in class org.jmol.shapespecial.Dots
 
bsOrderSet - Variable in class org.jmol.shape.Sticks
 
Bspf - Class in org.jmol.bspt
A Binary Space Partitioning Forest
Bspf(int) - Constructor for class org.jmol.bspt.Bspf
 
bspf - Variable in class org.jmol.modelset.AtomCollection
Binary Space Partitioning Forest
bspf - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
bsPolygons - Variable in class org.jmol.render.MeshRenderer
 
bsPolygons - Variable in class org.jmol.util.MeshSurface
 
bsPolygonsToExport - Variable in class org.jmol.render.MeshRenderer
 
Bspt - Class in org.jmol.bspt
a Binary Space Partitioning Tree
Bspt(int, int) - Constructor for class org.jmol.bspt.Bspt
Create a bspt with the specified number of dimensions.
bspt - Variable in class org.jmol.bspt.CubeIterator
 
bspt - Variable in class org.jmol.bspt.Element
 
bspts - Variable in class org.jmol.bspt.Bspf
 
bsptsValid - Variable in class org.jmol.bspt.Bspf
 
bsr - Variable in class org.jmol.renderbio.NucleicRenderer
 
bsRenderableAtoms - Variable in class org.jmol.viewer.ShapeManager
 
bsRenderMesh - Variable in class org.jmol.renderbio.BioShapeRenderer
 
bsRequired - Variable in class org.jmol.smiles.SmilesSearch
 
bsReturn - Variable in class org.jmol.smiles.SmilesSearch
 
bsRotateBranch - Variable in class org.jmol.viewer.Viewer
 
bsSelected - Variable in class org.jmol.atomdata.AtomData
 
bsSelected - Variable in class org.jmol.jvxl.readers.Parameters
 
bsSelected - Variable in class org.jmol.minimize.Minimizer
 
bsSelected - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
bsSelected - Variable in class org.jmol.modelset.BondIteratorSelected
 
bsSelected - Variable in class org.jmol.quantum.MepCalculation
 
bsSelected - Variable in class org.jmol.shape.Measures
 
bsSelected - Variable in class org.jmol.shapebio.Backbone
 
bsSelected - Variable in class org.jmol.shapespecial.Dots
 
bsSelected - Variable in class org.jmol.smiles.SmilesGenerator
 
bsSelected - Variable in class org.jmol.smiles.SmilesSearch
 
bsSelectedAtoms - Variable in class org.jmol.viewer.TransformManager
 
bsSelectedMonomers - Variable in class org.jmol.modelsetbio.BioPolymer
 
bsSelection - Variable in class org.jmol.viewer.SelectionManager
 
bsSelectRange(T, int) - Static method in class org.jmol.script.SV
 
bsSelectToken(T) - Static method in class org.jmol.script.SV
 
bsSelectVar(SV) - Static method in class org.jmol.script.SV
 
bsSets - Variable in class org.jmol.adapter.readers.cif.CifReader
 
bsSizeDefault - Variable in class org.jmol.shape.AtomShape
 
bsSizeSet - Variable in class org.jmol.shape.Shape
 
bsSlabDisplay - Variable in class org.jmol.util.MeshSurface
 
bsSlabGhost - Variable in class org.jmol.util.MeshSurface
 
bsSolvent - Variable in class org.jmol.jvxl.readers.Parameters
 
bsStickBonds - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsStructureDefined - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
bsStructuredModels - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
bsSubset - Variable in class org.jmol.viewer.SelectionManager
 
bsSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
bsSurface - Variable in class org.jmol.modelset.AtomCollection
 
bsSurfaceDone - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
bsSurfacePoints - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
bsSurfaceVoxels - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
bsSymmetry - Variable in class org.jmol.adapter.smarter.Atom
 
bsSymmetry - Variable in class org.jmol.modelset.ModelSet
 
bsTaint - Variable in class org.jmol.minimize.Minimizer
 
bsTemp - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
bsTemp - Variable in class org.jmol.renderbio.BioShapeRenderer
 
bsTemp - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
bsTemp - Variable in class org.jmol.shape.Mesh
 
bsTemp - Variable in class org.jmol.shapespecial.Polyhedra
 
bsTemp - Variable in class org.jmol.smiles.VTemp
 
bsTemp - Variable in class org.jmol.viewer.SelectionManager
 
bsToDo - Variable in class org.jmol.smiles.SmilesGenerator
 
bsTranslucent - Variable in class org.jmol.render.RepaintManager
 
bsUniqueBonds - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
bsUserVdws - Variable in class org.jmol.viewer.Viewer
 
BSUtil - Class in org.jmol.util
 
BSUtil() - Constructor for class org.jmol.util.BSUtil
 
bsValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bsVdw - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
bsVdw - Variable in class org.jmol.minimize.MinAtom
 
bsVdw - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
bsVertexCount - Variable in class org.jmol.shapespecial.Polyhedra
 
bsVertices - Variable in class org.jmol.shapespecial.Polyhedra
 
bsVisible - Variable in class org.jmol.modelset.AtomCollection
 
bsVisible - Variable in class org.jmol.renderbio.BioShapeRenderer
 
bsVisibleModels - Variable in class org.jmol.viewer.AnimationManager
 
bsVoxelBitSet - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
bsVoxels - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
bTest - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
btSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
BTYPE - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
BUFF - Static variable in class org.jmol.minimize.forcefield.MMFFESCalc
 
buffer - Variable in class org.openscience.jmol.app.InputScannerThread
 
bufferedImage - Variable in class org.jmol.g3d.Platform3D
 
bufferHeight - Variable in class org.jmol.g3d.Platform3D
 
bufferSize - Variable in class org.jmol.g3d.Platform3D
 
bufferSize - Variable in class org.jmol.util.GData
 
bufferSizeT - Variable in class org.jmol.g3d.Platform3D
 
bufferWidth - Variable in class org.jmol.g3d.Platform3D
 
build - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
BUILD - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
buildAdvancedPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
buildAtomsPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buildBasicPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
buildBondPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buildBox(P3, V3, V3, V3) - Method in class org.jmol.renderbio.RocketRenderer
 
buildButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
buildButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
buildDispPanel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
buildFilePanel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
buildFilePanel() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
buildLeftPanel() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
buildPolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
 
buildRightPanel() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
buildScene(String, Lst<Object>, Map<String, Lst<Object>>, Map<String, Lst<Object>>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Build a scene at file reading time.
buildSpaceGroup(String) - Method in class org.jmol.symmetry.SpaceGroup
 
buildStructure(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
buildStructure(String) - Method in class org.jmol.popup.MainPopupResourceBundle
 
buildStructure(String) - Method in class org.jmol.popup.PopupResource
 
button - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
 
BUTTON_MASK - Static variable in class org.jmol.viewer.binding.Binding
 
button_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
button_mode_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
BUTTON_MODIFIER_MASK - Static variable in class org.jmol.viewer.binding.Binding
 
buttonGroup - Variable in class org.jmol.popup.AwtSwingPopupHelper
 
buttonGroup - Variable in class org.jmol.popup.GenericSwingPopup
 
buttonGroup - Variable in class org.jmol.popup.JSSwingPopupHelper
 
buttonModelkit - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
buttonPanel - Variable in class org.jmol.console.ScriptEditor
 
buttonPanel - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
buttonRotate - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
bValue(T) - Static method in class org.jmol.script.SV
 
BW - Static variable in class org.jmol.util.ColorEncoder
 
BWR - Static variable in class org.jmol.util.ColorEncoder
 
bwSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
byChain - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
BYELEMENT_JMOL - Static variable in class org.jmol.util.ColorEncoder
 
BYELEMENT_PREFIX - Static variable in class org.jmol.util.ColorEncoder
 
BYELEMENT_RASMOL - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_AMINO - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_PREFIX - Static variable in class org.jmol.util.ColorEncoder
 
BYRESIDUE_SHAPELY - Static variable in class org.jmol.util.ColorEncoder
 
bySymop - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
byteArrayOS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
byteFactor - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
bytes - Variable in class org.jmol.io.FileReader
 

C

c - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
c - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
c - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
c - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
c - Variable in class org.jmol.jvxl.readers.MapFileReader
 
c - Variable in class org.jmol.minimize.forcefield.Calculation
 
C - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
c - Variable in class org.jmol.quantum.MOCalculation
 
c - Static variable in class org.jmol.quantum.NciCalculation
 
C - Class in org.jmol.util
Note: Color table is now in javajs/util/CU.java
C() - Constructor for class org.jmol.util.C
 
c - Variable in class org.jmol.util.SimpleUnitCell
 
c1 - Variable in class org.jmol.g3d.HermiteRenderer
 
C1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c2 - Variable in class org.jmol.g3d.HermiteRenderer
 
C2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c2 - Static variable in class org.jmol.symmetry.PointGroup
 
C2P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c3 - Static variable in class org.jmol.symmetry.PointGroup
 
C3P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
C4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c4 - Static variable in class org.jmol.symmetry.PointGroup
 
C4P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
C5 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c5 - Static variable in class org.jmol.symmetry.PointGroup
 
C5P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
C6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c6 - Static variable in class org.jmol.symmetry.PointGroup
 
C8 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
c8 - Static variable in class org.jmol.symmetry.PointGroup
 
c_ - Variable in class org.jmol.util.SimpleUnitCell
 
CA - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
cA_ - Variable in class org.jmol.util.SimpleUnitCell
 
cache - Static variable in class org.jmol.script.T
 
cache() - Method in class org.jmol.scriptext.CmdExt
 
cache - Variable in class org.jmol.viewer.FileManager
 
cache_display - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cache_frames - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cache_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cache_memory - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cache_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cacheClear() - Method in class org.jmol.viewer.FileManager
 
cacheClear() - Method in class org.jmol.viewer.Viewer
 
cacheFileByName(String, boolean) - Method in class org.jmol.appletjs.Jmol
 
cacheFileByName(String, boolean) - Method in class org.jmol.viewer.Viewer
 
cacheFileByNameAdd(String, boolean) - Method in class org.jmol.viewer.FileManager
 
cacheGet(String, boolean) - Method in class org.jmol.viewer.FileManager
 
cacheID - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
cacheList() - Method in class org.jmol.viewer.FileManager
 
cacheName - Variable in class org.jmol.script.FileLoadThread
 
cachePngFiles() - Method in class org.jmol.viewer.Viewer
 
cachePngjFile(JmolBinary, String[]) - Method in interface org.jmol.api.JmolZipUtilities
 
cachePngjFile(JmolBinary, String[]) - Method in class org.jmol.io.JmolUtil
 
cachePut(String, Object) - Method in class org.jmol.appletjs.Jmol
 
cachePut(String, Object) - Method in class org.jmol.viewer.FileManager
 
cachePut(String, Object) - Method in class org.jmol.viewer.Viewer
JSInterface -- allows saving files in memory for later retrieval
caf - Variable in class org.jmol.viewer.AnimationManager
current animation frame
CageRenderer - Class in org.jmol.render
 
CageRenderer() - Constructor for class org.jmol.render.CageRenderer
 
cai - Variable in class org.jmol.viewer.AnimationManager
 
calc(int, boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
calc - Variable in class org.jmol.minimize.forcefield.ForceField
 
calc1Screen(P3, V3, short, float, P3i) - Method in class org.jmol.renderbio.BioShapeRenderer
 
CALC_ANGLE - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_DISTANCE - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_ES - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_MAX - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_OOP - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_STRETCH_BEND - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_TORSION - Static variable in class org.jmol.minimize.forcefield.Calculations
 
CALC_VDW - Static variable in class org.jmol.minimize.forcefield.Calculations
 
calcArgbEndcap(boolean, boolean) - Method in class org.jmol.g3d.CylinderRenderer
 
calcArgbsGreyscale() - Static method in class org.jmol.util.C
 
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.api.JmolViewer
 
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.modelset.ModelSet
 
calcAtomsMinMax(BS, BoxInfo) - Method in class org.jmol.viewer.Viewer
 
calcAxis() - Method in class org.jmol.modelsetbio.Helix
 
calcAxis() - Method in class org.jmol.modelsetbio.ProteinStructure
 
calcAxis() - Method in class org.jmol.modelsetbio.Sheet
 
calcBfactorRange(BS) - Method in class org.jmol.modelset.AtomCollection
 
calcBfactorRange() - Method in class org.jmol.shapebio.BioShape
 
calcBioParameters() - Method in class org.jmol.modelsetbio.Monomer
 
calcBoundBoxDimensions(BS, float) - Method in class org.jmol.modelset.ModelSet
 
calcBoundBoxDimensions(BS, float) - Method in class org.jmol.viewer.Viewer
 
calcCameraFactors() - Method in class org.jmol.viewer.TransformManager
sets all camera and scale factors needed by the specific perspective model instantiated
calcContourPoint(float, float, float, P3) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
calcConvexBits() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calcConvexMap(boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calcCosSin(float, float, float) - Method in class org.jmol.g3d.CylinderRenderer
 
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcEtaThetaAngles() - Method in class org.jmol.modelsetbio.NucleicPolymer
 
calcFactors(int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
calcHbondEnergy(P3, P3, AminoMonomer, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
based on RasMol 2.7.2.1.1 model checkDistances: When we are seriously looking for H bonds, we want to also check that distCN > distCH and that the OH distance is less than 3 Angstroms.
calcLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcLegendre(int) - Method in class org.jmol.util.Modulation
 
calcMeanPositionalDisplacement(int) - Method in class org.jmol.shapebio.BioShape
Calculates the mean positional displacement in milliAngstroms.
calcMetrics() - Method in class org.jmol.shape.Frank
 
calcNavCameraFactors(float) - Method in class org.jmol.viewer.TransformManager
 
calcNavigationDepthPercent() - Method in class org.jmol.navigate.Navigator
 
calcNavigationPoint() - Method in interface org.jmol.api.JmolNavigatorInterface
 
calcNavigationPoint() - Method in class org.jmol.navigate.Navigator
 
calcNavigationPoint() - Method in class org.jmol.viewer.TransformManager
All the magic happens here.
calcNavSlabAndDepthValues() - Method in class org.jmol.navigate.Navigator
 
calcOptions - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
calcParameters() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcPhiPsiAngles() - Method in class org.jmol.modelsetbio.BioPolymer
 
calcPhiPsiAngles2(AminoMonomer, AminoMonomer) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcPlane(int, float[]) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
Fill this plane with data based on the current set of raw data planes.
calcPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
For reduced density only; coloring is done point by point.
calcPoints(int, boolean) - Method in class org.jmol.g3d.CylinderRenderer
 
calcRasmolHydrogenBonds(ModelSet, BS, BS, Lst<Bond>, boolean, int, boolean, BS) - Method in class org.jmol.modelset.Model
 
calcRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS) - Method in class org.jmol.modelset.ModelSet
These are not actual hydrogen bonds.
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calcRasmolHydrogenBonds(ModelSet, BS, BS, Lst<Bond>, boolean, int, boolean, BS) - Method in class org.jmol.modelsetbio.BioModel
 
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
calcRasmolHydrogenBonds(BioPolymer, BS, BS, Lst<Bond>, int, int[][][], boolean, boolean) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
calcRectRubberBand() - Method in class org.jmol.viewer.ActionManager
 
calcRopeMidPoints() - Method in class org.jmol.renderbio.RocketsRenderer
 
calcRotatedPoint(float, int, boolean, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
 
calcRotationRadius(int, P3) - Method in class org.jmol.modelset.ModelSet
 
calcRotationRadiusBs(BS) - Method in class org.jmol.modelset.ModelSet
 
calcs - Variable in class org.jmol.minimize.forcefield.Calculation
 
calcScreenControlPoints() - Method in class org.jmol.renderbio.BioShapeRenderer
 
calcScreenPoints(BS, float, int, int, int) - Method in class org.jmol.renderspecial.DotsRenderer
calculates the screen xy coordinates for the dots or faces
calcScreens(float, short[]) - Method in class org.jmol.renderbio.BioShapeRenderer
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
calcSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
 
calcSelectedGroupsCount(BS) - Method in class org.jmol.modelset.Chain
prior to coloring by group, we need the chain count per chain that is selected
calcSelectedGroupsCount(BS) - Method in class org.jmol.modelset.Model
 
calcSelectedGroupsCount() - Method in class org.jmol.modelset.ModelSet
 
calcSelectedMoleculesCount() - Method in class org.jmol.modelset.ModelSet
 
calcSelectedMonomersCount(BS) - Method in class org.jmol.modelset.Model
 
calcSelectedMonomersCount() - Method in class org.jmol.modelset.ModelSet
 
calcSelectedMonomersCount(BS) - Method in class org.jmol.modelsetbio.BioModel
 
calcSelectedMonomersCount(BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
calcSheetUnitVectors() - Method in class org.jmol.modelsetbio.Sheet
 
calcSlabAndDepthValues() - Method in class org.jmol.viewer.TransformManager
sets slab and depth, possibly using visual range considerations for setting the slab-clipping plane.
calcSP(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
 
calcSphereShading() - Method in class org.jmol.util.Shader
 
calcSurfaceDistances() - Method in class org.jmol.modelset.AtomCollection
 
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager
 
calcTransformMatrix() - Method in class org.jmol.viewer.TransformManager4D
 
calcType - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in interface org.jmol.api.JmolEnvCalc
 
calculate(VolumeDataInterface, BS, P3[], float[], int) - Method in interface org.jmol.api.MepCalculationInterface
 
calculate(RadiusData, float, BS, BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
calculate(VolumeDataInterface, BS, P3[], float[], int) - Method in class org.jmol.quantum.MepCalculation
 
calculate - Static variable in class org.jmol.script.T
 
calculate() - Method in class org.jmol.scriptext.CmdExt
 
calculate(T3, boolean) - Method in class org.jmol.util.ModulationSet
Calculate r_I internal d-space coordinate of an atom.
calculateAllPolymers(ModelSet, Group[], int, int, BS) - Method in class org.jmol.modelset.Model
 
calculateAllPolymers(ModelSet, Group[], int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
 
calculateAnglesInDegrees() - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculateCodes(float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculateCutoff() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
 
calculatedArea - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
calculatedArea - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
calculatedDipole - Variable in class org.jmol.shapespecial.Dipoles
 
calculateDssp(Object[], int, Object, boolean, boolean, boolean) - Method in interface org.jmol.api.DSSPInterface
 
calculateDssp(Object[], int, Object, boolean, boolean, boolean) - Method in class org.jmol.dssx.DSSP
 
calculateDSSRStructure(Viewer, BS) - Method in interface org.jmol.api.JmolAnnotationParser
 
calculateDSSRStructure(Viewer, BS) - Method in class org.jmol.dssx.AnnotationParser
 
calculateDssx(Lst<Bond>, boolean, boolean, boolean) - Method in class org.jmol.modelsetbio.BioModel
 
calculatedVolume - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
calculatedVolume - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
calculateElectronDensity() - Method in class org.jmol.quantum.MOCalculation
 
calculateFormalCharges(BS) - Method in class org.jmol.viewer.Viewer
 
calculateFractionalPoint(float, P3, P3, float, float, P3) - Method in class org.jmol.jvxl.data.VolumeData
 
calculateGeodesicSurface(BS, float) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
calculateGeodesicSurface(BS, float) - Method in class org.jmol.shapesurface.Isosurface
 
calculateHydrogens(BS, int[], boolean, boolean, Lst<Atom>) - Method in class org.jmol.modelset.AtomCollection
get a list of potential H atom positions based on elemental valence and formal charge
calculateMad(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
 
calculateMolecularDipole(int, BS) - Method in class org.jmol.modelset.ModelSet
 
calculateMolecularDipole(BS) - Method in class org.jmol.viewer.Viewer
 
calculatePartialCharges(Bond[], int, Atom[], BS) - Method in interface org.jmol.api.MinimizerInterface
 
calculatePartialCharges(Bond[], int[], Atom[], int[], BS, boolean) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
assign partial charges ala MMFF94
calculatePartialCharges(Bond[], int, Atom[], BS) - Method in class org.jmol.minimize.Minimizer
 
calculatePartialCharges(BS) - Method in class org.jmol.viewer.Viewer
 
calculatePointGroup(BS) - Method in class org.jmol.modelset.ModelSet
 
calculatePointGroupForFirstModel(BS, boolean, boolean, boolean, String, int, float) - Method in class org.jmol.modelset.ModelSet
 
calculatePolymers(Group[], int, int, BS) - Method in class org.jmol.modelset.ModelSet
 
calculatePolymers(ModelSet, Group[], int, int, BS) - Static method in class org.jmol.modelsetbio.BioModel
 
calculateQCoefs(double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
determine simple linear combination assuming simple -3 to 3 no more than two dimensions.
calculateR0(double, double, double, double, double) - Static method in class org.jmol.minimize.forcefield.CalculationsUFF
 
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calculateRamachandranHelixAngle(int, char) - Method in class org.jmol.modelsetbio.BioPolymer
 
calculateRunsFourOrMore(AlphaPolymer.Code[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculateStraightness() - Method in class org.jmol.modelset.ModelSet
 
calculateStraightness() - Method in class org.jmol.viewer.Viewer
 
calculateStraightnessAll(ModelSet) - Method in class org.jmol.modelset.Model
 
calculateStraightnessAll(ModelSet) - Method in class org.jmol.modelsetbio.BioModel
 
calculateStructures(boolean, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.Model
 
calculateStructures(BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
calculateStructures(boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
 
calculateStructures(boolean, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelsetbio.BioModel
 
calculateStructures(BS, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
calculateStructuresAllExcept(BS, boolean, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
allows rebuilding of PDB structures; also accessed by ModelManager from Eval
calculateStruts(ModelSet, BS, BS) - Method in class org.jmol.modelset.Model
 
calculateStruts(BS, BS) - Method in class org.jmol.modelset.ModelSet
see comments in org.jmol.modelsetbio.AlphaPolymer.java Struts are calculated for atoms in bs1 connecting to atoms in bs2.
calculateStruts(ModelSet, BS, BS, Lst<Atom>, float, int, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
Algorithm of George Phillips phillips@biochem.wisc.edu originally a contribution to pyMol as struts.py; adapted here by Bob Hanson for Jmol 1/2010 Return a vector of support posts for rapid prototyping models along the lines of George Phillips for Pymol except on actual molecular segments (biopolymers), not PDB chains (which may or may not be continuous).
calculateStruts(ModelSet, BS, BS) - Method in class org.jmol.modelsetbio.BioModel
 
calculateStruts(ModelSet, BS, BS, Lst<Atom>, float, int, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
calculateStruts(BS, BS) - Method in class org.jmol.viewer.Viewer
 
calculateStrutsStatic(ModelSet, BS, BS, Lst<Atom>, float, int, boolean) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
calculateSurface(BS, float) - Method in class org.jmol.modelset.AtomCollection
 
calculateSurface(BS, float) - Method in class org.jmol.viewer.Viewer
 
calculateVolume(BS, VDW) - Method in class org.jmol.modelset.AtomCollection
 
calculateVolumeOrArea(MeshData, int, boolean, boolean) - Static method in class org.jmol.jvxl.data.MeshData
 
calculateVolumeOrArea(boolean) - Method in class org.jmol.shapesurface.Isosurface
 
Calculation - Class in org.jmol.minimize.forcefield
 
Calculation() - Constructor for class org.jmol.minimize.forcefield.Calculation
 
calculationNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
The number of the calculation being interpreted.
calculationNumber - Variable in class org.jmol.adapter.readers.quantum.QchemReader
The number of the calculation being interpreted.
Calculations - Class in org.jmol.minimize.forcefield
 
Calculations(ForceField, MinAtom[], MinBond[], MinAngle[], MinTorsion[], MinPosition[], Lst<Object[]>) - Constructor for class org.jmol.minimize.forcefield.Calculations
 
calculations - Variable in class org.jmol.minimize.forcefield.Calculations
 
CalculationsMMFF - Class in org.jmol.minimize.forcefield
 
CalculationsMMFF(ForceField, Map<Object, Object>, MinAtom[], MinBond[], MinAngle[], MinTorsion[], MinPosition[], Lst<Object[]>) - Constructor for class org.jmol.minimize.forcefield.CalculationsMMFF
 
CalculationsUFF - Class in org.jmol.minimize.forcefield
 
CalculationsUFF(ForceField, Map<Object, Object>, MinAtom[], MinBond[], MinAngle[], MinTorsion[], MinPosition[], Lst<Object[]>) - Constructor for class org.jmol.minimize.forcefield.CalculationsUFF
 
calculationType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
calculationType - Variable in class org.jmol.jvxl.readers.Parameters
 
calculationType - Variable in class org.jmol.quantum.MOCalculation
 
calcUnitCellMinMax() - Method in class org.jmol.modelset.ModelSet
 
calcVertexPoint(int, int, int, int, P3) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
calcVoxelPlaneDistance(int, int, int) - Method in interface org.jmol.api.VolumeDataInterface
 
calcVoxelPlaneDistance(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
calcVoxelVertexVectors() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
callbacks - Variable in class org.jmol.util.GenericApplet
 
camera - Variable in class org.jmol.viewer.TransformManager
 
cameraDepth - Variable in class org.jmol.modelset.Orientation
 
cameradepth - Static variable in class org.jmol.script.T
 
cameraDepth - Variable in class org.jmol.thread.MoveToThread
 
cameraDepth - Variable in class org.jmol.viewer.TransformManager
 
cameraDepthSetting - Variable in class org.jmol.viewer.TransformManager
 
cameraDistance - Variable in class org.jmol.export.___Exporter
 
cameraDistance - Variable in class org.jmol.viewer.TransformManager
 
cameraDistanceFromCenter - Variable in class org.jmol.viewer.TransformManager
 
cameraPosition - Variable in class org.jmol.export.___Exporter
 
cameraScaleFactor - Variable in class org.jmol.viewer.TransformManager
 
cameraSetting - Variable in class org.jmol.viewer.TransformManager
 
cameraX - Variable in class org.jmol.modelset.Orientation
 
cameraX - Variable in class org.jmol.thread.MoveToThread
 
cameraY - Variable in class org.jmol.modelset.Orientation
 
cameraY - Variable in class org.jmol.thread.MoveToThread
 
canAdd(Bridge) - Method in class org.jmol.dssx.Bridge
 
canBeNormalized(V3d) - Static method in class org.jmol.minimize.Util
 
canBeSquared(double) - Static method in class org.jmol.minimize.Util
 
cancel - Static variable in class org.jmol.script.T
 
cancel() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
cancel() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cancel() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cancelButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
cancelPressed() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Responds to cancel being press- or equivalent eg window closed.
canDoLineTo() - Method in interface org.jmol.api.GenericGraphics
 
canDoLineTo() - Method in class org.jmol.awt.AwtG2D
 
canDoLineTo() - Method in class org.jmol.awtjs2d.JsG2D
 
canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
 
canDownsample - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
canImport(JComponent, DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
canIncrement() - Method in class org.jmol.script.SV
 
CANONICAL_DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
CANONICAL_DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
CANONICAL_FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
CANONICAL_FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
canonicalizeQuantumSubshellTag(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
canonicalSeitzList - Static variable in class org.jmol.symmetry.SpaceGroup
 
canonizeAlphaDigit(char) - Static method in class org.jmol.api.JmolAdapter
 
canonizeAlternateLocationID(char) - Static method in class org.jmol.api.JmolAdapter
 
canonizeInsertionCode(char) - Static method in class org.jmol.api.JmolAdapter
 
canSkipLoad - Variable in class org.jmol.modelset.AtomCollection
 
canvas - Variable in class org.jmol.awtjs2d.Platform
 
cap - Static variable in class org.jmol.script.T
 
capCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
capData(P4, float) - Method in interface org.jmol.api.VolumeDataInterface
 
capData(P4, float) - Method in class org.jmol.jvxl.data.VolumeData
 
capMap - Variable in class org.jmol.util.MeshCapper
initialization only
capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
capOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
capper - Variable in class org.jmol.util.MeshSlicer
 
cappingObject - Variable in class org.jmol.shape.Mesh
 
cappingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
 
capPlanesPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
capture - Static variable in class org.jmol.script.T
 
capture() - Method in class org.jmol.scriptext.CmdExt
 
captureParams - Variable in class org.jmol.viewer.Viewer
 
CapVertex(T3, int) - Constructor for class org.jmol.util.MeshCapper.CapVertex
 
carbohydrate - Static variable in class org.jmol.script.T
 
CarbohydrateMonomer - Class in org.jmol.modelsetbio
 
CarbohydrateMonomer() - Constructor for class org.jmol.modelsetbio.CarbohydrateMonomer
 
CarbohydratePolymer - Class in org.jmol.modelsetbio
 
CarbohydratePolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.CarbohydratePolymer
 
cardinality() - Method in class org.jmol.java.BS
Returns the number of bits set to true in this BitSet.
cardinalityN(int) - Method in class org.jmol.java.BS
 
cardinalityOf(BS) - Static method in class org.jmol.util.BSUtil
cardinality = "total number of set bits"
cartesianOffset - Variable in class org.jmol.symmetry.UnitCell
 
cartesianProduct(T3, T3) - Method in class org.jmol.adapter.readers.xtal.JanaReader
dual-purpose function for cross products, proper rotations, and improper rotations
CARTN_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CARTN_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CARTN_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
cartoon - Static variable in class org.jmol.script.T
 
Cartoon - Class in org.jmol.shapebio
 
Cartoon() - Constructor for class org.jmol.shapebio.Cartoon
 
cartoon_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_cylindrical_helices - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_discrete_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_dumbbell_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_dumbbell_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_dumbbell_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_fancy_helices - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_fancy_sheets - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_flat_cycles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_flat_sheets - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_helix_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_highlight_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_ladder_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_ladder_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_ladder_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_loop_cap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_loop_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_loop_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_nucleic_acid_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_nucleic_acid_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_nucleic_acid_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_oval_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_oval_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_oval_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_power_b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_putty_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_putty_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_putty_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_putty_scale_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_putty_scale_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_putty_scale_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_putty_transform - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_rect_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_rect_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_refine - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_refine_normals - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_refine_tips - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_ring_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_ring_finder - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_ring_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_ring_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_ring_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_ring_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_round_helices - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_sampling - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_side_chain_helper - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_smooth_cycles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_smooth_first - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_smooth_last - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_smooth_loops - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_throw - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_trace_atoms - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_tube_cap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_tube_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_tube_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoon_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cartoonbaseedges - Static variable in class org.jmol.script.T
 
cartoonBaseEdges - Variable in class org.jmol.viewer.GlobalSettings
 
cartoonColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
cartoonFancy - Variable in class org.jmol.viewer.GlobalSettings
 
cartoonLadderMode - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
cartoonladders - Static variable in class org.jmol.script.T
 
cartoonLadders - Variable in class org.jmol.viewer.GlobalSettings
 
CartoonRenderer - Class in org.jmol.renderbio
 
CartoonRenderer() - Constructor for class org.jmol.renderbio.CartoonRenderer
 
cartoonribose - Static variable in class org.jmol.script.T
 
cartoonRibose - Variable in class org.jmol.viewer.GlobalSettings
 
cartoonRockets - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
cartoonrockets - Static variable in class org.jmol.script.T
 
cartoonRockets - Variable in class org.jmol.viewer.GlobalSettings
 
cartoons - Variable in class org.jmol.dialog.FilePreview
 
cartoonsFancy - Variable in class org.jmol.renderbio.BioShapeRenderer
 
cartoonsfancy - Static variable in class org.jmol.script.T
 
cartoonTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
cartoonTypes - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
casecmd - Static variable in class org.jmol.script.T
 
CastepDensityReader - Class in org.jmol.jvxl.readers
 
CastepDensityReader() - Constructor for class org.jmol.jvxl.readers.CastepDensityReader
 
CastepReader - Class in org.jmol.adapter.readers.xtal
CASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer "q={1/4 1/4 0}" "q=ALL" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example note: following was never implemented? -- following this with ".1" ".2" etc.
CastepReader() - Constructor for class org.jmol.adapter.readers.xtal.CastepReader
 
catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
 
catalogStructureUnits(Viewer, SV, int[], Map<String, int[]>, Object, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
 
catalogUnit(Viewer, float[][], String, float, BS, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
Carried out for each unit
catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in interface org.jmol.api.JmolAnnotationParser
 
catalogValidations(Viewer, SV, int[], Map<String, int[]>, Map<String, Integer>, Map<String, Integer>) - Method in class org.jmol.dssx.AnnotationParser
Returns a Lst of property data in the form name(String), data(float[]), modelIndex (Integer), isGroup (Boolean);
catchcmd - Static variable in class org.jmol.script.T
 
cationLookupTable - Static variable in class org.jmol.util.Elements
 
cavity - Static variable in class org.jmol.script.T
 
cavity_cull - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cavityRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
cavityRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
cb - Variable in class org.jmol.dialog.Dialog
 
CB - Static variable in class org.jmol.minimize.forcefield.MMFFAngleCalc
 
cB_ - Variable in class org.jmol.util.SimpleUnitCell
 
cbAxesOrientationRasmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cbClearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
CBK - Enum in org.jmol.c
 
CBK() - Constructor for enum org.jmol.c.CBK
 
cbl - Variable in class org.jmol.viewer.StatusManager
 
cbOpenFilePreview - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cbPerspectiveDepth - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cbShowAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cbShowBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
CC_ATOM_CHARGE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CC_ATOM_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CC_ATOM_SYM - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CC_ATOM_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CC_ATOM_X_IDEAL - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CC_ATOM_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CC_ATOM_Y_IDEAL - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CC_ATOM_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CC_ATOM_Z_IDEAL - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CC_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CCDC_GEOM_BOND_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
cchScript - Variable in class org.jmol.script.ScriptCompiler
 
cchToken - Variable in class org.jmol.script.ScriptCompiler
 
cd - Static variable in class org.jmol.script.T
 
cd(String) - Method in class org.jmol.viewer.Viewer
 
ce - Variable in class org.jmol.util.ColorEncoder
 
ce - Variable in class org.jmol.viewer.ColorManager
 
CELL - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
cell() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
cell() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
cell - Static variable in class org.jmol.script.T
 
cell0 - Variable in class org.jmol.render.UccageRenderer
 
cell1 - Variable in class org.jmol.render.UccageRenderer
 
cellLattice - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
 
cellParameterType - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
cellParamNames - Static variable in class org.jmol.api.JmolAdapter
 
cellParams - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
 
cellParams - Variable in class org.jmol.adapter.readers.xtal.MagresReader
 
cellRange - Variable in class org.jmol.symmetry.SymmetryInfo
 
celOn - Variable in class org.jmol.util.Shader
 
celPower - Variable in class org.jmol.util.Shader
 
celRGB - Variable in class org.jmol.util.Shader
 
celshading - Static variable in class org.jmol.script.T
 
celshadingpower - Static variable in class org.jmol.script.T
 
celZ - Variable in class org.jmol.util.Shader
 
center - Variable in class org.jmol.export.___Exporter
 
center - Variable in class org.jmol.jvxl.readers.Parameters
 
center - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
center - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
 
center - Variable in class org.jmol.modelset.Orientation
 
center - Variable in class org.jmol.navigate.Navigator
 
center - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
center - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
center - Static variable in class org.jmol.script.T
 
center - Variable in class org.jmol.shapespecial.Dipole
 
center - Variable in class org.jmol.shapespecial.Ellipsoid
 
center - Variable in class org.jmol.shapesurface.Isosurface
 
center - Variable in class org.jmol.symmetry.PointGroup
 
center - Variable in class org.jmol.thread.MoveToThread
 
center - Variable in class org.jmol.util.Modulation
 
center - Static variable in class org.jmol.viewer.JC
 
center - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
centerat - Static variable in class org.jmol.script.T
 
centerAt() - Method in class org.jmol.scriptext.CmdExt
 
centerAt(int, int, P3) - Method in class org.jmol.viewer.TransformManager
 
centerAtomIndex - Variable in class org.jmol.symmetry.PointGroup
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
Centers the dialog on the screen.
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Centers the dialog on the screen.
centerDialog() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
centerDipole() - Method in class org.jmol.shapespecial.Dipole
 
centerI - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
centering - Variable in class org.jmol.symmetry.SymmetryOperation
 
centerings - Variable in class org.jmol.symmetry.SymmetryInfo
 
centerParameter(int) - Method in class org.jmol.script.ScriptParam
 
centerParameter(int) - Method in class org.jmol.scriptext.CmdExt
 
centerParameterForModel(int, int) - Method in class org.jmol.script.ScriptParam
 
centers - Variable in class org.jmol.shapespecial.Polyhedra
 
centers - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
centerStart - Variable in class org.jmol.navigate.Navigator
 
centerT - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
centralAtom - Variable in class org.jmol.shapespecial.Polyhedron
 
centralize() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
centroid - Static variable in class org.jmol.script.T
 
centroidPacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
centroidPacked - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
cgdLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CgdReader - Class in org.jmol.adapter.readers.xtal
A reader for TOPOS systre file Crystal Graph Data format.
CgdReader() - Constructor for class org.jmol.adapter.readers.xtal.CgdReader
 
cgo - Static variable in class org.jmol.script.T
 
cgo() - Method in class org.jmol.scriptext.IsoExt
 
CGO - Class in org.jmol.shapecgo
 
CGO() - Constructor for class org.jmol.shapecgo.CGO
 
cgo_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_dot_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_dot_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_ellipsoid_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_line_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_line_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_ray_width_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_shader_ub_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_shader_ub_flags - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_shader_ub_normal - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_sphere_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgo_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cgoMesh - Variable in class org.jmol.rendercgo.CGORenderer
 
cgoMesh - Variable in class org.jmol.shapecgo.CGO
 
CGOMesh - Class in org.jmol.shapecgo
 
CGOMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapecgo.CGOMesh
 
CGORenderer - Class in org.jmol.rendercgo
 
CGORenderer() - Constructor for class org.jmol.rendercgo.CGORenderer
 
cH - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
ch1 - Variable in class org.jmol.modelset.LabelToken
 
Chain - Class in org.jmol.modelset
 
Chain(Model, int, int) - Constructor for class org.jmol.modelset.Chain
 
chain - Variable in class org.jmol.modelset.Group
 
chain - Static variable in class org.jmol.script.T
 
chainAtomCount - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
chainAtomCounts - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
chainAtomMap - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
chaincasesensitive - Static variable in class org.jmol.script.T
 
chainCaseSensitive - Variable in class org.jmol.viewer.GlobalSettings
 
chainCaseSpecified - Variable in class org.jmol.viewer.Viewer
 
chainCount - Variable in class org.jmol.modelset.Model
 
chainID - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
chainID - Variable in class org.jmol.adapter.smarter.Atom
 
chainID - Variable in class org.jmol.modelset.Chain
 
chainList - Variable in class org.jmol.viewer.Viewer
 
chainMap - Variable in class org.jmol.viewer.Viewer
 
chainno - Static variable in class org.jmol.script.T
 
chainOf - Variable in class org.jmol.modelset.ModelLoader
 
chains - Variable in class org.jmol.modelset.Model
 
chainSum - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
chainToUpper(int) - Static method in class org.jmol.modelset.AtomCollection
 
CHANGEABLE_MASK - Static variable in class org.jmol.util.C
 
changeableColixMap - Variable in class org.jmol.util.GData
 
changeColixArgb(int, int) - Method in class org.jmol.util.GData
 
CHAR - Static variable in class org.jmol.shapecgo.CGOMesh
 
characters(char[], int, int) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
charAt(int) - Method in class org.jmol.script.ScriptCompiler
 
charge - Variable in class org.jmol.smiles.SmilesAtom
 
charge - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
chargesFound - Variable in class org.jmol.adapter.readers.simple.MopacReader
 
ChargesOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
chargeSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
chargeType - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
chars - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
check - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
check - Static variable in class org.jmol.script.T
 
check() - Method in class org.jmol.smiles.SmilesMeasure
 
check(int, int, int, int, long, long) - Method in class org.jmol.viewer.MouseState
 
check - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
CHECK1 - Static variable in class org.jmol.thread.JmolThread
 
CHECK2 - Static variable in class org.jmol.thread.JmolThread
 
CHECK3 - Static variable in class org.jmol.thread.JmolThread
 
checkAction(ActionEvent) - Method in class org.jmol.console.ScriptEditor
 
checkAims(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkAlchemy(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkAll - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
checkAllocColixes() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
checkAromaticDefined(Node[], BS) - Static method in class org.jmol.smiles.SmilesAromatic
set aromatic atoms based on predefined BOND_AROMATIC definitions
checkAromaticStrict(Node[], BS, Lst<Object>, Lst<Object>) - Static method in class org.jmol.smiles.SmilesAromatic
 
checkAromaticStrict2(Node[], BS, Lst<Object>, Lst<Object>, BS, boolean) - Static method in class org.jmol.smiles.SmilesAromatic
uses an MMFF94 strategy for determining aromaticity for a specific ring.
checkAtomArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkAtomLine(boolean, boolean, String, String, SB) - Static method in class org.jmol.jvxl.readers.VolumeFileReader
checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
checkAxisOrder(int, V3, P3) - Method in class org.jmol.symmetry.PointGroup
 
checkBetaSheetAlphaHelixOverlap(AlphaPolymer.Code[], float[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
checkBinary(String) - Method in class org.jmol.jvxl.readers.PmeshReader
 
checkBioType(String, int) - Method in class org.jmol.smiles.SmilesParser
 
checkBlock() - Method in class org.jmol.adapter.readers.xtal.MagresReader
looking for tags here.
checkBondArrayLength(int) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkBoolean(String) - Method in class org.jmol.popup.JmolGenericPopup
 
checkBoundsMinMax(P3, P3) - Method in class org.jmol.shape.Shape
 
checkBoxListener - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
CheckBoxMenuItemAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.CheckBoxMenuItemAction
 
checkBrace(SmilesSearch, char, char) - Method in class org.jmol.smiles.SmilesParser
 
checkBridge(Bridge, boolean, int, int) - Method in class org.jmol.dssx.DSSP
check to see if another bridge exists offset by n1 and n2 from the two ends of a bridge
checkBulge(Bridge, boolean, int) - Method in class org.jmol.dssx.DSSP
 
checkButton - Variable in class org.jmol.console.ScriptEditor
 
checkButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
checkByteCount - Variable in class org.jmol.shape.Mesh
 
checkCalculationType() - Method in class org.jmol.quantum.MOCalculation
 
checkCarbohydrate(String) - Static method in class org.jmol.modelsetbio.Resolver
 
checkCastep(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkCharge(String, int, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
 
checkChirality(String, int, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
 
checkClick(TouchPoint, List<Event>, boolean) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
 
checkClickAction(int, int, long, int) - Method in class org.jmol.viewer.ActionManager
 
checkCommand() - Method in class org.openscience.jmol.app.InputScannerThread
 
checkCommand() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
checkComment() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
checkContinue() - Method in class org.jmol.script.ScriptEval
checks to see if there is a pause condition, during which commands can still be issued, but with the ! first.
checkContour(MarchingSquares.Triangle, int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
checkCoordinatesChanged() - Method in class org.jmol.viewer.Viewer
 
checkCp(ContactPair, ContactPair, int, int) - Static method in class org.jmol.shapesurface.Contact
 
checkCrystal(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkCube(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkCurrentLineForScript() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkCutoff(int, int, int, float[]) - Static method in class org.jmol.jvxl.data.MeshData
 
checkDiameter(int) - Method in class org.jmol.renderbio.BioShapeRenderer
 
checkDistance(P3, P3, float, float, int, int, int, P3) - Method in interface org.jmol.api.SymmetryInterface
 
checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.symmetry.Symmetry
 
checkDistance(P3, P3, float, float, int, int, int, P3) - Method in class org.jmol.symmetry.UnitCell
 
checkDragWheelAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
 
checkDSSR() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
checkedSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkExplicit(String) - Method in class org.jmol.shape.MeshCollection
 
checkExtension(int) - Method in class org.jmol.script.ScriptEval
 
checkField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
checkFilenames - Variable in class org.openscience.chimetojmol.ChimePanel
 
checkFileStart(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkFilter(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkFilterKey(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkFloatRange(float, float, float) - Static method in class org.jmol.viewer.Viewer
 
checkFlowCommand(String) - Method in class org.jmol.script.ScriptCompiler
 
checkFlowEnd(int, String, int) - Method in class org.jmol.script.ScriptCompiler
 
checkFlowEndBrace() - Method in class org.jmol.script.ScriptCompiler
 
checkFlowStartBrace(boolean) - Method in class org.jmol.script.ScriptCompiler
 
checkFoldingXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkForceEndIf() - Method in class org.jmol.script.ScriptFlowContext
 
checkForCheckBoxScript(SC, String, boolean) - Method in class org.jmol.popup.GenericSwingPopup
 
checkForCoordinate(boolean) - Method in class org.jmol.script.ScriptTokenParser
 
checkForItemSelector(boolean) - Method in class org.jmol.script.ScriptTokenParser
 
checkForResidualBFactors(SymmetryInterface) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
checkFrankclicked(int, int) - Method in class org.jmol.viewer.ShapeManager
 
checkGenNBO(String[], String) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkGreater - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
checkGromacs(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkHalt(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
checkHalt(String, boolean) - Method in class org.jmol.api.JmolViewer
 
checkHalt(String, boolean) - Method in class org.jmol.script.ScriptManager
 
checkHalt(String, boolean) - Method in class org.jmol.viewer.Viewer
 
checkHeaderContains(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkHover() - Method in class org.jmol.viewer.ActionManager
 
checkID(String) - Method in class org.jmol.shapespecial.Ellipsoids
 
checkImpliedScriptCmd - Variable in class org.jmol.script.ScriptCompiler
 
checkIn(String, Object) - Static method in class org.jmol.util.GenericApplet
 
checking - Variable in class org.jmol.console.ScriptEditor.EditorTextPane
 
checking - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
checkInheritedShapes() - Method in class org.jmol.viewer.ShapeManager
starting with Jmol 13.1.13, isosurfaces can use "property color" to inherit the color of the underlying atoms.
checkInMotion(int) - Method in class org.jmol.viewer.Viewer
 
checkInterrupted(JmolThread) - Method in class org.jmol.thread.JmolThread
 
checkIntRange(int, int, int) - Static method in class org.jmol.viewer.Viewer
 
checkJSpecView(boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
checkKey(String, boolean) - Method in class org.jmol.adapter.readers.cif.MSRdr
Filter keys only for this model.
checkKey(String) - Method in class org.jmol.popup.GenericSwingPopup
 
checkLast(int) - Method in class org.jmol.script.ScriptParam
 
checkLastModel() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
sets continuing and doProcessLines
checkLatticeOnly - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
checkLength(int) - Method in class org.jmol.script.ScriptParam
 
checkLength(int) - Method in class org.jmol.scriptext.CmdExt
 
checkLength23() - Method in class org.jmol.script.ScriptParam
 
checkLength34() - Method in class org.jmol.script.ScriptParam
 
checkLengthErrorPt(int, int) - Method in class org.jmol.script.ScriptParam
 
checkLine() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
checkLine() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
checkLine() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
checkLine() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Reads a Collection of AtomSets from a BufferedReader.
checkLine() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
checkLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.AmpacReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.InputReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
 
checkLine() - Method in class org.jmol.adapter.readers.simple.MopacReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.MagresReader
Valid blocks include [calculation] [atoms] [magres]; all magres entries must be prefaced with a corresponding unit; Use of < > instead of [ ] is allowed.
checkLine() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.VaspChgcarReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
checkLine() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
checkLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkLineContinuation() - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
checkLineForScript(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkLineStarts(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkLogic(SmilesSearch, String, SmilesAtom, SmilesBond, SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
 
checkM2() - Method in class org.jmol.viewer.TransformManager4D
 
checkMap(Map<String, ?>, String, boolean, Lst<Object>, Object, int) - Method in class org.jmol.viewer.PropertyManager
 
checkMatch(SmilesAtom, int, int, boolean) - Method in class org.jmol.smiles.SmilesSearch
Check for a specific match of a model set atom with a pattern position
checkMatchBond(SmilesAtom, SmilesAtom, SmilesBond, int, int, Edge) - Method in class org.jmol.smiles.SmilesSearch
 
checkMemory() - Static method in class org.jmol.util.Logger
 
checkMenuUpdate() - Method in class org.jmol.viewer.Viewer
 
checkMesh(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
checkMeshBB(Shape[], int, BoxInfo) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
checkMinAttachedAngle(Atom, float, V3, V3, boolean) - Static method in class org.jmol.modelset.ModelSet
 
checkMinimization() - Method in class org.jmol.viewer.Viewer
 
checkMinZ(Atom, int[]) - Method in class org.jmol.modelset.Group
 
checkMol(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkMopacGraphf(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkMOs() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
checkMotionRendering(int) - Method in class org.jmol.viewer.Viewer
check motion for rendering during mouse movement, spin, vibration, and animation
checkMotionRotateZoom(int, int, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
 
checkNboLine() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
checkNested(SmilesSearch, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesParser
 
checkNewDotsArray() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
checkNewGroup(JmolAdapter, int, String, int, char, boolean, boolean) - Method in class org.jmol.modelset.ModelLoader
 
checkNewSetCommand() - Method in class org.jmol.script.ScriptCompiler
 
checkNormals(short, short, short) - Method in class org.jmol.render.MeshRenderer
 
checkNotPDB() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
checkNucleicObject(BS, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
checkObject(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
checkObjectClicked(boolean, int, int, BS) - Method in class org.jmol.modelset.Object2d
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Object2dShape
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Shape
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shape.Sticks
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapespecial.Draw
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.shapesurface.Isosurface
 
checkObjectClicked(int, int, int, BS, boolean) - Method in class org.jmol.viewer.ShapeManager
 
checkObjectClicked(int, int, int) - Method in class org.jmol.viewer.Viewer
 
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Labels
 
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shape.Shape
 
checkObjectDragged(int, int, int, int, int, BS) - Method in class org.jmol.shapespecial.Draw
 
checkObjectDragged(int, int, int, int, int, BS, int) - Method in class org.jmol.viewer.ShapeManager
 
checkObjectDragged(int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Frank
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Object2dShape
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Shape
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shape.Sticks
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapespecial.Draw
 
checkObjectHovered(int, int, BS) - Method in class org.jmol.shapesurface.Isosurface
 
checkObjectHovered(int, int, BS, boolean) - Method in class org.jmol.viewer.ShapeManager
 
checkObjectHovered(int, int) - Method in class org.jmol.viewer.Viewer
 
checkOdyssey(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkOperation(Quat, P3, int) - Method in class org.jmol.symmetry.PointGroup
 
checkOption(Object) - Static method in class org.openscience.jmol.app.webexport.WebPanel
 
checkOption2(String, String) - Method in class org.jmol.viewer.Viewer
 
checkOptional(byte[], byte, int, int) - Static method in class org.jmol.modelsetbio.Monomer
 
checkOptions(CommandLine, Options) - Method in class org.openscience.jmol.app.JmolApp
 
checkOrbitalType(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
checkOut(String) - Static method in class org.jmol.util.GenericApplet
 
checkPacked(int, Map<String, Object>, SB) - Method in class org.jmol.script.ScriptEval
 
checkPhiPsi(float[], float, float) - Static method in class org.jmol.modelsetbio.AminoPolymer
 
checkPoint(T3) - Method in class org.jmol.export._IdtfExporter
 
checkPoint(Point3fi) - Method in class org.jmol.modelset.MeasurementPending
 
checkPressedAction(int, int, long) - Method in class org.jmol.viewer.ActionManager
 
checkPrimitiveAtom(SmilesAtom, int) - Method in class org.jmol.smiles.SmilesSearch
 
checkPrimitiveBond(SmilesBond, int, int, Edge) - Method in class org.jmol.smiles.SmilesSearch
 
checkPrivateKey(double) - Method in class org.jmol.viewer.Viewer
Simple method to ensure that the image creator (which writes files) was in fact opened by this vwr and not by some manipulation of the applet.
checkPropertyParameter(String) - Method in interface org.jmol.api.JmolPropertyManager
 
checkPropertyParameter(String) - Method in class org.jmol.viewer.PropertyManager
 
checkPropertyParameter(String) - Method in class org.jmol.viewer.Viewer
 
checkPt(float[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
two values -- v1, and v2, which need not be ordered v1 < v2.
checkRasmolHydrogenBond(AminoMonomer, BioPolymer, int, P3, BS, Lst<Bond>, int[][], boolean) - Method in class org.jmol.modelsetbio.AminoPolymer
 
checkReleaseAction(int, int, long, boolean) - Method in class org.jmol.viewer.ActionManager
 
checkResume(String) - Method in class org.jmol.script.ScriptManager
 
checkRings(Lst<BS>, int[], int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
checkScript() - Method in class org.jmol.console.ScriptEditor
 
checkScriptExecution(String, boolean) - Method in class org.jmol.script.ScriptManager
 
checkScriptSilent(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
checkScriptSilent(String) - Method in class org.jmol.script.ScriptEval
a method for just checking a script
checkSecurity(String) - Method in class org.jmol.viewer.FileManager
 
checkSelect(Map<String, SV>, T[]) - Method in interface org.jmol.api.JmolScriptEvaluator
 
checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptEval
Check a map for a WHERE phrase
checkSelect(Map<String, SV>, T[]) - Method in class org.jmol.viewer.Viewer
 
checkShades(int) - Method in class org.jmol.util.Shader
 
checkSigned - Variable in class org.openscience.chimetojmol.ChimePanel
 
checkSkip(T, int) - Method in class org.jmol.script.ScriptMathProcessor
 
checkSlab(int, T3, float, float, BS) - Method in class org.jmol.util.MeshSlicer
 
checkSlideZoom(int) - Method in class org.jmol.viewer.ActionManager
 
checkSpecial - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
checkSpecial1(int, String[], String) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkSpecial2(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkSpecialData(GenericZipTools, InputStream, String[]) - Static method in class org.jmol.io.JmolUtil
called by SmarterJmolAdapter to see if we have a Spartan directory and, if so, open it and get all the data into the correct order.
checkSpecialInZip(String[]) - Static method in class org.jmol.io.JmolUtil
called by SmarterJmolAdapter to see if we can automatically assign a file from the zip file.
checkSpecialParameterSyntax() - Method in class org.jmol.script.ScriptCompiler
Check for special parameters, including: +, -, \, *, /, &, |, =, period, or [, single or double quote, command-specific parameters, $....
checkSpecialVoxel(P3, P3, P3) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
checkStandardDeviation(V3[], V3, int, float) - Static method in class org.jmol.smiles.SmilesAromatic
 
checkStepping(String) - Method in class org.jmol.script.ScriptManager
 
checkStereochemistry() - Method in class org.jmol.smiles.SmilesSearch
 
checkStereochemistryAll(boolean, Node, int, int, Node, Node, Node, Node, Node, Node, VTemp) - Static method in class org.jmol.smiles.SmilesSearch
 
checkStereoPairs(Node, int, Node[], int) - Method in class org.jmol.smiles.SmilesGenerator
 
checkSubs - Variable in class org.openscience.chimetojmol.ChimePanel
 
checkSymmetry() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
checkTimer(String, boolean) - Static method in class org.jmol.util.Logger
 
checkToken(int) - Method in class org.jmol.script.ScriptParam
 
checkTranslucent(boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
checkTranslucent(boolean) - Method in class org.jmol.export.Export3D
 
checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
 
checkTwoAtomAction(Point3fi, int) - Method in class org.jmol.viewer.ActionManager
 
checkType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
checkUnitCell(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkUnitCell(SymmetryInterface, P3, P3, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
checkUnitCell(SymmetryInterface, P3, P3, boolean) - Method in class org.jmol.symmetry.Symmetry
 
checkUnitCellItem(String[], String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
checkUnitCellOffset() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
checkUnquotedFileName() - Method in class org.jmol.script.ScriptCompiler
 
checkUserAction(int, int, int, int, int, long, int) - Method in class org.jmol.viewer.ActionManager
 
checkVasp(String[], boolean) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkVisible() - Method in class org.jmol.modelset.Atom
 
checkWien2k(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkWinding(MeshCapper.CapVertex, MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
Check for CCW winding.
checkWithin(T3, Lst<P3>, float, boolean) - Static method in class org.jmol.shape.Mesh
 
checkXyz(String[]) - Static method in class org.jmol.adapter.smarter.Resolver
 
checkXYZlist(String) - Method in class org.jmol.symmetry.SpaceGroup
 
CHEM_COMP_BOND_AROMATIC_FLAG - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CHEM_COMP_BOND_ATOM_ID_1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CHEM_COMP_BOND_ATOM_ID_2 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CHEM_COMP_BOND_VALUE_ORDER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CHEM_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
CHEM_COMP_NAME - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
chemCompBondFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
chemCompFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
chemFileProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
chemical - Static variable in class org.jmol.script.T
 
chemicalName - Variable in class org.jmol.adapter.readers.cif.CifReader
 
chemicalshift - Static variable in class org.jmol.script.T
 
chFirst - Variable in class org.jmol.script.ScriptCompiler
 
ChimePanel - Class in org.openscience.chimetojmol
 
ChimePanel() - Constructor for class org.openscience.chimetojmol.ChimePanel
 
chimePath - Variable in class org.openscience.chimetojmol.ChimePanel
 
ChimeToJmol - Class in org.openscience.chimetojmol
 
ChimeToJmol() - Constructor for class org.openscience.chimetojmol.ChimeToJmol
 
ChimeToJmol.ApplicationCloser - Class in org.openscience.chimetojmol
 
chiralClass - Variable in class org.jmol.smiles.SmilesAtom
 
chiralOrder - Variable in class org.jmol.smiles.SmilesAtom
 
chk - Variable in class org.jmol.script.ScriptContext
 
chk - Variable in class org.jmol.script.ScriptError
 
chk - Variable in class org.jmol.script.ScriptMathProcessor
 
chk - Variable in class org.jmol.scriptext.CmdExt
 
choice - Variable in class org.jmol.dialog.Dialog
 
chooseBestBoundBox() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
chooser - Variable in class org.jmol.dialog.FilePreview
 
chooser - Variable in class org.openscience.chimetojmol.ChimePanel
 
chop(String) - Static method in class org.jmol.viewer.StateCreator
 
chord - Variable in class org.jmol.util.ContactPair
 
chpt0 - Variable in class org.jmol.script.ScriptFunction
 
CHRG - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
cifLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CifReader - Class in org.jmol.adapter.readers.cif
A true line-free CIF file reader for CIF files.
CifReader() - Constructor for class org.jmol.adapter.readers.cif.CifReader
 
circle - Static variable in class org.jmol.script.T
 
circle3d - Variable in class org.jmol.g3d.Graphics3D
 
CIRCLE_FRACTION - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
circleNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
CircleRenderer - Class in org.jmol.g3d
Implements flat circle drawing/filling routines.
CircleRenderer() - Constructor for class org.jmol.g3d.CircleRenderer
 
CITATION_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
CITATION_TITLE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
citationFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
cJvxlEdgeNaN - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
clamp_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
clash - Static variable in class org.jmol.script.T
 
classBase - Static variable in class org.jmol.adapter.smarter.Resolver
 
ClassPreloader - Class in org.jmol.applet
 
ClassPreloader(AppletWrapper) - Constructor for class org.jmol.applet.ClassPreloader
 
clauseAlternateSpec() - Method in class org.jmol.script.ScriptTokenParser
check for %x or % (null alternate)
clauseAnd() - Method in class org.jmol.script.ScriptTokenParser
 
clauseAtomSpec() - Method in class org.jmol.script.ScriptTokenParser
 
clauseCell(int) - Method in class org.jmol.script.ScriptTokenParser
 
clauseChainSpec(int) - Method in class org.jmol.script.ScriptTokenParser
[:] [chars] [:] ["chars"] [:] [*] [:] [0-9] [:] [?] [:] (empty chain)
clauseComparator(boolean) - Method in class org.jmol.script.ScriptTokenParser
 
clauseConnected() - Method in class org.jmol.script.ScriptTokenParser
 
clauseDefine(boolean, boolean) - Method in class org.jmol.script.ScriptTokenParser
 
clauseItemSelector() - Method in class org.jmol.script.ScriptTokenParser
 
clauseModelSpec() - Method in class org.jmol.script.ScriptTokenParser
process /1 /1.1 /* no longer accept just "/" here for implicit /1
clauseNot() - Method in class org.jmol.script.ScriptTokenParser
 
clauseOr(boolean) - Method in class org.jmol.script.ScriptTokenParser
 
clausePrimitive() - Method in class org.jmol.script.ScriptTokenParser
 
clauseResidueSpec() - Method in class org.jmol.script.ScriptTokenParser
 
clauseResNameSpec() - Method in class org.jmol.script.ScriptTokenParser
[a] or just a
clauseSequenceSpec() - Method in class org.jmol.script.ScriptTokenParser
 
clauseSubstructure() - Method in class org.jmol.script.ScriptTokenParser
 
clauseWithin(boolean) - Method in class org.jmol.script.ScriptTokenParser
 
clean() - Method in class org.jmol.shape.MeshCollection
 
clean() - Method in class org.jmol.shapecgo.CGO
 
clean() - Method in class org.jmol.shapespecial.Draw
 
clean_electro_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cleanLine() - Method in class org.jmol.adapter.readers.simple.InputReader
 
cleanPattern(String) - Static method in class org.jmol.smiles.SmilesParser
 
cleanRegistry() - Static method in class org.jmol.applet.Jmol
 
cleanScriptComments(String) - Method in class org.jmol.script.ScriptCompiler
allows for three kinds of comments.
cleanSingletons(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
PyMOL does not display cartoons or traces for single-residue runs.
cleanUp() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
clear() - Method in interface org.jmol.api.JmolDataManager
 
clear(int) - Method in interface org.jmol.api.JmolRepaintManager
 
clear(boolean) - Method in interface org.jmol.api.JmolScriptManager
 
clear() - Method in class org.jmol.awt.Mouse
 
clear() - Method in class org.jmol.awtjs2d.Mouse
 
clear() - Method in class org.jmol.g3d.Graphics3D
 
clear(int) - Method in class org.jmol.java.BS
Sets the bit specified by the index to false.
clear() - Method in class org.jmol.jvxl.data.JvxlData
 
clear() - Method in class org.jmol.minimize.forcefield.ForceField
 
clear() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
clear() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
clear() - Method in class org.jmol.minimize.Minimizer
 
clear(BS, Atom, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
 
clear() - Method in class org.jmol.multitouch.ActionManagerMT
 
clear(int) - Method in class org.jmol.render.RepaintManager
 
clear(boolean) - Method in class org.jmol.script.ScriptManager
 
clear - Static variable in class org.jmol.script.T
 
clear() - Method in class org.jmol.shape.Measures
 
clear(String) - Method in class org.jmol.shape.Mesh
 
clear(String) - Method in class org.jmol.shapecgo.CGOMesh
 
clear(boolean) - Method in class org.jmol.shapespecial.Dipoles
 
clear(String) - Method in class org.jmol.shapespecial.DrawMesh
 
clear() - Static method in exception org.jmol.smiles.InvalidSmilesException
 
clear() - Method in class org.jmol.smiles.SmilesSearch
 
clear(Map<String, Object>) - Static method in class org.jmol.thread.TimeoutThread
 
clear() - Method in class org.jmol.util.CommandHistory
clears the history.
clear() - Method in class org.jmol.util.GData
 
clear() - Method in class org.jmol.util.MeshCapper.CapVertex
Free all links.
clear() - Method in class org.jmol.util.MeshCapper
 
clear() - Method in class org.jmol.util.TempArray
 
clear() - Method in class org.jmol.viewer.ActionManager
 
clear() - Method in class org.jmol.viewer.AnimationManager
 
clear() - Method in class org.jmol.viewer.DataManager
 
clear() - Method in class org.jmol.viewer.FileManager
 
clear() - Method in class org.jmol.viewer.GlobalSettings
 
clear() - Method in class org.jmol.viewer.SelectionManager
 
clear(GlobalSettings) - Method in class org.jmol.viewer.StateManager
 
clear() - Method in class org.jmol.viewer.TransformManager
 
clear() - Method in class org.openscience.jmol.app.HistoryFile
 
clear() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
clear() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
clearAll() - Method in class org.jmol.java.BS
Sets all of the bits in this BitSet to false.
clearAllMeasurements() - Method in class org.jmol.viewer.Viewer
 
clearAndCachePngjFile(String[]) - Method in class org.jmol.io.JmolBinary
 
clearAtomSets() - Method in class org.jmol.viewer.Viewer
 
clearBfactorRange() - Method in class org.jmol.modelset.AtomCollection
 
clearBindings() - Method in class org.jmol.viewer.ActionManager
 
clearBioPolymers() - Method in class org.jmol.modelset.Model
 
clearBioPolymers() - Method in class org.jmol.modelsetbio.BioModel
 
clearBits(int, int) - Method in class org.jmol.java.BS
Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to false.
clearBsFound(int) - Method in class org.jmol.smiles.SmilesSearch
 
clearBuffer() - Method in class org.jmol.g3d.Platform3D
 
clearButton - Variable in class org.jmol.console.ScriptEditor
 
clearButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
clearButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
clearCache() - Method in class org.jmol.modelset.ModelSet
 
clearClickCount() - Method in class org.jmol.viewer.Viewer
 
clearCommandWatcherThread() - Method in class org.jmol.script.ScriptManager
 
clearConsole() - Method in class org.jmol.viewer.StatusManager
 
clearContent(String) - Method in class org.jmol.console.GenericConsole
 
clearContent() - Method in class org.jmol.console.ScriptEditor.EditorDocument
Removes all content of the script window, and add a new prompt.
clearContent() - Method in class org.jmol.console.ScriptEditor.EditorTextPane
 
clearContent(String) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
 
clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
clearContent() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
Removes all content of the script window, and add a new prompt.
clearContent(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
clearDataFrameReference(int) - Method in class org.jmol.modelset.ModelSet
 
clearDefinedVariableAtomSets() - Method in class org.jmol.script.ScriptEval
 
clearDefinedVariableAtomSets() - Method in class org.jmol.script.ScriptExpr
 
clearFontCache() - Method in class org.jmol.g3d.Graphics3D
 
clearFontCache() - Static method in class org.jmol.g3d.TextRenderer
 
clearFontCache() - Method in class org.jmol.util.GData
 
clearForces() - Method in class org.jmol.minimize.forcefield.ForceField
 
clearFunctions() - Method in class org.jmol.viewer.Viewer
 
clearGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
clearHighlight() - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
clearHistory - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
clearInButton - Variable in class org.jmol.console.GenericConsole
 
clearKeyBuffer() - Method in class org.jmol.awt.Mouse
 
clearKeyBuffer() - Method in class org.jmol.awtjs2d.Mouse
 
clearLineCache() - Method in class org.jmol.g3d.LineRenderer
 
clearListener(AbstractButton) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
clearListeners(Object[]) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
clearMeasurements() - Method in class org.jmol.api.JmolViewer
 
clearMeasurements() - Method in class org.jmol.viewer.Viewer
 
clearMesh(String) - Method in class org.jmol.shape.Mesh
 
clearMinimization() - Method in class org.jmol.viewer.Viewer
 
clearModelDependentObjects() - Method in class org.jmol.viewer.Viewer
 
clearMouseInfo() - Method in class org.jmol.viewer.ActionManager
 
clearOutButton - Variable in class org.jmol.console.GenericConsole
 
clearPixel(int, int) - Method in class org.jmol.g3d.Pixelator
 
clearPixel(int, int) - Method in class org.jmol.g3d.PixelatorT
 
clearPngjCache(String) - Method in class org.jmol.io.JmolBinary
 
clearPngjCache(String) - Method in class org.jmol.viewer.FileManager
 
clearQueue() - Method in interface org.jmol.api.JmolScriptManager
 
clearQueue() - Method in class org.jmol.script.ScriptManager
 
clearRasmolHydrogenBonds(ModelSet, BioModel, BS) - Static method in class org.jmol.modelsetbio.BioModel
 
clearReaderData() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
clearRepaintManager(int) - Method in class org.jmol.viewer.Viewer
 
clearScreenBuffer() - Method in class org.jmol.g3d.Platform3D
 
clearScreenBufferThreaded() - Method in class org.jmol.g3d.Platform3D
 
clearScriptQueue() - Method in class org.jmol.viewer.Viewer
 
clearSelection() - Method in class org.jmol.api.JmolViewer
 
clearSelection(boolean) - Method in class org.jmol.viewer.SelectionManager
 
clearSelection() - Method in class org.jmol.viewer.Viewer
 
clearSg() - Method in class org.jmol.shapesurface.Isosurface
 
clearSg() - Method in class org.jmol.shapesurface.MolecularOrbital
 
clearShapeManager(Error) - Method in class org.jmol.script.ScriptParallelProcessor
 
clearShapeRenderers() - Method in class org.jmol.viewer.Viewer
 
clearSpin() - Method in class org.jmol.viewer.TransformManager
 
clearState(boolean) - Method in class org.jmol.script.ScriptEval
 
clearStructures() - Method in class org.jmol.modelsetbio.AlphaPolymer
 
clearStructures() - Method in class org.jmol.modelsetbio.BioPolymer
 
clearTBuffer() - Method in class org.jmol.g3d.Platform3D
 
clearTemp() - Method in class org.jmol.viewer.StateCreator
 
clearTempPoints() - Method in class org.jmol.util.TempArray
 
clearTempScreens() - Method in class org.jmol.util.TempArray
 
clearThreads() - Method in class org.jmol.viewer.TransformManager
 
clearThreads() - Method in class org.jmol.viewer.Viewer
 
clearTimeout(String) - Method in class org.jmol.viewer.Viewer
 
clearTimeouts() - Method in class org.jmol.viewer.Viewer
 
clearType(String, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
clearUnitCell() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
clearVibration() - Method in class org.jmol.viewer.TransformManager
 
clearVisibleSets() - Method in class org.jmol.modelset.AtomCollection
 
CLICK - Static variable in class org.jmol.multitouch.ActionManagerMT
 
CLICK - Static variable in class org.jmol.viewer.binding.Binding
 
CLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
clickabilityFlags - Variable in class org.jmol.modelset.Atom
 
clickable - Static variable in class org.jmol.script.T
 
clickableMax - Static variable in class org.jmol.viewer.ShapeManager
 
clickAction - Variable in class org.jmol.viewer.ActionManager
 
clicked(long, int, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
 
clicked - Variable in class org.jmol.viewer.ActionManager
 
clickedCount - Variable in class org.jmol.viewer.ActionManager
 
client - Variable in class org.jmol.modelset.MeasurementData
 
client - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
clipboard - Static variable in class org.jmol.script.T
 
clipCode(int, int, int) - Method in class org.jmol.export.Export3D
 
clipCode(int) - Method in class org.jmol.util.GData
 
clipCode3(int, int, int) - Method in class org.jmol.util.GData
 
clipImageOrPasteText(String) - Method in class org.jmol.api.JmolViewer
 
clipImageOrPasteText(String) - Method in class org.jmol.viewer.OutputManager
 
clipImageOrPasteText(String) - Method in class org.jmol.viewer.OutputManagerAwt
 
clipImageOrPasteText(String) - Method in class org.jmol.viewer.OutputManagerJS
 
clipImageOrPasteText(String) - Method in class org.jmol.viewer.Viewer
 
clipped - Variable in class org.jmol.g3d.CylinderRenderer
 
cList - Variable in class org.jmol.shapecgo.CGOMesh
 
clockBaseline - Variable in class org.jmol.applet.AppletWrapper
 
clockWidth - Variable in class org.jmol.applet.AppletWrapper
 
clockX - Variable in class org.jmol.applet.AppletWrapper
 
clone() - Method in class org.jmol.java.BS
Cloning this BitSet produces a new BitSet that is equal to it.
clone() - Method in class org.jmol.util.Vibration
 
cloneAtomSetWithBonds(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneFirstAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneLastAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneLastAtomSet(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
cloneLastAtomSetFromPoints(int, P3[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
cloneV() - Method in class org.jmol.util.MeshCapper.CapVertex
 
close(Object) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
close() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
close() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
close() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
close() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
closeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
CloseAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CloseAction
 
closeButton - Variable in class org.jmol.console.ScriptEditor
 
closeButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
closeButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
closePressed() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
Responds to cancel being press- or equivalent eg window closed.
closePreview() - Method in class org.jmol.dialog.Dialog
 
closeReader() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
closeReader() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
closeReader() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
closeReader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
closeReaderSFR() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
closest - Variable in class org.jmol.modelset.ModelSet
 
cm - Variable in class org.jmol.viewer.Viewer
 
cM - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
cMapSourceBRIX - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cMapSourceCCP4 - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cMapSourceChempyBrick - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cMapSourceCrystallographic - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cMapSourceDesc - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cMapSourceFLD - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cMapSourceGeneralPurpose - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cMapSourceGRD - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cMapSourceObsolete - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cMapSourceVMDPlugin - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
cmdAnimation() - Method in class org.jmol.script.ScriptEval
 
cmdAxes(int) - Method in class org.jmol.script.ScriptEval
 
cmdBackground(int) - Method in class org.jmol.script.ScriptEval
 
cmdBind() - Method in class org.jmol.script.ScriptEval
 
cmdBondorder() - Method in class org.jmol.script.ScriptEval
 
cmdBoundbox(int) - Method in class org.jmol.script.ScriptEval
 
cmdCD() - Method in class org.jmol.script.ScriptEval
 
cmdCenter(int) - Method in class org.jmol.script.ScriptEval
 
cmdColor() - Method in class org.jmol.script.ScriptEval
 
cmdDefine() - Method in class org.jmol.script.ScriptEval
 
cmdDelay() - Method in class org.jmol.script.ScriptEval
 
cmdDelete() - Method in class org.jmol.script.ScriptEval
 
cmdDisplay(boolean) - Method in class org.jmol.script.ScriptEval
 
cmdDots(int) - Method in class org.jmol.script.ScriptEval
 
cmdEcho(int) - Method in class org.jmol.script.ScriptEval
 
cmdExt - Variable in class org.jmol.script.ScriptExpr
 
CmdExt - Class in org.jmol.scriptext
 
CmdExt() - Constructor for class org.jmol.scriptext.CmdExt
 
cmdFile() - Method in class org.jmol.script.ScriptEval
 
cmdFixed() - Method in class org.jmol.script.ScriptEval
 
cmdFlow(int, boolean, Lst<T[]>) - Method in class org.jmol.script.ScriptEval
 
cmdFlowSwitch(ContextToken, int) - Method in class org.jmol.script.ScriptEval
 
cmdFont(int, float) - Method in class org.jmol.script.ScriptEval
 
cmdFrank(int) - Method in class org.jmol.script.ScriptEval
 
cmdFunc() - Method in class org.jmol.script.ScriptEval
 
cmdGetProperty() - Method in class org.jmol.script.ScriptEval
 
cmdGoto(boolean) - Method in class org.jmol.script.ScriptEval
 
cmdHbond() - Method in class org.jmol.script.ScriptEval
 
cmdHelp() - Method in class org.jmol.script.ScriptEval
 
cmdHistory(int) - Method in class org.jmol.script.ScriptEval
 
cmdHover() - Method in class org.jmol.script.ScriptEval
 
cmdInvertSelected() - Method in class org.jmol.script.ScriptEval
 
cmdIso - Variable in class org.jmol.script.ScriptEval
 
cmdLabel(int) - Method in class org.jmol.script.ScriptEval
 
cmdLoad() - Method in class org.jmol.script.ScriptEval
 
cmdLog() - Method in class org.jmol.script.ScriptEval
 
cmdLoop() - Method in class org.jmol.script.ScriptEval
 
cmdMessage() - Method in class org.jmol.script.ScriptEval
 
cmdModel(int) - Method in class org.jmol.script.ScriptEval
ONE difference between FRAME and MODEL: model 1 sets model NAMED one in the case of PDB frame 1 always sets the first model
cmdMove() - Method in class org.jmol.script.ScriptEval
 
cmdMoveto() - Method in class org.jmol.script.ScriptEval
 
cmdPause() - Method in class org.jmol.script.ScriptEval
 
cmdPrint() - Method in class org.jmol.script.ScriptEval
 
cmdPrompt() - Method in class org.jmol.script.ScriptEval
 
cmdpt0 - Variable in class org.jmol.script.ScriptFunction
 
cmdReset() - Method in class org.jmol.script.ScriptEval
 
cmdRestore() - Method in class org.jmol.script.ScriptEval
 
cmdRestrict() - Method in class org.jmol.script.ScriptEval
 
cmdReturn(SV) - Method in class org.jmol.script.ScriptEval
 
cmdRotate(boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
cmds - Variable in class org.jmol.rendercgo.CGORenderer
 
cmds - Variable in class org.jmol.shapecgo.CGOMesh
 
cmdSave() - Method in class org.jmol.script.ScriptEval
 
cmdScript(int, String, String) - Method in class org.jmol.script.ScriptEval
 
cmdSelect(int) - Method in class org.jmol.script.ScriptEval
 
cmdSelectionHalos(int) - Method in class org.jmol.script.ScriptEval
 
cmdSet() - Method in class org.jmol.script.ScriptEval
 
cmdSetEcho() - Method in class org.jmol.script.ScriptEval
 
cmdSetLabel(String) - Method in class org.jmol.script.ScriptEval
 
cmdSetPicking() - Method in class org.jmol.script.ScriptEval
 
cmdSetPickingStyle() - Method in class org.jmol.script.ScriptEval
 
cmdSlab(boolean) - Method in class org.jmol.script.ScriptEval
 
cmdSsbond() - Method in class org.jmol.script.ScriptEval
 
cmdStructure() - Method in class org.jmol.script.ScriptEval
 
cmdSubset() - Method in class org.jmol.script.ScriptEval
 
cmdSync() - Method in class org.jmol.script.ScriptEval
 
cmdThrow() - Method in class org.jmol.script.ScriptEval
 
cmdTimeout(int) - Method in class org.jmol.script.ScriptEval
 
cmdTranslate(boolean) - Method in class org.jmol.script.ScriptEval
 
cmdUnbind() - Method in class org.jmol.script.ScriptEval
 
cmdUndoRedoMove() - Method in class org.jmol.script.ScriptEval
 
cmdUnitcell(int) - Method in class org.jmol.script.ScriptEval
 
cmdVector() - Method in class org.jmol.script.ScriptEval
 
cmdVibration() - Method in class org.jmol.script.ScriptEval
 
cmdWireframe() - Method in class org.jmol.script.ScriptEval
 
cmdZap(boolean) - Method in class org.jmol.script.ScriptEval
 
cmdZoom(boolean) - Method in class org.jmol.script.ScriptEval
 
cmeshes - Variable in class org.jmol.shapecgo.CGO
 
cmi - Variable in class org.jmol.viewer.AnimationManager
current model index
CML - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CML_NAMESPACE_URI - Static variable in class org.jmol.adapter.smarter.Resolver
 
cnmrPeaks - Variable in class org.jmol.popup.JmolGenericPopup
 
code - Variable in class org.jmol.adapter.readers.cif.Subsystem
 
code - Variable in enum org.jmol.c.FIL
 
code - Variable in class org.jmol.i18n.Language
 
Code() - Constructor for enum org.jmol.modelsetbio.AlphaPolymer.Code
 
code - Variable in enum org.jmol.util.Edge.EnumBondOrder
 
codeBase - Variable in class org.jmol.util.GenericApplet
 
codePath - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
coef - Variable in class org.jmol.g3d.SphereRenderer
 
coef - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
coef - Variable in class org.jmol.quantum.SlaterData
 
coef1 - Static variable in class org.jmol.quantum.NciCalculation
 
coef2 - Static variable in class org.jmol.quantum.NciCalculation
 
coef3 - Static variable in class org.jmol.quantum.NciCalculation
 
COEF_INDICES - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
coefCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
coeffs - Variable in class org.jmol.quantum.MOCalculation
 
coefs - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
coefs - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
coefs - Variable in class org.jmol.quantum.MOCalculation
 
coefs - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
col - Static variable in class org.jmol.script.T
 
colix - Variable in class org.jmol.adapter.smarter.Bond
 
colix - Variable in class org.jmol.export.Export3D
 
colix - Variable in class org.jmol.modelset.Bond
 
colix - Variable in class org.jmol.modelset.Measurement
 
colix - Variable in class org.jmol.modelset.MeasurementData
 
colix - Variable in class org.jmol.modelset.Object2d
 
colix - Variable in class org.jmol.render.ShapeRenderer
 
colix - Variable in class org.jmol.renderbio.NucleicRenderer
 
colix - Variable in class org.jmol.renderbio.RocketRenderer
 
colix - Variable in class org.jmol.shape.Measures
 
colix - Variable in class org.jmol.shape.MeshCollection
 
colix - Variable in class org.jmol.shapespecial.Dipole
 
colix - Variable in class org.jmol.shapespecial.Dipoles
 
colix - Variable in class org.jmol.shapespecial.Ellipsoid
 
colix - Variable in class org.jmol.util.MeshSurface
 
colix - Variable in class org.jmol.viewer.Connection
 
colix0 - Variable in class org.jmol.rendercgo.CGORenderer
 
colix1 - Variable in class org.jmol.rendercgo.CGORenderer
 
colix2 - Variable in class org.jmol.rendercgo.CGORenderer
 
colixA - Variable in class org.jmol.g3d.CylinderRenderer
 
colixA - Variable in class org.jmol.render.FontLineShapeRenderer
 
colixA - Variable in class org.jmol.renderspecial.DipolesRenderer
 
colixAtom - Variable in class org.jmol.modelset.Atom
 
colixB - Variable in class org.jmol.g3d.CylinderRenderer
 
colixB - Variable in class org.jmol.render.FontLineShapeRenderer
 
colixB - Variable in class org.jmol.renderspecial.DipolesRenderer
 
colixBack - Variable in class org.jmol.renderbio.BioShapeRenderer
 
colixBack - Variable in class org.jmol.util.MeshSurface
 
colixBackgroundContrast - Variable in class org.jmol.viewer.ColorManager
 
colixCurrent - Variable in class org.jmol.util.GData
 
colixEndcap - Variable in class org.jmol.g3d.CylinderRenderer
 
colixes - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
colixes - Variable in class org.jmol.render.AxesRenderer
 
colixes - Variable in class org.jmol.renderbio.BioShapeRenderer
 
colixes - Variable in class org.jmol.shape.AtomShape
 
colixesBack - Variable in class org.jmol.renderbio.BioShapeRenderer
 
colixesBack - Variable in class org.jmol.shapebio.BioShape
 
colixHash - Static variable in class org.jmol.util.C
 
colixHighlight - Variable in class org.jmol.shape.Halos
 
colixMax - Static variable in class org.jmol.util.C
 
colixRubberband - Variable in class org.jmol.viewer.ColorManager
 
colixSelection - Variable in class org.jmol.shape.Halos
 
collapsed - Static variable in class org.jmol.script.T
 
collapsed - Variable in class org.jmol.shapespecial.Polyhedron
 
COLLECTION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
String for prefix/resource identifier for the collection area.
collectionName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
colon - Static variable in class org.jmol.script.T
 
color - Variable in enum org.jmol.c.STR
 
color - Variable in class org.jmol.jvxl.data.JvxlData
 
color - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
 
color - Static variable in class org.jmol.script.T
 
COLOR - Static variable in class org.jmol.shape.Echo
 
color - Variable in class org.jmol.shape.Mesh
 
color - Variable in class org.jmol.shape.MeshCollection
 
COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
 
color - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
color4(short) - Method in class org.jmol.export._PovrayExporter
 
COLOR_BACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
COLOR_BLACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
COLOR_FRONT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
colorByPhase - Variable in class org.jmol.jvxl.readers.Parameters
 
colorBySets - Variable in class org.jmol.jvxl.readers.Parameters
 
colorBySign - Variable in class org.jmol.jvxl.readers.Parameters
 
colorCommand - Variable in class org.jmol.shape.Mesh
 
colorCommand(SimpleAttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
colorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
colorData - Variable in class org.jmol.viewer.ColorManager
 
colorDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
colorDensity - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
colorDensity - Variable in class org.jmol.jvxl.data.JvxlData
 
colorDensity - Variable in class org.jmol.jvxl.readers.Parameters
 
colorDensity - Variable in class org.jmol.shape.Mesh
 
colorEncoder - Variable in class org.jmol.jvxl.readers.Parameters
 
colorEncoder - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
ColorEncoder - Class in org.jmol.util
 
ColorEncoder(ColorEncoder, Viewer) - Constructor for class org.jmol.util.ColorEncoder
 
colorFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
 
colorFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
colorFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
 
colorFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
colorIndex(float, int) - Static method in class org.jmol.util.ColorEncoder
 
colorIndexRepeat(float, int) - Static method in class org.jmol.util.ColorEncoder
 
colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
colorIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
ColorManager - Class in org.jmol.viewer
 
ColorManager(Viewer, GData) - Constructor for class org.jmol.viewer.ColorManager
 
colorNames - Static variable in class org.jmol.applet.AppletWrapper
 
colorNeg - Variable in class org.jmol.jvxl.readers.Parameters
 
colorNegLCAO - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPhase - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPhased - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
colorPhases - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
colorPos - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPosLCAO - Variable in class org.jmol.jvxl.readers.Parameters
 
colorPtr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
colorPtr - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
colorrasmol - Static variable in class org.jmol.script.T
 
colorRgb - Variable in class org.jmol.jvxl.readers.Parameters
 
colors - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
colors - Static variable in class org.jmol.applet.AppletWrapper
 
colorScheme - Variable in class org.jmol.jvxl.data.JvxlData
 
colorscheme - Static variable in class org.jmol.script.T
 
colorSchemes - Static variable in class org.jmol.util.ColorEncoder
 
colorSchemeTranslucent - Variable in class org.jmol.jvxl.readers.Parameters
 
colorSetting(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
colorSettingClamped(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
colorsExplicit - Variable in class org.jmol.util.MeshSurface
 
colorShape(int, int, boolean) - Method in class org.jmol.script.ScriptEval
 
colorType - Variable in class org.jmol.shape.Mesh
 
colorType - Variable in class org.jmol.shapesurface.Isosurface
 
colorVertices(short, BS, boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
color a specific set of vertices a specific color
combineModulation(String, float, float) - Method in class org.jmol.adapter.readers.xtal.JanaReader
Retrieve cataloged displacement and add in this component, returning a new double[3].
combineSurfaces(Lst<ContactPair>, int, int, float[], Object, boolean, boolean) - Method in class org.jmol.shapesurface.Contact
 
comma - Static variable in class org.jmol.script.T
 
command - Static variable in class org.jmol.script.T
 
commandDelay - Static variable in class org.jmol.script.CommandWatcherThread
 
commandExpected() - Method in class org.jmol.script.ScriptTokenParser
 
CommandHistory - Class in org.jmol.util
Implements a queue for a bash-like command history.
CommandHistory() - Constructor for class org.jmol.util.CommandHistory
Creates a new instance using the default size (100)
commandHistory - Variable in class org.jmol.viewer.Viewer
 
commandHistoryLevelMax - Variable in class org.jmol.script.ScriptEval
 
commandLineOptions - Variable in class org.jmol.export.___Exporter
 
commandList - Variable in class org.jmol.util.CommandHistory
Array of commands.
commandLoop(boolean) - Method in class org.jmol.script.ScriptEval
 
commandOptions - Variable in class org.jmol.viewer.Viewer
 
commands - Static variable in class org.jmol.script.T
 
commands - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
commands - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
commandStart - Variable in class org.jmol.script.ScriptFlowContext
 
CommandWatcherThread - Class in org.jmol.script
 
CommandWatcherThread() - Constructor for class org.jmol.script.CommandWatcherThread
 
commandWatcherThread - Variable in class org.jmol.script.ScriptManager
 
commensurateSection1 - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
comment - Variable in class org.jmol.script.ScriptCompiler
 
commentChar - Variable in class org.jmol.export.___Exporter
 
COMP_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
comparator - Static variable in class org.jmol.script.T
 
compare(Object, Object) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
 
compare(Map<String, Object>, Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
 
compare(SlaterData, SlaterData) - Method in class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
 
compare(TextString, TextString) - Method in class org.jmol.g3d.TextString
 
compare(MeshData.SSet, MeshData.SSet) - Method in class org.jmol.jvxl.data.MeshData.SortSet
 
compare(Atom, Atom) - Method in class org.jmol.modelset.AtomCollection.AtomSorter
 
compare(String[], String[]) - Method in class org.jmol.modelsetbio.Resolver.BondSorter
 
compare(SV, SV) - Method in class org.jmol.script.SV.Sort
 
compare - Static variable in class org.jmol.script.T
 
compare() - Method in class org.jmol.scriptext.CmdExt
 
compare(Object[], Object[]) - Method in class org.jmol.util.EigenSort
 
compare(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.CapVertex
 
compare(Option, Option) - Method in class org.openscience.jmol.app.JmolApp.OptSort
 
compareAtoms(int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
compareAtoms(int, int) - Method in interface org.jmol.api.PymolAtomReader
 
compareFloat(int, float, float) - Method in class org.jmol.script.ScriptExpr
 
compareFloatData(int, float[], int, float) - Method in class org.jmol.script.ScriptExpr
 
compareInt(int, int, int) - Method in class org.jmol.script.ScriptExpr
 
compareString(int, int, String) - Method in class org.jmol.script.ScriptExpr
 
compareStringValues(int, String, String) - Method in class org.jmol.script.ScriptExpr
 
compile(String, boolean) - Method in interface org.jmol.api.JmolPatternMatcher
 
compile(Viewer, String, char, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
Compiles a set of tokens for each primitive element of a label.
compile(String, String, boolean, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptCompiler
 
compile(String, boolean) - Method in class org.jmol.util.PatternMatcher
 
compile0(boolean) - Method in class org.jmol.script.ScriptCompiler
 
compileCommand() - Method in class org.jmol.script.ScriptCompiler
 
compileExpr(String) - Method in class org.jmol.viewer.Viewer
 
compileExpression() - Method in class org.jmol.script.ScriptTokenParser
 
compileExpressions() - Method in class org.jmol.script.ScriptTokenParser
 
compiler - Variable in class org.jmol.script.ScriptEval
 
compiler - Variable in class org.jmol.script.ScriptFlowContext
 
compiler - Variable in class org.jmol.viewer.Viewer
 
compileScript(String, String, boolean) - Method in class org.jmol.script.ScriptEval
 
compileScriptFile(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
compileScriptFile(String, boolean) - Method in class org.jmol.script.ScriptEval
 
compileScriptFileInternal(String, String, String, String) - Method in class org.jmol.script.ScriptEval
 
compileScriptString(String, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
compileScriptString(String, boolean) - Method in class org.jmol.script.ScriptEval
 
compileSelect(SV[]) - Method in class org.jmol.viewer.PropertyManager
 
completeCommand(String) - Method in class org.jmol.console.GenericConsole
 
completeCommand(Map<String, ?>, boolean, boolean, String, int) - Static method in class org.jmol.script.T
 
completeInitialization(Graphics, Dimension) - Method in class org.jmol.applet.AppletWrapper
 
compnd - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
compnd(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
component - Variable in class org.jmol.smiles.SmilesAtom
 
componentHidden(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
componentMoved(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
componentResized(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
componentShown(ComponentEvent) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
 
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.Calculations
 
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
 
compute(int, Object[]) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFAngleCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFDistanceCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFESCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFOOPCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFSBCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFTorsionCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.MMFFVDWCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFAngleCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFDistanceCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFOOPCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFTorsionCalc
 
compute(Object[]) - Method in class org.jmol.minimize.forcefield.UFFVDWCalc
 
comSSMat - Variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
concatList(SV, SV, boolean) - Static method in class org.jmol.script.SV
 
CONE - Static variable in class org.jmol.shapecgo.CGOMesh
 
cone_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
conect() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
coneNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
CONF_TYPE_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
configuration - Static variable in class org.jmol.script.T
 
configuration() - Method in class org.jmol.scriptext.CmdExt
 
configurationPtr - Variable in class org.jmol.adapter.readers.cif.CifReader
 
configurationPtr - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
configurationSelected - Variable in class org.jmol.popup.JmolGenericPopup
 
conformationIndex - Variable in class org.jmol.adapter.readers.cif.CifReader
 
conformationIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
connect(float[][]) - Method in class org.jmol.modelset.ModelSet
 
connect - Static variable in class org.jmol.script.T
 
connect(int) - Method in class org.jmol.scriptext.CmdExt
 
connect_bonded - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
connect_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
connect_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
connectAll(int, boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
connectAllBad(int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
connected - Static variable in class org.jmol.script.T
 
Connection - Class in org.jmol.viewer
 
Connection(int, int, short, short, int, float, int) - Constructor for class org.jmol.viewer.Connection
 
connections - Variable in class org.jmol.shape.Mesh
 
connections - Variable in class org.jmol.shape.MeshCollection
 
Connections - Class in org.jmol.viewer
 
Connections(Viewer) - Constructor for class org.jmol.viewer.Connections
 
connections - Variable in class org.jmol.viewer.Connections
 
connectivity - Variable in class org.jmol.smiles.SmilesAtom
 
connectLast - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
connectNextAtomIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
connectNextAtomSet - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
connectorFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
connectorFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
connectors - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
console - Static variable in class org.jmol.script.T
 
console() - Method in class org.jmol.scriptext.CmdExt
 
console - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
consoleAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ConsoleAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ConsoleAction
 
consoleButton - Variable in class org.jmol.console.ScriptEditor
 
consoleDoc - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
ConsoleDocument() - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
consoleframe - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
consoleMessage(String) - Method in class org.jmol.util.GenericApplet
 
ConsoleTextArea - Class in org.openscience.jmol.app.jmolpanel.console
 
ConsoleTextArea(InputStream[]) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
 
ConsoleTextArea(boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
 
consoleTextPane - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
ConsoleTextPane(AppConsole) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
ConsoleWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
 
constrainQuadratic(double, double, double, int) - Method in class org.jmol.minimize.forcefield.Calculations
 
constraint - Static variable in class org.jmol.script.T
 
constraintEnergy(int) - Method in class org.jmol.minimize.forcefield.Calculations
 
constraintMap - Variable in class org.jmol.minimize.Minimizer
 
constraints - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
constraints - Variable in class org.jmol.minimize.forcefield.Calculations
 
constraints - Variable in class org.jmol.minimize.Minimizer
 
constructBitSetPolyhedron(int) - Method in class org.jmol.shapespecial.Polyhedra
 
constructBondsPolyhedron(int) - Method in class org.jmol.shapespecial.Polyhedra
 
constructDismissButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
constructMeasurementButtonPanel() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
constructMeasurementTable() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
constructRadiusPolyhedron(int, AtomIndexIterator) - Method in class org.jmol.shapespecial.Polyhedra
 
contact - Static variable in class org.jmol.script.T
 
contact() - Method in class org.jmol.scriptext.IsoExt
 
Contact - Class in org.jmol.shapesurface
 
Contact() - Constructor for class org.jmol.shapesurface.Contact
 
contactPair - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
contactPair - Variable in class org.jmol.jvxl.readers.Parameters
 
ContactPair - Class in org.jmol.util
 
ContactPair(Atom[], int, int, float, float, float, float) - Constructor for class org.jmol.util.ContactPair
 
ContactRenderer - Class in org.jmol.rendersurface
 
ContactRenderer() - Constructor for class org.jmol.rendersurface.ContactRenderer
 
contactType - Variable in class org.jmol.util.ContactPair
 
container - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
contains(int, int) - Method in class org.jmol.util.Rectangle
 
contentDisabled - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
contentPath - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
context - Variable in class org.jmol.awtjs2d.Platform
 
context - Variable in class org.jmol.script.ScriptProcess
 
context - Static variable in class org.jmol.script.T
 
contextCount - Static variable in class org.jmol.script.ScriptContext
 
contextPath - Variable in class org.jmol.script.ScriptContext
 
contextPath - Variable in class org.jmol.script.ScriptEval
 
ContextToken - Class in org.jmol.script
 
ContextToken() - Constructor for class org.jmol.script.ContextToken
 
contextVariables - Variable in class org.jmol.script.ContextToken
 
contextVariables - Variable in class org.jmol.script.ScriptCompiler
 
contextVariables - Variable in class org.jmol.script.ScriptParam
 
CONTINUE - Static variable in class org.jmol.script.ScriptCompiler
 
continuecmd - Static variable in class org.jmol.script.T
 
continueMatch(int, int, boolean) - Method in class org.jmol.smiles.SmilesSearch
 
continuing - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
contour - Static variable in class org.jmol.script.T
 
CONTOUR_BITSET - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_COLIX - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_COLOR - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_FDATA - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_NPOLYGONS - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
CONTOUR_POINTS - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
CONTOUR_VALUE - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
contourColixes - Variable in class org.jmol.jvxl.data.JvxlData
 
contourColixes - Variable in class org.jmol.jvxl.readers.Parameters
 
contourColixes - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
contourColors - Variable in class org.jmol.jvxl.data.JvxlData
 
contourFromZero - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourFromZero - Variable in class org.jmol.jvxl.readers.Parameters
 
contourIncrements - Variable in class org.jmol.jvxl.readers.Parameters
 
contourIndex - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
contourlines - Static variable in class org.jmol.script.T
 
contourPlaneMaximumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourPlaneMinimumValue - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contours - Static variable in class org.jmol.script.T
 
contoursDiscrete - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contoursDiscrete - Variable in class org.jmol.jvxl.readers.Parameters
 
contourType - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
contourType - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourType - Variable in class org.jmol.jvxl.readers.Parameters
 
contourValues - Variable in class org.jmol.jvxl.data.JvxlData
 
contourValues - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
contourValuesUsed - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourValuesUsed - Variable in class org.jmol.jvxl.data.JvxlData
 
ContourVertex(P3) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
contourVertexCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
contourVertexCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
contourVertexes - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
CONTRACTIONS - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
ControlEnterTextArea() - Constructor for class org.jmol.console.AppletConsole.ControlEnterTextArea
 
controlHermites - Variable in class org.jmol.renderbio.BioShapeRenderer
 
controlHermites - Variable in class org.jmol.renderspecial.DrawRenderer
 
controlPoints - Variable in class org.jmol.modelsetbio.BioPolymer
 
controlPoints - Variable in class org.jmol.renderbio.BioShapeRenderer
 
controlPointScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
 
converged - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
convertPointFromScreen(Object, P3) - Static method in class org.jmol.awt.Display
 
convertPointFromScreen(Object, P3) - Method in class org.jmol.awt.Platform
 
convertPointFromScreen(Object, P3) - Static method in class org.jmol.awtjs2d.Display
 
convertPointFromScreen(Object, P3) - Method in class org.jmol.awtjs2d.Platform
 
convertToMegabytes(long) - Static method in class org.jmol.popup.GenericSwingPopup
 
coord - Variable in class org.jmol.minimize.MinAtom
 
coord - Static variable in class org.jmol.script.T
 
coordinateInRange(int, int, T3, int, P3i) - Method in class org.jmol.shape.Shape
 
coordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
coordinatesAreFractional(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
coordinatesAreFractional(Object) - Method in class org.jmol.api.JmolAdapter
Get the boolean whether coordinates are fractional.
coordinatesAreFractional - Variable in class org.jmol.script.ScriptParam
 
coordinatesAreFractional - Variable in class org.jmol.symmetry.SymmetryInfo
 
coordinatesArePrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
coords - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
coords - Variable in class org.jmol.shapespecial.Dipole
 
coordSaved - Variable in class org.jmol.minimize.forcefield.ForceField
 
coordSaved - Variable in class org.jmol.minimize.Minimizer
 
copy(BS) - Static method in class org.jmol.util.BSUtil
 
copy() - Method in class org.jmol.util.Point3fi
 
copy2(BS, BS) - Static method in class org.jmol.util.BSUtil
 
copyandUnzip(String, String, String) - Method in class org.openscience.jmol.app.webexport.WebPanel
Based on code available at Java2s.com
copyBinaryFile(String, String) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
copyColixTranslucency(short, short) - Static method in class org.jmol.util.C
 
copyDirectory(String, File, File, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
copyFile(String, File, File, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
copyImageAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
CopyImageAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyImageAction
 
copyImageActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
copyInvert(BS, int) - Static method in class org.jmol.util.BSUtil
 
copyModulations(String, String) - Method in class org.jmol.adapter.readers.xtal.JanaReader
Create a new catalog entry for an atom's modulation components.
copyright - Static variable in class org.jmol.viewer.JC
 
copyScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
CopyScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CopyScriptAction
 
copyScriptActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
copyTensor() - Method in class org.jmol.util.Tensor
 
cordMidPoints - Variable in class org.jmol.renderbio.RocketsRenderer
 
corner - Variable in class org.jmol.shape.Axes
 
corners - Variable in class org.jmol.renderbio.RocketRenderer
 
corners - Static variable in class org.jmol.script.T
 
cos - Static variable in class org.jmol.script.T
 
cosAlpha - Variable in class org.jmol.util.SimpleUnitCell
 
cosASB2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
cosBeta - Variable in class org.jmol.util.SimpleUnitCell
 
cosGamma - Variable in class org.jmol.util.SimpleUnitCell
 
cosPhi - Variable in class org.jmol.g3d.CylinderRenderer
 
cossin - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
cosTheta - Variable in class org.jmol.g3d.CylinderRenderer
 
cosTolerance - Variable in class org.jmol.symmetry.PointGroup
 
coulomb_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
coulomb_dielectric - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
coulomb_units_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
count - Variable in class org.jmol.bspt.Element
 
count - Variable in class org.jmol.modelset.Measurement
 
count - Variable in class org.jmol.render.MeasuresRenderer
 
count - Static variable in class org.jmol.script.T
 
COUNT_MASK - Static variable in class org.jmol.viewer.binding.Binding
 
countData(String) - Method in class org.jmol.jvxl.readers.JvxlReader
 
countData(String) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
counter - Variable in class org.jmol.script.ScriptParallelProcessor
 
countGroup(int, String, String) - Method in class org.jmol.modelset.ModelLoader
 
countInternalPairs(Node[], BS, boolean) - Static method in class org.jmol.smiles.SmilesAromatic
Counts the electron pairs that are internal to this ring.
countPlusIndices - Variable in class org.jmol.modelset.Measurement
 
countStereo(String) - Static method in class org.jmol.smiles.SmilesMatcher
 
countsXYZ - Variable in class org.jmol.quantum.QuantumCalculation
 
covalentHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
 
covalentradius - Static variable in class org.jmol.script.T
 
covalentVersion - Static variable in class org.jmol.util.Elements
 
cr - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
create - Static variable in class org.jmol.script.T
 
createAndShowGUI(Viewer, HistoryFile, String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
createAtomDataSet(Viewer, ModelSet, int, Object, BS) - Static method in class org.jmol.modelset.ModelLoader
 
createAtomDataSet(Object, int) - Method in class org.jmol.viewer.ModelManager
 
createAtomSeCollectionFromArrayData(Lst<Object>, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
createAtomSeCollectionFromStrings(String[], SB, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
createAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
 
createAtomSetCollectionFromFile(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
createAtomSetCollectionFromFiles(String[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
createAtomSetCollectionFromReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
not used in Jmol project -- will close reader
createAtomSetCollectionFromString(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
createAtomsFromCoordLines() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
Now create atoms from the coordinate lines.
createBonds(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
Use the site bitset to check for atoms that are within +/-dx Angstroms of the specified distances in GEOM_BOND where dx is determined by the uncertainty (dx) in the record.
createCap(V3) - Method in class org.jmol.util.MeshCapper
Entry point when finished generating edges.
createCartoonObject(String, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
createColorScheme(String, boolean, boolean) - Method in class org.jmol.util.ColorEncoder
 
createContours(float, float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
createCube() - Method in interface org.jmol.api.MOCalculationInterface
 
createCube() - Method in class org.jmol.quantum.MepCalculation
 
createCube() - Method in class org.jmol.quantum.MOCalculation
 
createCube() - Method in class org.jmol.quantum.NciCalculation
 
createDialog(Component) - Method in class org.jmol.dialog.FileChooser
 
createEllipsoidShades() - Method in class org.jmol.util.Shader
 
createExportPanel(String[], String[], String) - Method in class org.jmol.dialog.Dialog
 
createFunction(String, String, String) - Method in class org.jmol.scriptext.IsoExt
for the ISOSURFACE command
createGeodesic() - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
createGeodesic(int) - Static method in class org.jmol.util.Geodesic
 
createImage(String, String, Object, int) - Method in interface org.jmol.api.JmolStatusListener
Starting with Jmol 11.8.RC5, for a context where the Jmol application is embedded in another application simply to send the returned message to the application.
createImage(Object) - Static method in class org.jmol.awt.Image
 
createImage(Object) - Method in class org.jmol.awt.Platform
could be byte[] (from ZIP file) or String (local file name) or URL
createImage(Object) - Method in class org.jmol.awtjs2d.Platform
could be byte[] (from ZIP file) or String (local file name) or URL
createImage(String, String, Object, int) - Method in class org.jmol.util.GenericApplet
 
createImage(String, String, String, byte[], int) - Method in class org.jmol.viewer.StatusManager
offer to let application do the image creation.
createImage(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
createImageStatus(String, String, Object, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Starting with Jmol 11.8.RC5, this is just informational if type == null and null is returned, then it means "Jmol, you handle it"
createIsosurface(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
createLadders(Lst<Bridge>, boolean) - Method in class org.jmol.dssx.DSSP
"ladder =: one or more consecutive bridges of identical type" (p.
createLanguageList() - Method in class org.jmol.i18n.GT
 
createLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
 
createLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
 
createLcaoLobe(V3, float, int) - Method in class org.jmol.shapesurface.Isosurface
 
createMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create a menu for the app.
createMenubar() - Method in class org.jmol.console.AppletConsole
 
createMenubar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create the menubar for the app.
createMenuItem(String) - Method in class org.jmol.console.AppletConsole
 
createMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
This is the hook through which all menu items are created.
createMesh() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
 
createMesh(int, int, int, int, float, int) - Method in class org.jmol.renderbio.BioShapeRenderer
Cartoon meshes are triangulated objects.
createModels(int) - Method in class org.jmol.modelset.ModelSet
 
createModelSet(JmolAdapter, Object, BS) - Method in class org.jmol.modelset.ModelLoader
 
createModelSet(String, String, SB, Object, BS, boolean) - Method in class org.jmol.viewer.ModelManager
 
createModelSetAndReturnError(Object, boolean, SB, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
finally(!) we are ready to create the "model set" from the "atom set collection" - does NOT repaint
createMonteCarloOrbital() - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
createMovie(Viewer, String[], int, int, int, String) - Method in interface org.jmol.api.JmolMovieCreatorInterface
create a movie from a set of image files
createMovie(Viewer, String[], int, int, int, String) - Method in class org.jmol.image.AviCreator
 
createNewAtomSet() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
createOrbital() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
createParticle(String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
createPdfDocument(OC, Object) - Method in interface org.jmol.api.JmolPdfCreatorInterface
 
createPuttyObject(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
"Putty" shapes scaled in a variety of ways.
createRibbonObject(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
PyMOL "ribbons" could be Jmol backbone or trace, depending upon the value of PyMOL.ribbon_sampling.
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManager
 
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerAwt
 
createSceneSet(String, String, int, int) - Method in class org.jmol.viewer.OutputManagerJS
 
createSet(int, int, int) - Method in class org.jmol.jvxl.data.MeshData
 
createSGFromList(String, Lst<?>) - Static method in class org.jmol.symmetry.SpaceGroup
 
createShapeObject(int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Create JmolObjects for each shape.
createShapeObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create JmolObjects for all the molecular shapes; not executed for a state script.
createShapeObjects(BS[], boolean, int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
create all objects for a given molecule or scene
createSlaterData(int, String, String) - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
createSpacefillObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Create a BALLS JmolObject for each radius.
createSpaceGroup(int, String, Object) - Method in interface org.jmol.api.SymmetryInterface
 
createSpaceGroup(int, String, Object) - Static method in class org.jmol.symmetry.SpaceGroup
 
createSpaceGroup(int, String, Object) - Method in class org.jmol.symmetry.Symmetry
 
createSpaceGroupN(String) - Static method in class org.jmol.symmetry.SpaceGroup
 
createSpaceGroups() - Static method in class org.jmol.symmetry.SpaceGroup
 
createSphericalSlaterByType(int, int, String, float, float) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
We have the type as a string and need to translate that to exponents for x, y, z, and r.
createSurfaceTool() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
createTextureFile(String, MeshSurface, int[]) - Method in class org.jmol.export._ObjExporter
Writes a texture file with the colors in the colixes array in a way that it can be mapped by the texture coordinates vt.
createTheImage(Object, String, OC, Map<String, Object>, String[]) - Method in class org.jmol.viewer.OutputManager
 
createTool(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Hook through which every toolbar item is created.
createToolbar() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create the toolbar.
createToolbarButton(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Create a button to go inside of the toolbar.
createTopoMap(BS) - Method in class org.jmol.smiles.SmilesSearch
 
createTraceObject(BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
trace, or cartoon in the case of cartoon ladders.
createTransferable(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
createTreeModel() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Creates the treeModel of the AtomSets available in the JmolViewer
createVCRController(String) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Creates a VCR type set of controller inside a JPanel.
createVoxelData() - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
Developer must customize this method
createWebExport() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
createZip(String, String, Object) - Method in class org.jmol.viewer.Viewer
 
createZipSet(String, String[], boolean, OC, String) - Method in class org.jmol.viewer.OutputManager
 
creatingImage - Variable in class org.jmol.viewer.Viewer
 
creditsAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
CreditsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.CreditsAction
 
CreditsDialog - Class in org.openscience.jmol.app.jmolpanel
 
CreditsDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.CreditsDialog
 
crit - Variable in class org.jmol.minimize.Minimizer
 
criterion - Variable in class org.jmol.minimize.forcefield.ForceField
 
criterion - Static variable in class org.jmol.script.T
 
cross - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
cross - Static variable in class org.jmol.script.T
 
cross0 - Variable in class org.jmol.renderspecial.DipolesRenderer
 
cross1 - Variable in class org.jmol.renderspecial.DipolesRenderer
 
crossBinary(String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
crossed - Static variable in class org.jmol.script.T
 
crossEnd - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
crossOffset - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
crossWidth - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
crossWidthPixels - Variable in class org.jmol.renderspecial.DipolesRenderer
 
crtval - Static variable in class org.jmol.shapespecial.Ellipsoid
 
cryst1 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
cryst1() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
CRYSTAL - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
CRYSTAL_SYMMETRY_TRANSFORM3 - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
crystalContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CrystalReader - Class in org.jmol.adapter.readers.xtal
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
CrystalReader() - Constructor for class org.jmol.adapter.readers.xtal.CrystalReader
 
CS - Static variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
 
CS2 - Static variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
 
csfLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CsfReader - Class in org.jmol.adapter.readers.quantum
CSF file reader based on CIF idea -- fluid property fields.
CsfReader() - Constructor for class org.jmol.adapter.readers.quantum.CsfReader
 
CTRL - Static variable in class org.jmol.viewer.binding.Binding
 
CTRL_ALT - Static variable in class org.jmol.viewer.binding.Binding
 
CTRL_SHIFT - Static variable in class org.jmol.viewer.binding.Binding
 
cubeCountX - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeCountY - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeCountZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cubeFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
CubeIterator - Class in org.jmol.bspt
Iterator used for finding all points within a box or a hemi-box
CubeIterator(Bspt) - Constructor for class org.jmol.bspt.CubeIterator
 
cubeIterator - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
cubeIterators - Variable in class org.jmol.bspt.Bspf
 
CubeReader - Class in org.jmol.adapter.readers.simple
Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.
CubeReader() - Constructor for class org.jmol.adapter.readers.simple.CubeReader
 
CubeReader - Class in org.jmol.jvxl.readers
 
CubeReader() - Constructor for class org.jmol.jvxl.readers.CubeReader
 
cubeVertexOffsets - Static variable in class org.jmol.util.BoxInfo
 
cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
 
cubeVertexVectors - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
cull_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
current - Variable in class org.jmol.thread.HoverWatcherThread
 
current - Variable in class org.jmol.viewer.ActionManager
 
currentAtomSetIndex - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
currentBgColor - Variable in class org.jmol.shape.Object2dShape
 
currentBgTranslucentLevel - Variable in class org.jmol.shape.Object2dShape
 
currentBlock - Variable in class org.jmol.adapter.readers.xtal.MagresReader
 
currentChain - Variable in class org.jmol.modelset.ModelLoader
 
currentChainID - Variable in class org.jmol.modelset.ModelLoader
 
currentColor - Variable in class org.jmol.shape.Object2dShape
 
currentCompnd - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
currentCursor - Variable in class org.jmol.viewer.Viewer
 
currentDipole - Variable in class org.jmol.shapespecial.Dipoles
 
currentDirection - Variable in class org.jmol.viewer.AnimationManager
 
currentFont - Variable in class org.jmol.shape.Object2dShape
 
currentFont - Variable in class org.jmol.util.GData
 
currentFrameIs(int) - Method in class org.jmol.viewer.AnimationManager
 
currentFrankId - Variable in class org.jmol.popup.JmolGenericPopup
 
currentGroup3 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
currentGroup3 - Variable in class org.jmol.modelset.ModelLoader
 
currentGroupInsertionCode - Variable in class org.jmol.modelset.ModelLoader
 
currentGroupSequenceNumber - Variable in class org.jmol.modelset.ModelLoader
 
currentIndex - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
currentIsLast() - Method in class org.jmol.viewer.AnimationManager
 
currentKey - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
currentLevel - Static variable in class org.jmol.util.Geodesic
 
currentlocalpath - Static variable in class org.jmol.script.T
 
currentlyRendering - Variable in class org.jmol.util.GData
 
currentMenuItemId - Variable in class org.jmol.popup.GenericSwingPopup
 
currentMesh - Variable in class org.jmol.shape.MeshCollection
 
currentMetricsFont3d - Variable in class org.jmol.shape.Frank
 
currentMorphModel - Variable in class org.jmol.viewer.AnimationManager
 
currentNormalOrigin - Variable in class org.jmol.export._ObjExporter
Wavefront OBJ refers to vertices and normals and textures by their location in the file.
currentObject - Variable in class org.jmol.shape.Object2dShape
 
currentPalette - Variable in class org.jmol.util.ColorEncoder
 
currentPoints - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
currentProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
currentResno - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
currentSegmentCount - Variable in class org.jmol.util.ColorEncoder
 
currentShadeIndex - Variable in class org.jmol.g3d.Graphics3D
 
currentShapeID - Variable in class org.jmol.viewer.Viewer
 
currentShapeState - Variable in class org.jmol.viewer.Viewer
 
currentSize - Variable in class org.jmol.dialog.FilePreview.FPPanel
 
currentStep - Variable in class org.jmol.minimize.forcefield.ForceField
 
currentTextureOrigin - Variable in class org.jmol.export._ObjExporter
Wavefront OBJ refers to vertices and normals and textures by their location in the file.
currentThread - Variable in class org.jmol.script.ScriptEval
 
currentTime - Variable in class org.jmol.thread.JmolThread
 
currentTranslucentLevel - Variable in class org.jmol.shape.Object2dShape
 
currentVertexOrigin - Variable in class org.jmol.export._ObjExporter
Wavefront OBJ refers to vertices and normals and textures by their location in the file.
cursor - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
 
cursorPos - Variable in class org.jmol.util.CommandHistory
Current position of the cursor;
curve - Static variable in class org.jmol.script.T
 
CUSTOM - Static variable in class org.jmol.util.ColorEncoder
 
CUSTOM_CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
 
CUT - Static variable in class org.jmol.quantum.MOCalculation
 
cutoff - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
cutoff - Variable in class org.jmol.jvxl.data.JvxlData
 
cutoff - Variable in class org.jmol.jvxl.readers.Parameters
 
cutoff - Static variable in class org.jmol.script.T
 
cutoffAutomatic - Variable in class org.jmol.jvxl.readers.Parameters
 
cutoffRange - Variable in class org.jmol.shapesurface.Isosurface
 
cx - Variable in class org.jmol.bspt.CubeIterator
 
CX - Variable in class org.jmol.quantum.MOCalculation
 
cxyz - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
 
cy - Variable in class org.jmol.bspt.CubeIterator
 
CY - Variable in class org.jmol.quantum.MOCalculation
 
CYAN - Static variable in class org.jmol.util.C
 
cylinder - Static variable in class org.jmol.script.T
 
CYLINDER - Static variable in class org.jmol.shapecgo.CGOMesh
 
cylinder3d - Variable in class org.jmol.g3d.Graphics3D
 
cylinder_shader_ff_workaround - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cylinderBase - Static variable in class org.jmol.renderspecial.DipolesRenderer
 
cylinderMatrix - Variable in class org.jmol.export._IdtfExporter
 
cylinderNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
CylinderRenderer - Class in org.jmol.g3d
Draws shaded cylinders in 3D.
CylinderRenderer(Graphics3D) - Constructor for class org.jmol.g3d.CylinderRenderer
 
cylinders_shader_filter_faces - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
cz - Variable in class org.jmol.bspt.CubeIterator
 
CZ - Variable in class org.jmol.quantum.MOCalculation
 

D

d - Variable in class org.jmol.adapter.readers.cif.Subsystem
 
d - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
d - Variable in class org.jmol.minimize.forcefield.Calculation
 
d - Variable in class org.jmol.util.ContactPair
 
d1 - Variable in class org.jmol.g3d.HermiteRenderer
 
d2 - Variable in class org.jmol.g3d.HermiteRenderer
 
d2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
da - Variable in class org.jmol.minimize.forcefield.Calculations
 
DA_D - Static variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
DA_DA - Static variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
dAB - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
dAB2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
dash_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dash_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dash_gap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dash_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dash_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dash_round_ends - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dash_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dash_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dashDots - Variable in class org.jmol.render.FontLineShapeRenderer
 
dashes - Static variable in class org.jmol.render.FontLineShapeRenderer
 
data - Variable in class org.jmol.adapter.readers.cif.CifReader
 
data - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
data - Variable in class org.jmol.jvxl.readers.DelPhiBinaryReader
 
data - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
data - Variable in class org.jmol.jvxl.readers.IsoFxyzReader
 
data - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
data - Variable in class org.jmol.minimize.MinObject
 
data - Variable in class org.jmol.modelset.LabelToken
 
data - Static variable in class org.jmol.script.T
 
data() - Method in class org.jmol.scriptext.CmdExt
 
data - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
DATA_SAVE_IN_STATE - Static variable in class org.jmol.viewer.DataManager
 
DATA_SELECTION_MAP - Static variable in class org.jmol.viewer.DataManager
 
DATA_TYPE - Static variable in class org.jmol.viewer.DataManager
 
DATA_TYPE_AF - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_AFF - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_AFFF - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_STRING - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_TYPE_UNKNOWN - Static variable in interface org.jmol.api.JmolDataManager
 
DATA_VALUE - Static variable in class org.jmol.viewer.DataManager
 
databases - Variable in class org.jmol.viewer.GlobalSettings
 
databases - Static variable in class org.jmol.viewer.JC
 
dataFrames - Variable in class org.jmol.modelset.Model
 
dataIsReducedDensity - Variable in class org.jmol.quantum.NciCalculation
 
DataManager - Class in org.jmol.viewer
 
DataManager() - Constructor for class org.jmol.viewer.DataManager
 
dataMax - Variable in class org.jmol.jvxl.data.JvxlData
 
dataMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
dataMean - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
dataMin - Variable in class org.jmol.jvxl.data.JvxlData
 
dataMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
dataOnly - Variable in class org.jmol.util.MeshSurface
 
dataOnly - Variable in class org.jmol.viewer.Viewer
 
dataPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
dataReaders - Variable in class org.jmol.io.FilesReader
 
dataScaling - Variable in class org.jmol.quantum.NciCalculation
 
dataseparator - Static variable in class org.jmol.script.T
 
dataSeparator - Variable in class org.jmol.viewer.GlobalSettings
 
dataSourceFrame - Variable in class org.jmol.modelset.Model
 
dataT - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
dataType - Variable in class org.jmol.jvxl.readers.Parameters
 
dataType - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
dataType - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
dataValues - Variable in class org.jmol.viewer.DataManager
 
dataXYReversed - Variable in class org.jmol.jvxl.data.JvxlData
 
dataXYReversed - Variable in class org.jmol.jvxl.readers.Parameters
 
date - Static variable in class org.jmol.viewer.JC
 
db - Variable in class org.jmol.minimize.forcefield.Calculations
 
dBb(BS, boolean) - Method in class org.jmol.modelset.BondCollection
 
DBLCLK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
DBLCLK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
dBm(BS, boolean) - Method in class org.jmol.modelset.BondCollection
send request up to ModelCollection level.
dc - Variable in class org.jmol.minimize.forcefield.Calculations
 
DC - Static variable in class org.jmol.quantum.QS
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
 
DC_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
dcdFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
dd - Variable in class org.jmol.minimize.forcefield.Calculations
 
dData - Variable in class org.jmol.minimize.forcefield.Calculation
 
ddata - Variable in class org.jmol.minimize.MinObject
 
dE - Variable in class org.jmol.minimize.forcefield.Calculation
 
dE - Variable in class org.jmol.minimize.forcefield.ForceField
 
DEATH - Static variable in class org.jmol.multitouch.ActionManagerMT
 
debug - Static variable in class org.jmol.export._ObjExporter
Flag to cause debugging output to stdout.
debug - Static variable in class org.jmol.script.T
 
debug(String) - Method in class org.jmol.util.DefaultLogger
 
debug(String) - Static method in class org.jmol.util.Logger
Writes a log at DEBUG level.
debug(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at DEBUG level.
debug_pick - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
debugContext - Variable in class org.jmol.adapter.readers.xml.XmlHandler
 
debugging - Static variable in class org.jmol.util.Logger
 
debuggingHigh - Static variable in class org.jmol.util.Logger
 
debugHigh - Variable in class org.jmol.script.ScriptExpr
 
debugHigh - Variable in class org.jmol.script.ScriptMathProcessor
 
debugPrint(String) - Method in class org.jmol.export._ObjExporter
Debug print utility.
debugScript - Variable in class org.jmol.script.ScriptEval
 
debugscript - Static variable in class org.jmol.script.T
 
debugScript - Variable in class org.jmol.viewer.GlobalSettings
 
decimal - Static variable in class org.jmol.script.T
 
decodeAssemblyOperators(String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
decodeKey(Integer) - Static method in class org.jmol.minimize.MinObject
 
deduceElementSymbol(String, String) - Method in class org.jmol.adapter.readers.more.GromacsReader
 
deduceElementSymbol(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed.
deducePdbElementSymbol(boolean, String, String) - Static method in class org.jmol.adapter.readers.more.ForceFieldReader
 
DEFAULT - Static variable in class org.jmol.g3d.TriangleRenderer
 
default_2fofc_map_rep - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
DEFAULT_BASIS - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JC
 
DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JC
 
DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JC
 
default_buster_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
DEFAULT_CAMERA_DEPTH - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_CHARGE - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
DEFAULT_DISTANCE_FACTOR - Static variable in class org.jmol.shapespecial.Polyhedra
 
DEFAULT_FACECENTEROFFSET - Static variable in class org.jmol.shapespecial.Polyhedra
 
default_fofc_map_rep - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_GESTURE_SWIPE_FACTOR - Static variable in class org.jmol.viewer.ActionManager
 
DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JC
 
DEFAULT_MAD - Static variable in class org.jmol.shapespecial.Dipoles
 
DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_MAX_SIZE - Static variable in class org.jmol.util.CommandHistory
 
DEFAULT_METHOD - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JC
 
DEFAULT_MOUSE_DRAG_FACTOR - Static variable in class org.jmol.viewer.ActionManager
 
DEFAULT_MOUSE_WHEEL_FACTOR - Static variable in class org.jmol.viewer.ActionManager
 
DEFAULT_MULT - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
DEFAULT_NAV_FPS - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_OFFSETSIDE - Static variable in class org.jmol.shapespecial.Dipoles
 
DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JC
 
DEFAULT_PERSPECTIVE_DEPTH - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_PERSPECTIVE_MODEL - Static variable in class org.jmol.viewer.TransformManager
 
default_phenix_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
default_phenix_no_fill_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
default_refmac_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
DEFAULT_RHOPARAM - Variable in class org.jmol.quantum.NciCalculation
 
DEFAULT_RHOPLOT_PRO - Variable in class org.jmol.quantum.NciCalculation
 
DEFAULT_RHOPLOT_SCF - Variable in class org.jmol.quantum.NciCalculation
 
DEFAULT_SPIN_FPS - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_SPIN_Y - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_STEREO_DEGREES - Static variable in class org.jmol.viewer.TransformManager
 
DEFAULT_STRUT_RADIUS - Static variable in class org.jmol.viewer.JC
 
DEFAULT_VISUAL_RANGE - Static variable in class org.jmol.viewer.TransformManager
 
defaultActions - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
Actions defined by the Jmol class
defaultAlignment - Variable in class org.jmol.shape.Labels
 
defaultanglelabel - Static variable in class org.jmol.script.T
 
defaultAngleLabel - Variable in class org.jmol.viewer.GlobalSettings
 
defaultBgcolix - Variable in class org.jmol.shape.Labels
 
defaultBondingMars - Static variable in class org.jmol.util.Elements
Default table of bonding radii stored as a short mar ...
defaultChoice - Static variable in class org.jmol.dialog.Dialog
 
defaultcmd - Static variable in class org.jmol.script.T
 
defaultColix - Variable in class org.jmol.shape.Labels
 
defaultColix - Variable in class org.jmol.shapesurface.Isosurface
 
defaultColorFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultColorFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultColorFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorNegative - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorNegativeLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorPositive - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultColorPositiveLCAO - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultcolorscheme - Static variable in class org.jmol.script.T
 
defaultContourCount - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
defaultContourCount - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultCovalentMad - Variable in class org.jmol.modelset.BondCollection
 
defaultCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultCutoff - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
defaultdirectory - Static variable in class org.jmol.script.T
 
defaultDirectory - Variable in class org.jmol.viewer.GlobalSettings
 
defaultdistancelabel - Static variable in class org.jmol.script.T
 
defaultDistanceLabel - Variable in class org.jmol.viewer.GlobalSettings
 
defaultdrawarrowscale - Static variable in class org.jmol.script.T
 
defaultDrawArrowScale - Variable in class org.jmol.viewer.GlobalSettings
 
defaultdropscript - Static variable in class org.jmol.script.T
 
defaultDropScript - Variable in class org.jmol.viewer.GlobalSettings
 
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultEdgeFractionBase - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
defaultEdgeFractionRange - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultFontId - Variable in class org.jmol.shape.Labels
 
defaultFontName - Static variable in class org.jmol.shape.Frank
 
defaultFontSize - Static variable in class org.jmol.shape.Frank
 
defaultFontStyle - Static variable in class org.jmol.shape.Frank
 
defaultGroupCount - Static variable in class org.jmol.modelset.ModelLoader
 
defaultlabelpdb - Static variable in class org.jmol.script.T
 
defaultLabelPDB - Variable in class org.jmol.viewer.GlobalSettings
 
defaultlabelxyz - Static variable in class org.jmol.script.T
 
defaultLabelXYZ - Variable in class org.jmol.viewer.GlobalSettings
 
defaultlattice - Static variable in class org.jmol.script.T
 
defaultloadfilter - Static variable in class org.jmol.script.T
 
defaultLoadFilter - Variable in class org.jmol.viewer.GlobalSettings
 
defaultloadscript - Static variable in class org.jmol.script.T
 
defaultLoadScript - Variable in class org.jmol.viewer.GlobalSettings
 
defaultLobeCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
DefaultLogger - Class in org.jmol.util
Default implementation of the logger.
DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
 
defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMappedDataMax - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMappedDataMin - Static variable in class org.jmol.jvxl.readers.SurfaceReader
 
defaultMepCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMepMax - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMepMin - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultMessage - Variable in class org.jmol.console.GenericConsole
 
defaultMode - Variable in class org.jmol.viewer.TransformManager
 
defaultOffset - Variable in class org.jmol.shape.Labels
 
defaultON - Static variable in class org.jmol.script.T
 
defaultOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultOrbitalCutoffOld - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultPaletteID - Variable in class org.jmol.shape.Labels
 
defaultPointer - Variable in class org.jmol.shape.Labels
 
defaultQMElectronDensityCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultQMOrbitalCutoff - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultRotationRadius - Variable in class org.jmol.modelset.Model
 
defaults - Static variable in class org.jmol.script.T
 
defaultScaleToScreen(float) - Method in class org.jmol.viewer.TransformManager
 
defaultSolventRadius - Static variable in class org.jmol.jvxl.readers.Parameters
 
defaultsOnlyForNone - Variable in class org.jmol.shape.Labels
 
defaultStructure - Variable in class org.jmol.modelset.Model
 
defaultstructuredssp - Static variable in class org.jmol.script.T
 
defaultStructureDSSP - Variable in class org.jmol.viewer.GlobalSettings
 
defaultTickInfo - Variable in class org.jmol.shape.Measures
 
defaulttorsionlabel - Static variable in class org.jmol.script.T
 
defaultTorsionLabel - Variable in class org.jmol.viewer.GlobalSettings
 
defaulttranslucent - Static variable in class org.jmol.script.T
 
defaultTranslucent - Variable in class org.jmol.viewer.GlobalSettings
 
defaultvdw - Static variable in class org.jmol.script.T
 
defaultVdw - Variable in class org.jmol.viewer.Viewer
 
defaultZPos - Variable in class org.jmol.shape.Labels
 
defer_builds_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
defer_updates - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
define(JmolMeasurementClient, ModelSet) - Method in class org.jmol.modelset.MeasurementData
called by the client to generate a set of measurements
define - Static variable in class org.jmol.script.T
 
define(MeasurementData, int) - Method in class org.jmol.shape.Measures
 
defineAll(int, Measurement, boolean, boolean, boolean) - Method in class org.jmol.shape.Measures
 
defineAtoms(String, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
defineAtomSet(String) - Method in class org.jmol.script.ScriptEval
 
defineAtomSets(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
defineCenterAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
DefineCenterAction() - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.DefineCenterAction
 
definedAtomSets - Variable in class org.jmol.script.ScriptEval
 
definedAtomSets - Variable in class org.jmol.viewer.Viewer
 
defineMeasurement(int, Measurement, boolean) - Method in class org.jmol.shape.Measures
 
defineSets() - Method in class org.jmol.script.ScriptEval
support for @xxx or define xxx commands
defineStructure(STR, String, int, int, int, int, char, int, int, char, int[], int[], BS) - Method in class org.jmol.modelsetbio.Resolver
 
DEG_TO_RAD - Static variable in class org.jmol.minimize.forcefield.Calculations
 
DEG_TO_RAD - Static variable in class org.jmol.minimize.Util
 
degree - Variable in class org.jmol.smiles.SmilesAtom
 
degrees - Variable in class org.jmol.navigate.Navigator
 
DEGREES - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
degreesPerRadian - Static variable in class org.jmol.export.___Exporter
 
degreesPerRadian - Static variable in class org.jmol.viewer.TransformManager
 
degreeStep - Variable in class org.jmol.navigate.Navigator
 
delay - Static variable in class org.jmol.script.T
 
delaymaximumms - Static variable in class org.jmol.script.T
 
delayMaximumMs - Variable in class org.jmol.viewer.GlobalSettings
 
delayScript(int) - Method in class org.jmol.script.ScriptEval
 
delete - Static variable in class org.jmol.script.T
 
delete() - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
deleteAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
deleteAllBonds() - Method in class org.jmol.modelset.ModelSet
 
deleteAllBonds2() - Method in class org.jmol.modelset.BondCollection
 
deleteAllButton - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
deleteAtomReferences() - Method in class org.jmol.modelset.Bond
 
deleteAtoms(int, int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
deleteAtoms(BS) - Method in class org.jmol.modelset.ModelSet
 
deleteAtoms(int, BS, BS) - Method in class org.jmol.modelset.StateScript
 
deleteAtoms(BS) - Method in class org.jmol.modelsetbio.Resolver
called from org.jmol.modelsetbio.resolver when adding hydrogens.
deleteAtoms(int) - Method in class org.jmol.shapespecial.DrawMesh
 
deleteAtoms(BS) - Method in class org.jmol.viewer.SelectionManager
 
deleteAtoms(BS, boolean) - Method in class org.jmol.viewer.Viewer
 
deleteAtomsInVariables(BS) - Method in interface org.jmol.api.JmolScriptEvaluator
 
deleteAtomsInVariables(BS) - Method in class org.jmol.script.ScriptEval
 
deleteAtomTensors(BS) - Method in class org.jmol.modelset.AtomCollection
 
deleteBits(BS, BS) - Static method in class org.jmol.util.BSUtil
this one slides deleted bits out of a pattern.
deleteBond(Bond) - Method in class org.jmol.modelset.Atom
 
deleteBondAt(int) - Method in class org.jmol.modelset.Atom
 
deleteBonds(BS) - Method in class org.jmol.modelset.Atom
 
deleteBonds(BS, boolean) - Method in class org.jmol.modelset.ModelSet
 
deleteBonds(BS) - Method in class org.jmol.viewer.Viewer
 
deleteButton - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
deleteConnections(float, float, int, BS, BS, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
 
deleteContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
deleteDipole(Dipole) - Method in class org.jmol.shapespecial.Dipoles
 
deleteDirectory(File) - Static method in class org.openscience.chimetojmol.ChimePanel
 
deleteI(int) - Method in class org.jmol.shape.Measures
 
deleteInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
deleteLcaoCartoon() - Method in class org.jmol.shapesurface.LcaoCartoon
 
deleteLcaoCartoon(int) - Method in class org.jmol.shapesurface.LcaoCartoon
 
deleteM(Measurement) - Method in class org.jmol.shape.Measures
 
deleteMeasurement(int) - Method in class org.jmol.api.JmolViewer
 
deleteMeasurement(int) - Method in class org.jmol.viewer.Viewer
 
deleteMesh() - Method in class org.jmol.shape.MeshCollection
 
deleteMeshElement(int) - Method in class org.jmol.shapecgo.CGO
 
deleteMeshElement(int) - Method in class org.jmol.shapespecial.Draw
 
deleteMeshI(int) - Method in class org.jmol.shape.MeshCollection
 
deleteMeshKey(String) - Method in class org.jmol.shape.MeshCollection
 
deleteModel(int, int, int, BS, BS) - Method in class org.jmol.modelset.ModelSet
 
deleteModelAtoms(int, int, BS) - Method in interface org.jmol.api.JmolDataManager
 
deleteModelAtoms(int, int, BS) - Method in class org.jmol.modelset.AtomCollection
 
deleteModelAtoms(int, int, BS) - Method in class org.jmol.viewer.DataManager
 
deleteModelAtoms(int, int, int, BS) - Method in class org.jmol.viewer.Viewer
 
deleteModels(BS) - Method in class org.jmol.modelset.ModelSet
 
deleteModels(int) - Method in class org.jmol.shapespecial.Draw
 
deleteModels(int, BS) - Method in class org.jmol.viewer.Viewer
called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1
deleteO(Object) - Method in class org.jmol.shape.Measures
 
deletePolyhedra() - Method in class org.jmol.shapespecial.Polyhedra
 
deleteSaved(String) - Method in class org.jmol.viewer.StateManager
 
deleteSavedType(String) - Method in class org.jmol.viewer.StateManager
 
deleteShapeAtoms(Object[], BS) - Method in class org.jmol.viewer.ShapeManager
 
deleteUnneededAtoms() - Method in class org.jmol.modelsetbio.Resolver
Delete hydrogen atoms that are still in bsAddedHydrogens, because they were not actually added.
deleteVdwDependentShapes(BS) - Method in class org.jmol.viewer.ShapeManager
 
deleteWidget(int) - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
DELPHI_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.io.JmolUtil
 
DelPhiBinaryReader - Class in org.jmol.jvxl.readers
 
DelPhiBinaryReader() - Constructor for class org.jmol.jvxl.readers.DelPhiBinaryReader
 
delta - Variable in class org.jmol.minimize.forcefield.Calculation
 
delta - Variable in class org.jmol.thread.MoveToThread.Slider
 
delta2 - Variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
 
delta2 - Variable in class org.jmol.util.Modulation
 
density - Static variable in class org.jmol.script.T
 
DEPR_FD_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DEPR_FD_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DEPR_FO_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DEPR_FO_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DEPR_FU_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DEPR_FU_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
deprecatedparam - Static variable in class org.jmol.script.T
 
depth - Variable in class org.jmol.export.Export3D
 
depth - Variable in class org.jmol.g3d.SphereRenderer
 
depth - Static variable in class org.jmol.script.T
 
depth - Variable in class org.jmol.util.GData
 
depth1 - Variable in class org.jmol.g3d.HermiteRenderer
 
depth_cue - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
depthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
 
depthByPixels(int) - Method in class org.jmol.viewer.Viewer
 
depthDelta - Variable in class org.jmol.navigate.Navigator
 
depthPercent - Variable in class org.jmol.navigate.Navigator
 
depthPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
depthPlane - Variable in class org.jmol.viewer.TransformManager
 
depthStart - Variable in class org.jmol.navigate.Navigator
 
depthToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
depthValue - Variable in class org.jmol.viewer.TransformManager
 
depthZ - Variable in class org.jmol.export.___Exporter
 
desc - Variable in class org.jmol.symmetry.Symmetry
 
DESCENDER - Static variable in class org.jmol.util.MeshCapper
 
descent - Variable in class org.jmol.modelset.Text
 
descent - Variable in class org.jmol.render.LabelsRenderer
 
descr - Variable in class org.jmol.minimize.forcefield.AtomType
 
desiredModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
desiredQ - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
desiredQpt - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
desiredSpaceGroupIndex - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
desiredVibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
destroy() - Method in interface org.jmol.api.JmolAppletInterface
 
destroy() - Method in class org.jmol.applet.AppletWrapper
 
destroy() - Method in class org.jmol.applet.Jmol
 
destroy() - Method in class org.jmol.g3d.Graphics3D
 
destroy() - Method in class org.jmol.util.GData
 
destroy() - Method in class org.jmol.util.GenericApplet
 
destroyConsole() - Method in class org.jmol.console.GenericConsole
 
detectExplosion() - Method in class org.jmol.minimize.forcefield.ForceField
 
determineAtomSetCollectionReader(Object, boolean) - Static method in class org.jmol.adapter.smarter.Resolver
the main resolver method.
determineSpaceGroup(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroupIndex(String, float, float, float, float, float, float, int) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroupN(String) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroupNA(String, float[]) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSpaceGroupNS(String, SpaceGroup) - Static method in class org.jmol.symmetry.SpaceGroup
 
determineSurfaceFileType(BufferedReader) - Method in interface org.jmol.api.JmolZipUtilities
 
determineSurfaceFileType(BufferedReader) - Method in class org.jmol.io.JmolBinary
 
determineSurfaceFileType(BufferedReader) - Method in class org.jmol.io.JmolUtil
 
determineSurfaceTypeIs(InputStream) - Method in class org.jmol.io.JmolBinary
 
determineUniqueAxis(float, float, float, float, float, float) - Static method in class org.jmol.symmetry.SpaceGroup
 
DF_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
dfact2 - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
dfBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
dfCoefMaps - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
dfCoefMaps - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
dfCoefMaps - Variable in class org.jmol.quantum.MOCalculation
 
dFixed - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
DFT_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
dgridContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
DgridReader - Class in org.jmol.adapter.readers.quantum
A reader for Dgrid BASISFILE data.
DgridReader() - Constructor for class org.jmol.adapter.readers.quantum.DgridReader
 
diagonal - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
diagonalReferenceAxis - Variable in class org.jmol.symmetry.HallRotationTerm
 
Dialog - Class in org.jmol.dialog
 
Dialog() - Constructor for class org.jmol.dialog.Dialog
 
dialog - Variable in class org.jmol.dialog.FileChooser
 
Dialog.ExportChoiceListener - Class in org.jmol.dialog
 
Dialog.QualityListener - Class in org.jmol.dialog
 
Dialog.TypeFilter - Class in org.jmol.dialog
 
dialogAsk(String, String) - Method in class org.jmol.viewer.StatusManager
 
dialogAsk(String, String) - Method in class org.jmol.viewer.Viewer
 
dialogLocation - Variable in class org.jmol.dialog.FileChooser
 
dialogSize - Variable in class org.jmol.dialog.FileChooser
 
dialogType - Variable in class org.jmol.dialog.Dialog
 
diameter - Variable in class org.jmol.g3d.CylinderRenderer
 
diameter - Variable in class org.jmol.g3d.SphereRenderer
 
diameter - Variable in class org.jmol.jvxl.data.JvxlData
 
diameter - Variable in class org.jmol.render.MeshRenderer
 
diameter - Variable in class org.jmol.renderspecial.DipolesRenderer
 
diameter - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
diameter - Variable in class org.jmol.renderspecial.VectorsRenderer
 
diameter - Static variable in class org.jmol.script.T
 
diameter - Variable in class org.jmol.shape.Mesh
 
diameter - Variable in class org.jmol.shapespecial.Draw
 
diameter0 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
diameterBeg - Variable in class org.jmol.renderbio.BioShapeRenderer
 
diameterEnd - Variable in class org.jmol.renderbio.BioShapeRenderer
 
diameterMid - Variable in class org.jmol.renderbio.BioShapeRenderer
 
diameterP - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.util.Rgb16
 
diffuseFactor - Variable in class org.jmol.util.Shader
 
diffusepercent - Static variable in class org.jmol.script.T
 
diffusePercent - Variable in class org.jmol.util.Shader
 
dihedral_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dihedral_label_position - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dihedral_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dihedralList - Variable in class org.jmol.thread.SpinThread
 
dim - Variable in class org.jmol.bspt.Node
 
dimension - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
dimension - Variable in class org.jmol.util.SimpleUnitCell
 
dimMax - Variable in class org.jmol.bspt.Bspf
 
dimMax - Variable in class org.jmol.bspt.Bspt
 
dimScreen - Variable in class org.jmol.viewer.Viewer
 
dimSize - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
DIPOLAR_FACTOR - Static variable in class org.jmol.quantum.NMRCalculation
 
DIPOLE - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
dipole - Static variable in class org.jmol.script.T
 
dipole() - Method in class org.jmol.scriptext.IsoExt
 
Dipole - Class in org.jmol.shapespecial
 
Dipole() - Constructor for class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_ATOMS - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_BOND - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_MOLECULAR - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_POINTS - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_POINTVECTOR - Static variable in class org.jmol.shapespecial.Dipole
 
DIPOLE_TYPE_UNKNOWN - Static variable in class org.jmol.shapespecial.Dipole
 
dipoleCount - Variable in class org.jmol.shapespecial.Dipoles
 
dipoleInfo - Variable in class org.jmol.shapespecial.Dipole
 
Dipoles - Class in org.jmol.shapespecial
 
Dipoles() - Constructor for class org.jmol.shapespecial.Dipoles
 
dipoles - Variable in class org.jmol.shapespecial.Dipoles
 
dipolescale - Static variable in class org.jmol.script.T
 
dipoleScale - Variable in class org.jmol.viewer.GlobalSettings
 
DipolesRenderer - Class in org.jmol.renderspecial
 
DipolesRenderer() - Constructor for class org.jmol.renderspecial.DipolesRenderer
 
dipoleValue - Variable in class org.jmol.shapespecial.Dipole
 
dipoleValue - Variable in class org.jmol.shapespecial.Dipoles
 
dipoleVectorScale - Variable in class org.jmol.renderspecial.DipolesRenderer
 
direct - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
direction - Static variable in class org.jmol.script.T
 
directLatticeVectors - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
DISABLE - Static variable in class org.jmol.shapecgo.CGOMesh
 
disableField(int) - Method in class org.jmol.adapter.readers.cif.CifReader
used for turning off fractional or nonfractional coord.
disablepopupmenu - Static variable in class org.jmol.script.T
 
disablePopupMenu - Variable in class org.jmol.viewer.GlobalSettings
 
discardLinesUntilBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilContains(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilContains(String) - Method in interface org.jmol.api.JmolJDXMOLReader
 
discardLinesUntilContains2(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilContains2(String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
 
discardLinesUntilNonBlank() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardLinesUntilNonBlank() - Method in interface org.jmol.api.JmolJDXMOLReader
 
discardLinesUntilStartsWith(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
discardPreviousAtoms() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
discardTempData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
discardTempData(boolean) - Method in class org.jmol.shapesurface.Isosurface
 
discardTempDataSR(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
discrete - Static variable in class org.jmol.script.T
 
DISORDER_ASSEMBLY - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
DISORDER_GROUP - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
disorderAssembly - Variable in class org.jmol.adapter.readers.cif.CifReader
 
DISP_SAW_AX - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DISP_SAW_AY - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DISP_SAW_AZ - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DISP_SAW_C - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DISP_SAW_W - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
DISP_SPEC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
dispatch(int, boolean, T[]) - Method in interface org.jmol.script.JmolCmdExtension
 
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.CmdExt
 
dispatch(int, boolean, T[]) - Method in class org.jmol.scriptext.IsoExt
 
dispatchCommands(boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
displacement - Static variable in class org.jmol.script.T
 
Display - Class in org.jmol.awt
methods required by Jmol that access java.awt.Component private to org.jmol.awt
Display() - Constructor for class org.jmol.awt.Display
 
Display - Class in org.jmol.awtjs2d
methods required by Jmol that access java.awt.Component private to org.jmol.awt
Display() - Constructor for class org.jmol.awtjs2d.Display
 
display - Variable in class org.jmol.dialog.FilePreview
 
display - Variable in class org.jmol.i18n.Language
 
display - Static variable in class org.jmol.script.T
 
display(ModelSet, BS, int, boolean) - Method in class org.jmol.viewer.SelectionManager
 
display - Variable in class org.jmol.viewer.Viewer
 
display - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
display - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
displayAtoms(BS, boolean, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
 
displayBonds(BondSet, boolean) - Method in class org.jmol.modelset.BondCollection
 
displaycellparameters - Static variable in class org.jmol.script.T
 
displayCellParameters - Variable in class org.jmol.viewer.GlobalSettings
 
displayConsole() - Method in class org.jmol.console.GenericConsole
 
displayed - Static variable in class org.jmol.script.T
 
displayLoadErrors - Variable in class org.jmol.viewer.Viewer
 
displayLoadErrorsSave - Variable in class org.jmol.script.ScriptContext
 
displayMaxX - Variable in class org.jmol.util.GData
 
displayMaxY - Variable in class org.jmol.util.GData
 
displayMinX - Variable in class org.jmol.util.GData
 
displayMinY - Variable in class org.jmol.util.GData
 
DisplayPanel - Class in org.openscience.jmol.app.jmolpanel
 
DisplayPanel(JmolPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
DisplayPanel.CheckBoxMenuItemAction - Class in org.openscience.jmol.app.jmolpanel
Action calling evalStringQuiet(<action> + CheckBoxState)
DisplayPanel.DefineCenterAction - Class in org.openscience.jmol.app.jmolpanel
 
DisplayPanel.HomeAction - Class in org.openscience.jmol.app.jmolpanel
 
DisplayPanel.MoveToAction - Class in org.openscience.jmol.app.jmolpanel
Action calling moveTo()
DisplayPanel.SetStatusAction - Class in org.openscience.jmol.app.jmolpanel
Action calling setStatus()
displaySpeed - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
displayWhileRenderingCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
displayWithinDistance2 - Variable in class org.jmol.shape.MeshCollection
 
displayWithinPoints - Variable in class org.jmol.shape.MeshCollection
 
dispose() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
dispose() - Method in interface org.jmol.api.JmolGestureServerInterface
 
dispose() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
dispose() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
dispose() - Method in class org.jmol.api.JmolViewer
 
dispose() - Method in class org.jmol.awt.FileDropper
 
dispose() - Method in class org.jmol.awt.Mouse
 
dispose() - Method in class org.jmol.awtjs2d.Mouse
 
dispose() - Method in class org.jmol.console.GenericConsole
 
dispose() - Method in class org.jmol.console.JmolConsole
 
dispose() - Method in class org.jmol.console.ScriptEditor
 
dispose() - Method in class org.jmol.consolejs.AppletConsole
 
dispose() - Method in class org.jmol.multitouch.ActionManagerMT
 
dispose() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
dispose() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
dispose() - Method in class org.jmol.multitouch.jni.JmolJniClientAdapter
 
dispose() - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
dispose() - Method in class org.jmol.viewer.ActionManager
 
dispose() - Method in class org.jmol.viewer.Viewer
end of life for this viewer
dispose() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
dispose(JFrame, boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
dispose() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
disposeGraphics(Object) - Static method in class org.jmol.awt.Image
 
disposeGraphics(Object) - Method in class org.jmol.awt.Platform
 
disposeGraphics(Object) - Static method in class org.jmol.awtjs.Image
 
disposeGraphics(Object) - Method in class org.jmol.awtjs.Platform
 
disposeGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
 
disregardNeighbors - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
dist_counter - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
distance - Variable in class org.jmol.jvxl.readers.Parameters
 
distance - Variable in class org.jmol.modelset.AtomIteratorWithinModelSet
 
distance - Static variable in class org.jmol.script.T
 
distance2(double[], double[]) - Static method in class org.jmol.minimize.Util
 
distance2V(V3d, V3d) - Static method in class org.jmol.minimize.Util
 
distance_exclusion - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
distancefactor - Static variable in class org.jmol.script.T
 
distanceFactor - Variable in class org.jmol.shapespecial.Polyhedra
 
distanceFactor - Variable in class org.jmol.shapespecial.Polyhedron
 
distanceMode - Variable in class org.jmol.quantum.MepCalculation
 
distancePointToPlane(T3) - Method in interface org.jmol.api.VolumeDataInterface
 
distancePointToPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
 
distanceSquared - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
distanceTolerance - Variable in class org.jmol.symmetry.PointGroup
 
distanceToMappingPlane(T3) - Method in class org.jmol.jvxl.data.VolumeData
 
distanceToPlane(V3, float, P3) - Static method in class org.jmol.smiles.SmilesSearch
 
distanceVerticalToPlane(float, float, P3, P3, P3) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
distinguishAndPropagateGroup(Chain, String, int, int, int, int, int[], Atom[]) - Method in interface org.jmol.api.JmolBioResolver
 
distinguishAndPropagateGroup(int, Chain, String, int, int, int) - Method in class org.jmol.modelset.ModelLoader
 
distinguishAndPropagateGroup(Chain, String, int, int, int, int, int[], Atom[]) - Method in class org.jmol.modelsetbio.Resolver
 
div - Static variable in class org.jmol.script.T
 
divide - Static variable in class org.jmol.script.T
 
dList - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
dm - Variable in class org.jmol.viewer.Viewer
 
dmax - Variable in class org.jmol.jvxl.readers.MapFileReader
 
dMax - Static variable in class org.jmol.quantum.NciCalculation
 
dmean - Variable in class org.jmol.jvxl.readers.MapFileReader
 
dmesh - Variable in class org.jmol.renderspecial.DrawRenderer
 
dmeshes - Variable in class org.jmol.shapespecial.Draw
 
dmin - Variable in class org.jmol.jvxl.readers.MapFileReader
 
dmolContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
DmolReader - Class in org.jmol.adapter.readers.xtal
 
DmolReader() - Constructor for class org.jmol.adapter.readers.xtal.DmolReader
 
dna - Static variable in class org.jmol.script.T
 
doAction(Object) - Method in class org.jmol.console.GenericConsole
 
doAction(MeasurementData, String, int) - Method in class org.jmol.shape.Measures
 
doAddHydrogens - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
doAddHydrogens - Variable in class org.jmol.modelset.ModelLoader
 
doApplySymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doBrowse() - Method in class org.openscience.chimetojmol.ChimePanel
 
doCache - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
doCache - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
doCalcArea - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
doCalculateTroughs - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
doCap - Variable in class org.jmol.util.MeshSlicer
 
doCap0 - Variable in class org.jmol.renderbio.BioShapeRenderer
 
doCap1 - Variable in class org.jmol.renderbio.BioShapeRenderer
 
doCentralize - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doCentroidUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doCentroidUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
doCheckUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doClear - Variable in class org.jmol.util.MeshSlicer
 
doClose(boolean) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
doColor - Variable in class org.jmol.rendercgo.CGORenderer
 
doConvertToFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
documentBase - Variable in class org.jmol.util.GenericApplet
 
doDebug - Variable in class org.jmol.quantum.QuantumCalculation
 
doDelay(int) - Method in class org.jmol.script.ScriptEval
 
doDisplace - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
 
doDrop(PropertyChangeEvent) - Method in class org.jmol.awt.FileDropper
 
doEndMove - Variable in class org.jmol.thread.MoveToThread
 
doEval(String) - Method in class org.jmol.applet.Jmol
 
doEval(String) - Method in class org.jmol.appletjs.Jmol
 
doEval(String) - Method in class org.jmol.util.GenericApplet
 
doFinalize() - Method in class org.jmol.symmetry.SymmetryOperation
 
doFinalTransform() - Method in class org.jmol.thread.MoveToThread
 
doFixFilenames - Variable in class org.openscience.chimetojmol.ChimePanel
 
doFixPeriodic - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
doFormatText - Variable in class org.jmol.modelset.Text
 
doFullMolecular - Variable in class org.jmol.jvxl.readers.Parameters
 
doFunctionXY(String, int, int) - Method in class org.jmol.applet.Jmol
 
doFunctionXY(String, int, int) - Method in class org.jmol.appletjs.Jmol
 
doFunctionXY(String, int, int) - Method in class org.jmol.util.GenericApplet
 
doFunctionXYZ(String, int, int, int) - Method in class org.jmol.applet.Jmol
 
doFunctionXYZ(String, int, int, int) - Method in class org.jmol.appletjs.Jmol
 
doFunctionXYZ(String, int, int, int) - Method in class org.jmol.util.GenericApplet
 
doGetModel(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doGetVibration(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doGhost - Variable in class org.jmol.util.MeshSlicer
 
doGo() - Method in class org.openscience.chimetojmol.ChimePanel
 
doHaveJDX() - Method in class org.jmol.viewer.Viewer
 
doHighlight(int, int, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
doIterate - Variable in class org.jmol.jvxl.data.VolumeData
 
doJustify - Variable in class org.jmol.render.MeasuresRenderer
 
dollarsign - Static variable in class org.jmol.script.T
 
doLogLevel(boolean) - Static method in class org.jmol.util.Logger
Indicates if the level is logged.
domains - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
domains - Static variable in class org.jmol.script.T
 
domAttributes - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
doMinimize - Variable in class org.jmol.modelset.ModelLoader
 
domObj - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
DOMReader - Class in org.jmol.io
 
DOMReader() - Constructor for class org.jmol.io.DOMReader
 
DOMResolve(Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.Resolver
a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page.
doNavStep(int) - Method in class org.jmol.navigate.Navigator
 
done - Variable in class org.jmol.dssx.DSSP
 
doneHere - Variable in class org.jmol.multitouch.ActionManagerMT
 
doneHere - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
doNew() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
doNormalize - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
doNormalize - Variable in class org.jmol.quantum.MOCalculation
 
doNormalize - Variable in class org.jmol.symmetry.SpaceGroup
 
doNormalize - Variable in class org.jmol.symmetry.SymmetryOperation
 
dontsave - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
doOpen() - Method in class org.jmol.console.ScriptEditor
 
doOverWrite(JFileChooser, File) - Static method in class org.jmol.dialog.Dialog
 
doPackUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doPackUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
doPoly(Object, int[], int[], int, boolean) - Method in class org.jmol.awtjs2d.JsG2D
 
doPopPush - Variable in class org.jmol.script.ScriptDelayThread
 
doPreSymmetry() - Method in class org.jmol.adapter.readers.cif.CifReader
 
doPreSymmetry() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
doPreSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doProcessLines - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doReadMolecularOrbitals - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doRender - Variable in class org.jmol.render.MeshRenderer
 
doReport - Variable in class org.jmol.dssx.DSSP
 
doReport() - Method in class org.jmol.script.ScriptEval
 
doReportProperty(String) - Static method in class org.jmol.viewer.GlobalSettings
 
doResize - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
doResume() - Method in class org.jmol.console.ScriptEditor
 
doSaveSurfacePoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
doSelection() - Method in class org.jmol.script.ScriptMathProcessor
 
doSelections - Variable in class org.jmol.script.ScriptMathProcessor
 
doSendCallback(String, Object[], String) - Method in class org.jmol.applet.Jmol
 
doSendCallback(String, Object[], String) - Method in class org.jmol.appletjs.Jmol
 
doSendCallback(String, Object[], String) - Method in class org.jmol.util.GenericApplet
 
doSendJsTextareaStatus(String) - Method in class org.jmol.applet.Jmol
 
doSendJsTextareaStatus(String) - Method in class org.jmol.appletjs.Jmol
 
doSendJsTextareaStatus(String) - Method in class org.jmol.util.GenericApplet
 
doSendJsTextStatus(String) - Method in class org.jmol.applet.Jmol
 
doSendJsTextStatus(String) - Method in class org.jmol.appletjs.Jmol
 
doSendJsTextStatus(String) - Method in class org.jmol.util.GenericApplet
 
doSetOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
doShowDocument(URL) - Method in class org.jmol.applet.Jmol
 
doShowDocument(URL) - Method in class org.jmol.appletjs.Jmol
 
doShowDocument(URL) - Method in class org.jmol.util.GenericApplet
 
doShowShellType - Variable in class org.jmol.quantum.MOCalculation
 
doShowStatus(String) - Method in class org.jmol.applet.Jmol
 
doShowStatus(String) - Method in class org.jmol.appletjs.Jmol
 
doShowStatus(String) - Method in class org.jmol.util.GenericApplet
 
doSmoothProperty - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
doSort - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
doStep() - Method in class org.jmol.console.ScriptEditor
 
doStepTransform() - Method in class org.jmol.thread.MoveToThread
 
doStroke(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
 
doStroke(Object, boolean) - Method in class org.jmol.awt.AwtG2D
 
doStroke(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
 
doSubdirectories - Variable in class org.openscience.chimetojmol.ChimePanel
 
doSymmetry - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
 
doSync() - Method in class org.jmol.viewer.StatusManager
 
dot - Static variable in class org.jmol.script.T
 
dot_as_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_density - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_hydrogens - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_normals - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dot_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dotColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
dotCount - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
dotdensity - Static variable in class org.jmol.script.T
 
dotDensity - Variable in class org.jmol.viewer.GlobalSettings
 
doTransform() - Method in class org.jmol.thread.SpinThread
 
doTransform4D - Variable in class org.jmol.viewer.TransformManager
 
doTranslate - Variable in class org.jmol.i18n.GT
 
doTranslate - Variable in class org.jmol.util.GenericApplet
 
dots - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
dots - Static variable in class org.jmol.script.T
 
Dots - Class in org.jmol.shapespecial
 
Dots() - Constructor for class org.jmol.shapespecial.Dots
 
dotScale - Variable in class org.jmol.renderspecial.DotsRenderer
 
dotScale - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
dotscale - Static variable in class org.jmol.script.T
 
dotScale - Variable in class org.jmol.viewer.GlobalSettings
 
dotsConvexMaps - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
dotsConvexMax - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
dotsOrDashes - Variable in class org.jmol.render.FontLineShapeRenderer
 
DotsRenderer - Class in org.jmol.renderspecial
 
DotsRenderer() - Constructor for class org.jmol.renderspecial.DotsRenderer
 
dotsselectedonly - Static variable in class org.jmol.script.T
 
dotsSelectedOnly - Variable in class org.jmol.viewer.GlobalSettings
 
dotsurface - Static variable in class org.jmol.script.T
 
dotSurface - Variable in class org.jmol.viewer.GlobalSettings
 
dotted - Static variable in class org.jmol.script.T
 
DOTWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
 
DOUBLE - Static variable in class org.jmol.viewer.binding.Binding
 
doubleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
doubleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
doUseIterator - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
doUseSigned - Variable in class org.openscience.chimetojmol.ChimePanel
 
DOWN - Static variable in class org.jmol.viewer.binding.Binding
 
DownLoadWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
 
downsample - Static variable in class org.jmol.script.T
 
downsample2d(int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
 
downsample2dZ(int[], int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
 
downsampleFactor - Variable in class org.jmol.jvxl.readers.Parameters
 
downsampleFactor - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
downsampleFullSceneAntialiasing(boolean) - Method in class org.jmol.g3d.Graphics3D
 
downsampleRemainders - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
dPlane - Variable in class org.jmol.util.MeshSlicer
 
DRAG - Static variable in class org.jmol.viewer.binding.Binding
 
DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
dragAction - Variable in class org.jmol.viewer.ActionManager
 
dragAtomIndex - Variable in class org.jmol.viewer.ActionManager
 
dragBinding - Variable in class org.jmol.viewer.ActionManager
 
DragBinding - Class in org.jmol.viewer.binding
 
DragBinding() - Constructor for class org.jmol.viewer.binding.DragBinding
 
dragEnter(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
 
dragExit(DropTargetEvent) - Method in class org.jmol.awt.FileDropper
 
dragged(long, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
 
dragged - Variable in class org.jmol.viewer.ActionManager
 
dragGesture - Variable in class org.jmol.viewer.ActionManager
 
dragMinimizeAtom(int) - Method in class org.jmol.viewer.Viewer
 
dragOver(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
 
dragselected - Static variable in class org.jmol.script.T
 
dragSelected - Variable in class org.jmol.viewer.GlobalSettings
 
dragSelectedMode - Variable in class org.jmol.viewer.ActionManager
 
drange - Variable in class org.jmol.jvxl.readers.MapFileReader
 
draw - Static variable in class org.jmol.script.T
 
draw() - Method in class org.jmol.scriptext.IsoExt
 
Draw - Class in org.jmol.shapespecial
 
Draw() - Constructor for class org.jmol.shapespecial.Draw
 
Draw.EnumDrawType - Enum in org.jmol.shapespecial
 
draw000 - Variable in class org.jmol.render.FontLineShapeRenderer
 
draw_frames - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
draw_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
drawArrowScale - Variable in class org.jmol.shapespecial.DrawMesh
 
drawAtom(Atom) - Method in interface org.jmol.api.JmolRendererInterface
 
drawAtom(Atom) - Method in class org.jmol.export.___Exporter
 
drawAtom(Atom) - Method in class org.jmol.export.__CartesianExporter
 
drawAtom(Atom) - Method in class org.jmol.export.__RayTracerExporter
 
drawAtom(Atom) - Method in class org.jmol.export.Export3D
 
drawAtom(Atom) - Method in class org.jmol.g3d.Graphics3D
 
drawBond(P3, P3, short, short, byte, short, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.export.Export3D
 
drawBond(P3, P3, short, short, byte, short, int) - Method in class org.jmol.g3d.Graphics3D
 
drawBond(int) - Method in class org.jmol.render.SticksRenderer
 
drawCap - Variable in class org.jmol.renderspecial.VectorsRenderer
 
drawCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.___Exporter
 
drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
drawCircle(int, int, int, int, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
drawCircle(short, int, int, int, int, boolean) - Method in class org.jmol.export.Export3D
draws a simple circle (draw circle)
drawCylinder(P3, P3, short, short, byte, int, int) - Method in class org.jmol.export.___Exporter
 
drawCylinder(P3, P3, short, short, byte, int, int) - Method in class org.jmol.export.__CartesianExporter
bond order -1 -- single bond, Cartesian bond order -2 -- multiple bond, Cartesian
drawCylinder(P3, P3, short, short, byte, int, int) - Method in class org.jmol.export.__RayTracerExporter
 
drawCylinderTriangle(int, int, int, int, int, int, int, int, int) - Method in class org.jmol.renderspecial.PolyhedraRenderer
 
drawDashed(int, int, int, int, int, int, int[]) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawDashedLine(int, int, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawDashedLine(int, int, P3i, P3i) - Method in class org.jmol.export.Export3D
 
drawDashedLine(int, int, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
 
drawDottedLine(P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawDottedLine(P3i, P3i) - Method in class org.jmol.export.Export3D
 
drawDottedLine(P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
 
drawEdges(P3i[], P3[], int) - Method in class org.jmol.renderbio.NucleicRenderer
 
drawEdges - Variable in class org.jmol.renderspecial.PolyhedraRenderer
 
drawEdges - Variable in class org.jmol.shapespecial.Polyhedra
 
drawEllipse(P3, P3, P3, boolean, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
drawEllipse(P3, P3, P3, short, boolean) - Method in class org.jmol.export.___Exporter
 
drawEllipse(P3, P3, P3, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
drawEllipse(P3, P3, P3, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.export.Export3D
 
drawEllipse(P3, P3, P3, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
 
drawFace(short, P3i, P3i, P3i) - Method in class org.jmol.renderspecial.PolyhedraRenderer
 
drawFilledCircle(short, short, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws a ring and filled circle (halos, draw CIRCLE, draw handles)
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.___Exporter
 
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.export.Export3D
draws a screened circle ...
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawfontsize - Static variable in class org.jmol.script.T
 
drawFontSize - Variable in class org.jmol.viewer.GlobalSettings
 
drawFrameLine(String, P3, V3, float, P3, SB, String, String) - Static method in class org.jmol.symmetry.SymmetryDesc
 
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawGrayScaleImage(Object, Object, int, int, int, int, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawHermite4(int, P3i, P3i, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawHermite4(int, P3i, P3i, P3i, P3i) - Method in class org.jmol.export.Export3D
 
drawHermite4(int, P3i, P3i, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
 
drawHermite7(boolean, boolean, int, P3i, P3i, P3i, P3i, P3i, P3i, P3i, P3i, int, short) - Method in interface org.jmol.api.JmolRendererInterface
 
drawHermite7(boolean, boolean, int, P3i, P3i, P3i, P3i, P3i, P3i, P3i, P3i, int, short) - Method in class org.jmol.export.Export3D
 
drawHermite7(boolean, boolean, int, P3i, P3i, P3i, P3i, P3i, P3i, P3i, P3i, int, short) - Method in class org.jmol.g3d.Graphics3D
 
drawHLine(int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawHLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawhover - Static variable in class org.jmol.script.T
 
drawHover - Variable in class org.jmol.viewer.GlobalSettings
 
drawImage(Object, int, int, int, int, short, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawImage(Object, Object, int, int, int, int) - Static method in class org.jmol.awt.Display
 
drawImage(Object, Object, int, int, int, int) - Method in class org.jmol.awt.Platform
 
drawImage(Object, Object, int, int, int, int) - Method in class org.jmol.awtjs.Platform
 
drawImage(Object, Object, int, int, int, int) - Static method in class org.jmol.awtjs2d.Display
Draw the completed image from rendering.
drawImage(Object, Object, int, int, int, int) - Method in class org.jmol.awtjs2d.Platform
 
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.export.Export3D
 
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Static method in class org.jmol.awt.Image
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Static method in class org.jmol.awtjs.Image
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awtjs.Platform
 
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
 
drawIndex - Variable in class org.jmol.symmetry.PointGroup
 
drawInfo(String, int, String) - Method in class org.jmol.render.UccageRenderer
 
drawInfo - Variable in class org.jmol.symmetry.PointGroup
 
drawing - Static variable in class org.jmol.script.T
 
drawLcaoCartoon(V3, V3, V3, int) - Method in class org.jmol.shapesurface.Isosurface
 
drawLine(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawLine(short, short, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLine(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawLine(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawLine(int, int, int, int, int, int, int) - Method in class org.jmol.render.MeasuresRenderer
 
drawLine(int, int, boolean, T3, T3, P3i, P3i) - Method in class org.jmol.render.MeshRenderer
 
drawLine(int, int, int, int, int, int) - Method in class org.jmol.render.StarsRenderer
 
drawLine(SB, String, float, P3, P3, String) - Static method in class org.jmol.symmetry.SymmetryDesc
 
drawLine2(int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawLineAB(P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLineAB(P3i, P3i) - Method in class org.jmol.export.Export3D
 
drawLineAB(P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
 
drawLineData(Lst<P3[]>) - Method in class org.jmol.renderspecial.DrawRenderer
 
drawLineXYZ(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
DrawMesh - Class in org.jmol.shapespecial
 
DrawMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapespecial.DrawMesh
 
drawMode - Variable in class org.jmol.viewer.ActionManager
 
drawpicking - Static variable in class org.jmol.script.T
 
drawPicking - Variable in class org.jmol.viewer.GlobalSettings
 
drawPixel(int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawPixel(short, int, int, int, int) - Method in class org.jmol.export.___Exporter
 
drawPixel(short, int, int, int, int) - Method in class org.jmol.export.__CartesianExporter
 
drawPixel(short, int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
 
drawPixel(int, int, int) - Method in class org.jmol.export.Export3D
 
drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
drawPointer(Text, JmolRendererInterface) - Static method in class org.jmol.render.TextRenderer
 
drawPoints(int, int[], int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawPoints(int, int[], int) - Method in class org.jmol.export.Export3D
 
drawPoints(int, int[], int) - Method in class org.jmol.g3d.Graphics3D
 
drawPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
 
drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
 
drawPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawQuadrilateral(short, P3i, P3i, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
drawQuadrilateral(short, P3i, P3i, P3i, P3i) - Method in class org.jmol.export.Export3D
 
drawQuadrilateral(short, P3i, P3i, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
 
drawQuat(Quat, String, String, P3, float) - Method in class org.jmol.modelsetbio.BioPolymer
 
drawQuat(Quat, String, String, P3, float) - Static method in class org.jmol.util.Escape
 
drawRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
draws a rectangle
drawRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
draws a rectangle
drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
draws a rectangle
DrawRenderer - Class in org.jmol.renderspecial
 
DrawRenderer() - Constructor for class org.jmol.renderspecial.DrawRenderer
 
drawSegment(Atom, Atom, short, short, float) - Method in class org.jmol.renderbio.BackboneRenderer
 
drawShaft - Variable in class org.jmol.renderspecial.VectorsRenderer
 
drawSlicePlane(SB, int, boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
drawString(Object, String, int, int) - Method in interface org.jmol.api.GenericGraphics
 
drawString(String, Font, int, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
draws the specified string in the current font.
drawString(Object, String, int, int) - Method in class org.jmol.awt.AwtG2D
 
drawString(Object, String, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.export.Export3D
draws the specified string in the current font.
drawString(String, Font, int, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
draws the specified string in the current font.
drawString(int, int, int, int, boolean, boolean, boolean, int, String) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawStringNoSlab(String, Font, int, int, int, short) - Method in interface org.jmol.api.JmolRendererInterface
draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.export.Export3D
draws the specified string in the current font.
drawStringNoSlab(String, Font, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
draws the specified string in the current font.
drawStringRotated(Object, String, int, int, double) - Method in interface org.jmol.api.GenericGraphics
 
drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awt.AwtG2D
 
drawStringRotated(Object, String, int, int, double) - Method in class org.jmol.awtjs2d.JsG2D
 
drawSurface(MeshSurface, short) - Method in interface org.jmol.api.JmolRendererInterface
 
drawSurface(MeshSurface, short) - Method in class org.jmol.export.___Exporter
 
drawSurface(MeshSurface, short) - Method in class org.jmol.export._ObjExporter
 
drawSurface(MeshSurface, short) - Method in class org.jmol.export.Export3D
 
drawSurface(MeshSurface, short) - Method in class org.jmol.g3d.Graphics3D
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export.___Exporter
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export.__CartesianExporter
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
 
drawTextPixel(int, int, int, int) - Method in class org.jmol.export._MayaExporter
 
drawTicks(Point3fi, Point3fi, int, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawTicks2(Point3fi, Point3fi, float, int, int, String[]) - Method in class org.jmol.render.FontLineShapeRenderer
 
drawTriangle(P3i, short, P3i, short, P3i, short, int, int) - Method in class org.jmol.render.MeshRenderer
 
drawTriangle(int, MeshCapper.CapVertex, MeshCapper.CapVertex, MeshCapper.CapVertex, String) - Method in class org.jmol.util.MeshCapper
for debugging
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in interface org.jmol.api.JmolRendererInterface
 
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.export.Export3D
 
drawTriangle3C(P3i, short, P3i, short, P3i, short, int) - Method in class org.jmol.g3d.Graphics3D
 
drawTriangles - Variable in class org.jmol.shape.Mesh
 
drawType - Variable in class org.jmol.renderspecial.DrawRenderer
 
drawType - Variable in class org.jmol.shapespecial.DrawMesh
 
drawType - Variable in class org.jmol.symmetry.PointGroup
 
drawTypes - Variable in class org.jmol.shapespecial.DrawMesh
 
drawVertexCount - Variable in class org.jmol.shapespecial.DrawMesh
 
drawVertexCounts - Variable in class org.jmol.shapespecial.DrawMesh
 
drawVLine(int, int, int, int) - Method in class org.jmol.export.Export3D
 
drawVLine(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
DRIVER_NONE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
drivingSync - Variable in class org.jmol.viewer.StatusManager
 
drop(DropTargetDropEvent) - Method in class org.jmol.awt.FileDropper
 
dropActionChanged(DropTargetDragEvent) - Method in class org.jmol.awt.FileDropper
 
dropper - Variable in class org.jmol.applet.Jmol
 
dRot - Variable in class org.jmol.thread.MoveToThread
 
DS - Static variable in class org.jmol.quantum.QS
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
 
DS_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
dSlab - Variable in class org.jmol.thread.MoveToThread
 
Dsn6BinaryReader - Class in org.jmol.jvxl.readers
 
Dsn6BinaryReader() - Constructor for class org.jmol.jvxl.readers.Dsn6BinaryReader
 
dSpherical - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
DSSP - Class in org.jmol.dssx
 
DSSP() - Constructor for class org.jmol.dssx.DSSP
 
dssp - Static variable in class org.jmol.script.T
 
dsspcalchydrogen - Static variable in class org.jmol.script.T
 
dsspCalcHydrogen - Variable in class org.jmol.viewer.GlobalSettings
 
dsspIgnoreHydrogens - Variable in class org.jmol.dssx.DSSP
 
DSSPInterface - Interface in org.jmol.api
 
dssr - Variable in class org.jmol.dssx.AnnotationParser
 
dssr - Static variable in class org.jmol.script.T
 
dssrCache - Variable in class org.jmol.modelset.Model
 
dTrans - Variable in class org.jmol.thread.MoveToThread
 
dtype - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
DUMMY_ATOM - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
dump() - Method in class org.jmol.bspt.Bspf
 
dump() - Method in class org.jmol.bspt.Bspt
 
dump(int, SB) - Method in class org.jmol.bspt.Element
 
dump(int, SB) - Method in class org.jmol.bspt.Leaf
 
dump(int, SB) - Method in class org.jmol.bspt.Node
 
dumpAll() - Static method in class org.jmol.symmetry.SpaceGroup
 
dumpAllSeitz() - Static method in class org.jmol.symmetry.SpaceGroup
 
dumpCanonicalSeitzList() - Method in class org.jmol.symmetry.SpaceGroup
 
dumpDipoles(String) - Method in class org.jmol.shapespecial.Dipoles
 
dumpInfo(int) - Method in class org.jmol.quantum.MOCalculation
 
dumpInfo() - Method in class org.jmol.symmetry.HallInfo
 
dumpInfo(String) - Method in class org.jmol.symmetry.HallRotationTerm
 
dumpInfo(SymmetryInterface) - Method in class org.jmol.symmetry.SpaceGroup
 
dumpInfo() - Method in class org.jmol.symmetry.SymmetryOperation
 
dumpInfo(boolean) - Method in class org.jmol.symmetry.UnitCell
 
dumping - Variable in class org.jmol.util.MeshCapper
for debugging
dumpLine(P3, T3, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
dumpLine2(P3, P3, String, float, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
dumpPoint(P3, String, String) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
dumpRegion() - Method in class org.jmol.util.MeshCapper.CapVertex
for debugging
dumpRingKeys(SB, Map<String, Object[]>) - Method in class org.jmol.smiles.SmilesGenerator
 
dumpSeitz(M4, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
dumpStacks(String) - Method in class org.jmol.script.ScriptMathProcessor
 
dumpStructure(String[][]) - Method in class org.jmol.popup.PopupResource
 
dumpSummary(AminoPolymer, char[]) - Method in class org.jmol.dssx.DSSP
 
dumpTags(AminoPolymer, String, BS, int) - Method in class org.jmol.dssx.DSSP
 
dumpWords() - Method in class org.jmol.popup.PopupResource
 
duplicateAtomProperties(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
dVal - Variable in class org.jmol.minimize.forcefield.FFParam
 
dval(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
dx - Variable in class org.jmol.bspt.CubeIterator
 
dx - Variable in class org.jmol.render.SticksRenderer
 
dx - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
dx - Variable in class org.jmol.shape.Frank
 
dxB - Variable in class org.jmol.g3d.CylinderRenderer
 
dxBf - Variable in class org.jmol.g3d.CylinderRenderer
 
dxStep - Variable in class org.jmol.render.SticksRenderer
 
DXY - Variable in class org.jmol.quantum.MOCalculation
 
dxyz - Variable in class org.jmol.g3d.SphereRenderer
 
DXZ - Variable in class org.jmol.quantum.MOCalculation
 
dy - Variable in class org.jmol.bspt.CubeIterator
 
dy - Variable in class org.jmol.render.SticksRenderer
 
dy - Variable in class org.jmol.shape.Frank
 
dyB - Variable in class org.jmol.g3d.CylinderRenderer
 
dyBf - Variable in class org.jmol.g3d.CylinderRenderer
 
dynamic_measures - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dynamic_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dynamic_width_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dynamic_width_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dynamic_width_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
dynamicmeasurements - Static variable in class org.jmol.script.T
 
dyStep - Variable in class org.jmol.render.SticksRenderer
 
DYZ - Variable in class org.jmol.quantum.MOCalculation
 
dz - Variable in class org.jmol.bspt.CubeIterator
 
dzB - Variable in class org.jmol.g3d.CylinderRenderer
 
dzBf - Variable in class org.jmol.g3d.CylinderRenderer
 
dZoom - Variable in class org.jmol.thread.MoveToThread
 

E

e - Variable in class org.jmol.scriptext.CmdExt
 
e - Variable in class org.jmol.scriptext.MathExt
 
e - Variable in class org.jmol.scriptext.SmilesExt
 
e(Object) - Static method in class org.jmol.util.Escape
 
e0 - Variable in class org.jmol.minimize.forcefield.ForceField
 
E_ANG_PER_DEBYE - Static variable in class org.jmol.shapespecial.Dipoles
 
e_charge - Static variable in class org.jmol.quantum.NMRCalculation
 
E_MINUS_D - Static variable in class org.jmol.quantum.MepCalculation
 
E_MINUS_D_OVER_2 - Static variable in class org.jmol.quantum.MepCalculation
 
eAD(double[]) - Static method in class org.jmol.util.Escape
 
eAF(float[]) - Static method in class org.jmol.util.Escape
 
eAI(int[]) - Static method in class org.jmol.util.Escape
 
EANGLE - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eAP(T3[]) - Static method in class org.jmol.util.Escape
 
eAS(String[], boolean) - Static method in class org.jmol.util.Escape
 
EBOND - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eBond(BS) - Static method in class org.jmol.util.Escape
 
eBS(BS) - Static method in class org.jmol.util.Escape
 
eButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
ec - Variable in class org.jmol.shapespecial.Dots
 
eccentricity - Static variable in class org.jmol.script.T
 
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityMatrix - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityMatrixInverse - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
eccentricityRatio - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityRatio - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
eccentricityScale - Variable in class org.jmol.jvxl.readers.Parameters
 
eccentricityScale - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
echo - Static variable in class org.jmol.script.T
 
Echo - Class in org.jmol.shape
 
Echo() - Constructor for class org.jmol.shape.Echo
 
echoMessage(String) - Method in class org.jmol.viewer.Viewer
 
EchoRenderer - Class in org.jmol.render
 
EchoRenderer() - Constructor for class org.jmol.render.EchoRenderer
 
echoShapeActive - Variable in class org.jmol.modelset.ModelSet
 
ecosASB2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
eCounts - Variable in class org.jmol.symmetry.PointGroup
 
ed - Static variable in class org.jmol.script.T
 
Edge(IsoSolventReader, int, int, float) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
Edge - Class in org.jmol.util
 
Edge() - Constructor for class org.jmol.util.Edge
 
Edge.EnumBondOrder - Enum in org.jmol.util
 
EDGE_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
edgeCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgeData - Variable in class org.jmol.adapter.readers.xtal.CgdReader
 
edgeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgeDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
edgeFractionBase - Variable in class org.jmol.jvxl.data.JvxlData
 
edgeFractionBase - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgeFractionRange - Variable in class org.jmol.jvxl.data.JvxlData
 
edgeFractionRange - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
edgePointIndexes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edges - Static variable in class org.jmol.script.T
 
edges - Static variable in class org.jmol.util.BoxInfo
 
EDGES_ALL - Static variable in class org.jmol.shapespecial.Polyhedra
 
EDGES_FRONT - Static variable in class org.jmol.shapespecial.Polyhedra
 
EDGES_NONE - Static variable in class org.jmol.shapespecial.Polyhedra
 
edgeTypeTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVector - Variable in class org.jmol.jvxl.data.VolumeData
 
edgeVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexes - Static variable in class org.jmol.util.TriangleData
 
edgeVertexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPlanesHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPlanesLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPointers - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPointersHighToLow - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edgeVertexPointersLowToHigh - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
edit_light - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
editArea - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
editArea1 - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
editArea2 - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
editButton - Variable in class org.jmol.console.GenericConsole
 
editor - Variable in class org.jmol.console.ScriptEditor
 
editor_auto_dihedral - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
editor_auto_origin - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
editor_bond_cycle_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
editor_label_fragments - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
EDITOR_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
editorAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
editorDoc - Variable in class org.jmol.console.ScriptEditor.EditorTextPane
 
EditorDocument() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument
 
editorScrollPane - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
EditorTextPane - Variable in class org.jmol.console.ScriptEditor.EditorDocument
 
EditorTextPane() - Constructor for class org.jmol.console.ScriptEditor.EditorTextPane
 
editPane - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
editPane1 - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
editPane2 - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
edsurlcutoff - Static variable in class org.jmol.script.T
 
edsUrlCutoff - Variable in class org.jmol.viewer.GlobalSettings
 
edsurlformat - Static variable in class org.jmol.script.T
 
edsUrlFormat - Variable in class org.jmol.viewer.GlobalSettings
 
edsurlformatdiff - Static variable in class org.jmol.script.T
 
edsUrlFormatDiff - Variable in class org.jmol.viewer.GlobalSettings
 
EELECTROSTATIC - Static variable in class org.jmol.minimize.forcefield.ForceField
 
EfvetReader - Class in org.jmol.jvxl.readers
 
EfvetReader() - Constructor for class org.jmol.jvxl.readers.EfvetReader
 
EIG_VAL - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
EIG_VEC - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
EIG_VEC_COMPRESSED - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
eigen - Variable in class org.jmol.quantum.NciCalculation
 
eigenSignMask - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
eigenSignMask - Variable in class org.jmol.util.Tensor
 
EigenSort - Class in org.jmol.util
sort from smallest to largest absolute
EigenSort() - Constructor for class org.jmol.util.EigenSort
 
eigenValues - Variable in class org.jmol.quantum.NciCalculation
 
eigenValues - Variable in class org.jmol.util.Tensor
 
eigenVectors - Variable in class org.jmol.util.Tensor
 
eightPiSquared100 - Static variable in class org.jmol.shapebio.BioShape
 
electroNegativities - Static variable in class org.jmol.util.Elements
 
electronEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
eleLeft - Variable in class org.jmol.bspt.Node
 
Element - Class in org.jmol.bspt
the internal tree is made up of elements ...
Element() - Constructor for class org.jmol.bspt.Element
 
element - Static variable in class org.jmol.script.T
 
elementCharMasks - Static variable in class org.jmol.adapter.smarter.Atom
 
elementContext - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
elementCounts - Variable in class org.jmol.util.JmolMolecule
 
elementNameFromNumber(int) - Static method in class org.jmol.util.Elements
 
elementNames - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
elementNames - Static variable in class org.jmol.util.Elements
 
elementNumber - Variable in class org.jmol.adapter.smarter.Atom
 
elementNumber - Variable in class org.jmol.smiles.SmilesAtom
 
elementNumberFromName(String) - Static method in class org.jmol.util.Elements
 
elementNumberFromSymbol(String, boolean) - Static method in class org.jmol.util.Elements
 
elementNumberMax - Static variable in class org.jmol.util.Elements
one larger than the last elementNumber, same as elementSymbols.length
elementNumberMax - Variable in class org.jmol.util.JmolMolecule
 
elements - Variable in class org.jmol.symmetry.PointGroup
 
Elements - Class in org.jmol.util
 
Elements() - Constructor for class org.jmol.util.Elements
 
elementsPresent - Variable in class org.jmol.modelset.ModelSet
 
elementSymbol - Variable in class org.jmol.adapter.smarter.Atom
 
elementSymbolFromNumber(int) - Static method in class org.jmol.util.Elements
 
elementSymbols - Static variable in class org.jmol.util.Elements
The default elementSymbols.
elemisono - Static variable in class org.jmol.script.T
 
elemNo - Variable in class org.jmol.minimize.forcefield.AtomType
 
elemno - Static variable in class org.jmol.script.T
 
elemnoMax - Variable in class org.jmol.minimize.Minimizer
 
eleRight - Variable in class org.jmol.bspt.Node
 
eleRoot - Variable in class org.jmol.bspt.Bspt
 
ellipseNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
ellipsoid - Static variable in class org.jmol.script.T
 
ellipsoid() - Method in class org.jmol.scriptext.CmdExt
 
ELLIPSOID - Static variable in class org.jmol.shapecgo.CGOMesh
 
Ellipsoid - Class in org.jmol.shapespecial
 
Ellipsoid() - Constructor for class org.jmol.shapespecial.Ellipsoid
 
ellipsoid_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ellipsoid_probability - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ellipsoid_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ellipsoid_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ellipsoid_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ellipsoidarcs - Static variable in class org.jmol.script.T
 
ellipsoidArcs - Variable in class org.jmol.viewer.GlobalSettings
 
ellipsoidarrows - Static variable in class org.jmol.script.T
 
ellipsoidArrows - Variable in class org.jmol.viewer.GlobalSettings
 
ellipsoidaxes - Static variable in class org.jmol.script.T
 
ellipsoidAxes - Variable in class org.jmol.viewer.GlobalSettings
 
ellipsoidaxisdiameter - Static variable in class org.jmol.script.T
 
ellipsoidAxisDiameter - Variable in class org.jmol.viewer.GlobalSettings
 
ellipsoidball - Static variable in class org.jmol.script.T
 
ellipsoidBall - Variable in class org.jmol.viewer.GlobalSettings
 
ellipsoiddotcount - Static variable in class org.jmol.script.T
 
ellipsoidDotCount - Variable in class org.jmol.viewer.GlobalSettings
 
ellipsoiddots - Static variable in class org.jmol.script.T
 
ellipsoidDots - Variable in class org.jmol.viewer.GlobalSettings
 
ellipsoidfill - Static variable in class org.jmol.script.T
 
ellipsoidFill - Variable in class org.jmol.viewer.GlobalSettings
 
ellipsoidNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
ellipsoids - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
Ellipsoids - Class in org.jmol.shapespecial
 
Ellipsoids() - Constructor for class org.jmol.shapespecial.Ellipsoids
 
ellipsoidSet - Variable in class org.jmol.shapespecial.Ellipsoids
 
ellipsoidShades - Variable in class org.jmol.util.Shader
 
EllipsoidsRenderer - Class in org.jmol.renderspecial
 
EllipsoidsRenderer() - Constructor for class org.jmol.renderspecial.EllipsoidsRenderer
 
elsecmd - Static variable in class org.jmol.script.T
 
elseif - Static variable in class org.jmol.script.T
 
embed1 - Static variable in class org.openscience.chimetojmol.ChimePanel
 
embed2 - Static variable in class org.openscience.chimetojmol.ChimePanel
 
EMBEDDED_SCRIPT_TAG - Static variable in class org.jmol.viewer.JC
 
embeddedCrystal - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
embedScript(String) - Static method in class org.jmol.viewer.JC
 
empty - Variable in class org.jmol.viewer.SelectionManager
 
EMPTY_DICT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
EMPTY_LIST - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
EMPTY_SET - Static variable in class org.jmol.geodesic.EnvelopeCalculation
 
emptyBitmap - Static variable in class org.jmol.java.BS
 
emptyListPt - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
emptySet - Static variable in class org.jmol.util.BSUtil
 
ENABLE - Static variable in class org.jmol.shapecgo.CGOMesh
 
enableButton(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
enableButtons(JList<?>) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
enabled - Variable in class org.jmol.util.ModulationSet
 
ENC_CALC_MAX_DIST - Static variable in class org.jmol.viewer.JC
 
encapsulateData(String, Object, int) - Static method in class org.jmol.util.Escape
 
encodeColor(short) - Static method in class org.jmol.shape.Shape
 
encodeImage(int, int, Object) - Method in class org.jmol.viewer.OutputManager
general image encoder, allows for BufferedImage, int[], or HTML5 2D canvas
encodeRadiusParameter(int, boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
END - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
end - Static variable in class org.jmol.script.T
 
END - Static variable in class org.jmol.shapecgo.CGOMesh
 
END_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
END_INS_CODE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
END_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
endAssignment() - Method in class org.jmol.script.ScriptMathProcessor
 
endcap - Variable in class org.jmol.render.FontLineShapeRenderer
 
endcaps - Variable in class org.jmol.g3d.CylinderRenderer
 
endcaps - Variable in class org.jmol.render.SticksRenderer
 
ENDCAPS_FLAT - Static variable in class org.jmol.util.GData
 
ENDCAPS_NONE - Static variable in class org.jmol.util.GData
 
ENDCAPS_OPEN - Static variable in class org.jmol.util.GData
 
ENDCAPS_OPENEND - Static variable in class org.jmol.util.GData
 
ENDCAPS_SPHERICAL - Static variable in class org.jmol.util.GData
 
endcapShadeIndex - Variable in class org.jmol.g3d.CylinderRenderer
 
endChainID - Variable in class org.jmol.adapter.smarter.Structure
 
endChainStr - Variable in class org.jmol.adapter.smarter.Structure
 
endCheck - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
endCheck - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
endCoord - Variable in class org.jmol.shapespecial.Dipoles
 
endDegrees - Variable in class org.jmol.thread.SpinThread
 
endDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
endElement(String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
endFlag - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
 
endifcmd - Static variable in class org.jmol.script.T
 
endIndexPending - Variable in class org.jmol.renderbio.RocketRenderer
 
endInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
 
endMinimization() - Method in interface org.jmol.api.MinimizerInterface
 
endMinimization() - Method in class org.jmol.minimize.Minimizer
 
endOfData - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
endOfLine - Variable in class org.jmol.script.ScriptCompiler
 
endPositions - Variable in class org.jmol.thread.SpinThread
 
endRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
endRendering() - Method in class org.jmol.g3d.Graphics3D
 
endRendering() - Method in class org.jmol.util.GData
 
endSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
 
energy - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
energy - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
energy - Variable in class org.jmol.minimize.forcefield.Calculation
 
ENERGY - Static variable in class org.jmol.minimize.forcefield.ForceField
 
energy - Variable in class org.jmol.modelset.HBond
 
energy - Static variable in class org.jmol.script.T
 
energy - Variable in class org.jmol.viewer.Connection
 
energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyAngle(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyBond(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyBond(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyES(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyES(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyFull(boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyKey - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
Type of energy calculated, e.g., E(RB+HF-PW91).
energyKey - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
The type of energy last calculated.
energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyOOP(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyStrBnd(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyStretchBend(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyStretchBend(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyString - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
Calculated energy with units (if possible).
energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyTorsion(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyUnits - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
energyUnits - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
energyunits - Static variable in class org.jmol.script.T
 
energyUnits - Variable in class org.jmol.viewer.GlobalSettings
 
energyValue - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
The last calculated energy value.
energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
energyVDW(boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
energyWithUnits - Variable in class org.jmol.adapter.readers.simple.MopacArchiveReader
 
ensureCapacity(int) - Method in class org.jmol.java.BS
Ensures that the BitSet can hold enough words.
ensureFourier(int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
Make sure that F_n record is present.
ensureMeshSource() - Method in class org.jmol.shapesurface.Isosurface
 
enterListener - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
EnterListener - Interface in org.openscience.jmol.app.jmolpanel.console
 
enterMeasurementMode(int) - Method in class org.jmol.viewer.ActionManager
 
enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
enterPressed() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
enterPressed() - Method in interface org.openscience.jmol.app.jmolpanel.console.EnterListener
 
enthalpy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
entries - Variable in class org.jmol.util.Int2IntHash
 
entry(long, int, int, boolean) - Method in class org.jmol.awtjs2d.Mouse
 
entryCount - Variable in class org.jmol.util.Int2IntHash
 
EnumBondOrder(int, String, String) - Constructor for enum org.jmol.util.Edge.EnumBondOrder
 
EnumDrawType(int, String) - Constructor for enum org.jmol.shapespecial.Draw.EnumDrawType
 
EnumType() - Constructor for enum org.jmol.atomdata.RadiusData.EnumType
 
ENV_CALC_MAX_LEVEL - Static variable in class org.jmol.viewer.JC
 
EnvelopeCalculation - Class in org.jmol.geodesic
 
EnvelopeCalculation() - Constructor for class org.jmol.geodesic.EnvelopeCalculation
 
envelopeRadius - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
envelopeRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
EOL - Static variable in class org.jmol.script.ScriptCompiler
 
eol(char) - Method in class org.jmol.script.ScriptCompiler
look for end-of-line character \r, \n, or ; that is not within a command such as for (var i=0;i < 10; i++)
EOOP - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eP(T3) - Static method in class org.jmol.util.Escape
must be its own, because of the possibility of being null
eP4(P4) - Static method in class org.jmol.util.Escape
 
equalCount - Variable in class org.jmol.script.ScriptMathProcessor
 
equals(Object) - Method in class org.jmol.java.BS
Compares this object against the specified object.
equals(Object) - Method in class org.jmol.modelset.Atom
 
equals(Object) - Method in class org.jmol.script.T
 
equivalentAtomSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
The number of equivalent atom sets.
equivalentAtomSets - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
The number of equivalent atom sets.
equivalentTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
errCount - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
error(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
ERROR - Static variable in class org.jmol.script.ScriptCompiler
 
ERROR(int) - Method in class org.jmol.script.ScriptCompiler
 
ERROR(int, String) - Method in class org.jmol.script.ScriptCompiler
 
error - Variable in class org.jmol.script.ScriptError
 
error(int) - Method in class org.jmol.script.ScriptError
 
error - Variable in class org.jmol.script.ScriptParallelProcessor
 
error(int) - Method in class org.jmol.script.ScriptTokenParser
 
error - Static variable in class org.jmol.script.T
 
error(int) - Method in class org.jmol.scriptext.CmdExt
 
error(String) - Method in class org.jmol.util.DefaultLogger
 
error(String) - Static method in class org.jmol.util.Logger
Writes a log at ERROR level.
error(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level.
ERROR_axisExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_backgroundModelError - Static variable in class org.jmol.script.ScriptError
 
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptError
 
ERROR_badArgumentCount - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_badContext - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_badMillerIndices - Static variable in class org.jmol.script.ScriptError
 
ERROR_badRGBColor - Static variable in class org.jmol.script.ScriptError
 
ERROR_booleanExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_booleanOrNumberExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_booleanOrWhateverExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_cannotSet - Static variable in class org.jmol.script.ScriptError
 
ERROR_colorExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_colorOrPaletteRequired - Static variable in class org.jmol.script.ScriptError
 
ERROR_commandExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_commandExpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_coordinateExpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_coordinateOrNameOrExpressionRequired - Static variable in class org.jmol.script.ScriptError
 
ERROR_drawObjectNotDefined - Static variable in class org.jmol.script.ScriptError
 
ERROR_endOfCommandUnexpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_endOfExpressionExpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_endOfStatementUnexpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_expressionExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_expressionOrIntegerExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_filenameExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_fileNotFoundException - Static variable in class org.jmol.script.ScriptError
 
ERROR_FLAG - Static variable in class org.jmol.util.CommandHistory
 
ERROR_identifierOrResidueSpecificationExpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_incompatibleArguments - Static variable in class org.jmol.script.ScriptError
 
ERROR_insufficientArguments - Static variable in class org.jmol.script.ScriptError
 
ERROR_integerExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_integerOutOfRange - Static variable in class org.jmol.script.ScriptError
 
ERROR_invalidArgument - Static variable in class org.jmol.script.ScriptError
 
ERROR_invalidArgument - Static variable in class org.jmol.scriptext.CmdExt
 
ERROR_invalidAtomSpecification - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_invalidChainSpecification - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_invalidExpressionToken - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_invalidModelSpecification - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_invalidParameterOrder - Static variable in class org.jmol.script.ScriptError
 
ERROR_keywordExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_missingEnd - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_moCoefficients - Static variable in class org.jmol.script.ScriptError
 
ERROR_moIndex - Static variable in class org.jmol.script.ScriptError
 
ERROR_moModelError - Static variable in class org.jmol.script.ScriptError
 
ERROR_moOccupancy - Static variable in class org.jmol.script.ScriptError
 
ERROR_moOnlyOne - Static variable in class org.jmol.script.ScriptError
 
ERROR_multipleModelsDisplayedNotOK - Static variable in class org.jmol.script.ScriptError
 
ERROR_multipleModelsNotOK - Static variable in class org.jmol.script.ScriptError
 
ERROR_noData - Static variable in class org.jmol.script.ScriptError
 
ERROR_noPartialCharges - Static variable in class org.jmol.script.ScriptError
 
ERROR_noUnitCell - Static variable in class org.jmol.script.ScriptError
 
ERROR_numberExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_numberExpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_numberMustBe - Static variable in class org.jmol.script.ScriptError
 
ERROR_numberOrVariableNameExpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_numberOutOfRange - Static variable in class org.jmol.script.ScriptError
 
ERROR_objectNameExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_planeExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_propertyNameExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_residueSpecificationExpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_spaceGroupNotFound - Static variable in class org.jmol.script.ScriptError
 
ERROR_stringExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_stringOrIdentifierExpected - Static variable in class org.jmol.script.ScriptError
 
ERROR_tokenExpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_tokenUnexpected - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_tooManyPoints - Static variable in class org.jmol.script.ScriptError
 
ERROR_tooManyScriptLevels - Static variable in class org.jmol.script.ScriptError
 
ERROR_unrecognizedAtomProperty - Static variable in class org.jmol.script.ScriptError
 
ERROR_unrecognizedBondProperty - Static variable in class org.jmol.script.ScriptError
 
ERROR_unrecognizedCommand - Static variable in class org.jmol.script.ScriptError
 
ERROR_unrecognizedExpression - Static variable in class org.jmol.script.ScriptError
 
ERROR_unrecognizedExpressionToken - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_unrecognizedObject - Static variable in class org.jmol.script.ScriptError
 
ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptError
 
ERROR_unrecognizedParameter - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_unrecognizedParameterWarning - Static variable in class org.jmol.script.ScriptError
 
ERROR_unrecognizedShowParameter - Static variable in class org.jmol.script.ScriptError
 
ERROR_unrecognizedToken - Static variable in class org.jmol.script.ScriptTokenParser
 
ERROR_what - Static variable in class org.jmol.script.ScriptError
 
ERROR_writeWhat - Static variable in class org.jmol.script.ScriptError
 
errorEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
errorEx(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at ERROR level with detail on exception.
errorEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level with detail on exception.
errorIntStr2(int, String, String) - Method in class org.jmol.script.ScriptTokenParser
 
errorLine - Variable in class org.jmol.script.ScriptTokenParser
 
errorMessage - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
errorMessage - Variable in class org.jmol.script.ScriptContext
 
errorMessage - Variable in class org.jmol.script.ScriptError
 
errorMessage - Variable in class org.jmol.script.ScriptTokenParser
 
errorMessage - Variable in class org.jmol.viewer.Viewer
 
errorMessageUntranslated - Variable in class org.jmol.script.ScriptContext
 
errorMessageUntranslated - Variable in class org.jmol.script.ScriptError
 
errorMessageUntranslated - Variable in class org.jmol.script.ScriptTokenParser
 
errorMessageUntranslated - Variable in class org.jmol.viewer.Viewer
 
errorMore(int, String, String, String) - Method in class org.jmol.script.ScriptError
 
errorMsg - Variable in class org.jmol.image.AviCreator
 
errorOrWarn(int, String, String, String, boolean) - Method in class org.jmol.script.ScriptError
 
errorStr(int, String) - Method in class org.jmol.script.ScriptError
 
errorStr(int, String) - Method in class org.jmol.script.ScriptTokenParser
 
errorStr2(int, String, String) - Method in class org.jmol.script.ScriptError
 
errorStr2(String, String) - Method in class org.jmol.script.ScriptTokenParser
 
errorString(int, String, String, String, boolean) - Static method in class org.jmol.script.ScriptError
 
errorString(int, String, String, boolean) - Static method in class org.jmol.script.ScriptTokenParser
 
errorType - Variable in class org.jmol.script.ScriptContext
 
errorType - Variable in class org.jmol.script.ScriptError
 
errorType - Variable in class org.jmol.script.ScriptTokenParser
 
esCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
escape(BS, char, char) - Static method in class org.jmol.java.BS
 
escape() - Method in class org.jmol.script.SV
 
Escape - Class in org.jmol.util
 
Escape() - Constructor for class org.jmol.util.Escape
 
escapeColor(int) - Static method in class org.jmol.util.Escape
 
escapeFloatA(float[], boolean) - Static method in class org.jmol.util.Escape
 
escapeFloatAA(float[][], boolean) - Static method in class org.jmol.util.Escape
 
escapeFloatAAA(float[][][], boolean) - Static method in class org.jmol.util.Escape
 
escapeHelical(String, int, P3, P3, T3[]) - Static method in class org.jmol.util.Escape
Jmol-specific post-processing of the array data returned by Measure.computeHelicalAxis
escapeHTML(String) - Static method in class org.jmol.i18n.GT
 
escapeMap(Map<String, Object>) - Static method in class org.jmol.util.Escape
 
escapeModelFileNumber(int) - Static method in class org.jmol.util.Escape
 
escapeNice(String) - Static method in class org.jmol.util.Escape
 
espCharges - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
espressoContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
EspressoReader - Class in org.jmol.adapter.readers.xtal
 
EspressoReader() - Constructor for class org.jmol.adapter.readers.xtal.EspressoReader
 
ESTRBND - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eta - Static variable in class org.jmol.script.T
 
ETORSION - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eV(Lst<SV>) - Static method in class org.jmol.util.Escape
 
eval(String) - Method in interface org.jmol.api.JmolStatusListener
 
eval - Variable in exception org.jmol.script.ScriptException
 
eval - Variable in class org.jmol.script.ScriptManager
 
eval - Variable in class org.jmol.script.ScriptMathProcessor
 
eval(ScriptContext, ShapeManager) - Method in class org.jmol.script.ScriptParallelProcessor
 
eval - Static variable in class org.jmol.script.T
 
eval - Variable in class org.jmol.thread.JmolThread
 
eval(String) - Method in class org.jmol.util.GenericApplet
 
eval - Variable in class org.jmol.viewer.Viewer
 
eval(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
evalError(String, String) - Method in class org.jmol.script.ScriptError
 
evalFile(String) - Method in interface org.jmol.api.JmolScriptManager
 
evalFile(String) - Method in class org.jmol.api.JmolViewer
 
evalFile(String) - Method in class org.jmol.script.ScriptManager
 
evalFile(String) - Method in class org.jmol.viewer.Viewer
 
evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.api.JmolScriptEvaluator
 
evalFunctionFloat(Object, Object, float[]) - Method in interface org.jmol.atomdata.AtomDataServer
 
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.script.ScriptEval
 
evalFunctionFloat(Object, Object, float[]) - Method in class org.jmol.viewer.Viewer
 
evalOp(T) - Method in class org.jmol.script.ScriptMathProcessor
 
evalParallel(ScriptContext, ShapeManager) - Method in interface org.jmol.api.JmolScriptEvaluator
 
evalParallel(ScriptContext, ShapeManager) - Method in interface org.jmol.script.JmolCmdExtension
 
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.script.ScriptEval
 
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.scriptext.CmdExt
used for TRY command
evalParallel(ScriptContext, ShapeManager) - Method in class org.jmol.viewer.Viewer
 
evalString(String) - Method in class org.jmol.api.JmolViewer
 
evalString(String) - Method in class org.jmol.viewer.Viewer
 
evalStringQuiet(String) - Method in class org.jmol.api.JmolViewer
 
evalStringQuiet(String) - Method in class org.jmol.viewer.Viewer
 
evalStringQuietSync(String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
 
evalStringQuietSync(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.script.ScriptManager
 
evalStringWaitStatusQueued(String, String, String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
evalTemp - Variable in class org.jmol.script.ScriptManager
 
evaluate(ScriptMathProcessor, T, SV[], int) - Method in interface org.jmol.script.JmolMathExtension
 
evaluate(Object, boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
evaluate(ScriptMathProcessor, T, SV[], int) - Method in class org.jmol.scriptext.MathExt
 
evaluateArray(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
 
evaluateBin(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateCache(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateColor(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateCompare(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateCompiledScript(boolean, boolean, boolean, boolean, SB, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
evaluateCompiledScript(boolean, boolean, boolean, boolean, SB, boolean) - Method in class org.jmol.script.ScriptEval
 
evaluateConnected(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateContact(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateCross(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateData(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateDot(ScriptMathProcessor, SV[], int, int) - Method in class org.jmol.scriptext.MathExt
 
evaluateExpression(Object, boolean, boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
evaluateExpression(Object) - Method in class org.jmol.api.JmolViewer
 
evaluateExpression(Object, boolean, boolean) - Method in class org.jmol.script.ScriptEval
a general-use method to evaluate a "SET" type expression.
evaluateExpression(Object) - Method in class org.jmol.viewer.Viewer
synchronized here trapped the eventQueue; see also evaluateExpressionAsVariable
evaluateExpressionAsVariable(Object) - Method in class org.jmol.viewer.Viewer
 
evaluateFind(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateFormat(ScriptMathProcessor, int, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
 
evaluateFunction(int) - Method in class org.jmol.script.ScriptMathProcessor
 
evaluateGetProperty(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
 
evaluateHelix(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateIn(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateList(ScriptMathProcessor, int, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateLoad(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
 
evaluateMath(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
 
evaluateMeasure(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
 
evaluateModulation(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluatePlane(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
 
evaluatePoint(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluatePrompt(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateQuaternion(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
 
evaluateRandom(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateReplace(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateRowCol(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
 
evaluateScript(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
 
evaluateSort(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
sort() or sort(n) or count() or count("xxxx")
evaluateString(ScriptMathProcessor, int, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateSubstructure(ScriptMathProcessor, SV[], int) - Method in class org.jmol.scriptext.MathExt
 
evaluateSymop(ScriptMathProcessor, SV[], boolean) - Method in class org.jmol.scriptext.MathExt
 
evaluateTensor(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateUserFunction(ScriptMathProcessor, String, SV[], int, boolean) - Method in class org.jmol.scriptext.MathExt
 
evaluateValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
evaluateWithin(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evaluateWrite(ScriptMathProcessor, SV[]) - Method in class org.jmol.scriptext.MathExt
 
evalWait(String, String, String) - Method in class org.jmol.viewer.Viewer
 
EVDW - Static variable in class org.jmol.minimize.forcefield.ForceField
 
eventNames - Static variable in class org.jmol.multitouch.ActionManagerMT
 
EX - Variable in class org.jmol.quantum.MOCalculation
 
excl_display_lists_shaders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
excludeAtoms(BS, boolean) - Method in class org.jmol.viewer.SelectionManager
 
excludedTriangleCount - Variable in class org.jmol.jvxl.data.JvxlData
 
excludedTriangleCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
excludedVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
excludedVertexCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
excludeMaximumSet() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
excludeMinimumSet() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
excludePartialCubes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
excludeSelectionSet(BS) - Method in class org.jmol.viewer.SelectionManager
 
execThread - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
execute(String) - Method in class org.jmol.console.AppletConsole
 
execute(String) - Method in class org.jmol.console.GenericConsole
 
execute(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
executeCommand(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
executeCommandAsThread(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
executeCommands(boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
ExecuteCommandThread(String) - Constructor for class org.openscience.jmol.app.jmolpanel.console.AppConsole.ExecuteCommandThread
 
executeRaw() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
executeScriptAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ExecuteScriptAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExecuteScriptAction
 
executing - Variable in class org.jmol.script.ScriptEval
 
executionPaused - Variable in class org.jmol.script.ScriptContext
 
executionPaused - Variable in class org.jmol.script.ScriptEval
 
executionStepping - Variable in class org.jmol.script.ScriptContext
 
executionStepping - Variable in class org.jmol.script.ScriptEval
 
executionStopped - Variable in class org.jmol.script.ScriptEval
 
executor - Variable in class org.jmol.viewer.Viewer
 
exit - Static variable in class org.jmol.script.T
 
exitAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ExitAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExitAction
 
exitjmol - Static variable in class org.jmol.script.T
 
exitJmol() - Method in class org.jmol.viewer.Viewer
 
exitJSpecView(boolean, Object) - Method in interface org.jmol.api.JSVInterface
 
exitJSpecView(boolean, Object) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
exitMeasurementMode(String) - Method in class org.jmol.viewer.ActionManager
 
expandFloatArray(float[], int) - Method in class org.jmol.script.ScriptEval
Accepts a float array and expands [1 -3] to [1 2 3], for example.
expandMinMax(P3, SymmetryInterface, P3, P3) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
expandTo(int) - Method in class org.jmol.java.BS
Ensures that the BitSet can accommodate a given wordIndex, temporarily violating the invariants.
expdta() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
explicitContours - Variable in class org.jmol.shapesurface.Isosurface
 
explicitH - Variable in class org.jmol.smiles.SmilesGenerator
 
explicitID - Variable in class org.jmol.shape.MeshCollection
 
Export3D - Class in org.jmol.export
 
Export3D() - Constructor for class org.jmol.export.Export3D
 
EXPORT_CARTESIAN - Static variable in class org.jmol.util.GData
 
EXPORT_DRIVER_LIST - Static variable in class org.jmol.viewer.JC
 
EXPORT_NOT - Static variable in class org.jmol.util.GData
 
EXPORT_RAYTRACER - Static variable in class org.jmol.util.GData
 
exportAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ExportAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ExportAction
 
exportActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ExportChoiceListener() - Constructor for class org.jmol.dialog.Dialog.ExportChoiceListener
 
exportDone(JComponent, Transferable, int) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
exporter - Variable in class org.jmol.export.Export3D
 
exportName - Variable in class org.jmol.export.Export3D
 
exportPass - Variable in class org.jmol.render.MeshRenderer
 
exportScale - Variable in class org.jmol.export.___Exporter
 
exportscale - Static variable in class org.jmol.script.T
 
exportScale - Variable in class org.jmol.viewer.GlobalSettings
 
exportSurface(short) - Method in class org.jmol.render.MeshRenderer
 
exportType - Variable in class org.jmol.export.___Exporter
 
exportType - Variable in class org.jmol.render.ShapeRenderer
 
expression - Static variable in class org.jmol.script.T
 
expressionBegin - Static variable in class org.jmol.script.T
 
expressionEnd - Static variable in class org.jmol.script.T
 
expressionResult - Variable in class org.jmol.script.ScriptParam
 
extendGrid - Variable in class org.jmol.jvxl.readers.Parameters
 
extendLadder(int, int) - Method in class org.jmol.dssx.Bridge
 
extendRuns(STR[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
extension - Variable in class org.jmol.dialog.Dialog
 
extensions - Variable in class org.jmol.dialog.Dialog
 
extents - Variable in class org.jmol.jvxl.readers.JaguarReader
 
externalContainer - Variable in class org.jmol.console.JmolConsole
 
extractFloats(Map<String, Object>, String[]) - Method in class org.jmol.dssx.AnnotationParser
 
extractLatticeInfo(String) - Method in class org.jmol.symmetry.HallInfo
 
extractMolData(String) - Method in class org.jmol.api.JmolViewer
 
extractMolData(String) - Method in class org.jmol.viewer.Viewer
 
extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in interface org.jmol.api.JmolPropertyManager
 
extractProperty(Object, Object, int, Lst<Object>, boolean) - Method in class org.jmol.viewer.PropertyManager
 
extractProperty(Object, Object, int) - Method in class org.jmol.viewer.Viewer
 
extractRotationInfo(String, int, char) - Method in class org.jmol.symmetry.HallInfo
 
extractTag(String, String, String, boolean) - Static method in class org.jmol.jvxl.readers.XmlReader
 
extractTagOnly(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
 
extractVectorInfo(String) - Method in class org.jmol.symmetry.HallInfo
 
EY - Variable in class org.jmol.quantum.MOCalculation
 
EZ - Variable in class org.jmol.quantum.MOCalculation
 

F

Face(int, int, int, P3) - Constructor for class org.jmol.jvxl.readers.IsoSolventReader.Face
 
FACE_COUNT_MAX - Static variable in class org.jmol.shapespecial.Polyhedra
 
facecenteroffset - Static variable in class org.jmol.script.T
 
faceCenterOffset - Variable in class org.jmol.shapespecial.Polyhedra
 
faceCenterOffset - Variable in class org.jmol.shapespecial.Polyhedron
 
faceId(int, int, int) - Method in class org.jmol.shapespecial.Polyhedra
 
faceMap - Variable in class org.jmol.renderspecial.DotsRenderer
 
facePoints - Static variable in class org.jmol.util.BoxInfo
 
facePt1 - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
 
facePt2 - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
 
facePt3 - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
 
faceVertexesArrays - Static variable in class org.jmol.util.Geodesic
 
faceVertexesIcosahedron - Static variable in class org.jmol.util.Geodesic
 
fact(double, double, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.
fact - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
fact1 - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
factoredLengths - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
factorType - Variable in class org.jmol.atomdata.RadiusData
 
FALSE - Static variable in class org.jmol.viewer.SelectionManager
 
falsifyMesh() - Method in class org.jmol.shapebio.BioShape
 
falsifyNearbyMesh(int) - Method in class org.jmol.shapebio.BioShape
 
FAMILY_ASSEM - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
FAMILY_ATOM - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
FAMILY_COMPBOND - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
FAMILY_OPER - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
FAMILY_SGOP - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
FAMILY_SHEET - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
FAMILY_STRUCSITE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
FAMILY_STRUCTCONF - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
fast_idle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
fatal(String) - Method in class org.jmol.util.DefaultLogger
 
fatal(String) - Static method in class org.jmol.util.Logger
Writes a log at FATAL level.
fatal(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at FATAL level.
fatalError(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
fatalEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
fatalEx(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at FATAL level with detail on exception.
fatalEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at ERROR level with detail on exception.
FC - Static variable in class org.jmol.quantum.QS
 
fc(float) - Static method in class org.jmol.symmetry.SymmetryOperation
 
fc - Variable in class org.openscience.jmol.app.webexport.Test
 
fc - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
 
FC_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
fcadj - Variable in class org.jmol.minimize.forcefield.AtomType
 
fcoord(T3) - Method in interface org.jmol.api.SymmetryInterface
 
fcoord(T3) - Method in class org.jmol.symmetry.Symmetry
 
fcoord(T3) - Static method in class org.jmol.symmetry.SymmetryOperation
 
FD_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
fd_oldFileName - Variable in class org.jmol.awt.FileDropper
 
fd_propSupport - Variable in class org.jmol.awt.FileDropper
 
FDP_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
fetch_host - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
fetch_path - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ff - Variable in class org.jmol.minimize.forcefield.Calculations
 
ff - Variable in class org.jmol.minimize.Minimizer
 
FF - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
ffAtomType - Variable in class org.jmol.minimize.MinAtom
 
fFixed - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
FFParam - Class in org.jmol.minimize.forcefield
 
FFParam() - Constructor for class org.jmol.minimize.forcefield.FFParam
 
ffParams - Variable in class org.jmol.minimize.forcefield.Calculations
 
ffParams - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
ffParams - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
ffType - Variable in class org.jmol.minimize.MinAtom
 
ffTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
fid - Variable in class org.jmol.modelset.Text
 
fid - Variable in class org.jmol.render.LabelsRenderer
 
fidPrevious - Variable in class org.jmol.render.LabelsRenderer
 
fids - Variable in class org.jmol.shape.Labels
 
field - Variable in class org.jmol.adapter.readers.cif.CifReader
 
field - Variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
Field - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
field_of_view - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
fieldCount - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
fieldOf - Variable in class org.jmol.adapter.readers.cif.CifReader
 
fieldProperty(int) - Method in class org.jmol.adapter.readers.cif.CifReader
 
fieldProperty(CifReader, int) - Method in class org.jmol.adapter.readers.cif.MSCifRdr
 
fieldTypes - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
FIL - Enum in org.jmol.c
 
FIL(int) - Constructor for enum org.jmol.c.FIL
 
file - Static variable in class org.jmol.script.T
 
file - Variable in class org.openscience.jmol.app.HistoryFile
The location of the history file.
file - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
FILE_OPEN_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
fileAtomIndex - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
fileButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
FileButton - Variable in class org.openscience.jmol.app.webexport.Test
 
filecachedirectory - Static variable in class org.jmol.script.T
 
filecaching - Static variable in class org.jmol.script.T
 
FileChecker(String) - Constructor for class org.jmol.console.JmolConsole.FileChecker
 
FileChooser - Class in org.jmol.dialog
JFileChooser with possibility to fix size and location
FileChooser() - Constructor for class org.jmol.dialog.FileChooser
 
fileChooser - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
fileCoordinatesAreFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fileData - Variable in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
fileDotModel - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
FileDropper - Class in org.jmol.awt
A simple Dropping class to allow files to be dragged onto a target.
FileDropper(JmolStatusListener, Viewer) - Constructor for class org.jmol.awt.FileDropper
 
fileField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
fileHasUnitCell - Variable in class org.jmol.popup.JmolGenericPopup
 
fileHeader - Variable in class org.jmol.modelset.ModelLoader
 
fileIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
fileIndex - Variable in class org.jmol.modelset.Model
 
fileList - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
FileLoadThread - Class in org.jmol.script
 
FileLoadThread(JmolScriptEvaluator, Viewer, String, String, String) - Constructor for class org.jmol.script.FileLoadThread
JavaScript only
fileLoadThread - Variable in class org.jmol.script.ScriptEval
 
FileManager - Class in org.jmol.viewer
 
FileManager(Viewer) - Constructor for class org.jmol.viewer.FileManager
 
FileMolOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
fileName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fileName - Variable in class org.jmol.atomdata.AtomData
 
filename - Variable in class org.jmol.console.ScriptEditor
 
fileName - Variable in class org.jmol.export.___Exporter
 
fileName - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
fileName - Variable in class org.jmol.jvxl.readers.MsmsReader
 
fileName - Variable in class org.jmol.jvxl.readers.Parameters
 
fileName - Variable in class org.jmol.script.FileLoadThread
 
filename - Variable in class org.jmol.script.ScriptCompiler
 
fileName - Variable in class org.jmol.viewer.FileManager
 
fileName - Variable in exception org.jmol.viewer.JmolAsyncException
 
fileName - Variable in class org.jmol.viewer.ModelManager
 
fileNameIn - Variable in class org.jmol.io.FileReader
 
fileOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fileOffsetFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filePath - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
FilePreview - Class in org.jmol.dialog
File previsualisation before opening
FilePreview(Viewer, JFileChooser, boolean, Map<String, Object>) - Constructor for class org.jmol.dialog.FilePreview
Constructor
FilePreview.FPPanel - Class in org.jmol.dialog
 
filePt - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
FileReader - Class in org.jmol.io
 
FileReader(FileManager, Viewer, String, String, String, String, Object, Map<String, Object>, boolean) - Constructor for class org.jmol.io.FileReader
 
FileReader - Class in org.openscience.jvxl
 
FileReader() - Constructor for class org.openscience.jvxl.FileReader
 
files - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
fileScaling - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
FilesReader - Class in org.jmol.io
open a set of models residing in different files
FilesReader() - Constructor for class org.jmol.io.FilesReader
 
fileStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
fileType - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
fileTypeIn - Variable in class org.jmol.io.FileReader
 
fileTypeName - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
FileTyper - Class in org.openscience.jmol.app.jmolpanel
 
FileTyper() - Constructor for class org.openscience.jmol.app.jmolpanel.FileTyper
 
fileTypesIn - Variable in class org.jmol.io.FilesReader
 
FileUnitOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
fileWriter(File, JList<JmolInstance>) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
fill - Static variable in class org.jmol.script.T
 
fillADa(AtomData, int) - Method in class org.jmol.modelset.AtomCollection
 
fillArc - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
fillAtomData(AtomData, int) - Method in interface org.jmol.atomdata.AtomDataServer
 
fillAtomData(AtomData, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
fillAtomData(AtomData, int) - Method in class org.jmol.modelset.ModelSet
 
fillAtomData(AtomData, int) - Method in class org.jmol.viewer.Viewer
 
fillBackground(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
 
fillBackground(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
 
fillBackground(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
 
fillCircle(Object, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
fillCircle(Object, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
fillCircle(Object, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
fillConeSceen3f(byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
fillConeSceen3f(byte, int, P3, P3) - Method in class org.jmol.export.Export3D
 
fillConeSceen3f(byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
fillConeScreen(byte, int, P3i, P3i, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
fillConeScreen(short, byte, int, P3, P3, boolean) - Method in class org.jmol.export.___Exporter
 
fillConeScreen(short, byte, int, P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
 
fillConeScreen(short, byte, int, P3, P3, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
fillConeScreen(byte, int, P3i, P3i, boolean) - Method in class org.jmol.export.Export3D
 
fillConeScreen(byte, int, P3i, P3i, boolean) - Method in class org.jmol.g3d.Graphics3D
 
fillConeScreen(P3i, P3i, boolean) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export.__RayTracerExporter
 
fillConicalCylinder(P3, P3, int, short, byte) - Method in class org.jmol.export._TachyonExporter
 
fillCsfArray(String, String[], int, Object, boolean) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
fillCylinder(byte, int, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.export.Export3D
 
fillCylinder(byte, int, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinder(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.render.FontLineShapeRenderer
 
fillCylinderBits(byte, int, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.export.Export3D
 
fillCylinderBits(byte, int, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderScreen(short, byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.___Exporter
 
fillCylinderScreen(short, byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.__CartesianExporter
 
fillCylinderScreen(short, byte, int, P3, P3, P3, P3, float) - Method in class org.jmol.export.__RayTracerExporter
 
fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinderScreen3I(byte, int, P3i, P3i, P3, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderScreen3I(byte, int, P3i, P3i, P3, P3, float) - Method in class org.jmol.export.Export3D
 
fillCylinderScreen3I(byte, int, P3i, P3i, P3, P3, float) - Method in class org.jmol.g3d.Graphics3D
 
fillCylinderScreenMad(short, byte, int, P3, P3) - Method in class org.jmol.export.___Exporter
 
fillCylinderScreenMad(short, byte, int, P3, P3) - Method in class org.jmol.export.__CartesianExporter
 
fillCylinderScreenMad(short, byte, int, P3, P3) - Method in class org.jmol.export.__RayTracerExporter
 
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillDataBlock(String[][], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fills an array with a pre-defined number of lines of token data, skipping blank lines in the process
fillDataBlockFixed(String[][], int, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fills an array with a predefined number of lines of data that is arranged in fixed FORTRAN-like column format
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3i[]) - Method in interface org.jmol.api.JmolRendererInterface
 
fillEllipsoid(P3, P3[], short, int, int, int, int, M3, double[], M4, P3i[]) - Method in class org.jmol.export.___Exporter
 
fillEllipsoid(P3, P3[], short, int, int, int, int, M3, double[], M4, P3i[]) - Method in class org.jmol.export.__CartesianExporter
 
fillEllipsoid(P3, P3[], short, int, int, int, int, M3, double[], M4, P3i[]) - Method in class org.jmol.export.__RayTracerExporter
 
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3i[]) - Method in class org.jmol.export.Export3D
 
fillEllipsoid(P3, P3[], int, int, int, int, M3, double[], M4, int, P3i[]) - Method in class org.jmol.g3d.Graphics3D
 
fillFace(short, P3i, P3i, P3i) - Method in class org.jmol.renderspecial.PolyhedraRenderer
 
fillFloatArray(String, int, float[]) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
fills a float array with string data from a file
fillFrequencyData(int, int, int, boolean[], boolean, int, int, int[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
Extracts a block of frequency data from a file.
fillHermite(int, int, int, int, P3i, P3i, P3i, P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
fillHermite(int, int, int, int, P3i, P3i, P3i, P3i) - Method in class org.jmol.export.Export3D
 
fillHermite(int, int, int, int, P3i, P3i, P3i, P3i) - Method in class org.jmol.g3d.Graphics3D
 
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
fillMeshData(MeshData, int, IsosurfaceMesh) - Method in class org.jmol.shapesurface.Isosurface
 
fillOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
fillPolygon(Object, int[], int[], int) - Method in interface org.jmol.api.GenericGraphics
 
fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awt.AwtG2D
 
fillPolygon(Object, int[], int[], int) - Method in class org.jmol.awtjs2d.JsG2D
 
fillQuadrilateral(P3, P3, P3, P3) - Method in interface org.jmol.api.JmolRendererInterface
 
fillQuadrilateral(P3, P3, P3, P3) - Method in class org.jmol.export.Export3D
 
fillQuadrilateral(P3, P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
fillRect(Object, int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
fillRect(int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fills background rectangle for label
fillRect(Object, int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
fillRect(Object, int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
fillRect(int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
fills background rectangle for label
fillRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fills background rectangle for label
fillSlater(int[], int, int, int) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
fillSphere(int, P3) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphere(short, int, P3) - Method in class org.jmol.export.___Exporter
 
fillSphere(short, int, P3) - Method in class org.jmol.export.__CartesianExporter
 
fillSphere(short, int, P3) - Method in class org.jmol.export.__RayTracerExporter
 
fillSphere(int, P3) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphere(int, P3) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillSphereI(int, P3i) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphereI(int, P3i) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphereI(int, P3i) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in class org.jmol.export.Export3D
fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fills a solid sphere
fillTriangle(short, T3, T3, T3, boolean, boolean) - Method in class org.jmol.export.___Exporter
 
fillTriangle(short, T3, T3, T3, boolean, boolean) - Method in class org.jmol.export.__CartesianExporter
 
fillTriangle(short, T3, T3, T3, boolean, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
fillTriangle() - Method in class org.jmol.rendercgo.CGORenderer
 
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.export.Export3D
 
fillTriangle3CN(P3i, short, short, P3i, short, short, P3i, short, short) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle3f(P3, P3, P3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.export.Export3D
 
fillTriangle3f(P3, P3, P3, boolean) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangle3i(P3i, P3i, P3i, T3, T3, T3, boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangle3i(P3i, P3i, P3i, T3, T3, T3, boolean) - Method in class org.jmol.export.Export3D
 
fillTriangle3i(P3i, P3i, P3i, T3, T3, T3, boolean) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangleB(boolean) - Method in class org.jmol.g3d.TriangleRenderer
 
fillTriangleP3f(P3, P3, P3, boolean) - Method in class org.jmol.g3d.TriangleRenderer
 
fillTriangleP3i(P3i, P3i, P3i, boolean) - Method in class org.jmol.g3d.TriangleRenderer
 
fillTriangles - Variable in class org.jmol.shape.Mesh
 
fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
fillTriangleXYZ(int, int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.TriangleRenderer
 
filter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filter - Static variable in class org.jmol.script.T
 
filter1 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filter2 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterAltLoc - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterAssembly - Variable in class org.jmol.adapter.readers.cif.CifReader
 
filterAtom(Atom, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterAtomName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterAtomNameTerminator - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterAtomType - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterAtomTypeStr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterChain - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterCIFAtom(Atom, String) - Method in class org.jmol.adapter.readers.cif.CifReader
 
filterData(boolean, float) - Method in interface org.jmol.api.VolumeDataInterface
 
filterData(boolean, float) - Method in class org.jmol.jvxl.data.VolumeData
 
filterElement - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterEveryNth - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterGroup3 - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterHetero - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterIsNot - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
filterMO() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
filterN - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterPDBAtom(Atom, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
filterReject(String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterSymop - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
filterSymop - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
filterTokens - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
finalize() - Method in class org.jmol.viewer.Viewer
 
finalizeAtoms(BS, P3) - Method in class org.jmol.viewer.ShapeManager
 
finalized - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
finalizeEdges() - Method in class org.jmol.adapter.readers.xtal.CgdReader
Now that we have all the edge data we can add edges to atoms
finalizeGroupBuild() - Method in class org.jmol.modelset.ModelLoader
 
finalizeHydrogens() - Method in interface org.jmol.api.JmolBioResolver
 
finalizeHydrogens() - Method in class org.jmol.modelsetbio.Resolver
 
finalizeLoad(boolean, boolean, boolean, boolean, int, int, int) - Method in class org.jmol.script.ScriptEval
 
finalizeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
finalizeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
finalizeMOData(Map<String, Object>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalizeModels(int) - Method in class org.jmol.modelset.ModelLoader
Model numbers are considerably more complicated in Jmol 11.
finalizeModelSet() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
At the end of the day, we need to finalize all the JmolObjects, set the trajectories, and, if filtered with DOCACHE, cache a streamlined binary file for inclusion in the PNGJ file.
finalizeModelSet() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalizeModulation() - Method in class org.jmol.adapter.readers.cif.MSRdr
Create a script that will run to turn modulation on and to display only atoms with modulated occupancy >= 0.5.
finalizeModulation() - Method in interface org.jmol.adapter.smarter.MSInterface
 
finalizeNet() - Method in class org.jmol.adapter.readers.xtal.CgdReader
Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdges
finalizeObject(PyMOLScene, ModelSet, String, boolean) - Method in class org.jmol.adapter.readers.pymol.JmolObject
 
finalizeObject(int, int, float, int, boolean, Object, int, BS) - Method in class org.jmol.scriptext.CmdExt
 
finalizeObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Finally, we turn each JmolObject into its Jmol equivalent.
finalizeOutput() - Method in interface org.jmol.api.JmolRendererInterface
 
finalizeOutput() - Method in class org.jmol.export.___Exporter
 
finalizeOutput() - Method in class org.jmol.export._IdtfExporter
 
finalizeOutput() - Method in class org.jmol.export._ObjExporter
 
finalizeOutput() - Method in class org.jmol.export._PovrayExporter
 
finalizeOutput() - Method in class org.jmol.export.Export3D
 
finalizeOutput() - Method in class org.jmol.g3d.Graphics3D
 
finalizeOutput2() - Method in class org.jmol.export.___Exporter
 
finalizePdbCharges() - Method in class org.jmol.modelsetbio.Resolver
 
finalizePdbMultipleBonds() - Method in class org.jmol.modelsetbio.Resolver
 
finalizeReaderASCR() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalizeReaderMR() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
finalizeReaderPDB() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
finalizeRna3d(Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
 
finalizeSceneData() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Make sure atom uniqueID (vectorX) and cartoonType (vectorY) are made permanent
finalizeShapes() - Method in class org.jmol.modelset.ModelLoader
 
finalizeStructures() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
 
finalizeSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.cif.CifReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.P2nReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.simple.InputReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
Set final auxiliary info and symmetry, including "fileHeader", "magresUnits", and "interactionTensors"; note that print getProperty("auxiliaryInfo.models[1].magresUnits") should return a catalog of tensor types.
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspChgcarReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
finalizeSubclassReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
optional reader-specific method run first.
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
 
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
finalizeSubclassSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finalizeSymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
finalizeTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finalizeTrajectoryAs(Lst<P3[]>, Lst<V3[]>) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finalizeTransformParameters() - Method in class org.jmol.viewer.TransformManager
 
finalizeTransformParameters() - Method in class org.jmol.viewer.Viewer
 
finalizeUniqueBonds() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
finalizeUnitCell(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
Ensure that ModelLoader sets up the supercell unit cell.
finalizeValidations(Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
Create property_xxxx for each validation category.
finalizeVisibility() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Create group JmolObjects, and set hierarchical visibilities
finalOperations - Variable in class org.jmol.symmetry.SpaceGroup
 
find(String, String, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
find(Lst<Measurement>, Measurement) - Static method in class org.jmol.modelset.Measurement
 
find - Static variable in class org.jmol.script.T
 
find(Measurement) - Method in class org.jmol.shape.Measures
 
find(String, String, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
Searches for all matches of a pattern within a SMILES string.
find(String, SmilesSearch, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
 
find(String, int) - Method in class org.jmol.util.CommandHistory
 
findAdditionalAxes(int) - Method in class org.jmol.symmetry.PointGroup
 
findAnnotationAtoms(Viewer, String, Lst<SV>, String, BS) - Method in class org.jmol.dssx.AnnotationParser
find annotations; allows for wild cards InterPro.* where .....
findApplets(String, String, String, Lst<String>) - Static method in class org.jmol.util.GenericApplet
 
findAromaticNeighbor(int) - Method in class org.jmol.modelset.Atom
 
findAtom(int, int, int, int, boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
findAtom(P3) - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
findAtomDipole(Atom, Atom, boolean) - Method in class org.jmol.shapespecial.Dipoles
 
findAtomForRange(int, int, int, int, boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
findAtomsInRectangle(Rectangle) - Method in class org.jmol.modelset.ModelSet
 
findAtomsLike(String) - Method in class org.jmol.modelset.Atom
 
findAtomsLike(String) - Method in class org.jmol.smiles.SmilesAtom
 
findAtomsLike(String) - Method in interface org.jmol.util.Node
 
findBestFit(int, int[]) - Static method in class org.jmol.util.TempArray
 
findBondDipole(Bond) - Method in class org.jmol.shapespecial.Dipoles
 
findCAxes() - Method in class org.jmol.symmetry.PointGroup
 
findDipole(String) - Method in class org.jmol.shapespecial.Dipoles
 
findDipoleFor(String, String) - Method in class org.jmol.shapespecial.Dipoles
 
findEdge(int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
findElementsPresent() - Method in class org.jmol.modelset.ModelLoader
 
findFrequency(int, int) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Have the vwr show a particular frame with frequencies if it can be found.
findHelixes(int, int[][][]) - Method in class org.jmol.dssx.DSSP
(p.
findHelixes2(int, int, int[][][], STR, int, BS) - Method in class org.jmol.dssx.DSSP
 
findInversionCenter() - Method in class org.jmol.symmetry.PointGroup
 
findLeftLeaf() - Method in class org.jmol.bspt.CubeIterator
does the work
findMaxRadii() - Method in class org.jmol.modelset.AtomCollection
 
findModelById(String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
findNearest2(int, int, Atom[], BS, int) - Method in class org.jmol.modelset.AtomCollection
 
findNearestAtom(int, int, Point3fi, boolean) - Method in class org.jmol.viewer.ActionManager
 
findNearestAtomIndex(int, int) - Method in class org.jmol.api.JmolViewer
 
findNearestAtomIndex(int, int, BS, int) - Method in class org.jmol.modelset.ModelSet
 
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.AminoMonomer
 
findNearestAtomIndex(int, int, Atom[], short[], int, BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.Monomer
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
findNearestAtomIndex(int, int, Atom[], short, short) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shape.Shape
 
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShape
 
findNearestAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
findNearestAtomIndex(int, int) - Method in class org.jmol.viewer.Viewer
 
findNearestAtomIndexMovable(int, int, boolean) - Method in class org.jmol.viewer.Viewer
 
findNearestLabel(int, int) - Method in class org.jmol.shape.Labels
 
findNearestShapeAtomIndex(int, int, Atom[], BS) - Method in class org.jmol.viewer.ShapeManager
 
findNearestThreePoints(float, float, float[][], int[]) - Static method in class org.jmol.jvxl.readers.SurfaceGenerator
 
findNotAttached(int, int[][], int[], int) - Method in class org.jmol.modelset.AtomCollection
 
findPickedBond(int, int, BS, P3) - Method in class org.jmol.shape.Sticks
 
findPickedObject(int, int, boolean, BS) - Method in class org.jmol.shapespecial.Draw
 
findPlanes() - Method in class org.jmol.symmetry.PointGroup
 
findRecord(String) - Method in class org.jmol.jsv.JDXMOLParser
 
findSet(int) - Method in class org.jmol.jvxl.data.MeshData
 
findShorter(int, int[]) - Static method in class org.jmol.util.TempArray
 
findSpaceGroup(String) - Static method in class org.jmol.symmetry.SpaceGroup
 
findString - Variable in class org.jmol.jvxl.readers.KinemageReader
 
findValue(int, int, boolean, BS) - Method in class org.jmol.shapesurface.Isosurface
 
finish() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
finish() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
finish(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
finish(Object) - Method in class org.jmol.api.JmolAdapter
 
FINISH - Static variable in class org.jmol.thread.JmolThread
 
first - Variable in class org.jmol.modelset.TickInfo
 
first - Static variable in class org.jmol.script.T
 
firstAtom - Variable in class org.jmol.adapter.readers.cif.CifReader
 
firstAtomIndex - Variable in class org.jmol.atomdata.AtomData
 
firstAtomIndex - Variable in class org.jmol.modelset.Group
 
firstAtomIndex - Variable in class org.jmol.modelset.Model
 
firstAtomIndex - Variable in class org.jmol.util.JmolMolecule
 
firstAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
 
firstAtomOffset - Variable in class org.jmol.quantum.QuantumCalculation
 
firstChar - Variable in class org.jmol.adapter.readers.cif.CifReader
 
firstFrameDelay - Variable in class org.jmol.viewer.AnimationManager
 
firstFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
 
firstFrameIndex - Variable in class org.jmol.viewer.AnimationManager
 
firstIsotope - Static variable in class org.jmol.util.Elements
first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
firstLastStep - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
firstLine - Variable in class org.jmol.adapter.readers.simple.InputReader
 
firstMatchOnly - Variable in class org.jmol.smiles.SmilesSearch
 
firstModelIndex - Variable in class org.jmol.atomdata.AtomData
 
firstMoleculeIndex - Variable in class org.jmol.modelset.Model
 
firstNearbyAtom - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
firstPosition - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
firstProper - Static variable in class org.jmol.symmetry.PointGroup
 
firstRealVertex - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
firstSymmetryAtom - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
fit_iterations - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
fit_kabsch - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
fit_tolerance - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
fix(String, boolean) - Method in class org.jmol.dssx.AnnotationParser
A.T8 --> [T]8:A N1@A.G2673 --> [G]2673:A.N1 A.US3/4 --> [US3]4:A
fix(String) - Static method in class org.jmol.i18n.Resource
 
fix(float) - Method in class org.jmol.symmetry.UnitCell
 
fixACDAtomList(String, Map<String, String>, int) - Method in class org.jmol.jsv.JDXMOLParser
 
fixAnnotations(int, String, int) - Method in class org.jmol.modelsetbio.Resolver
 
fixAtomName(String) - Static method in class org.jmol.adapter.readers.xtal.CrystalReader
MN33 becomes Mn33
fixAtoms(int, SV, BS, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
 
fixAtoms(int, SV, BS, int, int) - Method in class org.jmol.dssx.AnnotationParser
Adjusts _atoms bitset to account for added hydrogen atoms.
fixBaseIndices() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fixBasisLine(String) - Static method in class org.jmol.adapter.readers.quantum.GamessReader
 
fixChime(String, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
fixChirality(SmilesSearch) - Method in class org.jmol.smiles.SmilesParser
 
fixD(float, boolean) - Method in class org.jmol.modelset.BondCollection
 
fixDataString(String) - Static method in class org.jmol.util.Parser
 
fixDouble(double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
fixed - Static variable in class org.jmol.script.T
 
fixedCount - Variable in class org.jmol.jvxl.readers.PmeshReader
 
fixedLattice - Variable in class org.jmol.jvxl.data.JvxlData
 
fixedOrigin - Variable in class org.jmol.shape.Axes
 
fixedRotationAxis - Variable in class org.jmol.viewer.TransformManager
 
fixedRotationCenter - Variable in class org.jmol.export.___Exporter
 
fixedRotationCenter - Variable in class org.jmol.viewer.TransformManager
 
fixedRotationOffset - Variable in class org.jmol.viewer.TransformManager
 
fixedtemp - Static variable in class org.jmol.script.T
 
fixedTranslation - Variable in class org.jmol.viewer.TransformManager
 
fixFileName(File) - Method in class org.openscience.chimetojmol.ChimePanel
 
fixFileNames(String, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
fixFileNames(String, String, char) - Method in class org.openscience.chimetojmol.ChimePanel
 
fixFileNameVariables(String, String) - Static method in class org.jmol.viewer.FileManager
 
fixFormalCharges(BS) - Method in class org.jmol.modelset.AtomCollection
 
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
 
fixHtml(String) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
fixIndices(int, BS) - Method in class org.jmol.modelset.Chain
 
fixIndices(int, BS) - Method in class org.jmol.modelset.Group
 
fixIndices(int, int, BS) - Method in class org.jmol.modelset.Model
 
fixIndices(int, int, BS) - Method in class org.jmol.modelsetbio.BioModel
 
fixIndicesM(int, int, BS) - Method in class org.jmol.modelset.Model
 
fixInlineString(String, char) - Static method in class org.jmol.viewer.Viewer
 
fixJavaFloat - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
fixKeyDSSR(String) - Method in class org.jmol.dssx.AnnotationParser
 
fixLabel(Atom, String) - Method in class org.jmol.render.HoverRenderer
 
fixLattice() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
fixLegendre() - Method in class org.jmol.adapter.readers.cif.MSRdr
 
fixModelSpec(T) - Method in class org.jmol.script.ScriptTokenParser
 
fixMovieCommands(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
Could possibly implement something here that interprets PyMOL script commands.
fixMovieViews(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
Could implement something here that creates a Jmol view.
fixName(String) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
fixName(String) - Static method in class org.jmol.util.ColorEncoder
 
fixOrbitalType() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
fixOrder(int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
fixOrder(int[], int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
fixPath(String) - Static method in class org.jmol.viewer.FileManager
 
fixPeriodic(P3, P3) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
 
fixPoint(float, float) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
 
fixPropertyValue(BS, Object, boolean) - Method in interface org.jmol.api.JmolBioResolver
 
fixPropertyValue(BS, Object, boolean) - Method in class org.jmol.modelsetbio.Resolver
 
fixRadius(float) - Static method in class org.jmol.adapter.readers.pdb.PdbReader
 
fixReps(BS[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
fixScriptPath(String, String) - Method in class org.jmol.script.ScriptEval
 
fixSettings(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Recent PyMOL files may not have all settings.
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
fixShellTag(String) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
fixSlaterTypes(int, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
fixTag(String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Returns a modified identifier for a tag, so that the element can be determined from it in the Atom.
fixText(String) - Method in class org.jmol.modelset.Text
 
fixTitleLine(int, Map<String, Object>) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
fixTrajectory(Atom) - Method in class org.jmol.modelset.AtomCollection
 
fixTypeOrder(int[], int, int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
fixTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
fixUnits(String) - Static method in class org.jmol.modelset.Measurement
 
fixValue(String, boolean) - Method in class org.jmol.modelset.Measurement
 
fixXY(float, float, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
FLAG_AROMATIC_DEFINED - Static variable in class org.jmol.util.Edge
 
FLAG_AROMATIC_DOUBLE - Static variable in class org.jmol.util.Edge
 
FLAG_AROMATIC_STRICT - Static variable in class org.jmol.util.Edge
 
FLAG_CANINCREMENT - Static variable in class org.jmol.script.SV
 
FLAG_exfoliate - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
FLAG_ignore - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
FLAG_IGNORE_STEREOCHEMISTRY - Static variable in class org.jmol.util.Edge
 
FLAG_inorganic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
FLAG_MASK - Static variable in class org.jmol.modelset.Atom
 
FLAG_MODIFIED - Static variable in class org.jmol.script.SV
 
FLAG_NO_AROMATIC - Static variable in class org.jmol.util.Edge
 
FLAG_no_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
FLAG_NOSURFACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
FLAG_organic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
FLAG_polymer - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
FLAG_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
flags - Variable in class org.jmol.script.SV
 
flags - Variable in class org.jmol.smiles.SmilesParser
 
flags - Variable in class org.jmol.smiles.SmilesSearch
 
flat - Static variable in class org.jmol.script.T
 
FLICK_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
FLICK_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
flipLighting(int) - Method in class org.jmol.shape.Mesh
 
fList - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
flistValue(T, int) - Static method in class org.jmol.script.SV
 
float_labels - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
floatArraySet(int, int, int) - Method in class org.jmol.scriptext.IsoExt
 
floatArraySetXYZ(int, int, int, int) - Method in class org.jmol.scriptext.IsoExt
 
floatAt(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
floatAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
floatparam - Static variable in class org.jmol.script.T
 
floatParameter(int) - Method in class org.jmol.script.ScriptParam
 
floatParameter(int) - Method in class org.jmol.scriptext.CmdExt
 
floatParameterRange(int, float, float) - Method in class org.jmol.script.ScriptParam
 
floatParameterSet(int, int, int) - Method in class org.jmol.script.ScriptParam
process a general string or set of parameters as an array of floats, allowing for relatively free form input
floatproperty - Static variable in class org.jmol.script.T
 
floatRange - Variable in class org.jmol.shapebio.BioShape
 
floats - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
floatsAt(Lst<Object>, int, float[], int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
floatSecondsTotal - Variable in class org.jmol.navigate.Navigator
 
floatSecondsTotal - Variable in class org.jmol.thread.MoveToThread
 
floatSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
floatValue() - Method in class org.jmol.script.ScriptTokenParser
 
flowCommand - Static variable in class org.jmol.script.T
 
flowContext - Variable in class org.jmol.script.ScriptCompiler
 
flush(Object) - Static method in class org.jmol.awt.Image
 
flush(Object) - Static method in class org.jmol.awtjs.Image
 
flushCaches() - Method in class org.jmol.util.Shader
 
flushImage(Object) - Method in class org.jmol.awt.Platform
 
flushImage(Object) - Method in class org.jmol.awtjs.Platform
 
flushImage(Object) - Method in class org.jmol.awtjs2d.Platform
 
flushQueue(String) - Method in class org.jmol.script.ScriptManager
 
fm - Variable in class org.jmol.io.DOMReader
 
fm - Variable in class org.jmol.io.FileReader
 
fm - Variable in class org.jmol.io.FilesReader
 
fm - Variable in class org.jmol.io.JmolBinary
 
fm - Variable in class org.jmol.viewer.Viewer
 
fmt(int) - Method in class org.jmol.applet.Jmol
 
fmt(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
FO_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
foccupancy - Variable in class org.jmol.adapter.smarter.Atom
 
fog - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
fog_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
FoldingXyzReader - Class in org.jmol.adapter.readers.simple
This reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.
FoldingXyzReader() - Constructor for class org.jmol.adapter.readers.simple.FoldingXyzReader
 
font - Variable in class org.jmol.applet.AppletWrapper
 
font - Variable in class org.jmol.g3d.TextString
 
font - Variable in class org.jmol.modelset.Text
 
font - Static variable in class org.jmol.script.T
 
FONT - Static variable in class org.jmol.shapecgo.CGOMesh
 
font3d - Variable in class org.jmol.render.FontLineShapeRenderer
 
font3d - Variable in class org.jmol.shape.FontShape
 
font3d - Variable in class org.jmol.shape.Measures
 
FONT_AXES - Static variable in class org.jmol.shapecgo.CGOMesh
 
FONT_SCALE - Static variable in class org.jmol.shapecgo.CGOMesh
 
FONT_VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
 
fontAscent - Variable in class org.jmol.applet.AppletWrapper
 
fontcaching - Static variable in class org.jmol.script.T
 
fontCaching - Variable in class org.jmol.viewer.GlobalSettings
 
fontFace - Static variable in class org.jmol.applet.AppletWrapper
 
FONTFACE - Static variable in class org.jmol.shape.Echo
 
FONTFACE - Static variable in class org.jmol.shape.Hover
 
fontHeight - Variable in class org.jmol.applet.AppletWrapper
 
FontLineShape - Class in org.jmol.shape
 
FontLineShape() - Constructor for class org.jmol.shape.FontLineShape
 
FontLineShapeRenderer - Class in org.jmol.render
 
FontLineShapeRenderer() - Constructor for class org.jmol.render.FontLineShapeRenderer
 
fontMetrics - Variable in class org.jmol.applet.AppletWrapper
 
fontScale - Variable in class org.jmol.modelset.Object2d
 
fontscaling - Static variable in class org.jmol.script.T
 
fontScaling - Variable in class org.jmol.viewer.GlobalSettings
 
FontShape - Class in org.jmol.shape
 
FontShape() - Constructor for class org.jmol.shape.FontShape
 
fontSize - Variable in class org.jmol.applet.AppletWrapper
 
fontsize - Static variable in class org.jmol.script.T
 
FONTSIZE - Static variable in class org.jmol.shape.Echo
 
FONTSIZE - Static variable in class org.jmol.shape.Hover
 
fontSizeDivisor - Static variable in class org.jmol.applet.AppletWrapper
 
fontStringWidth(Font, String) - Method in class org.jmol.awt.Platform
 
fontStringWidth(Font, String) - Method in class org.jmol.awtjs.Platform
 
fontStringWidth(Font, String) - Method in class org.jmol.awtjs2d.Platform
 
FONTSTYLE - Static variable in class org.jmol.shape.Hover
 
FOOP - Static variable in class org.jmol.minimize.forcefield.MMFFOOPCalc
 
FOOPD - Static variable in class org.jmol.minimize.forcefield.MMFFOOPCalc
 
FOP_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
force - Variable in class org.jmol.minimize.MinAtom
 
forceautobond - Static variable in class org.jmol.script.T
 
forceAutoBond - Variable in class org.jmol.viewer.GlobalSettings
 
forceEndIf - Variable in class org.jmol.script.ScriptFlowContext
 
ForceField - Class in org.jmol.minimize.forcefield
 
ForceField() - Constructor for class org.jmol.minimize.forcefield.ForceField
 
forcefield - Static variable in class org.jmol.script.T
 
forceField - Variable in class org.jmol.viewer.GlobalSettings
 
ForceFieldMMFF - Class in org.jmol.minimize.forcefield
MMFF94 implementation 5/14/2012 - fully validated for atom types and charges - reasonably well validated for energies (see below) - TODO: add UFF for preliminary/backup calculation
ForceFieldMMFF(Minimizer) - Constructor for class org.jmol.minimize.forcefield.ForceFieldMMFF
 
ForceFieldReader - Class in org.jmol.adapter.readers.more
 
ForceFieldReader() - Constructor for class org.jmol.adapter.readers.more.ForceFieldReader
 
ForceFieldUFF - Class in org.jmol.minimize.forcefield
 
ForceFieldUFF(Minimizer) - Constructor for class org.jmol.minimize.forcefield.ForceFieldUFF
 
forceFlowEnd(T) - Method in class org.jmol.script.ScriptCompiler
 
forceNoAddHydrogens - Variable in class org.jmol.script.ScriptEval
 
forcePacked - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
forceSymmetry(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
forcmd - Static variable in class org.jmol.script.T
 
FORMAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
 
FORMAL_CHARGE_MAX - Static variable in class org.jmol.util.Elements
 
FORMAL_CHARGE_MIN - Static variable in class org.jmol.util.Elements
ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
formalCharge - Variable in class org.jmol.adapter.smarter.Atom
 
formalCharge - Variable in class org.jmol.minimize.forcefield.AtomType
 
formalcharge - Static variable in class org.jmol.script.T
 
formalChargeAndFlags - Variable in class org.jmol.modelset.Atom
 
format(float, String, T3) - Method in class org.jmol.modelset.LabelToken
 
format(SV[], int) - Static method in class org.jmol.script.SV
Accepts arguments from the format() function First argument is a format string.
format - Static variable in class org.jmol.script.T
 
formatAngle(float) - Method in class org.jmol.modelset.Measurement
 
formatDistance(String) - Method in class org.jmol.modelset.Measurement
 
formatLabel(Viewer, Atom, String, P3) - Method in class org.jmol.modelset.LabelToken
 
formatLabelAtomArray(Viewer, Atom, LabelToken[], char, int[], P3) - Static method in class org.jmol.modelset.LabelToken
returns a formatted string based on the precompiled label tokens
formatLabelBond(Viewer, Bond, LabelToken[], Map<String, Object>, int[], P3) - Static method in class org.jmol.modelset.LabelToken
 
formatLabelMeasure(Viewer, Measurement, String, float, String) - Static method in class org.jmol.modelset.LabelToken
 
formatMeasurement(String) - Method in class org.jmol.modelset.Measurement
 
formatMeasurementAs(String, String, boolean) - Method in class org.jmol.modelset.Measurement
 
formats - Variable in class org.jmol.shape.Labels
 
formatString(float, String, String) - Method in class org.jmol.modelset.Measurement
 
formatText() - Method in class org.jmol.modelset.Text
 
formatText(JmolViewer, String) - Static method in class org.jmol.util.Txt
 
formul() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
formula - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
forPoint3 - Variable in class org.jmol.script.ScriptCompiler
 
forThermalEllipsoid - Variable in class org.jmol.util.Tensor
 
foundDistance2() - Method in interface org.jmol.api.AtomIndexIterator
 
foundDistance2() - Method in class org.jmol.bspt.CubeIterator
After calling nextElement(), allows one to find out the value of the distance squared.
foundDistance2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
foundDuringLastSync - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
fourdots - Static variable in class org.jmol.render.FontLineShapeRenderer
 
FPAR - Static variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
FPPanel(Map<String, Object>) - Constructor for class org.jmol.dialog.FilePreview.FPPanel
 
fps - Static variable in class org.jmol.script.T
 
fps - Variable in class org.jmol.thread.MoveToThread
 
FPS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for the fps slider.
fpsSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
fracs - Variable in class org.jmol.util.MeshSlicer
 
FRACT_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
FRACT_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
FRACT_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
fractionalOffset - Variable in class org.jmol.symmetry.UnitCell
 
fractionalOrigin - Variable in class org.jmol.util.SimpleUnitCell
 
fractionalPoint - Variable in class org.jmol.script.ScriptParam
 
fractionalrelative - Static variable in class org.jmol.script.T
 
fractionalRelative - Variable in class org.jmol.viewer.GlobalSettings
 
fractionData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
fractionPtr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
fracx - Static variable in class org.jmol.script.T
 
fracxyz - Static variable in class org.jmol.script.T
 
fracy - Static variable in class org.jmol.script.T
 
fracz - Static variable in class org.jmol.script.T
 
frame - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
frame - Static variable in class org.jmol.script.T
 
frame - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
frame - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
FRAME_FIRST - Static variable in class org.jmol.viewer.AnimationManager
 
FRAME_LAST - Static variable in class org.jmol.viewer.AnimationManager
 
frameControl(int) - Method in class org.jmol.script.ScriptEval
 
frameDelay - Variable in class org.jmol.modelset.Model
 
frameObj - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
frameOffset - Variable in class org.jmol.viewer.TransformManager
 
frameOffsets - Variable in class org.jmol.viewer.Viewer
 
framePointer1 - Variable in class org.jmol.thread.AnimationThread
 
framePointer2 - Variable in class org.jmol.thread.AnimationThread
 
frames - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
FramesOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
frameStep - Variable in class org.jmol.viewer.AnimationManager
 
frameTimeMillis - Variable in class org.jmol.navigate.Navigator
 
frameTimeMillis - Variable in class org.jmol.thread.MoveToThread
 
frameTitles - Variable in class org.jmol.modelset.ModelSet
 
frank - Static variable in class org.jmol.script.T
 
Frank - Class in org.jmol.shape
 
Frank() - Constructor for class org.jmol.shape.Frank
 
frankAscent - Variable in class org.jmol.shape.Frank
 
frankClicked(int, int) - Method in class org.jmol.viewer.Viewer
 
frankClickedModelKit(int, int) - Method in class org.jmol.viewer.Viewer
 
frankDescent - Variable in class org.jmol.shape.Frank
 
frankList - Variable in class org.jmol.popup.JmolGenericPopup
 
frankMargin - Static variable in class org.jmol.shape.Frank
 
frankOn - Variable in class org.jmol.viewer.Viewer
 
frankPopup - Variable in class org.jmol.popup.JmolGenericPopup
 
FrankRenderer - Class in org.jmol.render
 
FrankRenderer() - Constructor for class org.jmol.render.FrankRenderer
 
frankString - Variable in class org.jmol.shape.Frank
 
frankWidth - Variable in class org.jmol.shape.Frank
 
freeBonds - Variable in class org.jmol.modelset.BondCollection
 
freeEnum - Variable in class org.jmol.util.TempArray
 
freeEnumSize - Static variable in class org.jmol.util.TempArray
 
freePoints - Variable in class org.jmol.util.TempArray
 
freePointsSize - Static variable in class org.jmol.util.TempArray
 
freeScreens - Variable in class org.jmol.util.TempArray
 
freeScreensSize - Static variable in class org.jmol.util.TempArray
 
freeTempArrays() - Method in class org.jmol.renderbio.BioShapeRenderer
 
freeTempEnum(STR[]) - Method in class org.jmol.util.TempArray
 
freeTempEnum(STR[]) - Method in class org.jmol.viewer.Viewer
 
freeTempPoints(P3[]) - Method in class org.jmol.util.TempArray
 
freeTempPoints(P3[]) - Method in class org.jmol.viewer.Viewer
 
freeTempScreens(P3i[]) - Method in class org.jmol.util.TempArray
 
freeTempScreens(P3i[]) - Method in class org.jmol.viewer.Viewer
 
freeze(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
freeze() - Method in class org.jmol.modelset.Model
 
freeze() - Method in class org.jmol.modelset.ModelLoader
 
freeze() - Method in class org.jmol.modelsetbio.BioModel
 
freezeM() - Method in class org.jmol.modelset.Model
 
freezeModels() - Method in class org.jmol.modelset.ModelSet
 
freqAtom0 - Variable in class org.jmol.adapter.readers.simple.AmpacReader
 
fReturn - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
FRIENDLY - Static variable in class org.jmol.util.ColorEncoder
 
from - Static variable in class org.jmol.script.T
 
front - Static variable in class org.jmol.script.T
 
frontAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
frontedges - Static variable in class org.jmol.script.T
 
frontlit - Static variable in class org.jmol.script.T
 
frontOnly - Variable in class org.jmol.render.MeshRenderer
 
frontOnly - Variable in class org.jmol.renderspecial.PolyhedraRenderer
 
frontonly - Static variable in class org.jmol.script.T
 
frontOnly - Variable in class org.jmol.shape.Mesh
 
frontonly - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
FS - Static variable in class org.jmol.quantum.QS
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.QchemReader
 
FS_LIST - Static variable in class org.jmol.adapter.readers.quantum.WebMOReader
 
fset0 - Variable in class org.jmol.render.UccageRenderer
 
fSpherical - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
fStep - Variable in class org.jmol.thread.MoveToThread
 
FSTRETCH - Static variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
 
FU_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
full - Static variable in class org.jmol.script.T
 
full_screen - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
fullCommand - Variable in class org.jmol.script.ScriptEval
 
fullCommand - Variable in class org.jmol.shapesurface.LcaoCartoon
 
fullCubePolygon - Static variable in class org.jmol.util.TriangleData
 
fullName - Variable in class org.jmol.awtjs2d.JSFile
 
fullName - Variable in class org.jmol.util.GenericApplet
 
fullName - Variable in class org.jmol.viewer.Viewer
 
fullPathName - Variable in class org.jmol.viewer.FileManager
 
fullPathNameIn - Variable in class org.jmol.io.FileReader
 
fullPathNamesIn - Variable in class org.jmol.io.FilesReader
 
fullplane - Static variable in class org.jmol.script.T
 
fullyLit - Variable in class org.jmol.jvxl.readers.Parameters
 
fullylit - Static variable in class org.jmol.script.T
 
func - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
func - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
func - Variable in class org.jmol.jvxl.readers.Parameters
 
function - Variable in class org.jmol.script.ScriptFlowContext
 
function - Static variable in class org.jmol.script.T
 
functionInfo - Variable in class org.jmol.jvxl.readers.Parameters
 
functionName - Variable in class org.jmol.script.ScriptContext
 
functionName - Variable in class org.jmol.script.ScriptEval
 
functionXY(String, int, int) - Method in interface org.jmol.api.JmolStatusListener
for isosurface FUNCTIONXY
functionxy - Static variable in class org.jmol.script.T
 
functionXY(String, int, int) - Method in class org.jmol.util.GenericApplet
 
functionXY(String, int, int) - Method in class org.jmol.viewer.StatusManager
 
functionXY(String, int, int) - Method in class org.jmol.viewer.Viewer
fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.
functionXY(String, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
this is just a test method for isosurface FUNCTIONXY
functionXYZ(String, int, int, int) - Method in interface org.jmol.api.JmolStatusListener
for isosurface FUNCTIONXYZ
functionxyz - Static variable in class org.jmol.script.T
 
functionXYZ(String, int, int, int) - Method in class org.jmol.util.GenericApplet
 
functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.StatusManager
 
functionXYZ(String, int, int, int) - Method in class org.jmol.viewer.Viewer
 
functionXYZ(String, int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
funcType - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
FUP_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
fux - Static variable in class org.jmol.script.T
 
fuxyz - Static variable in class org.jmol.script.T
 
fuy - Static variable in class org.jmol.script.T
 
fuz - Static variable in class org.jmol.script.T
 
fval(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
fValue(T) - Static method in class org.jmol.script.SV
 
FWV_DISP_AXIS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_DISP_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_DISP_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_DISP_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_DISP_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_DISP_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_DISP_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_OCC_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_OCC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_OCC_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_OCC_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_OCC_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_OCC_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_SPIN_AXIS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_SPIN_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_SPIN_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_SPIN_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_SPIN_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_SPIN_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_SPIN_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_U_COS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_U_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_U_MODULUS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_U_PHASE - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_U_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_U_SIN - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_U_TENS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_X - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_Y - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
FWV_Z - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 

G

g - Variable in class org.jmol.g3d.Pixelator
 
g - Variable in class org.jmol.util.Rgb16
 
g - Variable in class org.jmol.viewer.Viewer
 
g1 - Variable in class org.jmol.modelsetbio.BasePair
 
g2 - Variable in class org.jmol.modelsetbio.BasePair
 
g3d - Variable in class org.jmol.g3d.CircleRenderer
 
g3d - Variable in class org.jmol.g3d.CylinderRenderer
 
g3d - Variable in class org.jmol.g3d.HermiteRenderer
 
g3d - Variable in class org.jmol.g3d.LineRenderer
 
g3d - Variable in class org.jmol.g3d.SphereRenderer
 
g3d - Variable in class org.jmol.g3d.TriangleRenderer
 
g3d - Variable in class org.jmol.modelset.AtomCollection
 
g3d - Variable in class org.jmol.render.ShapeRenderer
could be vwr.gdata or an exporter
g3d - Variable in class org.jmol.renderbio.NucleicRenderer
 
g3d - Variable in class org.jmol.renderbio.RocketRenderer
 
g3d - Variable in class org.jmol.viewer.ColorManager
 
G3DRenderer - Interface in org.jmol.g3d
 
GamessReader - Class in org.jmol.adapter.readers.quantum
 
GamessReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessReader
 
gamessUKContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GamessUKReader - Class in org.jmol.adapter.readers.quantum
 
GamessUKReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUKReader
 
gamessUSContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GamessUSReader - Class in org.jmol.adapter.readers.quantum
 
GamessUSReader() - Constructor for class org.jmol.adapter.readers.quantum.GamessUSReader
 
gamma - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gamma - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
gamma - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
gamma - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
gamma - Variable in class org.jmol.jvxl.readers.MapFileReader
 
gamma - Variable in class org.jmol.util.SimpleUnitCell
 
gammaE - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
gammaE - Variable in class org.jmol.util.ModulationSet
 
gammaIinv - Variable in class org.jmol.util.ModulationSet
 
gaussian_b_adjust - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gaussian_b_floor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gaussian_resolution - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gaussianAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
GaussianAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.GaussianAction
 
gaussianContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
gaussianCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
gaussianCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
GaussianDialog - Class in org.openscience.jmol.app.jmolpanel
 
GaussianDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
gaussianDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
gaussianFchkContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GaussianFchkReader - Class in org.jmol.adapter.readers.quantum
Reader for Gaussian fchk files also allows appended frequency info from the log file
GaussianFchkReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
gaussianPtr - Variable in class org.jmol.quantum.MOCalculation
 
GaussianReader - Class in org.jmol.adapter.readers.quantum
Reader for Gaussian 94/98/03/09 output files.
GaussianReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianReader
 
gaussians - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
gaussians - Variable in class org.jmol.quantum.MOCalculation
 
GaussianWfnReader - Class in org.jmol.adapter.readers.quantum
Reader for Gaussian Wfn files -- not implemented yet
GaussianWfnReader() - Constructor for class org.jmol.adapter.readers.quantum.GaussianWfnReader
 
GC - Static variable in class org.jmol.quantum.QS
 
gdata - Variable in class org.jmol.export.___Exporter
 
gdata - Variable in class org.jmol.export.Export3D
 
gdata - Variable in class org.jmol.g3d.HermiteRenderer
 
GData - Class in org.jmol.util
 
GData() - Constructor for class org.jmol.util.GData
It is possible to instantiate this class with no Graphics3D.
gdata - Variable in class org.jmol.viewer.Viewer
 
generalResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
generateAllOperators(HallInfo) - Method in class org.jmol.symmetry.SpaceGroup
 
generateBaseEllipsePrecisely(boolean) - Method in class org.jmol.g3d.CylinderRenderer
 
generateColors(Object[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Set PyMOL "atom-wise" colors -- the colors that are defined initially as element colors but possibly set with the PyMOL 'color' command and are used when representation colors (cartoon, dots, etc.) are not defined (-1).
generateContourData(boolean, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
generateCube() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
generateCube() - Method in class org.jmol.jvxl.readers.IsoMepReader
 
generateCube() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
generateCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
generateCube() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
generateOperatorsFromXyzInfo(String) - Method in class org.jmol.symmetry.SpaceGroup
 
generateOutputForExport(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
for POV-Ray
generateOutputForExport(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
generateRaster(int, int, int, int[], int[], int, Rgb16[]) - Method in class org.jmol.g3d.TriangleRenderer
 
generateResidueSpecCode(T) - Method in class org.jmol.script.ScriptTokenParser
 
generateScene(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Generate the saved scene using file settings preserved here and scene-specific information including frame, view, colors, visibilities, .
generateScene(Map<String, Object>) - Method in interface org.jmol.api.JmolSceneGenerator
 
generateShapes(Object[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Create all Jmol shape objects.
generateSolventCavity() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
generateSolventCube() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
generateSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
generateSurfaceData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
generateVisibilities(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Hide everything, then just make visible the sets of atoms specified in the visibility (i.e.
GenericApplet - Class in org.jmol.util
A collection of all methods necessary for initialization of and communication with the applet, whether it be JavaScript or Java.
GenericApplet() - Constructor for class org.jmol.util.GenericApplet
 
GenericConsole - Class in org.jmol.console
 
GenericConsole() - Constructor for class org.jmol.console.GenericConsole
 
GenericGraphics - Interface in org.jmol.api
 
GenericSwingPopup - Class in org.jmol.popup
 
GenericSwingPopup() - Constructor for class org.jmol.popup.GenericSwingPopup
 
GenericTextArea - Interface in org.jmol.console
 
GenericTextPane() - Constructor for class org.jmol.console.AppletConsole.GenericTextPane
 
GenNBOReader - Class in org.jmol.adapter.readers.quantum
NBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold
GenNBOReader() - Constructor for class org.jmol.adapter.readers.quantum.GenNBOReader
 
Geodesic - Class in org.jmol.util
J2SRequireImport is needed because we use ArrayUtil in a static method
Geodesic() - Constructor for class org.jmol.util.Geodesic
 
geodesicCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
geodesicMap - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
GEOM_BOND_ATOM_SITE_LABEL_1 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
GEOM_BOND_ATOM_SITE_LABEL_2 - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
GEOM_BOND_DISTANCE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
geomBondFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
geometry_export_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
geomOpt - Variable in class org.jmol.adapter.readers.xtal.DmolReader
 
geosurface - Static variable in class org.jmol.script.T
 
GeoSurface - Class in org.jmol.shapespecial
 
GeoSurface() - Constructor for class org.jmol.shapespecial.GeoSurface
 
GeoSurfaceRenderer - Class in org.jmol.renderspecial
 
GeoSurfaceRenderer() - Constructor for class org.jmol.renderspecial.GeoSurfaceRenderer
 
Gesture - Class in org.jmol.viewer
 
Gesture(int, Viewer) - Constructor for class org.jmol.viewer.Gesture
 
gestureServer - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
gestureswipefactor - Static variable in class org.jmol.script.T
 
gestureSwipeFactor - Variable in class org.jmol.viewer.ActionManager
 
get(int) - Method in class org.jmol.java.BS
Returns the value of the bit with the specified index.
get(int) - Method in class org.jmol.util.Int2IntHash
 
get(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
get(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
get2SidedNormix(V3, BS) - Static method in class org.jmol.util.Normix
 
get3(int, int, int) - Method in class org.jmol.awt.AwtColor
 
get3dContour(IsosurfaceMesh, Lst<Object>, float, short) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
get3DStraightness(String, Quat, Quat) - Static method in class org.jmol.modelsetbio.BioPolymer
 
get4(int, int, int, int) - Method in class org.jmol.awt.AwtColor
 
getACDPeakWidth(String) - Method in class org.jmol.jsv.JDXMOLParser
 
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Fetch the action that was created for the given command.
getAction(String) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
getActionCommand() - Method in class org.jmol.popup.AwtSwingComponent
 
getActionFromName(String) - Static method in class org.jmol.viewer.ActionManager
 
getActionName(int) - Static method in class org.jmol.viewer.ActionManager
 
getActions() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
getActions() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getActions() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
getAdditionalHydrogens(BS, boolean, boolean, Lst<Atom>) - Method in class org.jmol.viewer.Viewer
 
getADPMinMax(boolean) - Method in class org.jmol.modelset.Atom
 
getAlignment(int) - Static method in class org.jmol.shape.Labels
 
getAlignmentName(int) - Static method in class org.jmol.viewer.JC
 
getAllAtomInfo(BS) - Method in class org.jmol.viewer.PropertyManager
 
getAllAtoms() - Method in class org.jmol.viewer.Viewer
 
getAllAtomTensors(String) - Method in class org.jmol.modelset.AtomCollection
 
getAllAxes(V3) - Method in class org.jmol.symmetry.PointGroup
 
getAllBondInfo(Object) - Method in class org.jmol.viewer.PropertyManager
 
getAllChainInfo(BS) - Method in class org.jmol.viewer.PropertyManager
 
getAllInfo() - Method in class org.jmol.shape.Measures
 
getAllInfoAsString() - Method in class org.jmol.shape.Measures
 
getAllMolecularDipoles(BS) - Method in class org.jmol.shapespecial.Dipoles
 
getAllowedGestures(int) - Method in class org.jmol.multitouch.ActionManagerMT
 
getAllowedGestures(int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
 
getAllowedGestures(int) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
getAllowJSThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getAllowJSThreads() - Method in class org.jmol.script.ScriptEval
 
getAllPolymerInfo(BS, Map<String, Lst<Map<String, Object>>>, Lst<Map<String, Object>>) - Method in class org.jmol.modelset.Model
 
getAllPolymerInfo(BS, Map<String, Lst<Map<String, Object>>>, Lst<Map<String, Object>>) - Method in class org.jmol.modelsetbio.BioModel
 
getAllPolymerInfo(BS) - Method in class org.jmol.viewer.PropertyManager
 
getAllProperties(SV, String) - Method in class org.jmol.script.ScriptMathProcessor
 
getAllredRochowElectroNeg(int) - Static method in class org.jmol.util.Elements
 
getAllRenderers() - Method in class org.jmol.render.RepaintManager
 
getAllSettings(String) - Method in class org.jmol.viewer.JmolStateCreator
 
getAllSettings(String) - Method in class org.jmol.viewer.StateCreator
 
getAllSettings(String) - Method in class org.jmol.viewer.Viewer
 
getAllVariables() - Method in class org.jmol.viewer.GlobalSettings
 
getAlphasAndExponents() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
getAltLoc() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getAltLoc() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getAltLocCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getAltLocIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
 
getAltLocListInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getAmbientPercent() - Method in class org.jmol.util.GData
 
getAmino() - Method in class org.jmol.util.ColorEncoder
 
getAminoAcidValenceAndCharge(String, String, int[]) - Method in interface org.jmol.api.JmolBioResolver
 
getAminoAcidValenceAndCharge(String, String, int[]) - Method in class org.jmol.modelsetbio.Resolver
returns an array if we have special hybridization or charge
getAnglefromZ() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getAngleRadiansABC(double[], double[], double[]) - Static method in class org.jmol.minimize.Util
 
getAngles() - Method in class org.jmol.minimize.Minimizer
 
getAngleUnits() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getAngleUnitsList() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getAnimationInfo() - Method in class org.jmol.viewer.PropertyManager
 
getAnimRunTimeSeconds() - Method in class org.jmol.viewer.AnimationManager
 
getAnimState(AnimationManager, SB) - Method in class org.jmol.viewer.StateCreator
 
getAnnotationBits(String, int, String) - Method in class org.jmol.modelset.ModelSet
 
getAnnotationInfo(Viewer, SV, String, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
 
getAnnotationInfo(Viewer, SV, String, int, int) - Method in class org.jmol.dssx.AnnotationParser
Get a string report of annotation data
getAnnotationInfo(Object, int) - Method in class org.jmol.viewer.PropertyManager
 
getAnnotationInfo(SV, String, int) - Method in class org.jmol.viewer.Viewer
 
getAnnotationKVPairs(SV, String, String, SB, String, boolean, boolean, int) - Method in class org.jmol.dssx.AnnotationParser
Construct a nice listing for this annotation, including validation
getAnnotationParser() - Method in class org.jmol.viewer.Viewer
 
getAppletDefs(int, String, StringBuilder, JmolInstance) - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
getAppletDefs(int, String, StringBuilder, JmolInstance) - Method in class org.openscience.jmol.app.webexport.ScriptButtons
 
getAppletDefs(int, String, StringBuilder, JmolInstance) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getAppletDocumentBase() - Method in class org.jmol.viewer.FileManager
 
getAppletInfo() - Method in interface org.jmol.api.JmolAppletInterface
 
getAppletInfo() - Method in class org.jmol.applet.AppletWrapper
 
getAppletInfo() - Method in class org.jmol.util.GenericApplet
 
getAppletInfo() - Method in class org.jmol.viewer.PropertyManager
 
getAppletPath(boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getAppropriateRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getArgb(short) - Static method in class org.jmol.util.C
 
getArgb(float) - Method in class org.jmol.util.ColorEncoder
 
getArgb() - Method in class org.jmol.util.Rgb16
 
getArgbFromPalette(float, float, float, int) - Method in class org.jmol.util.ColorEncoder
 
getArgbGreyscale(short) - Static method in class org.jmol.util.C
 
getArgbHbondType(int) - Static method in class org.jmol.util.Edge
 
getArgbMinMax(float, float, float) - Method in class org.jmol.util.ColorEncoder
 
getArgbParam(int) - Method in class org.jmol.script.ScriptParam
 
getArgbParamLast(int, boolean) - Method in class org.jmol.script.ScriptParam
 
getArgbParamOrNone(int, boolean) - Method in class org.jmol.script.ScriptParam
 
getArgbs(int) - Method in interface org.jmol.api.JmolBioResolver
 
getArgbs(int) - Method in class org.jmol.modelsetbio.Resolver
 
getArgbs(int) - Method in class org.jmol.viewer.ColorManager
 
getArguments(String) - Method in class org.jmol.viewer.PropertyManager
 
getAromaticDottedBondMask() - Method in class org.jmol.render.SticksRenderer
 
getArrowScale() - Method in class org.jmol.renderspecial.DrawRenderer
 
getAscent(Object) - Static method in class org.jmol.awt.AwtFont
 
getAscent(Object) - Static method in class org.jmol.awtjs.JSFont
 
getAscent(Object) - Static method in class org.jmol.awtjs2d.JSFont
 
getAssocArray(int) - Method in class org.jmol.script.ScriptExpr
 
getAtom() - Method in class org.jmol.adapter.readers.simple.InputReader
 
getAtom(int) - Method in class org.jmol.modelset.Chain
 
getAtom(int) - Method in class org.jmol.modelset.Measurement
 
getAtom(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getAtomAndStateCount(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Look through all named objects for molecules, counting atoms and also states; see if trajectories are compatible (experimental).
getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in interface org.jmol.api.JmolAnnotationParser
 
getAtomBits(Viewer, String, Object, Map<String, Object>, int, int, BS) - Method in class org.jmol.dssx.AnnotationParser
 
getAtomBits(int, Object) - Method in class org.jmol.script.ScriptExpr
 
getAtomBitSet(Object) - Method in interface org.jmol.api.JmolScriptEvaluator
 
getAtomBitSet(Object) - Method in class org.jmol.script.ScriptEval
a general method to evaluate a string representing an atom set.
getAtomBitSet(Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in interface org.jmol.api.JmolScriptManager
 
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in class org.jmol.script.ScriptManager
 
getAtomBitSetEval(JmolScriptEvaluator, Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitSetVector(int, Object) - Method in interface org.jmol.api.JmolScriptEvaluator
 
getAtomBitSetVector(int, Object) - Method in class org.jmol.script.ScriptEval
just provides a vector list of atoms in a string-based expression
getAtomBitSetVector(Object) - Method in class org.jmol.viewer.Viewer
 
getAtomBitsMaybeDeleted(int, Object) - Method in class org.jmol.modelset.ModelSet
 
getAtomBitsMDa(int, Object) - Method in class org.jmol.modelset.AtomCollection
general unqualified lookup of atom set type
getAtomBitsMDb(int, Object) - Method in class org.jmol.modelset.BondCollection
 
getAtomCollectionReader(String, String, Object, Map<String, Object>, int) - Static method in class org.jmol.adapter.smarter.Resolver
the main method for reading files.
getAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
Get the estimated number of atoms contained in the file.
getAtomCount() - Method in class org.jmol.modelset.ModelLoader
 
getAtomCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getAtomDefs(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
getAtomFromName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomFromOffsetIndex(int) - Method in class org.jmol.modelsetbio.Monomer
 
getAtomGeneral(Atom, int, int) - Method in class org.jmol.adapter.readers.simple.InputReader
 
getAtomGroupQuaternions(BS, int, char) - Method in class org.jmol.modelset.ModelSet
 
getAtomGroupQuaternions(BS, int) - Method in class org.jmol.viewer.Viewer
 
getAtomicAndIsotopeNumber() - Method in class org.jmol.modelset.Atom
 
getAtomicAndIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
 
getAtomicAndIsotopeNumber() - Method in interface org.jmol.util.Node
 
getAtomicCharges() - Method in class org.jmol.modelset.AtomCollection
 
getAtomicMass() - Method in class org.jmol.smiles.SmilesAtom
Returns the atomic mass of the atom.
getAtomicMass(int) - Static method in class org.jmol.util.Elements
 
getAtomicNumber(String) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
getAtomicPotentials(String, String) - Method in class org.jmol.quantum.MepCalculation
 
getAtomicPotentials(BS, BS, String) - Method in class org.jmol.scriptext.IsoExt
 
getAtomicPropertyState(byte, BS) - Method in class org.jmol.viewer.JmolStateCreator
 
getAtomicPropertyState(byte, BS) - Method in class org.jmol.viewer.StateCreator
 
getAtomicPropertyState(SB, byte, BS, String, float[]) - Method in class org.jmol.viewer.Viewer
 
getAtomicPropertyStateBuffer(SB, byte, BS, String, float[]) - Method in class org.jmol.viewer.JmolStateCreator
 
getAtomicPropertyStateBuffer(SB, byte, BS, String, float[]) - Method in class org.jmol.viewer.StateCreator
 
getAtomIdentityInfo(int, Map<String, Object>, P3) - Method in class org.jmol.modelset.AtomCollection
 
getAtomIndex(int) - Method in class org.jmol.adapter.readers.simple.InputReader
 
getAtomIndex(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomIndex(String, int) - Method in class org.jmol.modelset.Group
 
getAtomIndex(int) - Method in class org.jmol.modelset.Measurement
 
getAtomIndex(String, int) - Method in class org.jmol.modelsetbio.Monomer
 
getAtomIndex1() - Method in class org.jmol.modelset.Bond
 
getAtomIndex1() - Method in class org.jmol.smiles.SmilesBond
 
getAtomIndex1() - Method in class org.jmol.util.Edge
 
getAtomIndex2() - Method in class org.jmol.modelset.Bond
 
getAtomIndex2() - Method in class org.jmol.smiles.SmilesBond
 
getAtomIndex2() - Method in class org.jmol.util.Edge
 
getAtomIndexFromAtomNumber(int, BS) - Method in class org.jmol.modelset.AtomCollection
 
getAtomIndexFromAtomNumber(int) - Method in class org.jmol.viewer.Viewer
 
getAtomIndexFromPrimitiveIndex(int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
getAtomIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getAtomIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getAtomIndices(BS) - Method in class org.jmol.modelset.AtomCollection
 
getAtomInfo(int, String, P3) - Method in class org.jmol.modelset.AtomCollection
 
getAtomInfo(int) - Method in class org.jmol.viewer.Viewer
 
getAtomInfoLong(int, P3) - Method in class org.jmol.viewer.PropertyManager
 
getAtomInfoXYZ(int, boolean) - Method in class org.jmol.viewer.Viewer
 
getAtomIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get an AtomIterator for retrieval of all atoms in the file.
getAtomLabel(int, int, int, int, int, boolean, String) - Static method in class org.jmol.smiles.SmilesAtom
 
getAtomList(String) - Method in class org.jmol.minimize.forcefield.Calculations
 
getAtomList(String) - Method in class org.jmol.minimize.forcefield.ForceField
 
getAtomMinMax(BS, BS[]) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getAtomName(String, String) - Static method in class org.jmol.adapter.readers.xtal.MagresReader
combine name and index
getAtomName() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getAtomName() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getAtomName() - Method in class org.jmol.modelset.Atom
 
getAtomName() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomName() - Method in interface org.jmol.util.Node
 
getAtomNames() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getAtomNumber() - Method in class org.jmol.modelset.Atom
 
getAtomPickingMode() - Method in class org.jmol.viewer.ActionManager
 
getAtomPoint(byte) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getAtomPointVector(BS) - Method in class org.jmol.modelset.AtomCollection
 
getAtomPropertiesLike(String) - Static method in class org.jmol.script.T
 
getAtomR0(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getAtomRecordMOL(ModelSet, SB, int, Atom, Quat, P3, P3, boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
 
getAtomResidueInfo(SB, Atom) - Static method in class org.jmol.viewer.PropertyManager
 
getAtoms(BS, boolean, boolean, boolean, boolean, boolean, boolean, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getAtoms(int, Object) - Method in class org.jmol.modelset.ModelSet
general lookup for integer type -- from Eval
getAtomsAndElements(Atom[], BS) - Method in class org.jmol.symmetry.PointGroup
 
getAtomsConnected(float, float, int, BS) - Method in class org.jmol.modelset.ModelSet
 
getAtomSetAtomCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAtomIndex(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetAuxiliaryInfo(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the auxiliary information for a particular atomSet.
getAtomSetAuxiliaryInfoValue(int, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetBondCount(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetCenter(BS) - Method in class org.jmol.modelset.ModelSet
 
getAtomSetCollection(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
Create the AtomSetCollection and return it
getAtomSetCollection(Object) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollection() - Method in interface org.jmol.api.JmolDomReaderInterface
 
getAtomSetCollection() - Method in interface org.jmol.api.JmolFilesReaderInterface
 
getAtomSetCollection() - Method in class org.jmol.io.FileReader
 
getAtomSetCollection() - Method in class org.jmol.io.FilesReader
 
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionAuxiliaryInfo(Object) - Method in class org.jmol.api.JmolAdapter
Get the auxiliary information for this atomSetCollection.
getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
Direct DOM HTML4 page reading; Egon was interested in this at one point.
getAtomSetCollectionFromDOM(Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionFromReader(String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionFromReaderType(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
all in one -- for TestSmarterJmolAdapter
getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]
getAtomSetCollectionFromSet(Object, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
getAtomSetCollectionName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionName(Object) - Method in class org.jmol.api.JmolAdapter
Get the name of the atom set collection, if known.
getAtomSetCollectionOrBufferedReaderFromZip(Viewer, JmolAdapter, InputStream, String, String[], Map<String, Object>, int, boolean) - Method in interface org.jmol.api.JmolZipUtilities
 
getAtomSetCollectionOrBufferedReaderFromZip(JmolAdapter, InputStream, String, String[], Map<String, Object>, boolean) - Method in class org.jmol.io.JmolBinary
A rather complicated means of reading a ZIP file, which could be a single file, or it could be a manifest-organized file, or it could be a Spartan directory.
getAtomSetCollectionOrBufferedReaderFromZip(Viewer, JmolAdapter, InputStream, String, String[], Map<String, Object>, int, boolean) - Method in class org.jmol.io.JmolUtil
 
getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
Read an atomSetCollection object from a bufferedReader and close the reader.
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
primary for String[] or File[] reading -- two options are implemented --- return a set of simultaneously open readers, or return one single collection using a single reader
getAtomSetCollectionReaders(JmolFilesReaderInterface, String[], String[], Map<String, Object>, boolean) - Method in class org.jmol.api.JmolAdapter
Associate an atomSetCollection object with an array of BufferedReader.
getAtomSetCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetCount(Object) - Method in class org.jmol.api.JmolAdapter
Get number of atomSets in the file.
getAtomSetIndex() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getAtomSetIndex() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getAtomSetIndex() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
 
getAtomSetName(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetName(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetName(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the name of an atomSet.
getAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getAtomSetNumber(Object, int) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getAtomSetNumber(Object, int) - Method in class org.jmol.api.JmolAdapter
Get the number identifying each atomSet.
getAtomShapeSetState(Shape, AtomShape[]) - Method in class org.jmol.viewer.JmolStateCreator
 
getAtomShapeSetState(Shape, AtomShape[]) - Method in class org.jmol.viewer.StateCreator
 
getAtomShapeSetState(Shape, AtomShape[]) - Method in class org.jmol.viewer.Viewer
 
getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.JmolStateCreator
 
getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.StateCreator
 
getAtomShapeState(AtomShape) - Method in class org.jmol.viewer.Viewer
 
getAtomShapeValue(int, Group, int) - Method in class org.jmol.viewer.ShapeManager
 
getAtomSite() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getAtomSite() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getAtomSite() - Method in class org.jmol.modelset.Atom
 
getAtomSite() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomSite() - Method in interface org.jmol.util.Node
 
getAtomSiteBS(BS) - Method in class org.jmol.quantum.NMRCalculation
Interaction tensors are not repeated for every possible combination.
getAtomsNearPlane(float, P4) - Method in class org.jmol.modelset.AtomCollection
 
getAtomsNearPt(float, P3) - Method in class org.jmol.viewer.Viewer
 
getAtomsNearPts(float, P3[], BS) - Method in class org.jmol.modelset.AtomCollection
 
getAtomsNearSurface(float, String) - Method in class org.jmol.scriptext.MathExt
 
getAtomsWithin(float, P3, BS, int) - Method in class org.jmol.modelset.ModelSet
 
getAtomsWithinRadius(float, BS, boolean, RadiusData) - Method in class org.jmol.modelset.ModelSet
Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms
getAtomSymmetry(Atom, SymmetryInterface) - Method in class org.jmol.adapter.readers.cif.MSRdr
When applying symmetry, this method allows us to use a set of symmetry operators unique to this particular atom -- or in this case, to its subsystem.
getAtomSymmetry(Atom, SymmetryInterface) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getAtomTensor(int, String) - Method in class org.jmol.modelset.AtomCollection
 
getAtomTensorList(int) - Method in class org.jmol.modelset.AtomCollection
 
getAtomType() - Method in class org.jmol.modelset.Atom
 
getAtomType() - Method in class org.jmol.smiles.SmilesAtom
 
getAtomType() - Method in interface org.jmol.util.Node
 
getAtomTypeDescriptions() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getAtomTypeDescs(int[]) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getAtomTypes() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getAtomTypes() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
getAtomTypes() - Method in class org.jmol.modelset.AtomCollection
 
getAtomUniqueID1() - Method in class org.jmol.adapter.smarter.BondIterator
 
getAtomUniqueID1() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getAtomUniqueID2() - Method in class org.jmol.adapter.smarter.BondIterator
 
getAtomUniqueID2() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getAtomValidation(Viewer, String, Atom) - Method in interface org.jmol.api.JmolAnnotationParser
 
getAtomValidation(Viewer, String, Atom) - Method in class org.jmol.dssx.AnnotationParser
Get all validation values corresponding to a specific validation type.
getAtomValidation(String, Atom) - Method in class org.jmol.viewer.Viewer
 
getAttached(Atom, int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getAttachedAtomForPDBH(String, String) - Method in class org.jmol.dssx.AnnotationParser
Finds the standard attached heavy atom for a PDB H atom; used in EBI clash validation.
getAttr(String, String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
getAttribute(String, String) - Method in interface org.jmol.api.JmolJDXMOLParser
 
getAttribute(String, String) - Method in class org.jmol.jsv.JDXMOLParser
 
getAuxiliaryFileData() - Method in class org.jmol.export._IdtfExporter
 
getAuxiliaryFileData() - Method in class org.jmol.export._PovrayExporter
 
getAuxiliaryInfo(BS) - Method in class org.jmol.modelset.ModelSet
 
getAuxiliaryInfo(Object) - Method in class org.jmol.viewer.PropertyManager
 
getAverageAtomPoint() - Method in class org.jmol.modelset.ModelSet
 
getAxesLengths() - Method in class org.jmol.util.ModulationSet
 
getAxisEndPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getAxisPoint(int, boolean) - Method in class org.jmol.shape.Axes
 
getAxisPoints() - Method in class org.jmol.viewer.Viewer
 
getAxisStartPoint() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getBackgroundArgb() - Method in class org.jmol.api.JmolViewer
 
getBackgroundArgb() - Method in class org.jmol.viewer.Viewer
 
getBaseModelBitSet() - Method in class org.jmol.viewer.Viewer
 
getBaseModelIndex(int) - Method in interface org.jmol.api.JmolJSpecView
 
getBaseModelIndex(int) - Method in class org.jmol.jsv.JSpecView
 
getBasePairBits(ModelSet, String) - Method in class org.jmol.modelset.Model
 
getBasePairBits(ModelSet, String) - Method in class org.jmol.modelsetbio.BioModel
 
getBasePairInfo(BS) - Method in class org.jmol.viewer.PropertyManager
 
getBasePairs() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getBaseRing6Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getBaseSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
Get the symmetry that was in place prior to any supercell business
getBBoxVertices() - Method in class org.jmol.modelset.ModelSet
 
getBfactor() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getBfactor() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getBfactor100() - Method in class org.jmol.modelset.Atom
 
getBfactor100Hi() - Method in class org.jmol.modelset.AtomCollection
 
getBfactor100Lo() - Method in class org.jmol.modelset.AtomCollection
 
getBFactors() - Method in class org.jmol.modelset.AtomCollection
 
getBgContrast(int) - Static method in class org.jmol.util.C
 
getBindingInfo(String) - Method in class org.jmol.viewer.ActionManager
 
getBindingInfo(String[], String[], String) - Method in class org.jmol.viewer.binding.Binding
 
getBindingInfo(String) - Method in class org.jmol.viewer.Viewer
 
getBindings() - Method in class org.jmol.viewer.binding.Binding
 
getBioBranches(Lst<BS>) - Method in class org.jmol.modelset.Model
 
getBioBranches(Lst<BS>) - Method in class org.jmol.modelsetbio.BioModel
 
getBioModel(int, int, String, Properties, Map<String, Object>) - Method in interface org.jmol.api.JmolBioResolver
 
getBioModel(int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelsetbio.Resolver
 
getBioPolymer(int) - Method in class org.jmol.modelsetbio.BioModel
 
getBioPolymerCount() - Method in class org.jmol.modelset.Model
 
getBioPolymerCount() - Method in class org.jmol.modelsetbio.BioModel
 
getBioPolymerCountInModel(ModelSet, int) - Method in class org.jmol.modelset.Model
 
getBioPolymerCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getBioPolymerCountInModel(ModelSet, int) - Method in class org.jmol.modelsetbio.BioModel
 
getBioPolymerIndexInModel() - Method in class org.jmol.modelset.Group
 
getBioPolymerIndexInModel() - Method in class org.jmol.modelsetbio.Monomer
 
getBioPolymerLength() - Method in class org.jmol.modelset.Group
 
getBioPolymerLength() - Method in class org.jmol.modelsetbio.Monomer
 
getBioShape(int) - Method in class org.jmol.shapebio.BioShapeCollection
 
getBioSmiles(BNode[], int, BS, boolean, boolean, String) - Method in class org.jmol.smiles.SmilesGenerator
 
getBioStructureTypeName(boolean) - Method in enum org.jmol.c.STR
 
getBioStructureTypeName() - Method in class org.jmol.modelset.Atom
 
getBioStructureTypeName() - Method in class org.jmol.smiles.SmilesAtom
 
getBioStructureTypeName() - Method in interface org.jmol.util.BNode
 
getBitSet(SV, boolean) - Static method in class org.jmol.script.SV
 
getBitSetForMF(Atom[], BS, String) - Static method in class org.jmol.util.JmolMolecule
 
getBitsetIdent(BS, String, Object, boolean, int, boolean) - Method in interface org.jmol.script.JmolCmdExtension
 
getBitsetIdent(BS, String, Object, boolean, int, boolean) - Method in class org.jmol.scriptext.CmdExt
 
getBitsetProperty(BS, int, P3, P4, Object, Object, boolean, int, boolean) - Method in class org.jmol.script.ScriptExpr
 
getBitsetPropertyFloat(BS, int, float, float) - Method in class org.jmol.script.ScriptExpr
 
getBitsetPropertySelector(int, boolean, boolean) - Method in class org.jmol.script.ScriptExpr
 
getBitSetTrajectories() - Method in class org.jmol.modelset.ModelSet
 
getBond(Atom) - Method in class org.jmol.modelset.Atom
 
getBond(int) - Method in class org.jmol.smiles.SmilesAtom
Returns the bond at index number.
getBondColix1(int) - Method in class org.jmol.modelset.BondCollection
 
getBondColix2(int) - Method in class org.jmol.modelset.BondCollection
 
getBondCount() - Method in class org.jmol.modelset.Model
 
getBondCount() - Method in class org.jmol.smiles.SmilesAtom
 
getBondCountInModel(int) - Method in class org.jmol.modelset.BondCollection
for general use
getBondCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getBondDipoles() - Method in class org.jmol.shapespecial.Dipoles
 
getBondedAtomIndex(int) - Method in class org.jmol.modelset.Atom
 
getBondedAtomIndex(int) - Method in class org.jmol.smiles.SmilesAtom
 
getBondedAtomIndex(int) - Method in interface org.jmol.util.Node
 
getBondedAtomIndexes() - Method in class org.jmol.minimize.MinAtom
 
getBondIndex(int) - Method in class org.jmol.minimize.MinAtom
 
getBondInfo(JmolAdapter, String, Object) - Method in class org.jmol.modelsetbio.Resolver
 
getBondInfo(int, P3) - Method in class org.jmol.viewer.PropertyManager
 
getBondingRadFromTable(int, int, short[]) - Static method in class org.jmol.util.Elements
 
getBondingRadii() - Method in class org.jmol.modelset.AtomCollection
 
getBondingRadius(int, int) - Static method in class org.jmol.api.JmolAdapter
 
getBondingRadius() - Method in class org.jmol.modelset.Atom
 
getBondingRadius(int, int) - Static method in class org.jmol.util.Elements
This method is used by: (1) the CIF reader to create molecular systems when no bonding information is present (2) Atom.getBondingRadiusFloat, used by AtomCollection.findMaxRadii and getWorkingRadius, BondCollection.deleteConnections, ModelCollection.autoBond and makeConnections (3) the MMFF minimizer for unidentified atoms In terms of bondingVersion, the critical ones are the first two.
getBondIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getBondIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get a BondIterator for retrieval of all bonds in the file.
getBondIterator(BS) - Method in class org.jmol.modelset.BondCollection
 
getBondIteratorForType(int, BS) - Method in class org.jmol.modelset.BondCollection
 
getBondLabelValues() - Static method in class org.jmol.modelset.LabelToken
 
getBondList(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create the bond set.
getBondList() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getBondList(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getBondList(Object) - Method in class org.jmol.api.JmolAdapter
 
getBondNotTo(SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesAtom
 
getBondOrder(String) - Method in class org.jmol.adapter.readers.cif.CifReader
 
getBondOrderFromFloat(float) - Static method in class org.jmol.util.Edge
 
getBondOrderFromString(String) - Static method in class org.jmol.script.ScriptParam
 
getBondOrderFromString(String) - Static method in class org.jmol.util.Edge
 
getBondOrderFull(float, float, float, float, float) - Static method in class org.jmol.modelset.BondCollection
 
getBondOrderNameFromOrder(int) - Static method in class org.jmol.util.Edge
 
getBondOrderNumberFromOrder(int) - Static method in class org.jmol.util.Edge
used for formatting labels and in the connect PARTIAL command
getBondOrderString(int) - Static method in class org.jmol.smiles.SmilesBond
 
getBondPicking() - Method in class org.jmol.viewer.Viewer
 
getBondRecordMOL(SB, int, Bond, int[], boolean, boolean) - Method in class org.jmol.viewer.PropertyManager
 
getBonds() - Method in class org.jmol.minimize.Minimizer
 
getBondsForSelectedAtoms(BS, boolean) - Method in class org.jmol.modelset.BondCollection
 
getBondsForSelectedAtoms(BS) - Method in class org.jmol.viewer.Viewer
 
getBondState(Shape, BS, boolean) - Method in class org.jmol.viewer.JmolStateCreator
 
getBondState(Shape, BS, boolean) - Method in class org.jmol.viewer.StateCreator
 
getBondState(Shape, BS, boolean) - Method in class org.jmol.viewer.Viewer
 
getBondStereochemistry(Edge, Node) - Method in class org.jmol.smiles.SmilesGenerator
Retrieves the saved character based on the index of the bond.
getBondTo(int) - Method in class org.jmol.minimize.MinAtom
 
getBondTo(SmilesAtom) - Method in class org.jmol.smiles.SmilesAtom
if atom is null, return bond TO this atom (bond.atom2 == this) otherwise, return bond connecting this atom with that atom
getBondType(Bond, AtomType, AtomType, int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getBondType() - Method in class org.jmol.smiles.SmilesBond
 
getBondTypeFromCode(char) - Static method in class org.jmol.smiles.SmilesBond
 
getBoolean(int) - Method in class org.jmol.api.JmolViewer
 
getBoolean(boolean) - Static method in class org.jmol.script.SV
 
getBoolean(int) - Method in class org.jmol.viewer.Viewer
 
getBooleanProperty(String) - Method in class org.jmol.api.JmolViewer
 
getBooleanProperty(String) - Method in class org.jmol.viewer.Viewer
 
getBooleanValue(String, boolean) - Method in class org.jmol.util.GenericApplet
 
getBoundBox(SV) - Method in class org.jmol.script.ScriptMathProcessor
 
getBoundBoxCenter() - Method in class org.jmol.api.JmolViewer
 
getBoundBoxCenter(int) - Method in class org.jmol.modelset.ModelSet
 
getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
 
getBoundBoxCenter() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCenterX() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCenterY() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxCommand(boolean) - Method in class org.jmol.modelset.ModelSet
 
getBoundBoxCornerVector() - Method in class org.jmol.api.JmolViewer
 
getBoundBoxCornerVector() - Method in class org.jmol.modelset.ModelSet
 
getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
 
getBoundBoxCornerVector() - Method in class org.jmol.viewer.Viewer
 
getBoundBoxInfo() - Method in class org.jmol.viewer.PropertyManager
 
getBoundBoxOrientation(int, BS) - Method in class org.jmol.modelset.ModelSet
 
getBoundBoxPoints(boolean) - Method in class org.jmol.util.BoxInfo
 
getBoundBoxVertices() - Method in class org.jmol.util.BoxInfo
 
getBoundingBox() - Method in class org.jmol.shape.Mesh
 
getBoundingBox() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getBox(int) - Method in class org.jmol.shape.Labels
 
getBoxInfo(BS, float) - Method in class org.jmol.modelset.ModelSet
 
getBoxVec() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getBPData(int, String, boolean) - Method in class org.jmol.dssx.AnnotationParser
 
getBranch2dZ(int, int, BS, BS, V3, V3, V3) - Method in class org.jmol.modelset.ModelLoader
 
getBranchBitSet(Node[], int, BS, Lst<BS>, int, boolean, boolean) - Static method in class org.jmol.util.JmolMolecule
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself, deliver the set of atoms constituting this branch.
getBranchBitSet(int, int, boolean) - Method in class org.jmol.viewer.Viewer
 
getBreakableContext(int) - Method in class org.jmol.script.ScriptFlowContext
 
getBrickValue(int) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
getBridge(int[][][][], int, int, int, int, Lst<Bridge>, Atom, Atom, AminoPolymer, AminoPolymer, Map<String, Boolean>, boolean) - Method in class org.jmol.dssx.DSSP
 
getBridges(int[][][][]) - Method in class org.jmol.dssx.DSSP
(p.
getBS(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getBsAtoms(Lst<Object>, int[], BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getBsBranches(float[]) - Method in class org.jmol.modelset.ModelSet
 
getBsOK() - Method in class org.jmol.quantum.NciCalculation
grid-based discrete SCF calculation needs to know which atoms to consider inter and which intramolecular
getBsReps(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getBSSideChain() - Method in class org.jmol.modelset.Group
 
getBSSideChain() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getBsSurfaceClone() - Method in interface org.jmol.api.JmolEnvCalc
 
getBsSurfaceClone() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getBufferedFileInputStream(String) - Static method in class org.jmol.awt.AwtFile
 
getBufferedFileInputStream(String) - Method in class org.jmol.awt.Platform
 
getBufferedFileInputStream(String) - Method in class org.jmol.awtjs2d.Platform
 
getBufferedInputStream(String) - Method in interface org.jmol.atomdata.AtomDataServer
 
getBufferedInputStream(String) - Method in class org.jmol.viewer.FileManager
 
getBufferedInputStream(String) - Method in class org.jmol.viewer.Viewer
 
getBufferedInputStreamOrErrorMessageFromName(String, String, boolean, boolean, byte[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getBufferedReader(String) - Method in class org.jmol.minimize.forcefield.ForceField
 
getBufferedReaderForResource(Viewer, Object, String, String) - Static method in class org.jmol.io.JmolBinary
 
getBufferedReaderOrBinaryDocument(int, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
 
getBufferedReaderOrBinaryDocument(int, boolean) - Method in class org.jmol.io.FilesReader
called by SmartJmolAdapter to request another buffered reader or binary document, rather than opening all the readers at once.
getBufferedReaderOrErrorMessageFromName(String, String[], boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getBufferedReaderOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
 
getButtonGroup() - Method in class org.jmol.popup.AwtSwingPopupHelper
 
getButtonGroup() - Method in class org.jmol.popup.JSSwingPopupHelper
 
getButtonGroup() - Method in interface org.jmol.popup.PopupHelper
 
getButtonMods(int) - Static method in class org.jmol.viewer.binding.Binding
 
getC1P() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getC2() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getC4P() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getCachedAnnotationMap(int, String, Object) - Method in class org.jmol.modelset.ModelSet
 
getCachedPngjBytes(JmolBinary, String) - Method in interface org.jmol.api.JmolZipUtilities
 
getCachedPngjBytes(String) - Method in class org.jmol.io.JmolBinary
 
getCachedPngjBytes(JmolBinary, String) - Method in class org.jmol.io.JmolUtil
 
getCallback(String) - Static method in enum org.jmol.c.CBK
 
getCameraDepth() - Method in class org.jmol.viewer.TransformManager
 
getCameraFactors() - Method in class org.jmol.viewer.TransformManager
This method returns data needed by the VRML, X3D, and IDTF/U3D exporters.
getCameraPosition() - Method in class org.jmol.export.__CartesianExporter
 
getCanonicalCopy(float, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getCanonicalCopy(float, boolean) - Method in class org.jmol.symmetry.Symmetry
 
getCanonicalCopy(float, boolean) - Method in class org.jmol.symmetry.UnitCell
 
getCanonicalCopy(float) - Method in class org.jmol.util.BoxInfo
 
getCanonicalCopy(P3[], float) - Static method in class org.jmol.util.BoxInfo
 
getCanonicalName(String) - Method in class org.jmol.viewer.FileManager
 
getCanonicalSeitzList() - Method in class org.jmol.symmetry.SpaceGroup
 
getCapOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getCapSlabInfo(String) - Method in class org.jmol.shapesurface.Isosurface
 
getCapSlabObject(int, boolean) - Method in class org.jmol.scriptext.IsoExt
 
getCapSlabObject(String, boolean) - Method in class org.jmol.shapesurface.Isosurface
legacy -- for some scripts with early isosurface slabbing
getCarbonylCarbonAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCarbonylOxygenAtom() - Method in class org.jmol.modelset.Group
 
getCarbonylOxygenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getCaretPosition() - Method in interface org.jmol.console.GenericTextArea
 
getCartesianOffset() - Method in interface org.jmol.api.SymmetryInterface
 
getCartesianOffset() - Method in class org.jmol.symmetry.Symmetry
 
getCartesianOffset() - Method in class org.jmol.symmetry.UnitCell
 
getCartoonType(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getCartoonType(int) - Method in interface org.jmol.api.PymolAtomReader
 
getCel() - Method in class org.jmol.util.GData
 
getCellRange() - Method in interface org.jmol.api.SymmetryInterface
 
getCellRange() - Method in class org.jmol.symmetry.Symmetry
 
getCellTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this
getCellWeight(P3) - Static method in class org.jmol.util.SimpleUnitCell
calculate weighting of 1 (interior), 0.5 (face), 0.25 (edge), or 0.125 (vertex)
getCellWeights(BS) - Method in class org.jmol.modelset.ModelSet
 
getCelPower() - Method in class org.jmol.util.GData
 
getCenter() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.modelset.ModelSet
 
getCenterAndPoints(Lst<Object[]>, boolean) - Method in class org.jmol.viewer.Viewer
 
getCenters() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getCenterText() - Method in class org.jmol.viewer.TransformManager
 
getCEState(ColorEncoder, SB) - Method in class org.jmol.viewer.StateCreator
 
getChain() - Method in class org.jmol.modelset.Atom
 
getChain(int) - Method in class org.jmol.modelset.Model
 
getChainAt(int) - Method in class org.jmol.modelset.Model
 
getChainBits(int) - Method in class org.jmol.modelset.AtomCollection
 
getChainCount(boolean) - Method in class org.jmol.modelset.Model
 
getChainCountInModelWater(int, boolean) - Method in class org.jmol.modelset.ModelSet
 
getChainID() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getChainID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getChainID() - Method in class org.jmol.modelset.Atom
 
getChainID() - Method in class org.jmol.smiles.SmilesAtom
 
getChainID() - Method in interface org.jmol.util.BNode
 
getChainID(String, boolean) - Method in class org.jmol.viewer.Viewer
Create a unique integer for any chain string.
getChainIDStr() - Method in class org.jmol.modelset.Atom
 
getChainIDStr() - Method in class org.jmol.smiles.SmilesAtom
 
getChainIDStr() - Method in interface org.jmol.util.BNode
 
getChainIDStr(int) - Method in class org.jmol.viewer.Viewer
 
getChainInfo(int, BS) - Method in class org.jmol.viewer.PropertyManager
 
getChangeableColix(int, int) - Method in class org.jmol.util.GData
 
getChangeableColixIndex(short) - Static method in class org.jmol.util.C
 
getChar(String, int) - Static method in class org.jmol.smiles.SmilesParser
 
getCharge() - Method in class org.jmol.smiles.SmilesAtom
Returns the charge of the atom.
getCharges() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getCheckBox(String, Map<Object, SC>) - Static method in class org.jmol.popup.AwtSwingComponent
 
getCheckBox(String) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
getCheckBox(String) - Method in class org.jmol.popup.JSSwingPopupHelper
 
getCheckBox(String) - Method in interface org.jmol.popup.PopupHelper
 
getChemicalInfo(String, T) - Method in class org.jmol.viewer.Viewer
 
getChemicalShift(Atom) - Method in interface org.jmol.api.JmolNMRInterface
If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shielding
getChemicalShift(Atom) - Method in class org.jmol.quantum.NMRCalculation
 
getChimeInfo(int, BS) - Method in interface org.jmol.api.JmolPropertyManager
 
getChimeInfo(SB, int) - Method in class org.jmol.modelset.Model
 
getChimeInfo(SB, int) - Method in class org.jmol.modelsetbio.BioModel
 
getChimeInfo(int, BS) - Method in class org.jmol.viewer.PropertyManager
 
getChimeInfo(int) - Method in class org.jmol.viewer.Viewer
 
getChimeInfoA(Atom[], int, BS) - Method in class org.jmol.viewer.PropertyManager
 
getChimeInfoM(SB, int) - Method in class org.jmol.modelset.Model
 
getChiralClass() - Method in class org.jmol.smiles.SmilesAtom
Returns the chiral class of the atom.
getChiralityClass(String) - Static method in class org.jmol.smiles.SmilesAtom
 
getChiralOrder() - Method in class org.jmol.smiles.SmilesAtom
Returns the chiral order of the atom.
getCifData(int) - Method in class org.jmol.viewer.Viewer
 
getCircleData() - Static method in class org.jmol.export.MeshData
Calculates the data (faces, vertices, normals) for a circle.
getCircleResource() - Method in class org.jmol.export._IdtfExporter
 
getClassifiedName(String, boolean) - Method in class org.jmol.viewer.FileManager
[0] and [2] may return same as [1] in the case of a local unsigned applet.
getClickableSet(boolean) - Method in class org.jmol.modelset.AtomCollection
 
getClickCount(int) - Static method in class org.jmol.viewer.binding.Binding
 
getClipboardText() - Method in class org.jmol.api.JmolViewer
 
getClipboardText() - Static method in class org.jmol.awt.AwtClipboard
Get the String residing on the clipboard.
getClipboardText() - Method in class org.jmol.viewer.OutputManager
 
getClipboardText() - Method in class org.jmol.viewer.OutputManagerAwt
 
getClipboardText() - Method in class org.jmol.viewer.OutputManagerJS
 
getClipboardText() - Method in class org.jmol.viewer.Viewer
 
getClone() - Method in class org.jmol.adapter.smarter.Atom
 
getCmd(int) - Method in class org.jmol.shapesurface.Isosurface
 
getCmdExt() - Method in class org.jmol.script.ScriptExpr
 
getCmlBondOrder(int) - Static method in class org.jmol.util.Edge
 
getCode() - Method in enum org.jmol.c.FIL
 
getCodeFromName(String) - Static method in enum org.jmol.util.Edge.EnumBondOrder
 
getColix(int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getColix() - Method in class org.jmol.adapter.smarter.BondIterator
 
getColix() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getColix(boolean) - Method in class org.jmol.rendercgo.CGORenderer
 
getColix(short[], int, Atom) - Static method in class org.jmol.shape.Shape
 
getColix(int) - Static method in class org.jmol.util.C
 
getColix2(int, Atom, boolean) - Method in class org.jmol.shape.Labels
 
getColixA(short, byte, Atom) - Method in class org.jmol.shape.Shape
 
getColixArray(String) - Static method in class org.jmol.util.C
 
getColixAtomPalette(Atom, byte) - Method in class org.jmol.viewer.ColorManager
 
getColixB(short, int, Bond) - Method in class org.jmol.shape.Shape
 
getColixBondPalette(Bond, int) - Method in class org.jmol.viewer.ColorManager
 
getColixI(short, byte, int) - Method in class org.jmol.shape.Shape
 
getColixInherited(short, short) - Static method in class org.jmol.util.C
 
getColixO(Object) - Static method in class org.jmol.util.C
 
getColixS(String) - Static method in class org.jmol.util.C
 
getColixTranslucencyFractional(short) - Static method in class org.jmol.util.C
 
getColixTranslucencyLabel(short) - Static method in class org.jmol.util.C
 
getColixTranslucencyLevel(short) - Static method in class org.jmol.util.C
 
getColixTranslucent(int) - Static method in class org.jmol.util.C
 
getColixTranslucent3(short, boolean, float) - Static method in class org.jmol.util.C
 
getColor() - Method in enum org.jmol.c.STR
 
getColor(short) - Method in class org.jmol.export.JSExporter
 
getColor(String) - Static method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getColor(String) - Method in class org.jmol.jvxl.readers.KinemageReader
 
getColor1(int) - Method in interface org.jmol.api.GenericGraphics
 
getColor1(int) - Method in class org.jmol.awt.AwtG2D
 
getColor1(int) - Method in class org.jmol.awtjs2d.JsG2D
 
getColor3(int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
getColor3(int, int, int) - Method in class org.jmol.awt.AwtG2D
 
getColor3(int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
getColor4(int, int, int, int) - Method in interface org.jmol.api.GenericGraphics
 
getColor4(int, int, int, int) - Method in class org.jmol.awt.AwtG2D
 
getColor4(int, int, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
getColorArgbOrGray(short) - Method in class org.jmol.util.GData
 
getColorCommand(String, byte, short, boolean) - Static method in class org.jmol.shape.Shape
 
getColorCommandUnk(String, short, boolean) - Static method in class org.jmol.shape.Shape
 
getColorEncoder(String) - Method in class org.jmol.viewer.ColorManager
 
getColorFromName(String) - Method in class org.jmol.applet.AppletWrapper
 
getColorIndex(float) - Method in class org.jmol.util.ColorEncoder
 
getColorIndexFromPalette(float, float, float, int, boolean) - Method in class org.jmol.util.ColorEncoder
 
getColorKey() - Method in class org.jmol.util.ColorEncoder
 
getColorList(int, short[], int, BS, Map<Short, Integer>) - Method in class org.jmol.export.___Exporter
input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color index
getColorPhaseIndex(String) - Static method in class org.jmol.jvxl.readers.SurfaceReader
 
getColorPointForPropertyValue(float) - Method in class org.jmol.viewer.Viewer
 
getColorPt(Object) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getColorRange(int) - Method in class org.jmol.script.ScriptEval
 
getColors(short[]) - Method in class org.jmol.export.JSExporter
 
getColorScheme() - Method in class org.jmol.util.ColorEncoder
 
getColorSchemeArray(int) - Method in class org.jmol.util.ColorEncoder
 
getColorSchemeList(int[]) - Static method in class org.jmol.util.ColorEncoder
 
getColorSchemeList(String) - Method in class org.jmol.viewer.ColorManager
 
getColorSchemeName(int) - Method in class org.jmol.util.ColorEncoder
 
getColorState(ColorManager, SB) - Method in class org.jmol.viewer.StateCreator
 
getColorTrans(ScriptEval, int, boolean, int[]) - Method in class org.jmol.scriptext.CmdExt
Checks color, translucent, opaque parameters.
getColorTriad(int) - Method in class org.jmol.script.ScriptParam
 
getColumnClass(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getColumnCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getColumnName(int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getCommand(int, boolean, boolean) - Method in class org.jmol.script.ScriptEval
used for recall of commands in the application console
getCommand(Mesh) - Method in class org.jmol.shapespecial.Draw
 
getCommand() - Method in class org.jmol.util.CommandHistory
Calculates the command to return.
getCommand(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
getCommand2(Mesh, int) - Method in class org.jmol.shapecgo.CGO
 
getCommand2(Mesh, int) - Method in class org.jmol.shapespecial.Draw
 
getCommandDown() - Method in class org.jmol.util.CommandHistory
Retrieves the following command from the top of the list, updates list position.
getCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Generates a commandline from the options set for povray path etc and sets in the textField.
getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.JmolStateCreator
 
getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.StateCreator
 
getCommands(Map<String, BS>, Map<String, BS>, String) - Method in class org.jmol.viewer.Viewer
 
getCommands2(Map<String, BS>, SB, String, String) - Method in class org.jmol.viewer.StateCreator
 
getCommandSet(String) - Static method in class org.jmol.script.T
retrieves an unsorted list of viable commands that could be completed by this initial set of characters.
getCommandString() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
getCommandString() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
getCommandUp() - Method in class org.jmol.util.CommandHistory
Retrieves the following command from the bottom of the list, updates list position.
getComparison(T, int, int, String, float[]) - Method in class org.jmol.script.ScriptExpr
 
getComponent(int) - Method in class org.jmol.popup.AwtSwingComponent
 
getComponentCount() - Method in class org.jmol.popup.AwtSwingComponent
 
getComponents() - Method in class org.jmol.popup.AwtSwingComponent
 
getConeData() - Static method in class org.jmol.export.MeshData
Calculates the data (faces, vertices, normals) for a cone.
getConeMesh(P3, M3, short) - Static method in class org.jmol.export.___Exporter
 
getConeResource() - Method in class org.jmol.export._IdtfExporter
 
getConformation(int, int, boolean) - Method in class org.jmol.modelset.ModelSet
 
getConformation(BS, int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getConformation(Atom[], BS, int) - Method in class org.jmol.modelsetbio.Monomer
clear out bits that are not associated with the nth conformation counting for each residue from the beginning of the file listing
getConnectionPoints() - Method in class org.jmol.renderspecial.DrawRenderer
 
getConstraintList() - Method in class org.jmol.minimize.forcefield.Calculations
 
getContext(boolean) - Method in class org.jmol.scriptext.CmdExt
 
getContext(String) - Method in class org.jmol.viewer.StateManager
 
getContextTrace(Viewer, ScriptContext, SB, boolean) - Static method in class org.jmol.script.ScriptEval
 
getContextVariableAsVariable(String) - Method in class org.jmol.script.ScriptParam
 
getContextVariables() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getContextVariables() - Method in class org.jmol.script.ScriptEval
 
getContextVariables() - Method in class org.jmol.viewer.Viewer
 
getContourList(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getContourPoint(T3[], int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
getContourPoint(T3[], int, int, float) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
getContours() - Method in class org.jmol.shapesurface.IsosurfaceMesh
create a set of contour data.
getContractionNormalization(int, int) - Method in class org.jmol.quantum.MOCalculation
 
getContrastingBlackOrWhite(Color) - Method in class org.jmol.applet.AppletWrapper
 
getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
getControlPoint(int, V3) - Method in class org.jmol.modelsetbio.BioPolymer
 
getControlPoints(boolean, float, boolean) - Method in class org.jmol.modelsetbio.BioPolymer
 
getControlPoints2(float) - Method in class org.jmol.modelsetbio.BioPolymer
 
getCoord(int) - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
getCoordinateMap(T3[], int[], BS) - Method in class org.jmol.export.__CartesianExporter
 
getCoordinatesAreFractional() - Method in interface org.jmol.api.SymmetryInterface
 
getCoordinatesAreFractional() - Method in class org.jmol.symmetry.Symmetry
 
getCoordinateState(BS) - Method in class org.jmol.viewer.Viewer
 
getCorrelationMaps(String, Node[], int, BS, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getCorrelationMaps(String, Node[], int, BS, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.
getCovalentBondCount() - Method in class org.jmol.modelset.Atom
 
getCovalentBondCount() - Method in class org.jmol.smiles.SmilesAtom
Returns the number of bonds of this atom.
getCovalentBondCount() - Method in interface org.jmol.util.Node
 
getCovalentBondOrder(int) - Static method in class org.jmol.util.Edge
 
getCovalentBondsForAtoms(Bond[], int, BS) - Static method in class org.jmol.viewer.PropertyManager
 
getCovalentHydrogenCount() - Method in class org.jmol.modelset.Atom
 
getCovalentHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getCovalentHydrogenCount() - Method in interface org.jmol.util.Node
 
getCovalentlyConnectedBitSet(Node[], Node, BS, boolean, boolean, Lst<BS>, BS) - Static method in class org.jmol.util.JmolMolecule
 
getCovalentOrder() - Method in class org.jmol.modelset.Bond
 
getCovalentOrder() - Method in class org.jmol.smiles.SmilesBond
 
getCovalentOrder() - Method in class org.jmol.util.Edge
 
getCovalentRadius(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getCovalentRadius(int) - Static method in class org.jmol.util.Elements
Prior to Jmol 14.1.11, this was OpenBabel 1.100.1, but now it is BODR
getCParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getCriticalPoints(P3[], T3) - Static method in class org.jmol.util.BoxInfo
 
getCrossLinkGroup(int, Lst<Integer>, Group) - Method in class org.jmol.modelsetbio.Monomer
 
getCrossLinkLead(Lst<Integer>) - Method in class org.jmol.modelset.Group
 
getCrossLinkLead(Lst<Integer>) - Method in class org.jmol.modelsetbio.Monomer
 
getCrossLinkLead(Lst<Integer>) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getCrossLinkLeadAtomIndexes(Lst<Integer>) - Method in class org.jmol.modelset.Atom
 
getCrossLinkLeadAtomIndexes(Lst<Integer>) - Method in class org.jmol.smiles.SmilesAtom
 
getCrossLinkLeadAtomIndexes(Lst<Integer>) - Method in interface org.jmol.util.BNode
 
getCubeIterator(int) - Method in class org.jmol.bspt.Bspf
 
getCurrentBondCount() - Method in class org.jmol.modelset.Atom
 
getCurrentColorRange() - Method in class org.jmol.viewer.Viewer
 
getCurrentColorSchemeName() - Method in class org.jmol.util.ColorEncoder
 
getCurrentFileAsString(String) - Method in class org.jmol.viewer.Viewer
 
getCurrentSolventProbeRadius() - Method in class org.jmol.viewer.Viewer
 
getCurrentStep() - Method in class org.jmol.minimize.forcefield.ForceField
 
getCurrentUnitCell() - Method in class org.jmol.viewer.Viewer
 
getCurrentX() - Method in class org.jmol.viewer.ActionManager
 
getCurrentY() - Method in class org.jmol.viewer.ActionManager
 
getCursorX() - Method in class org.jmol.viewer.Viewer
 
getCursorY() - Method in class org.jmol.viewer.Viewer
 
getCylinderData(boolean) - Static method in class org.jmol.export.MeshData
Calculates the data (faces, vertices, normals) for a cylinder.
getCylinderResource(boolean) - Method in class org.jmol.export._IdtfExporter
 
getData() - Method in class org.jmol.adapter.readers.cif.CifReader
 
getData(String) - Method in interface org.jmol.api.JmolDataManager
 
getData(String, String) - Method in class org.jmol.api.JmolViewer
 
getData(String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getData(Viewer, int, int, BioPolymer, char, char, int, BS, BS, boolean, boolean, boolean, boolean, boolean, boolean, float, boolean, boolean, LabelToken[], OC, SB, BS, P3) - Method in class org.jmol.modelsetbio.BioPolymer
 
getData() - Method in class org.jmol.quantum.NMRCalculation
Creates the data set necessary for doing NMR calculations.
getData(String) - Method in class org.jmol.script.ScriptCompiler
 
getData(String) - Method in class org.jmol.viewer.DataManager
 
getData(String) - Method in class org.jmol.viewer.Viewer
 
getData(String, String) - Method in class org.jmol.viewer.Viewer
 
getDataBaseList(String[]) - Method in class org.jmol.viewer.GlobalSettings
 
getDataBlock() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getDataFloat(String, int) - Method in interface org.jmol.api.JmolDataManager
 
getDataFloat(String, int) - Method in class org.jmol.viewer.DataManager
 
getDataFloat(String) - Method in class org.jmol.viewer.Viewer
 
getDataFloat2D(String) - Method in interface org.jmol.api.JmolDataManager
 
getDataFloat2D(String) - Method in class org.jmol.viewer.DataManager
 
getDataFloat2D(String) - Method in class org.jmol.viewer.Viewer
 
getDataFloat3D(String) - Method in interface org.jmol.api.JmolDataManager
 
getDataFloat3D(String) - Method in class org.jmol.viewer.DataManager
 
getDataFloat3D(String) - Method in class org.jmol.viewer.Viewer
 
getDataFloatA(String) - Method in interface org.jmol.api.JmolDataManager
 
getDataFloatA(String) - Method in class org.jmol.viewer.DataManager
 
getDataFloatAt(String, int) - Method in class org.jmol.viewer.Viewer
 
getDataKey(int) - Method in class org.jmol.dssx.AnnotationParser
 
getDataManager() - Method in class org.jmol.viewer.Viewer
 
getDataRange() - Method in class org.jmol.shapesurface.Isosurface
 
getDataSeparator() - Method in class org.jmol.viewer.Viewer
 
getDataState(JmolStateCreator, SB) - Method in interface org.jmol.api.JmolDataManager
 
getDataState(JmolStateCreator, SB) - Method in class org.jmol.viewer.DataManager
 
getDataState(SB) - Method in class org.jmol.viewer.StateCreator
 
getDateFormat(String) - Method in class org.jmol.awt.Platform
 
getDateFormat(String) - Method in class org.jmol.awtjs2d.Platform
 
getDE(MinAtom, int, int, double) - Method in class org.jmol.minimize.forcefield.ForceField
 
getDE(float[], int, int, int, int, boolean) - Method in class org.jmol.util.MeshSlicer
 
getDebugFooter(int, double) - Method in class org.jmol.minimize.forcefield.Calculations
 
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.Calculations
 
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
 
getDebugHeader(int) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getDebugHeader2(int) - Method in class org.jmol.minimize.forcefield.Calculations
 
getDebugLine(int, Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
 
getDebugLine(int, Calculation) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
 
getDebugLineC(int, Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
 
getDef(String) - Method in class org.jmol.export.UseTable
This Hashtable contains references to _n where n is a number.
getDefaultColix() - Method in class org.jmol.shapesurface.Isosurface
 
getDefaultCount(int, boolean) - Static method in class org.jmol.smiles.SmilesAtom
 
getDefaultDirectory(String) - Method in class org.jmol.viewer.FileManager
 
getDefaultDirectory() - Method in class org.jmol.viewer.Viewer
 
getDefaultLabelState(Labels) - Method in class org.jmol.viewer.StateCreator
 
getDefaultLargePDBRendering(SB, int) - Method in class org.jmol.modelset.Model
 
getDefaultLargePDBRendering(SB, int) - Method in class org.jmol.modelsetbio.BioModel
 
getDefaultLattice() - Method in class org.jmol.viewer.Viewer
 
getDefaultMadFromOrder(int) - Method in class org.jmol.modelset.BondCollection
When creating a new bond, determine bond diameter from order
getDefaultMeasurementLabel(int) - Method in class org.jmol.viewer.Viewer
 
getDefaultPropertyParam(int) - Method in interface org.jmol.api.JmolPropertyManager
 
getDefaultPropertyParam(int) - Method in class org.jmol.viewer.PropertyManager
 
getDefaultPropertyParam(int) - Method in class org.jmol.viewer.Viewer
 
getDefaultSetting(int, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
 
getDefaultStructure(BS, BS) - Method in class org.jmol.modelset.ModelSet
 
getDefaultUnitCell() - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getDefaultVdwNameOrData(VDW, BS) - Method in interface org.jmol.api.JmolDataManager
 
getDefaultVdwNameOrData(VDW, BS) - Method in class org.jmol.viewer.DataManager
 
getDefaultVdwNameOrData(int, VDW, BS) - Method in class org.jmol.viewer.Viewer
 
getDefaultVdwType(int) - Method in class org.jmol.modelset.ModelSet
 
getDefinedAtomSet(String) - Method in class org.jmol.viewer.Viewer
 
getDefinedAtomSets() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getDefinedAtomSets() - Method in class org.jmol.script.ScriptEval
 
getDefinedState(SB, boolean) - Method in class org.jmol.viewer.StateCreator
 
getDefRet(String, String[]) - Method in class org.jmol.export.UseTable
Used by JSExporter for WebGL
getDegrees(float, boolean) - Method in class org.jmol.multitouch.ActionManagerMT
 
getDegrees(float, boolean) - Method in class org.jmol.viewer.ActionManager
Transform a screen pixel change to an angular change such that a full sweep of the dimension (up to 500 pixels) corresponds to 180 degrees of rotation.
getDelayMaximumMs() - Method in class org.jmol.viewer.Viewer
 
getDerivedSpaceGroup() - Method in class org.jmol.symmetry.SpaceGroup
 
getDesc(ModelSet) - Method in class org.jmol.symmetry.Symmetry
 
getDescent(Object) - Static method in class org.jmol.awt.AwtFont
 
getDescent(Object) - Static method in class org.jmol.awtjs.JSFont
 
getDescent(Object) - Static method in class org.jmol.awtjs2d.JSFont
 
getDescription() - Method in class org.jmol.dialog.Dialog.TypeFilter
 
getDescription(SymmetryOperation, SymmetryInterface, P3, P3, String, ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
 
getDfCoefMaps() - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getDFMap(String, int, String, int) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
finds the position in the Jmol-required list of function types.
getDialog() - Method in class org.jmol.dialog.FileChooser
 
getDialogs() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getDiameter(int, int) - Method in class org.jmol.render.FontLineShapeRenderer
 
getDictRefValue() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
getDiffusePercent() - Method in class org.jmol.util.GData
 
getDigits(String, int, int[]) - Static method in class org.jmol.smiles.SmilesParser
 
getDihedralMap(int[]) - Method in class org.jmol.modelset.ModelSet
 
getDimensionValue(P3, int) - Static method in class org.jmol.bspt.Node
 
getDimensionValue(int) - Method in class org.jmol.modelset.Atom
 
getDipolarConstantHz(Atom, Atom) - Method in interface org.jmol.api.JmolNMRInterface
 
getDipolarConstantHz(Atom, Atom) - Method in class org.jmol.quantum.NMRCalculation
 
getDipolarCouplingHz(Atom, Atom, V3) - Method in interface org.jmol.api.JmolNMRInterface
 
getDipolarCouplingHz(Atom, Atom, V3) - Method in class org.jmol.quantum.NMRCalculation
 
getDipoleIndex(int, int) - Method in class org.jmol.shapespecial.Dipoles
 
getDipoleIndexFor(String, String) - Method in class org.jmol.shapespecial.Dipoles
 
getDistance(ScriptMathProcessor, SV, SV, int) - Method in class org.jmol.scriptext.MathExt
 
getDistanceUnits(String) - Method in class org.jmol.viewer.Viewer
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
getDOMAttributes() - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
getDOMAttributesA(Object[]) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
getDoTranslate() - Static method in class org.jmol.i18n.GT
 
getDotsConvexMaps() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getDouble(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
getDragDropFileTypeName(String) - Method in class org.jmol.script.ScriptManager
 
getDragSelected() - Method in class org.jmol.viewer.Viewer
 
getDrawHover() - Method in class org.jmol.viewer.Viewer
 
getDSSRAtoms(Viewer, String, Lst<?>, BS, Map<String, BS>) - Method in class org.jmol.dssx.AnnotationParser
parsing a residue designation for tokens in DSSR.
getDSSRForModel(Viewer, int) - Method in class org.jmol.dssx.AnnotationParser
 
getDualHydrogenBondArray() - Method in class org.jmol.dssx.DSSP
(p.
getDX(int, int) - Method in class org.jmol.viewer.Gesture
 
getDY(int, int) - Method in class org.jmol.viewer.Gesture
 
getEchoStateActive() - Method in class org.jmol.modelset.ModelSet
 
getEdgeData() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getEdgePoints(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getEdges() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getEdges() - Method in class org.jmol.modelset.Atom
 
getEdges() - Method in class org.jmol.smiles.SmilesAtom
 
getEdges() - Method in interface org.jmol.util.Node
 
getEigenSort() - Static method in class org.jmol.util.Tensor
 
getElement(String) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
getElementCounts() - Method in class org.jmol.symmetry.PointGroup
 
getElementName(int) - Method in class org.jmol.modelset.AtomCollection
 
getElementNumber() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getElementNumber(String) - Static method in class org.jmol.api.JmolAdapter
 
getElementNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getElementNumber() - Method in class org.jmol.modelset.Atom
 
getElementNumber() - Method in class org.jmol.smiles.SmilesAtom
Returns the atomic number of the element or 0
getElementNumber(int) - Static method in class org.jmol.util.Elements
 
getElementNumber() - Method in interface org.jmol.util.Node
 
getElementsPresentBitSet(int) - Method in class org.jmol.api.JmolViewer
 
getElementsPresentBitSet(int) - Method in class org.jmol.modelset.ModelSet
 
getElementsPresentBitSet(int) - Method in class org.jmol.viewer.Viewer
 
getElementSymbol(Atom, String) - Method in class org.jmol.adapter.readers.more.ForceFieldReader
 
getElementSymbol() - Method in class org.jmol.adapter.smarter.Atom
 
getElementSymbol(int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getElementSymbol(int) - Static method in class org.jmol.api.JmolAdapter
 
getElementSymbol() - Method in class org.jmol.modelset.Atom
 
getElementSymbol(int) - Static method in class org.jmol.util.Elements
 
getElementSymbolIso(boolean) - Method in class org.jmol.modelset.Atom
 
getEllipsoidForAtomTensor(Tensor, P3) - Static method in class org.jmol.shapespecial.Ellipsoid
 
getEllipsoidShade(float, float, float, int, M4) - Method in class org.jmol.util.Shader
 
getEmbeddedFileState(String, boolean) - Method in class org.jmol.viewer.FileManager
 
getEmbeddedScript(String) - Static method in class org.jmol.io.JmolBinary
 
getEmptyEllipsoid(String, int) - Static method in class org.jmol.shapespecial.Ellipsoid
 
getEncodedOrder() - Method in class org.jmol.adapter.smarter.BondIterator
 
getEncodedOrder() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getEncodedVertexData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
retrieve Jvxl 2.0 format vertex/triangle/edge/color data found within element
getEncoding(String) - Static method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getEndChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getEndChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getEndInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getEndInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getEndSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getEndSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getEnergies(int, boolean) - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergy() - Method in class org.jmol.minimize.forcefield.Calculation
 
getEnergy() - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergy() - Method in class org.jmol.modelset.Bond
 
getEnergy() - Method in class org.jmol.modelset.HBond
 
getEnergy(double, double, double, double) - Static method in class org.jmol.modelset.HBond
 
getEnergyDiff() - Method in class org.jmol.minimize.forcefield.ForceField
 
getEnergyOnly() - Method in class org.jmol.minimize.Minimizer
 
getEntryIcon(String[]) - Method in class org.jmol.popup.GenericSwingPopup
 
getEquationForQuadricWithCenter(float, float, float, M3, V3, M3, double[], M4) - Static method in class org.jmol.shapespecial.Ellipsoid
 
getEquivalentType(int, int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
equivalent types for OOP and torsions
getErrorLineMessage(String, String, int, int, String) - Static method in class org.jmol.script.ScriptError
 
getErrorLineMessage2() - Method in class org.jmol.script.ScriptEval
 
getErrorMessage() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getErrorMessage() - Method in class org.jmol.api.JmolViewer
 
getErrorMessage() - Method in class org.jmol.script.ScriptError
 
getErrorMessage() - Method in class org.jmol.viewer.Viewer
 
getErrorMessageUn() - Method in class org.jmol.api.JmolViewer
 
getErrorMessageUn() - Method in class org.jmol.viewer.Viewer
 
getErrorMessageUntranslated() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getErrorMessageUntranslated() - Method in class org.jmol.script.ScriptError
 
getErrorMessageUntranslated() - Method in exception org.jmol.script.ScriptException
 
getEvalContextAndHoldQueue(JmolScriptEvaluator) - Method in class org.jmol.viewer.Viewer
 
getEventName(int) - Static method in class org.jmol.multitouch.ActionManagerMT
 
getExecutor() - Method in interface org.jmol.api.JmolParallelProcessor
 
getExecutor() - Method in class org.jmol.script.ScriptParallelProcessor
 
getExecutor() - Method in class org.jmol.viewer.Viewer
 
getExitRate() - Method in class org.jmol.viewer.ActionManager
 
getExplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getExplicitNH() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getExportDate() - Method in class org.jmol.export.___Exporter
 
getExportDriverList() - Method in class org.jmol.viewer.Viewer
 
getExportName() - Method in interface org.jmol.api.JmolRendererInterface
 
getExportName() - Method in class org.jmol.export.Export3D
 
getExportName() - Method in class org.jmol.g3d.Graphics3D
 
getExportType() - Method in interface org.jmol.api.JmolRendererInterface
 
getExportType() - Method in class org.jmol.export.Export3D
 
getExportType() - Method in class org.jmol.g3d.Graphics3D
 
getExt(String) - Method in class org.jmol.script.ScriptExpr
 
getFaces() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getFaces() - Method in class org.jmol.util.MeshSurface
 
getFacesFromCriticalPoints(P3[]) - Static method in class org.jmol.util.BoxInfo
 
getFaceVertexes(int) - Static method in class org.jmol.util.Geodesic
 
getFactoredValue(int) - Method in class org.jmol.util.Tensor
Returns a factored eigenvalue; thermal ellipsoids use sqrt(abs(eigenvalue)) for ellipsoid axes; others use just use abs(eigenvalue); all cases get factored by typeFactor
getFFParameters() - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
getField(String) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
getFile(int) - Method in class org.jmol.console.JmolConsole.FileChecker
 
getFile() - Method in class org.openscience.jmol.app.HistoryFile
 
getFile() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
getFile31() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
getFile46() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
getFileAsBytes(String, OC) - Method in class org.jmol.viewer.FileManager
 
getFileAsMap(String) - Method in class org.jmol.viewer.FileManager
 
getFileAsString3(String, boolean, String) - Method in class org.jmol.viewer.Viewer
 
getFileAsString4(String, int, boolean, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
 
getFileContents(File) - Method in class org.openscience.chimetojmol.ChimePanel
 
getFileData(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
getFileData(int) - Method in class org.jmol.modelset.ModelSet
 
getFileData() - Method in class org.jmol.viewer.Viewer
 
getFileDataAsString(String[], int, boolean, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getFileHeader(int) - Method in class org.jmol.modelset.ModelSet
 
getFileHeader() - Method in class org.jmol.viewer.Viewer
 
getFileInfo() - Method in class org.jmol.viewer.FileManager
 
getFileInfo(Object, String) - Static method in class org.jmol.viewer.PropertyManager
 
getFileList() - Method in class org.openscience.chimetojmol.ChimePanel
 
getFileName() - Method in class org.jmol.viewer.FileManager
 
getFileName() - Method in exception org.jmol.viewer.JmolAsyncException
 
getFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
 
getFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
 
getFilePath(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getFileReferences(String, Lst<String>) - Static method in class org.jmol.io.JmolBinary
 
getFiles() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
getFileState(SB) - Method in class org.jmol.viewer.StateCreator
 
getFileType(BufferedReader) - Static method in class org.jmol.adapter.smarter.Resolver
From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issues
getFileTypeName(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
Just get the resolved file type; if a file, does NOT close the reader
getFileTypeName(Object) - Method in class org.jmol.api.JmolAdapter
Get the type of this file or molecular model, if known.
getFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getFirstAtomIndex(int) - Method in class org.jmol.modelset.ModelLoader
 
getFlag(int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
safely get a one-character 0 or 1 as a boolean
getFlexFitList(BS, BS, String, boolean) - Method in interface org.jmol.script.JmolSmilesExtension
 
getFlexFitList(BS, BS, String, boolean) - Method in class org.jmol.scriptext.SmilesExt
 
getFloat() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
getFloat(int, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
getFloat(int) - Method in class org.jmol.api.JmolViewer
 
getFloat() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
 
getFloat() - Method in class org.jmol.jvxl.readers.PmeshReader
 
getFloat(Lst<Object>, int) - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
 
getFloat(int) - Method in class org.jmol.shapecgo.CGOMesh
 
getFloat(int) - Method in class org.jmol.viewer.Viewer
 
getFloatEncodedInt(String) - Static method in class org.jmol.script.ScriptParam
Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders.
getFont(float) - Method in class org.jmol.shape.Frank
 
getFont3D(float) - Method in class org.jmol.util.GData
 
getFont3D(String, String, float) - Method in class org.jmol.viewer.Viewer
 
getFont3DCurrent() - Method in class org.jmol.util.GData
 
getFont3DFS(String, float) - Method in class org.jmol.util.GData
 
getFont3DFSS(String, String, float) - Method in class org.jmol.util.GData
 
getFont3DScaled(Font, float) - Method in class org.jmol.util.GData
 
getFontAscent(Object) - Method in class org.jmol.awt.Platform
 
getFontAscent(Object) - Method in class org.jmol.awtjs.Platform
 
getFontAscent(Object) - Method in class org.jmol.awtjs2d.Platform
 
getFontCommand(String, Font) - Static method in class org.jmol.shape.Shape
 
getFontDescent(Object) - Method in class org.jmol.awt.Platform
 
getFontDescent(Object) - Method in class org.jmol.awtjs.Platform
 
getFontDescent(Object) - Method in class org.jmol.awtjs2d.Platform
 
getFontFid(float) - Method in class org.jmol.util.GData
 
getFontFidFS(String, float) - Method in class org.jmol.util.GData
 
getFontLineShapeState(String, String, TickInfo[]) - Method in class org.jmol.viewer.JmolStateCreator
 
getFontLineShapeState(String, String, TickInfo[]) - Method in class org.jmol.viewer.StateCreator
 
getFontLineShapeState(String, String, TickInfo[]) - Method in class org.jmol.viewer.Viewer
 
getFontMetrics(Font, Object) - Static method in class org.jmol.awt.AwtFont
 
getFontMetrics(Font, Object) - Method in class org.jmol.awt.Platform
 
getFontMetrics(Object, Object) - Static method in class org.jmol.awtjs.JSFont
 
getFontMetrics(Font, Object) - Method in class org.jmol.awtjs.Platform
 
getFontMetrics(Font, Object) - Static method in class org.jmol.awtjs2d.JSFont
 
getFontMetrics(Font, Object) - Method in class org.jmol.awtjs2d.Platform
 
getFontMetrics() - Method in class org.jmol.modelset.Text
 
getFontState(String, Font) - Method in class org.jmol.viewer.JmolStateCreator
 
getFontState(String, Font) - Method in class org.jmol.viewer.StateCreator
 
getFontState(String, Font) - Method in class org.jmol.viewer.Viewer
 
getForceField(String) - Method in class org.jmol.minimize.Minimizer
 
getFormalCharge() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getFormalCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getFormalCharge() - Method in class org.jmol.modelset.Atom
 
getFormalCharge() - Method in class org.jmol.smiles.SmilesAtom
 
getFormalCharge() - Method in interface org.jmol.util.Node
 
getFormatType(String) - Static method in class org.jmol.script.SV
 
getFortranFormatLengths(String) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
get all integers after letters negative entries are spaces (1Xn)
getForVar(String) - Method in class org.jmol.script.ScriptEval
 
getFractional2DValue(float, float, float, float, float, float) - Static method in class org.jmol.jvxl.data.VolumeData
 
getFractionalCoord(V3) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
getFractionalCoord(boolean, char, boolean, P3) - Method in class org.jmol.modelset.Atom
 
getFractionalCoordPt(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
 
getFractionalOffset() - Method in interface org.jmol.api.SymmetryInterface
 
getFractionalOffset() - Method in class org.jmol.symmetry.Symmetry
 
getFractionalOffset() - Method in class org.jmol.symmetry.UnitCell
 
getFractionalOrigin() - Method in interface org.jmol.api.SymmetryInterface
 
getFractionalOrigin() - Method in class org.jmol.symmetry.Symmetry
 
getFractionalOrigin() - Method in class org.jmol.util.SimpleUnitCell
 
getFractionalUnitCoord(boolean, char, P3) - Method in class org.jmol.modelset.Atom
 
getFractionalUnitCoordPt(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
 
getFractionalUnitDistance(P3, P3, P3) - Method in class org.jmol.modelset.Atom
 
getFrame() - Method in interface org.jmol.awt.JmolFrame
 
getFrame() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
getFrame() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
getFrame() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getFrameCount() - Method in class org.jmol.viewer.AnimationManager
 
getFrameDelayMs(int) - Method in class org.jmol.modelset.ModelSet
 
getFrameOffsets(BS) - Method in class org.jmol.modelset.ModelSet
 
getFrameScenes(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
remove all scenes that do not define a frame.
getFrameStep(int) - Method in class org.jmol.viewer.AnimationManager
 
getFrameTitle(int) - Method in class org.jmol.modelset.ModelSet
 
getFrameTitle() - Method in class org.jmol.viewer.Viewer
 
getFullMap() - Method in class org.jmol.script.ScriptContext
 
getFullName() - Method in class org.jmol.appletjs.Jmol
 
getFullPath() - Method in class org.jmol.awt.AwtFile
 
getFullPath() - Method in class org.jmol.awtjs2d.JSFile
 
getFullPathName() - Method in class org.jmol.script.ScriptEval
 
getFullPathName(boolean) - Method in class org.jmol.viewer.FileManager
 
getFullPathNameOrError(String, boolean, String[]) - Method in class org.jmol.viewer.FileManager
just check for a file as being readable.
getFullPathNameOrError(String) - Method in class org.jmol.viewer.Viewer
 
getFullPDBHeader() - Method in class org.jmol.modelset.Model
 
getFullPDBHeader() - Method in class org.jmol.modelsetbio.BioModel
 
getFullProteinStructureState(ModelSet, BS, boolean, boolean, int) - Method in class org.jmol.modelset.Model
 
getFullProteinStructureState(ModelSet, BS, boolean, boolean, int) - Method in class org.jmol.modelsetbio.BioModel
 
getFullScreenDimensions(Object, int[]) - Static method in class org.jmol.awt.Display
 
getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awt.Platform
 
getFullScreenDimensions(Object, int[]) - Static method in class org.jmol.awtjs2d.Display
 
getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awtjs2d.Platform
 
getFunction(String) - Method in class org.jmol.viewer.Viewer
 
getFunctionCalls(String) - Method in class org.jmol.viewer.JmolStateCreator
 
getFunctionCalls(String) - Method in class org.jmol.viewer.StateCreator
 
getFunctionCalls(String) - Method in class org.jmol.viewer.Viewer
 
getFunctions(boolean) - Method in class org.jmol.viewer.Viewer
 
getFunctionZfromXY() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getGestureType() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
 
getGestureType() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
getGhostOn() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getGLmolView() - Method in class org.jmol.appletjs.Jmol
 
getGLmolView() - Method in class org.jmol.viewer.Viewer
This method is only called by JmolGLmol applet._refresh();
getGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getGraphics(Object) - Static method in class org.jmol.awt.Image
 
getGraphics(Object) - Method in class org.jmol.awt.Platform
 
getGraphics(Object) - Static method in class org.jmol.awtjs.Image
 
getGraphics(Object) - Method in class org.jmol.awtjs.Platform
 
getGraphics(Object) - Static method in class org.jmol.awtjs2d.Image
 
getGraphics(Object) - Method in class org.jmol.awtjs2d.Platform
 
getGraphicsForMetrics() - Method in class org.jmol.g3d.Platform3D
 
getGraphicsForTextOrImage(int, int) - Method in class org.jmol.g3d.Platform3D
 
getGroup(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getGroup1(char) - Method in class org.jmol.modelset.Atom
 
getGroup1() - Method in class org.jmol.modelset.Group
 
getGroup1() - Method in class org.jmol.modelsetbio.Monomer
 
getGroup1(char) - Method in class org.jmol.smiles.SmilesAtom
 
getGroup1(char) - Method in interface org.jmol.util.BNode
 
getGroup1b() - Method in class org.jmol.modelsetbio.Monomer
 
getGroup1b() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getGroup3() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getGroup3() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getGroup3(boolean) - Method in class org.jmol.modelset.Atom
 
getGroup3() - Method in class org.jmol.modelset.Group
 
getGroup3(int) - Method in class org.jmol.modelset.ModelLoader
 
getGroup3(boolean) - Method in class org.jmol.smiles.SmilesAtom
 
getGroup3(boolean) - Method in interface org.jmol.util.BNode
 
getGroupBits(BS) - Method in class org.jmol.modelset.Atom
 
getGroupBits(BS) - Method in class org.jmol.smiles.SmilesAtom
 
getGroupBits(BS) - Method in interface org.jmol.util.BNode
 
getGroupCount() - Method in class org.jmol.modelset.Model
 
getGroupCountHetero(boolean) - Method in class org.jmol.modelset.Model
 
getGroupCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getGroupID(String) - Method in interface org.jmol.api.JmolBioResolver
 
getGroupID() - Method in class org.jmol.modelset.Atom
 
getGroupID(String) - Method in class org.jmol.modelsetbio.Resolver
 
getGroupID(int, int) - Method in class org.jmol.multitouch.ActionManagerMT
 
getGroupID(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
 
getGroupID(Location) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
getGroupIdFor(String) - Static method in class org.jmol.modelsetbio.Resolver
 
getGroupInfo(int, P3) - Method in class org.jmol.modelset.Group
 
getGroupParameter(int) - Method in class org.jmol.modelset.Atom
 
getGroupParameter(int) - Method in class org.jmol.modelset.Group
Monomers only
getGroupParameter(int) - Method in class org.jmol.modelsetbio.Monomer
 
getGroups() - Method in class org.jmol.modelset.Group
 
getGroups() - Method in class org.jmol.modelset.ModelSet
In versions earlier than 12.1.51, groups[] was a field of ModelCollection.
getGroups() - Method in class org.jmol.modelsetbio.Monomer
 
getGroupsWithin(int, BS) - Method in class org.jmol.modelset.ModelSet
 
getGroupsWithin(int, BS) - Method in class org.jmol.viewer.Viewer
 
getGroupsWithinAll(ModelSet, int, BS) - Method in class org.jmol.modelset.Model
 
getGroupsWithinAll(ModelSet, int, BS) - Method in class org.jmol.modelsetbio.BioModel
 
getHallLatticeEquivalent(int) - Static method in class org.jmol.symmetry.HallTranslation
 
getHallTerms() - Static method in class org.jmol.symmetry.HallRotation
 
getHallTerms() - Static method in class org.jmol.symmetry.HallTranslation
 
getHallTranslation(char, int) - Static method in class org.jmol.symmetry.HallTranslation
 
getHandedness(Node, Node, Node, Node, VTemp) - Static method in class org.jmol.smiles.SmilesSearch
compares the
getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in interface org.jmol.api.JmolAnnotationParser
 
getHBonds(ModelSet, int, Lst<Bond>, boolean) - Method in class org.jmol.dssx.AnnotationParser
 
getHeader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getHeader() - Method in class org.jmol.dssx.AnnotationParser
 
getHeader() - Method in class org.jmol.jvxl.readers.EfvetReader
 
getHeight(Object) - Static method in class org.jmol.awt.Image
 
getHeight(Object) - Static method in class org.jmol.awtjs2d.Image
 
getHelixData(int, char, int) - Method in class org.jmol.modelset.Group
 
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getHelixData(int, char, int) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getHelixData(BS, int) - Method in class org.jmol.scriptext.MathExt
 
getHelixData2(int, char, int) - Method in class org.jmol.modelsetbio.Monomer
 
getHelixOrStem(int, String, String, boolean) - Method in class org.jmol.dssx.AnnotationParser
 
getHelixType(int) - Static method in class org.jmol.adapter.smarter.Structure
 
getHelp(String) - Method in class org.jmol.viewer.Viewer
 
getHermiteLevel() - Method in class org.jmol.viewer.Viewer
 
getHermiteList(int, T3, T3, T3, T3, T3, T3[], int, int, boolean) - Static method in class org.jmol.util.GData
Used by Navigator, BioShapeRenderer, and DrawRenderer
getHeteroList(int) - Method in class org.jmol.modelset.ModelSet
 
getHexCode(short) - Static method in class org.jmol.util.C
 
getHexCodes(short[]) - Static method in class org.jmol.util.C
 
getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
 
getHexitValue(char) - Static method in class org.jmol.util.Escape
 
getHiddenSet() - Method in class org.jmol.viewer.SelectionManager
 
getHideNotSelected() - Method in class org.jmol.viewer.SelectionManager
 
getHigh - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
 
getHighestOrder() - Method in class org.jmol.symmetry.PointGroup
 
getHistoryWindowPosition(String) - Method in interface org.jmol.api.JmolAppAPI
 
getHistoryWindowPosition(String) - Method in class org.openscience.jmol.app.JmolApp
 
getHistoryWindowSize(String) - Method in interface org.jmol.api.JmolAppAPI
 
getHistoryWindowSize(String) - Method in class org.openscience.jmol.app.JmolApp
 
getHklPlane(P3) - Method in class org.jmol.script.ScriptParam
 
getHoverDelay() - Method in class org.jmol.viewer.Viewer
 
getHtmlResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getHybridizationAndAxes(int, int, V3, V3, String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getHybridizationAndAxes(int, V3, V3, String) - Method in class org.jmol.viewer.Viewer
 
getHybridizationAndAxesD(int, V3, V3, String) - Method in class org.jmol.modelset.AtomCollection
dsp3 (trigonal bipyramidal, see-saw, T-shaped) or d2sp3 (square planar, square pyramidal, octahedral)
getHydrogenAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getHydrogenAtomCount(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getHydrogenAtomCount(Object) - Method in class org.jmol.api.JmolAdapter
Get the hydrogen atom count -- for ligand files
getHydrogens(Node, BS) - Method in class org.jmol.smiles.SmilesSearch
 
getHydrophobicity() - Method in class org.jmol.modelset.Atom
 
getHydrophobicity() - Method in class org.jmol.modelset.AtomCollection
 
getHydrophobicity(int) - Static method in class org.jmol.util.Elements
 
getIcon() - Method in class org.jmol.popup.AwtSwingComponent
 
getIcon(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getIconX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getId() - Method in enum org.jmol.c.STR
 
getID(String, int) - Method in class org.jmol.shapesurface.LcaoCartoon
 
getId(int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getIdentifierOrNull(String) - Method in class org.jmol.modelset.AtomCollection
overhauled by RMH Nov 1, 2006.
getIdentity() - Method in class org.jmol.minimize.MinAtom
 
getIdentity(boolean) - Method in class org.jmol.modelset.Atom
 
getIdentity() - Method in class org.jmol.modelset.Bond
 
getIdentityXYZ(boolean, P3) - Method in class org.jmol.modelset.Atom
 
getIDStr() - Method in class org.jmol.modelset.Chain
 
getImage(Viewer, Object, String) - Method in interface org.jmol.api.JmolZipUtilities
 
getImage(Viewer, Object, String) - Method in class org.jmol.io.JmolBinary
 
getImage(Viewer, Object, String) - Method in class org.jmol.io.JmolUtil
 
getImage(String, boolean) - Method in class org.jmol.viewer.PropertyManager
 
getImage(boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.api.JmolViewer
 
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.viewer.OutputManager
Called when a simple image is required -- from x=getProperty("image") or for a simple preview PNG image for inclusion in a ZIP file from write xxx.zip or xxx.jmol, or for a PNGJ or PNG image that is being posted because of a URL that contains "?POST?_PNG_" or ?POST?_PNGJ_" or ?POST?_PNGJBIN_".
getImageAsBytes(String, int, int, int, String[]) - Method in class org.jmol.viewer.Viewer
 
getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in interface org.jmol.api.JmolDialogInterface
 
getImageFileNameFromDialog(Viewer, String, String, String[], String[], int, int) - Method in class org.jmol.dialog.Dialog
 
getImageFontScaling() - Method in class org.jmol.viewer.Viewer
 
getImageHeight(Object) - Method in class org.jmol.awt.Platform
 
getImageHeight(Object) - Method in class org.jmol.awtjs2d.Platform
 
getImageIcon(String) - Method in class org.jmol.awtjs2d.JmolJSPopup
 
getImageIcon(String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
getImageIcon(String) - Method in class org.jmol.modelkit.ModelKitPopup
 
getImageIcon(String) - Method in class org.jmol.popup.GenericSwingPopup
 
getImageIcon(String) - Method in class org.jmol.popup.JmolAwtPopup
 
getImageWidth(Object) - Method in class org.jmol.awt.Platform
 
getImageWidth(Object) - Method in class org.jmol.awtjs2d.Platform
 
getImplicitHydrogenCount() - Method in class org.jmol.modelset.Atom
 
getImplicitHydrogenCount(Atom, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getImplicitHydrogenCount() - Method in class org.jmol.smiles.SmilesAtom
 
getImplicitHydrogenCount() - Method in interface org.jmol.util.Node
 
getIndex() - Method in class org.jmol.modelset.Atom
 
getIndex(int, int, int, int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getIndex(Monomer) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getIndex() - Method in class org.jmol.smiles.SmilesAtom
Returns the atom index of the atom.
getIndex() - Method in interface org.jmol.util.Node
 
getIndexFromName(String) - Method in class org.jmol.shape.MeshCollection
 
getIndexFromName(String) - Method in class org.jmol.shape.Shape
 
getIndexFromName(String) - Method in class org.jmol.shapespecial.Dipoles
 
getIndexFromName(String) - Method in class org.jmol.shapespecial.Ellipsoids
 
getIndexOf(int) - Method in class org.jmol.modelset.MeasurementPending
 
getInfo(String) - Method in interface org.jmol.api.JmolNMRInterface
 
getInfo() - Method in class org.jmol.modelset.Atom
 
getInfo(int, String) - Method in class org.jmol.modelset.ModelSet
 
getInfo(Map<String, Object>) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getInfo(String) - Method in class org.jmol.quantum.NMRCalculation
 
getInfo(int) - Method in class org.jmol.shape.Measures
 
getInfo(boolean) - Method in class org.jmol.shape.Mesh
 
getInfo(int, boolean, boolean, String, int, float) - Method in class org.jmol.symmetry.PointGroup
 
getInfo(String, SymmetryInterface) - Static method in class org.jmol.symmetry.SpaceGroup
 
getInfo() - Method in class org.jmol.util.Modulation
 
getInfo(Map<String, Object>) - Method in class org.jmol.util.ModulationSet
 
getInfo(int) - Method in class org.jmol.util.SimpleUnitCell
 
getInfo(String) - Method in class org.jmol.util.Tensor
returns an object of the specified type, including "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"
getInfo(Map<String, Object>) - Method in class org.jmol.util.Vibration
 
getInfoAsString(String) - Method in class org.jmol.modelset.Measurement
 
getInfoAsString(int) - Method in class org.jmol.shape.AtomShape
 
getInfoAsString(int) - Method in class org.jmol.shape.Measures
 
getInfoB(int, String) - Method in class org.jmol.modelset.ModelSet
 
getInfoHeight() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInfoI(int, String) - Method in class org.jmol.modelset.ModelSet
 
getInfoIndex(String) - Static method in class org.jmol.util.Tensor
 
getInfoM(String) - Method in class org.jmol.modelset.ModelSet
 
getInfoWidth() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInfoXYZ(boolean, boolean, P3) - Method in class org.jmol.modelset.Atom
 
getINI() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Save INI file
getInitiatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getInitiatorAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getInitiatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
 
getInlineChar() - Method in class org.jmol.viewer.Viewer
 
getInlineData(int) - Method in class org.jmol.modelset.ModelSet
 
getInlineData(SB, String, boolean, String) - Method in class org.jmol.viewer.JmolStateCreator
 
getInlineData(SB, String, boolean, String) - Method in class org.jmol.viewer.StateCreator
 
getInMotion(boolean) - Method in class org.jmol.viewer.Viewer
 
getInputPoint(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
for debugging
getInputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
getInputStreamOrErrorMessageFromName(String) - Static method in class org.openscience.jvxl.FileReader
 
getInsertedCommand() - Method in class org.jmol.viewer.Viewer
 
getInsertionCode() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getInsertionCode() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getInsertionCode() - Method in class org.jmol.modelset.Atom
 
getInsertionCode() - Method in class org.jmol.modelset.Group
 
getInsertionCodeChar(int) - Static method in class org.jmol.modelset.Group
 
getInsertionCodeFor(int) - Static method in class org.jmol.modelset.Group
 
getInsertionCodeIndexInModel(int, char) - Method in class org.jmol.modelset.ModelSet
 
getInsertionCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getInsertionListInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getInstance() - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getInstance(JmolViewer, String, int, int, int) - Static method in class org.openscience.jmol.app.webexport.JmolInstance
 
getInstanceList() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInstanceName(int) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getInt(int, int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
safe int parsing of line.substring(col1, col2);
getInt(int) - Method in class org.jmol.api.JmolViewer
 
getInt() - Method in class org.jmol.jvxl.readers.EfvetReader
 
getInt() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
 
getInt() - Method in class org.jmol.jvxl.readers.PmeshReader
 
getInt(int) - Method in class org.jmol.shapecgo.CGOMesh
 
getInt(Map<String, Object>, String, int) - Static method in class org.jmol.viewer.OutputManager
 
getInt(int) - Method in class org.jmol.viewer.Viewer
 
getInt(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
getIntData() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
getInteractionTensorList(String, BS) - Method in class org.jmol.quantum.NMRCalculation
Returns a list of tensors that are of the specified type and have both atomIndex1 and atomIndex2 in bsA.
getInterface(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getInterface(String, Viewer, String) - Static method in class org.jmol.api.Interface
 
getInterface(String) - Static method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getIntersection(float, P4, P3[], Lst<P3[]>, float[], BS, MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSlicer
 
getInverseNormix(short) - Static method in class org.jmol.util.Normix
 
getISCtype(Atom, String) - Method in class org.jmol.quantum.NMRCalculation
 
getIsHetero() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getIsHetero() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getIsoExt() - Method in class org.jmol.script.ScriptEval
 
getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in interface org.jmol.api.JmolNMRInterface
If t is null, then a1, a2, and type are used to find the appropriate tensor.
getIsoOrAnisoHz(boolean, Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
 
getIsosurfaceJvxl(boolean, int) - Method in class org.jmol.scriptext.CmdExt
 
getIsosurfacePropertySmoothing(boolean) - Method in class org.jmol.viewer.Viewer
 
getIsotopeData(Atom, int) - Method in class org.jmol.quantum.NMRCalculation
Get magnetogyricRatio (gamma/10^7 rad s^-1 T^-1) and quadrupoleMoment (Q/10^-2 fm^2) for a given isotope or for the default isotope of an element.
getIsotopeNumber() - Method in class org.jmol.modelset.Atom
 
getIsotopeNumber() - Method in class org.jmol.smiles.SmilesAtom
 
getIsotopeNumber(int) - Static method in class org.jmol.util.Elements
 
getIsotopeNumber() - Method in interface org.jmol.util.Node
 
getItem(int) - Static method in class org.jmol.quantum.QS
 
getItemType(SC) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
getItemType(SC) - Method in class org.jmol.popup.JSSwingPopupHelper
 
getItemType(SC) - Method in interface org.jmol.popup.PopupHelper
 
getIterativeModels(boolean) - Method in class org.jmol.modelset.ModelSet
only some models can be iterated through.
getJavaConsole(Jmol) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
 
getJavaScript(int, JmolInstance) - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
Each Widget must implement this function and make sure to use the appletID number to specify the target applet i.e.
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
 
getJavaScriptFileName() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
A COPY OF THIS .JS FILE MUST BE STORED IN THE html PART OF WEBEXPORT
getJBR() - Method in class org.jmol.viewer.Viewer
 
getJCouplingHz(Atom, Atom, String, Tensor) - Method in class org.jmol.quantum.NMRCalculation
 
getJDXBaseModelIndex(int) - Method in class org.jmol.viewer.Viewer
get the model designated as "baseModel" in a JCamp-MOL file for example, the model used for bonding for an XYZVIB file or the model used as the base model for a mass spec file.
getJmol(JFrame, int, int, Map<String, Object>) - Static method in class org.openscience.jmol.app.Jmol
 
getJmol(int, int, String) - Static method in class org.openscience.jmol.app.JmolData
 
getJmol(JmolApp, JFrame) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getJmolAtom(int) - Method in class org.jmol.smiles.SmilesSearch
 
getJmolDataFrameIndex(int, String) - Method in class org.jmol.modelset.ModelSet
 
getJmolDataSourceFrame(int) - Method in class org.jmol.modelset.ModelSet
 
getJmolFrameType(int) - Method in class org.jmol.modelset.ModelSet
 
getJmolName(String) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getJmolObject(int, BS, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getJmolOrRasmolArgb(int, int) - Method in class org.jmol.viewer.ColorManager
 
getJmolParameter(String) - Method in class org.jmol.applet.Jmol
 
getJmolParameter(String) - Method in class org.jmol.appletjs.Jmol
 
getJmolParameter(String) - Method in class org.jmol.util.GenericApplet
 
getJmolPerspective() - Method in class org.jmol.export.___Exporter
 
getJmolValueAsString(Viewer, String) - Static method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
getJmolVersion() - Static method in class org.jmol.api.JmolViewer
 
getJmolVersion() - Static method in class org.jmol.viewer.Viewer
 
getJones() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
getJSliderLabelTable(JSlider) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awt.Platform
 
getJsObjectInfo(Object[], String, Object[]) - Method in class org.jmol.awtjs2d.Platform
 
getJSONArray(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
getJsonNioServer() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
getJspecViewProperties(String) - Method in class org.jmol.viewer.StatusManager
 
getJspecViewProperties(Object) - Method in class org.jmol.viewer.Viewer
 
getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolStatusListener
 
getJSpecViewProperty(String) - Method in interface org.jmol.api.JmolSyncInterface
 
getJSpecViewProperty(String) - Method in class org.jmol.util.GenericApplet
JSpecView shares the JmolSyncInterface; used to get JSpecView
getJSpecViewProperty(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
getJSV() - Method in class org.jmol.viewer.Viewer
 
getJSVSyncSignal(String) - Static method in class org.jmol.viewer.JC
 
getJzt() - Method in class org.jmol.viewer.Viewer
 
getJzu() - Method in class org.jmol.io.JmolBinary
 
getKey() - Method in interface org.jmol.api.JmolAbstractButton
 
getKey() - Method in class org.jmol.console.JmolButton
 
getKey() - Method in class org.jmol.console.JmolLabel
 
getKey() - Method in class org.jmol.console.JmolToggleButton
 
getKey() - Method in class org.jmol.console.KeyJCheckBox
 
getKey() - Method in class org.jmol.console.KeyJCheckBoxMenuItem
 
getKey() - Method in class org.jmol.console.KeyJMenu
 
getKey() - Method in class org.jmol.console.KeyJMenuItem
 
getKey() - Method in class org.jmol.console.KeyJRadioButtonMenuItem
 
getKey(Object, int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getKey(int, int, int, int, int) - Static method in class org.jmol.minimize.MinObject
 
getKey(int, int) - Method in class org.jmol.util.MeshSlicer
 
getKeyList(SV, boolean, Lst<String>, String) - Method in class org.jmol.script.ScriptMathProcessor
 
getKeys(SV, boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
getLabel(String) - Method in class org.jmol.console.GenericConsole
 
getLabel(LabelToken[]) - Static method in class org.jmol.modelset.LabelToken
 
getLabel(int, boolean, boolean) - Method in class org.jmol.modelset.Measurement
 
getLabel(int) - Method in class org.jmol.shape.Labels
 
getLabel() - Method in class org.jmol.symmetry.PointGroup.Operation
 
getLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getLabel1() - Method in class org.jmol.console.AppletConsole
 
getLabel1() - Method in class org.jmol.console.GenericConsole
 
getLabeler() - Method in class org.jmol.modelset.AtomCollection
 
getLabelString() - Method in class org.jmol.modelset.Measurement
 
getLabelWithoutMnemonic(String) - Static method in class org.jmol.console.GenericConsole
 
getLanguage() - Static method in class org.jmol.i18n.GT
 
getLanguage() - Static method in class org.jmol.i18n.Resource
 
getLanguageList(GT) - Static method in class org.jmol.i18n.GT
 
getLanguageList() - Static method in class org.jmol.i18n.Language
This is the place to put the list of supported languages.
getLastAtomSetAtomCount() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getLastAtomSetAtomIndex() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getLastConventional - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
getLastError() - Static method in exception org.jmol.smiles.InvalidSmilesException
 
getLastException() - Method in interface org.jmol.api.SmilesMatcherInterface
 
getLastException() - Method in class org.jmol.smiles.SmilesMatcher
 
getLastIndex() - Method in class org.jmol.modelset.Measurement
 
getLastPoint(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
Find the lowest ascender or descender above scan line bounding the region for this point.
getLastVibrationVector(int, int) - Method in class org.jmol.modelset.ModelSet
 
getLatticeCode(int) - Static method in class org.jmol.symmetry.HallTranslation
 
getLatticeDesignation() - Method in interface org.jmol.api.SymmetryInterface
 
getLatticeDesignation() - Method in class org.jmol.symmetry.HallInfo
 
getLatticeDesignation(int) - Static method in class org.jmol.symmetry.HallTranslation
 
getLatticeDesignation() - Method in class org.jmol.symmetry.SpaceGroup
 
getLatticeDesignation() - Method in class org.jmol.symmetry.Symmetry
 
getLatticeDesignation2(char, boolean) - Static method in class org.jmol.symmetry.HallTranslation
 
getLatticeExtension(char, boolean) - Static method in class org.jmol.symmetry.HallTranslation
 
getLatticeIndex(char) - Static method in class org.jmol.symmetry.HallTranslation
 
getLatticeOp() - Method in interface org.jmol.api.SymmetryInterface
 
getLatticeOp() - Method in class org.jmol.symmetry.Symmetry
 
getLeadAtom() - Method in class org.jmol.modelset.Group
 
getLeadAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getLeadAtomIndices() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadAtomOr(Atom) - Method in class org.jmol.modelset.Group
 
getLeadColix(int) - Method in class org.jmol.renderbio.BioShapeRenderer
 
getLeadColixBack(int) - Method in class org.jmol.renderbio.BioShapeRenderer
 
getLeadMidPoint(int, P3) - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadMidpoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeadPoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
getLeftPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getLength(int) - Method in class org.jmol.shapespecial.Ellipsoid
 
getLength() - Method in class org.openscience.jvxl.MonitorInputStream
 
getLevel(int) - Static method in class org.jmol.util.Logger
Returns the text corresponding to a level.
getLigandBondInfo(JmolAdapter, Object, String) - Method in class org.jmol.modelsetbio.Resolver
reads PDB ligand CIF info and creates a bondInfo object.
getLigandInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
 
getLigandInfo(Object) - Method in class org.jmol.viewer.PropertyManager
 
getLigandModel(String, String, String, String) - Method in class org.jmol.viewer.Viewer
obtain CIF data for a ligand for purposes of adding hydrogens
getLightingInfo() - Method in class org.jmol.export._TachyonExporter
 
getLightingState(boolean) - Method in class org.jmol.viewer.JmolStateCreator
 
getLightingState(boolean) - Method in class org.jmol.viewer.StateCreator
 
getLightingState() - Method in class org.jmol.viewer.Viewer
 
getLightSource() - Method in class org.jmol.util.GData
 
getLine() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
getLine() - Method in class org.jmol.jvxl.readers.XmlReader
 
getLine() - Method in class org.jmol.jvxl.readers.XplorReader
 
getLinearOffset(int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getLinenumber(ScriptContext) - Method in class org.jmol.script.ScriptEval
 
getLinesUntil(String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
getLinkNTList(String, String, Lst<Object>) - Method in class org.jmol.dssx.AnnotationParser
 
getList(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getList(Lst<Object>, int) - Static method in class org.jmol.jvxl.readers.PyMOLMeshReader
 
getList() - Method in class org.jmol.script.SV
 
getListCellRendererComponent(JList<?>, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
 
getListCellRendererComponent(JList<?>, Object, int, boolean, boolean) - Method in class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
 
getLoadFilesList(int, SB, SB, Map<String, Object>, Lst<String>) - Method in class org.jmol.script.ScriptEval
 
getLoadModelIndex(int, SB, Map<String, Object>) - Method in class org.jmol.script.ScriptEval
 
getLoadState(Map<String, Object>) - Method in class org.jmol.viewer.GlobalSettings
these settings are determined when the file is loaded and are kept even though they might later change.
getLoadSymmetryParams(int, SB, Map<String, Object>) - Method in class org.jmol.script.ScriptEval
 
getLocalDirectory(Viewer, boolean) - Static method in class org.jmol.viewer.FileManager
 
getLocalPathForWritingFile(Viewer, String) - Static method in class org.jmol.viewer.FileManager
 
getLocalUrl(GenericFileInterface) - Static method in class org.jmol.awt.AwtFile
 
getLocalUrl(String) - Method in class org.jmol.awt.Platform
 
getLocalUrl(String) - Method in class org.jmol.awtjs2d.Platform
 
getLocalUrl(String) - Method in class org.jmol.viewer.Viewer
 
getLogData() - Method in class org.jmol.minimize.forcefield.Calculations
 
getLogData() - Method in class org.jmol.minimize.forcefield.ForceField
 
getLogFileName() - Method in class org.jmol.viewer.Viewer
 
getLogLevel() - Static method in class org.jmol.util.Logger
 
getLogPath(String) - Method in class org.jmol.viewer.OutputManager
 
getLogPath(String) - Method in class org.jmol.viewer.OutputManagerAwt
 
getLogPath(String) - Method in class org.jmol.viewer.OutputManagerJS
 
getLong(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
getMad(int, short) - Method in class org.jmol.shapebio.BioShape
 
getMadBond() - Method in class org.jmol.api.JmolViewer
 
getMadBond() - Method in class org.jmol.viewer.Viewer
 
getMadParameter() - Method in class org.jmol.script.ScriptParam
 
getMagneticShielding(Atom) - Method in interface org.jmol.api.JmolNMRInterface
 
getMagneticShielding(Atom) - Method in class org.jmol.quantum.NMRCalculation
 
getMainItem(Map<String, SV>) - Method in class org.jmol.dssx.AnnotationParser
 
getManifestScriptPath(String) - Static method in class org.jmol.io.JmolBinary
check a JmolManifest for a reference to a script file (.spt)
getMap(boolean) - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
getMap() - Method in class org.jmol.script.SV
 
getMapKeys(int, boolean) - Method in class org.jmol.script.SV
 
getMapList(Map<String, Object>, String) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getMappedAtoms(Node, Node, Node[]) - Method in class org.jmol.smiles.SmilesSearch
 
getMaps - Variable in class org.jmol.smiles.SmilesSearch
 
getMark() - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
getMass() - Method in class org.jmol.modelset.Atom
 
getMasses() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getMatchingAtom() - Method in class org.jmol.smiles.SmilesAtom
Returns the number of a matching atom in a molecule.
getMatchingBondedAtom(int) - Method in class org.jmol.smiles.SmilesAtom
 
getMathExt() - Method in class org.jmol.script.ScriptEval
 
getMathExt() - Method in class org.jmol.script.ScriptMathProcessor
 
getMatrices(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getMatrix4f(M3, T3) - Static method in class org.jmol.script.ScriptMathProcessor
 
getMatrixFromString(String, float[], boolean, int) - Method in interface org.jmol.api.SymmetryInterface
 
getMatrixFromString(String, float[], boolean, int) - Method in class org.jmol.symmetry.Symmetry
 
getMatrixFromString(SymmetryOperation, String, float[], boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
Convert the Jones-Faithful notation "x, -z+1/2, y" or "x1, x3-1/2, x2, x5+1/2, -x6+1/2, x7..." to a linear array Also allows a-b,-5a-5b,-c;0,0,0 format
getMaxMathParams(int) - Static method in class org.jmol.script.T
 
getMaxVanderwaalsRadius() - Method in class org.jmol.modelset.AtomCollection
 
getMeasurement(Point3fi[]) - Method in class org.jmol.modelset.Measurement
 
getMeasurementCount() - Method in class org.jmol.api.JmolViewer
 
getMeasurementCount() - Method in class org.jmol.viewer.Viewer
 
getMeasurementCountPlusIndices(int) - Method in class org.jmol.api.JmolViewer
 
getMeasurementCountPlusIndices(int) - Method in class org.jmol.viewer.Viewer
 
getMeasurementInfo() - Method in class org.jmol.viewer.PropertyManager
 
getMeasurementInfoAsString() - Method in class org.jmol.viewer.Viewer
 
getMeasurements(boolean, boolean) - Method in class org.jmol.modelset.MeasurementData
if this is the client, then this method can be called to get the result vector, either as a string or as an array.
getMeasurementScript(String, boolean) - Method in class org.jmol.modelset.Measurement
Used by MouseManager and Picking Manager to build the script
getMeasurementState(Measures, Lst<Measurement>, int, Font, TickInfo) - Method in class org.jmol.viewer.JmolStateCreator
 
getMeasurementState(Measures, Lst<Measurement>, int, Font, TickInfo) - Method in class org.jmol.viewer.StateCreator
 
getMeasurementState(Measures, Lst<Measurement>, int, Font, TickInfo) - Method in class org.jmol.viewer.Viewer
 
getMeasurementStringValue(int) - Method in class org.jmol.api.JmolViewer
 
getMeasurementStringValue(int) - Method in class org.jmol.viewer.Viewer
 
getMemo(int) - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
getMenu(String, Map<Object, SC>) - Static method in class org.jmol.popup.AwtSwingComponent
 
getMenu(String) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
getMenu(String) - Method in class org.jmol.popup.JSSwingPopupHelper
 
getMenu(String) - Method in interface org.jmol.popup.PopupHelper
 
getMenu(String) - Method in class org.jmol.viewer.Viewer
 
getMenuAsText(String) - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
getMenuAsText(String) - Method in class org.jmol.popup.MainPopupResourceBundle
 
getMenuAsText(String) - Method in class org.jmol.popup.PopupResource
 
getMenuItem(String, Map<Object, SC>) - Static method in class org.jmol.popup.AwtSwingComponent
 
getMenuItem(String) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
getMenuItem(String) - Method in class org.jmol.popup.JSSwingPopupHelper
 
getMenuItem(String) - Method in interface org.jmol.popup.PopupHelper
 
getMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Fetch the menu item that was created for the given command.
getMenuName() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
getMenuName() - Method in class org.jmol.popup.MainPopupResourceBundle
 
getMenuName() - Method in class org.jmol.popup.PopupResource
 
getMenuPopup(String, char) - Method in class org.jmol.awt.Platform
 
getMenuPopup(String, char) - Method in class org.jmol.awtjs2d.Platform
 
getMenuText(String) - Method in class org.jmol.popup.JmolGenericPopup
 
getMesh(String) - Method in class org.jmol.shape.MeshCollection
 
getMeshCommand(SB, int) - Method in class org.jmol.shapesurface.Isosurface
 
getMeshData(String, int[][], T3[], T3[]) - Method in class org.jmol.export._IdtfExporter
 
getMeshHeader(String, int, int, int, int, SB) - Method in class org.jmol.export._IdtfExporter
 
getMeshList(String, boolean) - Method in class org.jmol.shape.MeshCollection
Get matching list of meshes, order reversed
getMeshSlicer() - Method in class org.jmol.util.MeshSurface
 
getMiddle() - Method in class org.openscience.jmol.app.surfacetool.Slice
 
getMinDistance2ForVertexGrouping() - Method in class org.jmol.shape.Mesh
 
getMinDistance2ForVertexGrouping() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getMinDistances(MeasurementData) - Method in interface org.jmol.api.JmolNMRInterface
 
getMinDistances(MeasurementData) - Method in class org.jmol.quantum.NMRCalculation
 
getMinimizationInfo() - Method in class org.jmol.viewer.Viewer
 
getMinimizer(boolean) - Method in class org.jmol.viewer.Viewer
 
getMiniPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
getMinMax() - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getMinMax(Object, int) - Method in interface org.jmol.script.JmolMathExtension
 
getMinMax(Object, int) - Method in class org.jmol.scriptext.MathExt
 
getMinMaxMappedValues(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getMinMaxPoint(Object, int) - Method in class org.jmol.scriptext.MathExt
calculates the statistical value for x, y, and z independently
getMinMaxQuaternion(Lst<SV>, int) - Method in class org.jmol.scriptext.MathExt
 
getMinZ(Atom[], int[]) - Method in class org.jmol.modelset.Group
 
getMissingHydrogenCount() - Method in class org.jmol.smiles.SmilesSearch
 
getMnemonic(String) - Static method in class org.jmol.console.GenericConsole
 
getMod(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
Modulation data keys are keyed by model number as well as type using [at]n, where n is the model number, starting with 0.
getMod(String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getModAtom(int) - Method in class org.jmol.render.MeasuresRenderer
 
getModel() - Method in class org.jmol.modelset.Group
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
getModelAdapter() - Method in class org.jmol.api.JmolViewer
 
getModelAdapter() - Method in class org.jmol.viewer.Viewer
 
getModelAtomBitSetIncludingDeleted(int, boolean) - Method in class org.jmol.modelset.ModelSet
Note that this method returns all atoms, included deleted ones.
getModelAtomBitSetIncludingDeletedBs(BS) - Method in class org.jmol.modelset.ModelSet
note -- this method returns ALL atoms, including deleted.
getModelAtomIndices() - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
prepare a list of starting atom indices for each model, adding one additional one to indicate 1 + last atom index
getModelAuxiliaryInfo(int) - Method in class org.jmol.modelset.ModelSet
 
getModelBS(BS, boolean) - Method in class org.jmol.modelset.ModelSet
 
getModelCellRange(int) - Method in class org.jmol.modelset.ModelSet
 
getModelCenter() - Method in class org.jmol.export.__CartesianExporter
 
getModelCml(BS, int, boolean) - Method in interface org.jmol.api.JmolPropertyManager
 
getModelCml(BS, int, boolean) - Method in class org.jmol.viewer.PropertyManager
 
getModelCml(BS, int, boolean) - Method in class org.jmol.viewer.Viewer
 
getModelData(boolean) - Method in class org.jmol.jsv.JDXMOLParser
 
getModelDipole(int) - Method in class org.jmol.modelset.ModelSet
 
getModelDipole() - Method in class org.jmol.viewer.Viewer
 
getModelExtract(BS, boolean, boolean, String) - Method in interface org.jmol.api.JmolPropertyManager
 
getModelExtract(BS, boolean, boolean, String) - Method in class org.jmol.viewer.PropertyManager
 
getModelExtract(Object, boolean, boolean, String) - Method in class org.jmol.viewer.Viewer
 
getModelFileInfo(BS) - Method in interface org.jmol.api.JmolPropertyManager
 
getModelFileInfo(BS) - Method in class org.jmol.viewer.PropertyManager
 
getModelFileInfo() - Method in class org.jmol.viewer.Viewer
 
getModelFileInfoAll() - Method in class org.jmol.viewer.Viewer
 
getModelFileName(int) - Method in class org.jmol.modelset.ModelSet
 
getModelFileNumber(int) - Method in class org.jmol.viewer.Viewer
 
getModelFileType(int) - Method in class org.jmol.modelset.ModelSet
 
getModelIndex(ModelSet) - Method in class org.jmol.adapter.readers.pymol.JmolObject
 
getModelIndex() - Method in class org.jmol.modelset.Atom
 
getModelIndex() - Method in class org.jmol.modelset.Group
 
getModelIndex() - Method in class org.jmol.smiles.SmilesAtom
 
getModelIndex() - Method in interface org.jmol.util.Node
 
getModelIndexFromId(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getModelIndexFromId(String) - Method in class org.jmol.api.JmolViewer
 
getModelIndexFromId(String) - Method in class org.jmol.modelset.ModelSet
 
getModelIndexFromId(String) - Method in class org.jmol.util.GenericApplet
 
getModelIndexFromId(String) - Method in class org.jmol.viewer.Viewer
 
getModelIndices() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getModelIndices() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getModelInfo(Object) - Method in interface org.jmol.api.JmolPropertyManager
 
getModelInfo(Object) - Method in class org.jmol.viewer.PropertyManager
 
getModelInfoAsString() - Method in class org.jmol.modelset.ModelSet
 
getModelKitStateBitset(BS, BS) - Method in class org.jmol.modelset.ModelSet
 
getModelName(int) - Method in class org.jmol.api.JmolViewer
 
getModelName(int) - Method in class org.jmol.modelset.ModelSet
 
getModelName(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumber() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
getModelNumber() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
getModelNumber(int) - Method in class org.jmol.api.JmolViewer
 
getModelNumber() - Method in class org.jmol.modelset.Atom
 
getModelNumber(int) - Method in class org.jmol.modelset.ModelSet
 
getModelNumber(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumberDotted(int) - Method in class org.jmol.api.JmolViewer
 
getModelNumberDotted(int) - Method in class org.jmol.modelset.ModelSet
 
getModelNumberDotted(int) - Method in class org.jmol.viewer.Viewer
 
getModelNumberForAtomLabel(int) - Method in class org.jmol.modelset.ModelSet
 
getModelNumberForLabel() - Method in class org.jmol.modelset.Atom
 
getModelNumberIndex(int, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
getModelOrientation(int) - Method in class org.jmol.modelset.ModelSet
 
getModelPanel() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
getModelProperties(int) - Method in class org.jmol.api.JmolViewer
 
getModelProperties(int) - Method in class org.jmol.viewer.Viewer
 
getModelProperty(int, String) - Method in class org.jmol.modelset.ModelSet
 
getModelSet() - Method in class org.jmol.modelset.Model
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
getModelSetAuxiliaryInfo() - Method in class org.jmol.api.JmolViewer
 
getModelSetAuxiliaryInfo() - Method in class org.jmol.viewer.Viewer
 
getModelSetFileName() - Method in class org.jmol.api.JmolViewer
 
getModelSetFileName() - Method in class org.jmol.viewer.Viewer
 
getModelSetPathName() - Method in class org.jmol.api.JmolViewer
 
getModelSetPathName() - Method in class org.jmol.viewer.Viewer
 
getModelSetProperties() - Method in class org.jmol.api.JmolViewer
 
getModelSetProperties() - Method in class org.jmol.viewer.Viewer
 
getModelSetTypeName() - Method in class org.jmol.modelset.ModelSet
 
getModelSpecial(int) - Method in class org.jmol.viewer.AnimationManager
 
getModelState(SB, boolean, boolean) - Method in class org.jmol.viewer.JmolStateCreator
 
getModelState(SB, boolean, boolean) - Method in class org.jmol.viewer.StateCreator
 
getModelSymmetryCount(int) - Method in class org.jmol.modelset.ModelSet
 
getModelTitle(int) - Method in class org.jmol.modelset.ModelSet
 
getModelUndeletedAtomsBitSet(int) - Method in class org.jmol.viewer.Viewer
 
getModelUndeletedAtomsBitSetBs(BS) - Method in class org.jmol.viewer.Viewer
 
getModMatrices() - Method in class org.jmol.adapter.readers.cif.Subsystem
 
getModPoint(boolean) - Method in interface org.jmol.api.JmolModulationSet
 
getModPoint(boolean) - Method in class org.jmol.util.ModulationSet
 
getModTemp() - Method in class org.jmol.util.ModulationSet
 
getModType(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getModType(String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getModulation(char, T3) - Method in interface org.jmol.api.JmolModulationSet
 
getModulation() - Method in class org.jmol.modelset.Atom
 
getModulation(int) - Method in class org.jmol.modelset.AtomCollection
 
getModulation(char, T3) - Method in class org.jmol.util.ModulationSet
 
getModulationCoord(char) - Method in class org.jmol.modelset.Atom
 
getModulationCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
 
getModulationList(BS, char, P3) - Method in class org.jmol.modelset.ModelSet
 
getModulationMap() - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getModulationMap() - Method in interface org.jmol.adapter.smarter.MSInterface
 
getModulationReader() - Method in class org.jmol.adapter.readers.cif.CifReader
 
getMOHeader(int, String[], Map<String, Object>[], int) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
getMoInfo(int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getMoJvxl(int, boolean) - Method in class org.jmol.scriptext.CmdExt
 
getMolecular(BS) - Method in class org.jmol.shapespecial.Dipoles
 
getMolecularFormula(String, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getMolecularFormula(String, boolean) - Method in class org.jmol.smiles.SmilesMatcher
 
getMolecularFormula(Node[], BS, boolean, float[], boolean) - Static method in class org.jmol.util.JmolMolecule
 
getMolecularFormula(boolean, float[], boolean) - Method in class org.jmol.util.JmolMolecule
 
getMolecule(String, boolean) - Static method in class org.jmol.smiles.SmilesParser
 
getMoleculeBitSet(BS) - Method in class org.jmol.modelset.ModelSet
 
getMoleculeBitSetForAtom(int) - Method in class org.jmol.modelset.ModelSet
 
getMoleculeCountInModel(int) - Method in class org.jmol.modelset.ModelSet
 
getMoleculeIndex(int, boolean) - Method in class org.jmol.modelset.ModelSet
 
getMoleculeInfo(Object) - Method in class org.jmol.viewer.PropertyManager
 
getMoleculeNumber(boolean) - Method in class org.jmol.modelset.Atom
 
getMolecules() - Method in class org.jmol.modelset.ModelSet
 
getMolecules(BNode[], BS[], Lst<BS>, BS) - Static method in class org.jmol.util.JmolMolecule
Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.
getMolName() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
 
getMonomerIndex() - Method in class org.jmol.modelset.Atom
 
getMonomerIndex() - Method in class org.jmol.modelset.Group
 
getMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
 
getMonomers() - Method in class org.jmol.shape.AtomShape
 
getMonomers() - Method in class org.jmol.shapebio.BioShape
 
getMonomerSequenceAtoms(BS, BS) - Method in class org.jmol.modelsetbio.Monomer
 
getMoreInfo() - Method in interface org.jmol.api.SymmetryInterface
 
getMoreInfo() - Method in class org.jmol.symmetry.Symmetry
 
getMOString(float[]) - Static method in class org.jmol.quantum.QS
 
getMotionEventNumber() - Method in class org.jmol.api.JmolViewer
 
getMotionEventNumber() - Method in class org.jmol.viewer.Viewer
 
getMotionFixedAtoms() - Method in class org.jmol.viewer.SelectionManager
 
getMotionFixedAtoms() - Method in class org.jmol.viewer.Viewer
 
getMoTokens(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
getMouseAction(int, int, int) - Static method in class org.jmol.viewer.binding.Binding
 
getMouseActionName(int, boolean) - Static method in class org.jmol.viewer.binding.Binding
 
getMouseActionStr(String) - Static method in class org.jmol.viewer.binding.Binding
create an action code from a string such as "CTRL-LEFT-double click"
getMouseEnabled() - Method in class org.jmol.viewer.Viewer
 
getMouseInfo() - Method in class org.jmol.viewer.PropertyManager
 
getMouseManager(double, Object) - Method in class org.jmol.awt.Platform
 
getMouseManager(double, Object) - Method in class org.jmol.awtjs2d.Platform
 
getMoveToText(boolean) - Method in class org.jmol.modelset.Orientation
 
getMoveToText(float, boolean) - Method in class org.jmol.viewer.TransformManager
 
getMP() - Method in class org.jmol.viewer.ActionManager
 
getMpsShapeCount() - Method in class org.jmol.shapebio.BioShapeCollection
 
getMSInfoB(String) - Method in class org.jmol.modelset.ModelSet
 
getMultipleBondSettings(boolean) - Method in class org.jmol.render.SticksRenderer
 
getMyInfo(P3) - Method in class org.jmol.modelsetbio.Monomer
 
getMyValue() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
 
getN0() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN1() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN2() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN3() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN4() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getN6() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getName(String) - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
getName() - Method in interface org.jmol.api.JmolAbstractButton
 
getName() - Method in interface org.jmol.api.JmolScriptFunction
 
getName() - Method in class org.jmol.awtjs2d.JSFile
 
getName() - Method in enum org.jmol.c.STER
 
getName() - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
 
getName() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
getName() - Method in class org.jmol.popup.AwtSwingComponent
 
getName() - Method in class org.jmol.script.ScriptFunction
 
getName() - Method in class org.jmol.symmetry.PointGroup
 
getName() - Method in class org.jmol.symmetry.SpaceGroup
 
getNameFromCode(int) - Static method in enum org.jmol.util.Edge.EnumBondOrder
 
getNameList() - Static method in enum org.jmol.c.CBK
 
getNaturalIsotope(int) - Static method in class org.jmol.api.JmolAdapter
 
getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
 
getNav() - Method in class org.jmol.viewer.TransformManager
 
getNavigationOffset() - Method in class org.jmol.viewer.TransformManager
 
getNavigationOffsetPercent(char) - Method in class org.jmol.viewer.TransformManager
 
getNavigationSlabOffsetPercent() - Method in class org.jmol.navigate.Navigator
 
getNavigationState() - Method in interface org.jmol.api.JmolNavigatorInterface
 
getNavigationState() - Method in class org.jmol.navigate.Navigator
 
getNavigationState() - Method in class org.jmol.viewer.TransformManager
 
getNavigationText(boolean) - Method in class org.jmol.viewer.TransformManager
 
getNavPtHeight() - Method in class org.jmol.viewer.TransformManager
 
getNBOCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
getNboCharges() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
getNBOs - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
getNboTypes() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
getNegCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getNeighbors(AtomIndexIterator) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getNeighborVertexArrays() - Static method in class org.jmol.util.Normix
 
getNeighborVertexesArrays() - Static method in class org.jmol.util.Geodesic
 
getNested(int) - Method in class org.jmol.smiles.SmilesSearch
 
getNewCubeIterator(int) - Method in class org.jmol.bspt.Bspf
 
getNewDfCoefMap() - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getNewDfCoefMap() - Static method in class org.jmol.quantum.QS
 
getNewFixedRotationCenter() - Method in class org.jmol.viewer.TransformManager
 
getNewSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getNextPreloadClassName() - Method in class org.jmol.applet.AppletWrapper
 
getNextStatement() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getNextStatement() - Method in class org.jmol.script.ScriptEval
when paused, indicates what statement will be next
getNextValue() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getNextVoxelValue() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getNHPoint(P3, V3, boolean, boolean) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNitrogenAtom() - Method in class org.jmol.modelset.Group
 
getNitrogenAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNitrogenHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getNMRCalculation() - Method in class org.jmol.viewer.Viewer
 
getNMRPredict(boolean) - Method in class org.jmol.viewer.Viewer
 
getNoCase(Map<String, Object>, String) - Static method in class org.jmol.viewer.StateManager
 
getNode(int) - Method in class org.jmol.viewer.Gesture
 
getNormalizedDE() - Method in class org.jmol.minimize.forcefield.ForceField
 
getNormalMap(T3[], int, BS, Lst<String>) - Method in class org.jmol.export.__CartesianExporter
 
getNormals(T3[], P4) - Method in class org.jmol.shape.Mesh
 
getNormalsTemp() - Method in class org.jmol.shape.Mesh
 
getNormalThroughPoints(Node, Node, Node, V3, V3, V3) - Static method in class org.jmol.smiles.SmilesAromatic
 
getNormix() - Method in class org.jmol.rendercgo.CGORenderer
 
getNormix(double, double, double, int, BS) - Static method in class org.jmol.util.Normix
 
getNormixCount() - Static method in class org.jmol.util.Normix
 
getNormixV(V3, BS) - Static method in class org.jmol.util.Normix
 
getNotInCentroid(BS, int[]) - Method in class org.jmol.modelset.ModelSet
 
getNotionalUnitCell() - Method in interface org.jmol.api.SymmetryInterface
 
getNotionalUnitcell() - Method in class org.jmol.modelset.ModelSet
deprecated due to multimodel issues, but required by an interface -- do NOT remove.
getNotionalUnitCell() - Method in class org.jmol.symmetry.Symmetry
 
getNotionalUnitCell() - Method in class org.jmol.util.SimpleUnitCell
 
getNoValue() - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
Get that value that represents "no value" so that it can be disregarded in terms of recording and reporting the min/max/mean.
getNoValue() - Method in class org.jmol.quantum.NciCalculation
 
getNPQ(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
getNPQd(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
for D orbitals, MOPAC adds 1 to n for noble gases but subtracts 1 from n for transition metals
getNPQp(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
for P orbitals, MOPAC adds 1 to n for helium only
getNPQs(int) - Static method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
for S orbitals, MOPAC adds 1 to n for noble gases other than helium
getNT(String, boolean) - Method in class org.jmol.dssx.AnnotationParser
 
getNTList() - Method in class org.jmol.dssx.AnnotationParser
 
getNTs(Lst<Object>, Lst<Object>, boolean, boolean) - Method in class org.jmol.dssx.AnnotationParser
 
getNucleicPhosphorusAtom(int) - Method in class org.jmol.modelsetbio.NucleicPolymer
 
getNull(boolean) - Static method in class org.jmol.symmetry.SpaceGroup
 
getNumberFromCode(int) - Static method in enum org.jmol.util.Edge.EnumBondOrder
 
getNumericalToken() - Method in class org.jmol.script.ScriptTokenParser
 
getO2() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getO4() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getO6() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getObj(Object) - Method in class org.jmol.viewer.PropertyManager
 
getObjectAsSections(String, String, Map<String, String>) - Method in class org.jmol.viewer.FileManager
delivers file contents and directory listing for a ZIP/JAR file into sb
getObjectBoundingBox(String) - Method in class org.jmol.script.ScriptEval
 
getObjectCenter(String, int, int) - Method in class org.jmol.script.ScriptEval
 
getObjectCenter(String, int, int) - Method in class org.jmol.script.ScriptParam
 
getObjectColix(int) - Method in class org.jmol.viewer.Viewer
 
getObjectID(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getObjectIdFromName(String) - Static method in class org.jmol.viewer.StateManager
 
getObjectMad(int) - Method in class org.jmol.viewer.Viewer
 
getObjectMap(Map<String, ?>, boolean) - Method in class org.jmol.viewer.ShapeManager
 
getObjectMap(Map<String, ?>, char) - Method in class org.jmol.viewer.Viewer
used in autocompletion in console using TAB
getObjectNameFromId(int) - Static method in class org.jmol.viewer.StateManager
 
getObjects(int) - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
getObjectSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getObjectSettings() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getObjectType(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getOccupancy() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getOccupancy() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getOccupancy100() - Method in class org.jmol.modelset.Atom
 
getOffset(int, int) - Static method in class org.jmol.viewer.JC
 
getOffsetResidueAtom(String, int) - Method in class org.jmol.modelset.Atom
 
getOffsetResidueAtom(String, int) - Method in class org.jmol.smiles.SmilesAtom
 
getOffsetResidueAtom(String, int) - Method in interface org.jmol.util.BNode
 
getOffsetVertices(P4) - Method in class org.jmol.shape.Mesh
 
geTokens() - Method in interface org.jmol.api.JmolScriptFunction
 
geTokens() - Method in class org.jmol.script.ScriptFunction
 
getOpacity255() - Method in class org.jmol.awt.AwtColor
 
getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in interface org.jmol.api.JmolDialogInterface
 
getOpenFileNameFromDialog(Map<String, Object>, Viewer, String, JmolAppAPI, String, boolean) - Method in class org.jmol.dialog.Dialog
 
getOperation(int) - Method in class org.jmol.symmetry.SpaceGroup
 
getOperationCount() - Method in class org.jmol.symmetry.SpaceGroup
 
getOperationRsVs(int) - Method in interface org.jmol.api.SymmetryInterface
 
getOperationRsVs(int) - Method in class org.jmol.symmetry.Symmetry
 
getOpMatrix(String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
getOption(String, Viewer, String) - Static method in class org.jmol.api.Interface
Note! Do not use this method with "viewer." or "util." because when the JavaScript is built, "org.jmol.util" and "org.jmol.viewer" are condensed to "JU" and "JV" (javajs.util is also JU)
getOptions() - Method in class org.openscience.jmol.app.JmolApp
 
getOrAddBond(Atom, Atom, int, short, BS, float, boolean) - Method in class org.jmol.modelset.BondCollection
 
getOrAllocateChain(Model, int) - Method in class org.jmol.modelset.ModelLoader
 
getOrbitals(float[], float[], int, int) - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
getOrientation() - Method in class org.jmol.viewer.StateManager
 
getOrientationFor(String) - Method in class org.jmol.viewer.StateManager
 
getOrientationInfo() - Method in class org.jmol.viewer.TransformManager
 
getOrientationText(int) - Method in class org.jmol.viewer.TransformManager
 
getOrientationText(int, String) - Method in class org.jmol.viewer.Viewer
 
getOriginFloat() - Method in interface org.jmol.api.VolumeDataInterface
 
getOriginFloat() - Method in class org.jmol.jvxl.data.VolumeData
 
getOriginPoint(boolean) - Method in class org.jmol.shape.Axes
 
getOrSaveImage(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
Creates an image of params.type form -- PNG, PNGJ, PNGT, JPG, JPG64, PDF, PPM, GIF, GIFT.
getOrSetNewVariable(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
 
getOtherAtom(int) - Method in class org.jmol.minimize.MinBond
 
getOtherAtom(Atom) - Method in class org.jmol.modelset.Bond
 
getOtherAtom(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
 
getOtherAtomNode(Node) - Method in class org.jmol.modelset.Bond
 
getOtherAtomNode(Node) - Method in class org.jmol.smiles.SmilesBond
 
getOtherAtomNode(Node) - Method in class org.jmol.util.Edge
 
getOutOfPlaneParameter(int[]) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getOutputChannel(String, String[]) - Method in class org.jmol.viewer.OutputManager
 
getOutputChannel(String, String[]) - Method in class org.jmol.viewer.Viewer
 
getOutputFileNameFromDialog(String, int) - Method in class org.jmol.viewer.OutputManager
 
getOutputFromExport(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
 
getOutputManager() - Method in class org.jmol.viewer.Viewer
 
getOutputStream() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
getP() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getP(String) - Method in class org.jmol.viewer.Viewer
 
getPageAuthorName() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getPairs(BS, BS, RadiusData, int, boolean) - Method in class org.jmol.shapesurface.Contact
 
getPalette(String) - Static method in enum org.jmol.c.PAL
 
getPaletteAC() - Method in class org.jmol.util.ColorEncoder
 
getPaletteAtoB(int, int, int) - Static method in class org.jmol.util.ColorEncoder
 
getPaletteBW() - Method in class org.jmol.util.ColorEncoder
 
getPaletteColorCount(int) - Method in class org.jmol.util.ColorEncoder
 
getPaletteID(String) - Static method in enum org.jmol.c.PAL
 
getPaletteName(byte) - Static method in enum org.jmol.c.PAL
 
getPaletteWB() - Method in class org.jmol.util.ColorEncoder
 
getPane() - Method in class org.jmol.console.JmolConsole
 
getPanel() - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
getPanel(int, int) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
getParam(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
 
getParameter(String) - Method in class org.jmol.api.JmolViewer
 
getParameter(Object) - Method in class org.jmol.minimize.forcefield.Calculations
 
getParameter(float[], int, double, String) - Static method in class org.jmol.quantum.NciCalculation
 
getParameter(String, int, boolean) - Method in class org.jmol.script.ScriptParam
 
getParameter(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
strictly a getter
getParameter(String) - Method in class org.jmol.viewer.Viewer
 
getParameterEscaped(String, int) - Method in class org.jmol.viewer.GlobalSettings
 
getParameterObj(MinObject) - Method in class org.jmol.minimize.forcefield.Calculations
 
getParameterObj(MinObject) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
 
getParameterObj(MinObject) - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getParameters() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getParameterState(GlobalSettings, SB) - Method in class org.jmol.viewer.StateCreator
note that these are not user variables, only global jmol parameters
getParamType(int) - Static method in class org.jmol.script.T
 
getParamType(int) - Static method in class org.jmol.viewer.PropertyManager
 
getParent() - Method in class org.jmol.popup.AwtSwingComponent
 
getParent() - Method in class org.jmol.script.ScriptFlowContext
 
getParentAsFile() - Method in class org.jmol.awt.AwtFile
 
getParentAsFile() - Method in class org.jmol.awtjs2d.JSFile
 
getParentItem(String, M4) - Method in class org.jmol.export._IdtfExporter
 
getPartialBondDotted(int) - Static method in class org.jmol.util.Edge
 
getPartialBondOrder(int) - Static method in class org.jmol.util.Edge
 
getPartialBondOrderFromFloatEncodedInt(int) - Static method in class org.jmol.script.ScriptParam
reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)
getPartialBondOrderFromString(String) - Static method in class org.jmol.script.ScriptParam
 
getPartialCharge() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getPartialCharge() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getPartialCharge() - Method in class org.jmol.modelset.Atom
 
getPartialCharges() - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getPartialCharges() - Method in class org.jmol.modelset.AtomCollection
 
getPartialCharges() - Method in class org.jmol.viewer.Viewer
 
getPartnerAtom(NucleicMonomer) - Method in class org.jmol.modelsetbio.BasePair
 
getPathForAllFiles() - Method in class org.jmol.viewer.FileManager
 
getPathHistory() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
Just recovers the path settings from last session.
getPathHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Just recovers the path settings from last session.
getPatternMatcher() - Method in class org.jmol.scriptext.MathExt
 
getPdbAtomData(BS, OC) - Method in interface org.jmol.api.JmolPropertyManager
 
getPdbAtomData(BS, OC) - Method in class org.jmol.viewer.PropertyManager
PDB or PQR only
getPdbAtomData(BS, OC) - Method in class org.jmol.viewer.Viewer
 
getPdbBondInfo(String, boolean) - Method in class org.jmol.modelsetbio.Resolver
 
getPdbCharge(String, String) - Method in class org.jmol.modelset.ModelLoader
Adjust known N and O atom formal charges.
getPdbConformation(BS, int) - Method in class org.jmol.modelset.Model
 
getPdbConformation(BS, int) - Method in class org.jmol.modelsetbio.BioModel
 
getPdbData(int, String, BS, Object[], OC, boolean) - Method in interface org.jmol.api.JmolPropertyManager
 
getPdbData(Viewer, String, char, boolean, BS, OC, LabelToken[], SB, BS) - Method in class org.jmol.modelset.Model
 
getPdbData(Viewer, String, char, boolean, BS, OC, LabelToken[], SB, BS) - Method in class org.jmol.modelsetbio.BioModel
 
getPdbData(Viewer, char, char, int, int, BS, BS, boolean, boolean, boolean, LabelToken[], OC, SB, BS, P3) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.PropertyManager
 
getPdbData(int, String, BS, Object[], OC, boolean) - Method in class org.jmol.viewer.Viewer
 
getPDBGroupLength(String) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
getPDBHeader(int) - Method in class org.jmol.modelset.ModelSet
 
getPeakAtomRecord(int) - Method in class org.jmol.jsv.JSpecView
 
getPendingMeasurement() - Method in class org.jmol.viewer.Viewer
 
getPercentageRead() - Method in class org.openscience.jvxl.MonitorInputStream
 
getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.CastepDensityReader
 
getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
getPeriodicVoxels() - Method in class org.jmol.jvxl.readers.VaspChgcarReader
 
getPerspectiveDepth() - Method in class org.jmol.viewer.TransformManager
 
getPerspectiveFactor(float) - Method in class org.jmol.viewer.TransformManager
calculate the perspective factor based on z
getPhase(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getPhongExponent() - Method in class org.jmol.util.GData
 
getPickedPoint(T3, int) - Method in class org.jmol.shape.MeshCollection
 
getPickingMode(String) - Static method in class org.jmol.viewer.ActionManager
 
getPickingMode() - Method in class org.jmol.viewer.Viewer
 
getPickingModeName(int) - Static method in class org.jmol.viewer.ActionManager
 
getPickingState() - Method in class org.jmol.viewer.ActionManager
 
getPickingStyle() - Method in class org.jmol.viewer.ActionManager
 
getPickingStyleIndex(String) - Static method in class org.jmol.viewer.ActionManager
 
getPickingStyleName(int) - Static method in class org.jmol.viewer.ActionManager
 
getPlane(int, float[]) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
 
getPlane(int) - Method in interface org.jmol.jvxl.api.VertexDataServer
 
getPlane(int, boolean) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getPlane(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getPlane(float[], boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getPlane(int, float[]) - Method in class org.jmol.quantum.NciCalculation
 
getPlane(int) - Method in class org.jmol.shapesurface.Isosurface
 
getPlane(V3) - Method in class org.jmol.symmetry.PointGroup
 
getPlane(String) - Static method in class org.openscience.jvxl.Jvxl
 
getPlane2(int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getPlaneForObject(String, V3) - Method in class org.jmol.script.ScriptEval
 
getPlaneForObject(String, V3) - Method in class org.jmol.script.ScriptParam
 
getPlaneIntersection(int, P4, float, int, SymmetryInterface) - Method in class org.jmol.modelset.ModelSet
 
getPlaneIntersection(int, P4, float, int) - Method in class org.jmol.viewer.Viewer
 
getPlaneNormals(Node, Node, Node, Node, VTemp) - Static method in class org.jmol.smiles.SmilesSearch
 
getPlaneProcessed(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
Retrieve raw file planes and pass them to the calculation object for processing into new data.
getPlaneValue(int) - Method in class org.jmol.quantum.NciCalculation
We always have four raw planes in hand; we just need to know which three to use in any particular case.
getPlotMinMax(float[], boolean, int) - Method in class org.jmol.scriptext.CmdExt
 
getPlotText3D(int, int, Graphics3D, String, Font, boolean) - Static method in class org.jmol.g3d.TextRenderer
 
getPoint() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
getPoint(String) - Method in class org.jmol.dssx.AnnotationParser
 
getPoint(int, P3) - Method in class org.jmol.jvxl.data.VolumeData
 
getPoint(String, int, int[], boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
 
getPoint(int, P3, P3i) - Method in class org.jmol.rendercgo.CGORenderer
 
getPoint(int, T3) - Method in class org.jmol.shapecgo.CGOMesh
 
getPoint(Map<String, Object>) - Method in class org.jmol.viewer.ActionManager
 
getPoint3f(int, boolean) - Method in class org.jmol.script.ScriptParam
 
getPoint3f(int, boolean) - Method in class org.jmol.scriptext.CmdExt
 
getPoint4f(int) - Method in class org.jmol.script.ScriptParam
 
getPoint4f(int) - Method in class org.jmol.scriptext.IsoExt
 
getPointArray(int, int, boolean) - Method in class org.jmol.script.ScriptParam
may return null values in some cases
getPointCount() - Method in class org.jmol.viewer.Gesture
 
getPointCount2(int, int) - Method in class org.jmol.viewer.Gesture
 
getPointer(int) - Static method in class org.jmol.viewer.JC
 
getPointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getPointers(Object[]) - Method in class org.jmol.minimize.forcefield.Calculation
 
getPointGroup(PointGroup, Atom[], BS, boolean, float, float) - Static method in class org.jmol.symmetry.PointGroup
 
getPointGroupAsString(BS, boolean, String, int, float) - Method in class org.jmol.modelset.ModelSet
 
getPointGroupInfo(int, boolean, boolean, String, int, float) - Method in interface org.jmol.api.SymmetryInterface
 
getPointGroupInfo(BS) - Method in class org.jmol.modelset.ModelSet
 
getPointGroupInfo(int, boolean, boolean, String, int, float) - Method in class org.jmol.symmetry.Symmetry
 
getPointGroupName() - Method in interface org.jmol.api.SymmetryInterface
 
getPointGroupName() - Method in class org.jmol.symmetry.Symmetry
 
getPointIndex(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
getPointOrBitsetOperation(T, SV) - Method in class org.jmol.script.ScriptMathProcessor
 
getPointOrPlane(int, boolean, boolean, boolean, boolean, int, int) - Method in class org.jmol.script.ScriptParam
 
getPoints() - Method in interface org.jmol.api.JmolEnvCalc
 
getPoints() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getPoints(byte[], P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getPoints() - Method in class org.jmol.render.MeasuresRenderer
 
getPointVector(T, int) - Method in class org.jmol.script.ScriptParam
 
getPolygonColorData(int, short[], int[][], BS) - Static method in class org.jmol.shapesurface.Isosurface
 
getPolymerIndexInModel() - Method in class org.jmol.modelset.Atom
 
getPolymerInfo(BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPolymerLength() - Method in class org.jmol.modelset.Atom
 
getPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelset.Model
 
getPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelset.ModelSet
 
getPolymerPointsAndVectors(BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioModel
 
getPolymerPointsAndVectors(int, BS, Lst<P3[]>, boolean, float) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPolymerPointsAndVectors(BS, Lst<P3[]>) - Method in class org.jmol.viewer.Viewer
 
getPolymerSequenceAtoms(int, int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
getPopInHeight() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getPopInWidth() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getPopup(String, Map<Object, SC>) - Static method in class org.jmol.popup.AwtSwingComponent
 
getPopupMenu() - Method in class org.jmol.popup.AwtSwingComponent
 
getPopupMenu() - Method in class org.jmol.viewer.Viewer
 
getPOrNull(String) - Method in class org.jmol.viewer.Viewer
 
getPort() - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
getPort() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
getPosCorner() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getPosition() - Method in class org.openscience.jvxl.MonitorInputStream
 
getPositionMin() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getPrecedence(int) - Static method in class org.jmol.script.T
 
getPrefixToken() - Method in class org.jmol.script.ScriptCompiler
 
getPreserveState() - Method in class org.jmol.viewer.Viewer
This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such.
getPrettyMatrix(SB, M4) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getPrivateKey() - Method in class org.jmol.export.Export3D
 
getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
 
getPropDataMC(String, Object[]) - Method in class org.jmol.shape.MeshCollection
 
getProperties() - Method in class org.openscience.jmol.app.HistoryFile
 
getProperty(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getProperty(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
getProperty(String, String, Object) - Method in interface org.jmol.api.JmolPropertyManager
 
getProperty(String, String, Object) - Method in class org.jmol.api.JmolViewer
 
getProperty(String, int) - Method in interface org.jmol.api.MinimizerInterface
 
getProperty(String, int) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getProperty(String, int) - Method in class org.jmol.minimize.Minimizer
 
getproperty - Static variable in class org.jmol.script.T
 
getProperty(String, int) - Method in class org.jmol.shape.Axes
 
getProperty(String, int) - Method in class org.jmol.shape.Labels
 
getProperty(String, int) - Method in class org.jmol.shape.Measures
 
getProperty(String, int) - Method in class org.jmol.shape.Shape
 
getProperty(String, int) - Method in class org.jmol.shape.Sticks
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Dipoles
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Draw
 
getProperty(String, int) - Method in class org.jmol.shapespecial.Vectors
 
getProperty(String, int) - Method in class org.jmol.shapesurface.Isosurface
 
getProperty(String, int) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getProperty(String) - Method in class org.jmol.util.GenericApplet
 
getProperty(String, String) - Method in class org.jmol.util.GenericApplet
 
getProperty(String, boolean) - Static method in class org.jmol.util.Logger
 
getProperty(String, String, Object) - Method in class org.jmol.viewer.PropertyManager
 
getProperty(Object) - Method in class org.jmol.viewer.ShapeManager
 
getProperty(String, String, Object) - Method in class org.jmol.viewer.Viewer
 
getProperty(String, String) - Method in class org.openscience.jmol.app.HistoryFile
Get the value of a property
getPropertyAsJSON(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsJSON(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsJSON(String) - Method in class org.jmol.util.GenericApplet
 
getPropertyAsJSON(String, String) - Method in class org.jmol.util.GenericApplet
 
getPropertyAsObject(String, Object, String) - Method in class org.jmol.viewer.PropertyManager
 
getPropertyAsString(String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsString(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
getPropertyAsString(String) - Method in class org.jmol.util.GenericApplet
 
getPropertyAsString(String, String) - Method in class org.jmol.util.GenericApplet
 
getPropertyColorRange() - Method in class org.jmol.viewer.ColorManager
 
getPropertyCount(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
getPropertyData(String, Object[]) - Method in class org.jmol.shape.Echo
 
getPropertyData(String, Object[]) - Method in class org.jmol.shape.Shape
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapecgo.CGO
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Dipoles
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Draw
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapespecial.Ellipsoids
 
getPropertyData(String, Object[]) - Method in class org.jmol.shapesurface.Isosurface
 
getPropertyManager() - Method in class org.jmol.viewer.Viewer
 
getPropertyName(int) - Static method in class org.jmol.viewer.PropertyManager
 
getPropertyNumber(String) - Method in interface org.jmol.api.JmolPropertyManager
 
getPropertyNumber(String) - Method in class org.jmol.viewer.PropertyManager
 
getPropertyNumber(String) - Method in class org.jmol.viewer.Viewer
 
getPropI(String) - Method in class org.jmol.shapesurface.Isosurface
 
getPropMC(String) - Method in class org.jmol.shape.MeshCollection
 
getProteinStructure(int) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
getProteinStructure(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getProteinStructureState(BS, boolean, boolean, int) - Method in class org.jmol.modelset.ModelSet
 
getProteinStructureState(ModelSet, BioModel, BS, boolean, boolean, int) - Static method in class org.jmol.modelsetbio.BioModel
 
getProteinStructureState() - Method in class org.jmol.viewer.Viewer
 
getProteinStructureSubType() - Method in class org.jmol.modelset.Atom
 
getProteinStructureSubType() - Method in class org.jmol.modelset.Group
 
getProteinStructureSubType() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructureTag() - Method in class org.jmol.modelset.Atom
 
getProteinStructureTag() - Method in class org.jmol.modelset.Group
 
getProteinStructureTag() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getProteinStructureType(String) - Static method in enum org.jmol.c.STR
In DRuMS, RasMol, and Chime, quoting from http://www.umass.edu/microbio/rasmol/rascolor.htm The RasMol structure color scheme colors the molecule by protein secondary structure.
getProteinStructureType() - Method in class org.jmol.modelset.Atom
 
getProteinStructureType() - Method in class org.jmol.modelset.Group
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.Monomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getProteinStructureType() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getPymolView(Lst<Object>, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
adds depth_cue, fog, and fog_start
getPymolXYOffset(float, int, float) - Method in class org.jmol.modelset.Text
 
getQCoefs(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getQCoefs(String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getQInfo(Quat) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getQuadrupolarConstant(Tensor) - Method in interface org.jmol.api.JmolNMRInterface
Quadrupolar constant, directly proportional to Vzz and dependent on the quadrupolar moment of the isotope considered
getQuadrupolarConstant(Tensor) - Method in class org.jmol.quantum.NMRCalculation
 
getQuadrupoleTensors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
getQuality(String) - Method in interface org.jmol.api.JmolDialogInterface
 
getQuality(String) - Method in class org.jmol.dialog.Dialog
 
getQuantumShell(String) - Static method in class org.jmol.quantum.QS
 
getQuantumShellTag(int) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getQuantumShellTag(int) - Static method in class org.jmol.quantum.QS
 
getQuantumShellTagID(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getQuantumShellTagID(String) - Static method in class org.jmol.quantum.QS
 
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
getQuantumShellTagIDSpherical(String) - Static method in class org.jmol.quantum.QS
 
getQuaternion(int, char) - Method in class org.jmol.modelset.AtomCollection
 
getQuaternion(char) - Method in class org.jmol.modelset.Group
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getQuaternion(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getQuaternionAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getQuaternionArray(Object, int) - Method in class org.jmol.script.ScriptEval
 
getQuaternionFrame(Atom[]) - Method in class org.jmol.modelset.Group
 
getQuaternionFrame() - Method in class org.jmol.viewer.Viewer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.AminoMonomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.Monomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getQuaternionFrameCenter(char) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getQuaternionFrameCenterAlpha(char) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getQuaternionP() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getQuaternionParameter(int) - Method in class org.jmol.script.ScriptParam
 
getQuaternionRotation(String) - Method in interface org.jmol.api.SymmetryInterface
 
getQuaternionRotation(String) - Method in class org.jmol.symmetry.Symmetry
 
getQuaternionRotation(String) - Method in class org.jmol.symmetry.UnitCell
Returns a quaternion that will take the standard frame to a view down a particular axis, expressed as its counterparts.
getQuaternionStraightness(String, Quat, Quat) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getQuotedString(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
getQuotedStringNext() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
getR0(MinBond) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getRadio(String, Map<Object, SC>) - Static method in class org.jmol.popup.AwtSwingComponent
 
getRadio(String) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
getRadio(String) - Method in class org.jmol.popup.JSSwingPopupHelper
 
getRadio(String) - Method in interface org.jmol.popup.PopupHelper
 
getRadius() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getRadius() - Method in class org.jmol.adapter.smarter.BondIterator
 
getRadius() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getRadius() - Method in class org.jmol.api.JmolAdapterBondIterator
 
getRadius(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
getRadius() - Method in class org.jmol.modelset.Atom
 
getRadiusVdwJmol(Atom) - Method in class org.jmol.modelset.AtomCollection
 
getRange(BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
getRangeGroups(int, BS, BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
getRasmolHydrogenBonds(BS, BS, Lst<Bond>, boolean, int, boolean, BS) - Method in class org.jmol.modelsetbio.BioModel
 
getRasMolRadius() - Method in class org.jmol.modelset.Atom
 
getRasmolScale() - Static method in class org.jmol.util.ColorEncoder
 
getReaderClassBase(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getReaderData() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getReaderFromType(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getReadingTimeMillis() - Method in class org.openscience.jvxl.MonitorInputStream
 
getRecord(String) - Method in interface org.jmol.api.JmolJDXMOLParser
 
getRecord(String) - Method in class org.jmol.jsv.JDXMOLParser
 
getRefreshing() - Method in class org.jmol.viewer.Viewer
 
getRegistryInfo() - Method in interface org.jmol.api.JmolStatusListener
 
getRegistryInfo() - Method in class org.jmol.util.GenericApplet
 
getRegistryInfo() - Method in class org.jmol.viewer.StatusManager
 
getRegistryInfo() - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
getRelationship(String, String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getRelationship(String, String) - Method in class org.jmol.smiles.SmilesMatcher
 
getRenderable(BS) - Method in class org.jmol.modelset.AtomCollection
 
getRenderer(String) - Method in class org.jmol.g3d.Graphics3D
 
getRenderer(int) - Method in class org.jmol.render.RepaintManager
 
getRendering() - Method in class org.jmol.shape.Mesh
 
getResidueLabels() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getResiduePointers() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
getResno() - Method in class org.jmol.modelset.Atom
 
getResno() - Method in class org.jmol.modelset.Group
 
getResno() - Method in class org.jmol.smiles.SmilesAtom
 
getResno() - Method in interface org.jmol.util.BNode
 
getResolution() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getResolution() - Method in class org.jmol.util.MeshSurface
 
getResource(Viewer, String, String) - Static method in class org.jmol.i18n.Resource
 
getResource(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getResource(Object, String, boolean) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getResourceFromPO(String) - Static method in class org.jmol.i18n.Resource
applet only -- Simple reading of .po file; necessary for JavaScript; works in Java as well and avoids all those signed applets.
getResourceStream(String) - Static method in class org.openscience.chimetojmol.ChimePanel
 
getResourceString(Object, String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
getResult() - Method in class org.jmol.script.ScriptMathProcessor
 
getRGB(int) - Static method in class org.jmol.adapter.readers.pymol.PyMOL
 
getRiboseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getRingCache(int, int, Map<String, Object[]>) - Method in class org.jmol.smiles.SmilesGenerator
 
getRingData(boolean, int, Lst<BS>[]) - Method in class org.jmol.smiles.SmilesSearch
 
getRingKey(int, int) - Static method in class org.jmol.smiles.SmilesGenerator
 
getRingPointer(int) - Static method in class org.jmol.smiles.SmilesParser
 
getRna3dMap(String) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
 
getRnd(float) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getRootExt(String, String[], int) - Static method in class org.jmol.viewer.OutputManager
 
getRotateBondIndex() - Method in class org.jmol.viewer.Viewer
 
getRotateXyzText() - Method in class org.jmol.viewer.TransformManager
 
getRotateZyzText(boolean) - Method in class org.jmol.viewer.TransformManager
 
getRotation(M3) - Method in class org.jmol.viewer.TransformManager
 
getRotationMatrix(P3, P3, float) - Method in class org.jmol.export.___Exporter
 
getRotationMatrix(P3, P3, float, P3, P3) - Method in class org.jmol.export.___Exporter
 
getRotationText() - Method in class org.jmol.viewer.TransformManager
 
getRowCount() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getRowFor(int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getRubberBand() - Method in class org.jmol.viewer.ActionManager
 
getRubberBandSelection() - Method in class org.jmol.viewer.Viewer
 
getRuleBondLength(MinAtom, MinAtom, int, boolean) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getRunPanel() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
getSavedCoordinates(String) - Method in class org.jmol.viewer.StateManager
 
getSavedOrientationText(String) - Method in class org.jmol.viewer.StateManager
 
getSavedState(String) - Method in class org.jmol.viewer.StateManager
 
getSavedStructure(String) - Method in class org.jmol.viewer.StateManager
 
getSaveFileNameFromDialog(Viewer, String, String) - Method in interface org.jmol.api.JmolDialogInterface
 
getSaveFileNameFromDialog(Viewer, String, String) - Method in class org.jmol.dialog.Dialog
 
getScale() - Method in interface org.jmol.api.JmolModulationSet
 
getScale() - Method in class org.jmol.util.ModulationSet
 
getScalePixelsPerAngstrom(boolean) - Method in class org.jmol.viewer.Viewer
 
getScaling(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
 
getSceneScript(String[], Map<String, String>, Lst<Integer>) - Method in class org.jmol.viewer.OutputManagerAwt
 
getSchemeIndex(String) - Static method in class org.jmol.util.ColorEncoder
 
getScreenDim() - Method in class org.jmol.viewer.Viewer
 
getScreenHeight() - Method in class org.jmol.api.JmolViewer
 
getScreenHeight() - Method in class org.jmol.viewer.Viewer
 
getScreenImage(boolean) - Method in class org.jmol.g3d.Graphics3D
 
getScreenImage(boolean) - Method in class org.jmol.util.GData
 
getScreenImageBuffer(Object, boolean) - Method in class org.jmol.api.JmolViewer
 
getScreenImageBuffer(Object, boolean) - Method in class org.jmol.viewer.Viewer
Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo
getScreenNormal(T3, T3, float) - Method in class org.jmol.export.__RayTracerExporter
 
getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager
 
getScreenTemp(T3) - Method in class org.jmol.viewer.TransformManager4D
 
getScreenWidth() - Method in class org.jmol.api.JmolViewer
 
getScreenWidth() - Method in class org.jmol.viewer.Viewer
 
getScript() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getScript() - Method in class org.jmol.script.ScriptEval
 
getScriptBitSets(String, BS[]) - Method in class org.jmol.shapesurface.Isosurface
 
getScriptButtonPercent() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
getScriptContext(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
getScriptContext(String) - Method in class org.jmol.script.ScriptEval
 
getScriptContext(String) - Method in class org.jmol.viewer.Viewer
 
getScriptEditor() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
getScriptEditor() - Method in class org.jmol.console.GenericConsole
 
getScriptEditor() - Method in class org.jmol.console.JmolConsole
 
getScriptEditor() - Method in class org.jmol.consolejs.AppletConsole
 
getScriptID(ScriptContext) - Method in class org.jmol.scriptext.CmdExt
 
getScriptItem(boolean, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
getScriptItem(boolean, boolean) - Method in class org.jmol.script.ScriptManager
 
getScriptManager() - Method in class org.jmol.viewer.Viewer
 
getScriptParams() - Method in class org.jmol.jvxl.readers.Parameters
 
getScriptQueue() - Method in interface org.jmol.api.JmolScriptManager
 
getScriptQueue() - Method in class org.jmol.script.ScriptManager
 
getScriptQueueInfo() - Method in class org.jmol.viewer.Viewer
 
getSearch(String, int, BS) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
getSearch(SmilesSearch, String, int) - Method in class org.jmol.smiles.SmilesParser
 
getSection(String, String, boolean) - Method in class org.jmol.adapter.readers.simple.JSONReader
 
getSegments() - Method in class org.jmol.modelsetbio.ProteinStructure
 
getSelectCodeRange(ModelSet, int[]) - Method in class org.jmol.modelset.Model
 
getSelectCodeRange(ModelSet, int[]) - Method in class org.jmol.modelsetbio.BioModel
 
getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in interface org.jmol.atomdata.AtomDataServer
 
getSelectedAtomIterator(BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
getSelectedAtomIterator(BS, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
getSelectedAtoms() - Method in class org.jmol.viewer.SelectionManager
 
getSelectedAtomsNoSubset() - Method in class org.jmol.viewer.SelectionManager
 
getSelectedGroupCountWithinChain() - Method in class org.jmol.modelset.Atom
 
getSelectedGroupIndex() - Method in class org.jmol.modelset.Group
 
getSelectedGroupIndexWithinChain() - Method in class org.jmol.modelset.Atom
 
getSelectedMonomerCount() - Method in class org.jmol.modelset.Group
 
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.BioPolymer
 
getSelectedMonomerCount() - Method in class org.jmol.modelsetbio.Monomer
 
getSelectedMonomerCountWithinPolymer() - Method in class org.jmol.modelset.Atom
 
getSelectedMonomerIndex() - Method in class org.jmol.modelset.Group
 
getSelectedMonomerIndex() - Method in class org.jmol.modelsetbio.Monomer
 
getSelectedMonomerIndexWithinPolymer() - Method in class org.jmol.modelset.Atom
 
getSelectionAtoms(Lst<Object>, int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Add selected atoms to a growing bit set.
getSelectionCount() - Method in class org.jmol.viewer.SelectionManager
 
getSelectionHaloEnabled() - Method in class org.jmol.modelset.ModelSet
 
getSelectionHaloEnabled(boolean) - Method in class org.jmol.viewer.Viewer
 
getSelections() - Method in class org.jmol.smiles.SmilesSearch
htNested may contain $(select xxxx) primitives.
getSelectionState(SelectionManager, SB) - Method in class org.jmol.viewer.StateCreator
 
getSeqcode() - Method in class org.jmol.modelset.Atom
 
getSeqCode(T) - Static method in class org.jmol.script.ScriptExpr
 
getSeqcodeBits(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getSeqcodeFor(int, char) - Static method in class org.jmol.modelset.Group
 
getSeqcodeString() - Method in class org.jmol.modelset.Atom
 
getSeqcodeString() - Method in class org.jmol.modelset.Group
 
getSeqcodeStringFor(int) - Static method in class org.jmol.modelset.Group
 
getSeqID() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getSeqID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getSeqID() - Method in class org.jmol.modelset.Atom
 
getSeqNo(int, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
getSeqNumberFor(int) - Static method in class org.jmol.modelset.Group
 
getSequence() - Method in class org.jmol.modelsetbio.BioPolymer
 
getSequence() - Method in class org.jmol.viewer.ActionManager
 
getSequenceBits(ModelSet, String, BS) - Method in class org.jmol.modelset.Model
 
getSequenceBits(String, BS) - Method in class org.jmol.modelset.ModelSet
 
getSequenceBits(ModelSet, String, BS) - Method in class org.jmol.modelsetbio.BioModel
 
getSequenceCode(boolean) - Method in class org.jmol.script.ScriptTokenParser
 
getSequenceNumber(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getSequenceNumber() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getSequenceNumber() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getSequenceNumber(int) - Method in interface org.jmol.api.PymolAtomReader
 
getSerial(int, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
getSerial() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getSerial() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getSerialID() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getSerialID() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getSetAxesTypeMad(int) - Method in class org.jmol.script.ScriptEval
 
getSetHistory(int) - Method in class org.jmol.api.JmolViewer
 
getSetHistory(int) - Method in class org.jmol.util.CommandHistory
Options include: all Integer.MAX_VALUE n prev n >= 1 next -1 set max to -2 - n n <= -3 just clear -2 clear and turn off; return "" 0 clear and turn on; return "" Integer.MIN_VALUE;
getSetHistory(int) - Method in class org.jmol.viewer.Viewer
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;
getSettableTokFromString(String) - Static method in class org.jmol.script.T
 
getSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getSettingFloat(int) - Method in class org.jmol.script.ScriptEval
 
getSettingInt(int) - Method in class org.jmol.script.ScriptEval
 
getSettings(String) - Method in class org.jmol.shapesurface.MolecularOrbital
 
getSettingStr(int, boolean) - Method in class org.jmol.script.ScriptEval
Accept an unquoted string if there is just one parameter regardless of its type.
getShadeB(float, float, float) - Method in class org.jmol.util.Shader
 
getShadeF(float, float, float) - Method in class org.jmol.util.Shader
 
getShadeFp8(float, float, float) - Method in class org.jmol.util.Shader
 
getShadeIndex(short) - Method in class org.jmol.g3d.Graphics3D
 
getShadeIndex(float, float, float) - Method in class org.jmol.util.Shader
 
getShadeIndexP3(P3, P3, P3) - Method in class org.jmol.g3d.Graphics3D
 
getShadeN(float, float, float, float) - Method in class org.jmol.util.Shader
 
getShades(short) - Method in class org.jmol.util.GData
 
getShades(short) - Method in class org.jmol.util.Shader
 
getShades2(int, boolean) - Method in class org.jmol.util.Shader
 
getShadesG(short) - Method in class org.jmol.util.Shader
 
getShape(int) - Method in class org.jmol.viewer.ShapeManager
 
getShapeClassName(int, boolean) - Static method in class org.jmol.viewer.JC
 
getShapeDetail() - Method in class org.jmol.shape.Shape
 
getShapeDetail() - Method in class org.jmol.shapespecial.Dipoles
 
getShapeDetail() - Method in class org.jmol.shapespecial.Draw
 
getShapeDetail() - Method in class org.jmol.shapesurface.Isosurface
 
getShapeErrorState() - Method in class org.jmol.viewer.Viewer
 
getShapeIdFromObjectName(String) - Method in class org.jmol.viewer.ShapeManager
Returns the shape type index for a shape object given the object name.
getShapeInfo() - Method in class org.jmol.viewer.PropertyManager
 
getShapely() - Method in class org.jmol.util.ColorEncoder
 
getShapeProperty(int, String) - Method in class org.jmol.script.ScriptEval
 
getShapeProperty(int, String) - Method in class org.jmol.scriptext.CmdExt
 
getShapeProperty(int, String) - Method in class org.jmol.viewer.Viewer
 
getShapePropertyAsInt(int, String) - Method in class org.jmol.viewer.Viewer
 
getShapePropertyData(int, String, Object[]) - Method in class org.jmol.script.ScriptEval
 
getShapePropertyData(int, String, Object[]) - Method in class org.jmol.viewer.ShapeManager
 
getShapePropertyIndex(int, String, int) - Method in class org.jmol.scriptext.CmdExt
 
getShapePropertyIndex(int, String, int) - Method in class org.jmol.viewer.ShapeManager
 
getShapes() - Method in class org.jmol.viewer.ShapeManager
 
getShapeSetState(AtomShape, Shape, int, Group[], BS, Map<String, BS>, Map<String, BS>) - Method in class org.jmol.viewer.JmolStateCreator
 
getShapeSetState(AtomShape, Shape, int, Group[], BS, Map<String, BS>, Map<String, BS>) - Method in class org.jmol.viewer.StateCreator
 
getShapeSetState(AtomShape, Shape, int, Group[], BS, Map<String, BS>, Map<String, BS>) - Method in class org.jmol.viewer.Viewer
 
getShapeState() - Method in class org.jmol.shape.AtomShape
 
getShapeState() - Method in class org.jmol.shape.Axes
 
getShapeState() - Method in class org.jmol.shape.Balls
 
getShapeState() - Method in class org.jmol.shape.Echo
 
getShapeState() - Method in class org.jmol.shape.FontLineShape
 
getShapeState() - Method in class org.jmol.shape.Frank
 
getShapeState() - Method in class org.jmol.shape.Halos
 
getShapeState() - Method in class org.jmol.shape.Hover
 
getShapeState() - Method in class org.jmol.shape.Labels
 
getShapeState() - Method in class org.jmol.shape.Measures
 
getShapeState() - Method in class org.jmol.shape.Shape
 
getShapeState() - Method in class org.jmol.shape.Sticks
 
getShapeState() - Method in class org.jmol.shape.Uccage
 
getShapeState() - Method in class org.jmol.shapebio.BioShapeCollection
 
getShapeState() - Method in class org.jmol.shapecgo.CGO
 
getShapeState() - Method in class org.jmol.shapespecial.Dipole
 
getShapeState() - Method in class org.jmol.shapespecial.Dipoles
 
getShapeState() - Method in class org.jmol.shapespecial.Dots
 
getShapeState() - Method in class org.jmol.shapespecial.Draw
 
getShapeState() - Method in class org.jmol.shapespecial.Ellipsoids
 
getShapeState() - Method in class org.jmol.shapespecial.Polyhedra
 
getShapeState() - Method in class org.jmol.shapesurface.Isosurface
 
getShapeState() - Method in class org.jmol.shapesurface.LcaoCartoon
 
getShapeState() - Method in class org.jmol.shapesurface.MolecularOrbital
 
getShapeState(Shape) - Method in class org.jmol.viewer.JmolStateCreator
 
getShapeState(SB, boolean, int) - Method in class org.jmol.viewer.StateCreator
 
getShapeState(Shape) - Method in class org.jmol.viewer.StateCreator
 
getShapeState(Shape) - Method in class org.jmol.viewer.Viewer
 
getShapeType(int) - Method in class org.jmol.script.ScriptEval
 
getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JC
 
getSheetStructures() - Method in class org.jmol.dssx.DSSP
"sheet =: a set of one or more ladders connected by shared residues" (p.
getShellOrder(int) - Static method in class org.jmol.quantum.MOCalculation
 
getShowAxes() - Method in class org.jmol.viewer.Viewer
 
getShowBbcage() - Method in class org.jmol.viewer.Viewer
 
getShowFrank() - Method in class org.jmol.viewer.Viewer
 
getShowNavigationPoint() - Method in class org.jmol.viewer.Viewer
 
getShowUnitCell() - Method in class org.jmol.viewer.Viewer
 
getSigma() - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getSignature() - Method in interface org.jmol.api.JmolScriptFunction
 
getSignature() - Method in class org.jmol.script.ScriptFunction
 
getSiteMultiplicity(P3) - Method in interface org.jmol.api.SymmetryInterface
 
getSiteMultiplicity(P3, UnitCell) - Method in class org.jmol.symmetry.SpaceGroup
 
getSiteMultiplicity(P3) - Method in class org.jmol.symmetry.Symmetry
 
getSize(int) - Method in class org.jmol.shape.AtomShape
 
getSize(int) - Method in class org.jmol.shape.Shape
overridden in Dots, CGOMesh, and AtomShape
getSize(int) - Static method in class org.jmol.shapecgo.CGOMesh
 
getSize(int) - Method in class org.jmol.shapespecial.Dots
 
getSizeG(Group) - Method in class org.jmol.shape.Shape
BioShapeCollection only
getSizeG(Group) - Method in class org.jmol.shapebio.BioShapeCollection
 
getSlabColor() - Method in class org.jmol.util.MeshSurface
 
getSlabDepthPlane(boolean) - Method in class org.jmol.viewer.TransformManager
 
getSlabObjectType(int, Object, boolean, Object) - Static method in class org.jmol.util.TempArray
 
getSlabPercentSetting() - Method in class org.jmol.viewer.TransformManager
 
getSlabType() - Method in class org.jmol.util.MeshSurface
 
getSlabWithinRange(float, float) - Static method in class org.jmol.util.TempArray
 
getSlaterConstCartesian(int, double, int, int, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
scales slater using double factorials involving quantum number n, l, and xyz exponents.
getSlaterConstDSpherical(int, double, int, int) - Static method in class org.jmol.adapter.readers.quantum.SlaterReader
spherical scaling factors specifically for x2-y2 and z2 orbitals see http://openmopac.net/Manual/real_spherical_harmonics.html dz2 sqrt((1/2p)(5/8))(2cos2(q) -sin2(q)) sqrt(5/16p)(3z2-r2)/r2 dxz sqrt((1/2p)(15/4))(cos(q)sin(q))cos(f) sqrt(15/4p)(xz)/r2 dyz sqrt((1/2p)(15/4))(cos(q)sin(q))sin(f) sqrt(15/4p)(yz)/r2 dx2-y2 sqrt((1/2p)(15/16))sin2(q)cos2(f) sqrt(15/16p)(x2-y2)/r2 dxy sqrt((1/2p)(15/16))sin2(q)sin2(f) sqrt(15/4p)(xy)/r2 The fact() method returns sqrt(15/4p) for both z2 and x2-y2.
getSlice() - Method in class org.openscience.jmol.app.surfacetool.Slice
 
getSliceAngleXY() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSliceMiddle() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSlicePosition() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSliceThickness() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSmartsMatch(String, BS) - Method in class org.jmol.api.JmolViewer
 
getSmartsMatch(String, BS) - Method in class org.jmol.viewer.Viewer
 
getSmiles(BS) - Method in class org.jmol.api.JmolViewer
 
getSmiles(Node[], int, BS, boolean, boolean, boolean, String, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSmiles(Node[], int, BS, boolean) - Method in class org.jmol.smiles.SmilesGenerator
 
getSmiles(SB, Node, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesGenerator
 
getSmiles(Node[], int, BS, boolean, boolean, boolean, String, boolean) - Method in class org.jmol.smiles.SmilesMatcher
 
getSmiles(BS) - Method in class org.jmol.viewer.Viewer
 
getSmilesComponent(Node, BS, boolean) - Method in class org.jmol.smiles.SmilesGenerator
creates a valid SMILES string from a model.
getSmilesCorrelation(BS, BS, String, Lst<P3>, Lst<P3>, M4, Lst<BS>, boolean, boolean, int[][], P3, boolean, boolean) - Method in interface org.jmol.script.JmolSmilesExtension
 
getSmilesCorrelation(BS, BS, String, Lst<P3>, Lst<P3>, M4, Lst<BS>, boolean, boolean, int[][], P3, boolean, boolean) - Method in class org.jmol.scriptext.SmilesExt
The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.
getSmilesExt() - Method in class org.jmol.script.ScriptEval
 
getSmilesMatcher() - Method in class org.jmol.viewer.Viewer
 
getSmilesMatches(String, String, BS, BS, boolean, boolean) - Method in interface org.jmol.script.JmolSmilesExtension
 
getSmilesMatches(String, String, BS, BS, boolean, boolean) - Method in class org.jmol.scriptext.SmilesExt
 
getSmilesOpt(BS, int, int, boolean, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
returns the SMILES string for a sequence or atom set does not include attached protons on groups
getSolventPoints(IsoSolventReader.Edge, int, int, int) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getSource(EventObject) - Method in class org.jmol.popup.AwtSwingPopupHelper
returns the SwingComponent wrapper for this item
getSourceActions(JComponent) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
getSpaceGroup() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroup() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupInfo(ModelSet, String) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupInfo(ModelSet, String) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupInfo(Symmetry, int, String, int, P3, P3, String, ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
 
getSpaceGroupInfoStr(String, SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupInfoStr(String, SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupName() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupName() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupOperation(int) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupOperation(int) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupOperationCode(int) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupOperationCode(int) - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroupOperationCount() - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupOperationCount() - Method in class org.jmol.symmetry.Symmetry
 
getSpaceGroups() - Static method in class org.jmol.symmetry.SpaceGroup
 
getSpaceGroupXyz(int, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getSpaceGroupXyz(int, boolean) - Method in class org.jmol.symmetry.Symmetry
 
getSpanningVectors() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getSparseMatrix(CifReader, String, int, int) - Method in class org.jmol.adapter.readers.cif.MSCifRdr
 
getSpartanDirs(String) - Static method in class org.jmol.io.JmolUtil
read the output file from the Spartan directory and decide from that what files need to be read and in what order - usually M0001 or a set of Profiles.
getSpartanFileList(String, String[]) - Static method in class org.jmol.io.JmolUtil
returns the list of files to read for every Spartan spardir.
getSpartanFileList(String) - Method in class org.jmol.viewer.FileManager
 
getSpecialAtom(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
 
getSpecialAtomName(int) - Static method in class org.jmol.modelsetbio.Resolver
 
getSpecialAtomPoint(byte[], byte) - Method in class org.jmol.modelsetbio.Monomer
 
getSpecialLabel(String, String) - Method in class org.jmol.popup.JmolGenericPopup
menus or menu items with SPECIAL in their name are sent here for on-the-fly labeling
getSpecName(String) - Method in class org.jmol.modelset.AtomCollection
 
getSpecNameOrNull(String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getSpecular() - Method in class org.jmol.util.GData
 
getSpecularExponent() - Method in class org.jmol.util.GData
 
getSpecularPercent() - Method in class org.jmol.util.GData
 
getSpecularPower() - Method in class org.jmol.util.GData
 
getSpeedPixelsPerMillisecond(int, int) - Method in class org.jmol.viewer.Gesture
 
getSPF(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSPFv(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getSphereData(int) - Static method in class org.jmol.util.MeshSurface
Calculates the data (faces, vertices, normals) for a sphere.
getSphereResource() - Method in class org.jmol.export._IdtfExporter
 
getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
 
getSpinAxis(String, int) - Method in class org.jmol.shapespecial.Draw
 
getSpinCenter(String, int, int) - Method in class org.jmol.shapespecial.Draw
 
getSpinOp(int) - Method in interface org.jmol.api.SymmetryInterface
 
getSpinOp(int) - Method in class org.jmol.symmetry.Symmetry
 
getSpinOp() - Method in class org.jmol.symmetry.SymmetryOperation
Magnetic spin operations have a flag m=1 or m=-1 (m or -m) that indicates how the vector quantity changes with symmetry.
getSpinState(boolean) - Method in class org.jmol.viewer.JmolStateCreator
 
getSpinState(boolean) - Method in class org.jmol.viewer.StateCreator
 
getSpinState() - Method in class org.jmol.viewer.Viewer
 
getSSMapAtom(String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getStandardLabelFormat(int) - Method in class org.jmol.viewer.Viewer
 
getStandardPdbHydrogenCount(String) - Static method in class org.jmol.modelsetbio.Resolver
 
getStartChainID() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStartChainID() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStartInsertionCode() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStartInsertionCode() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStartSequenceNumber() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStartSequenceNumber() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getState() - Method in interface org.jmol.api.JmolGestureServerInterface
 
getState() - Method in interface org.jmol.api.JmolModulationSet
 
getState(SB) - Method in interface org.jmol.api.JmolNMRInterface
 
getState(SB) - Method in class org.jmol.quantum.NMRCalculation
 
getState(String) - Method in class org.jmol.shape.Mesh
 
getState() - Method in class org.jmol.shapespecial.Polyhedron
 
getState() - Method in class org.jmol.symmetry.UnitCell
 
getState() - Method in class org.jmol.util.ModulationSet
 
getStateAtoms(SB) - Method in class org.jmol.shapespecial.Ellipsoids
 
getStateCreator() - Method in class org.jmol.viewer.Viewer
 
getStateID(SB) - Method in class org.jmol.shapespecial.Ellipsoids
 
getStateInfo() - Method in class org.jmol.api.JmolViewer
 
getStateInfo() - Method in class org.jmol.viewer.Viewer
 
getStateInfo3(String, int, int) - Method in class org.jmol.viewer.Viewer
 
getStateScript(String, int, int) - Method in class org.jmol.viewer.JmolStateCreator
 
getStateScript(String, int, int) - Method in class org.jmol.viewer.StateCreator
 
getStaticGraphics(Object, boolean) - Static method in class org.jmol.awt.Image
 
getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
 
getStaticGraphics(Object, boolean) - Static method in class org.jmol.awtjs.Image
 
getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs.Platform
 
getStaticGraphics(Object, boolean) - Static method in class org.jmol.awtjs2d.Image
 
getStaticGraphics(Object, boolean) - Method in class org.jmol.awtjs2d.Platform
 
getStatusChanged(String) - Method in class org.jmol.viewer.StatusManager
 
getStatusChanged(String) - Method in class org.jmol.viewer.Viewer
 
getStereoFlag(Node, Node[], int, VTemp) - Static method in class org.jmol.smiles.SmilesGenerator
 
getStereoMode(String) - Static method in enum org.jmol.c.STER
 
getStereoRotationMatrix(boolean) - Method in class org.jmol.viewer.TransformManager
 
getStr(int, int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
safe string parsing of line.substring(col1, col2);
getStraightness(float) - Static method in class org.jmol.modelsetbio.BioPolymer
 
getStrandCount() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStrandCount() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStrandCount(int) - Method in class org.jmol.viewer.Viewer
 
getString(String) - Method in class org.jmol.i18n.GT
 
getString(String) - Method in class org.jmol.i18n.Resource
 
getString() - Method in class org.jmol.modelset.Measurement
 
getString(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getString(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
getStringDetail() - Method in class org.jmol.modelset.Measurement
 
getStringInfo(String, String, String, String, String, Map<String, Object[]>, String, Lst<Object[]>, String) - Method in class org.jmol.jsv.JDXMOLParser
 
getStringObjectAsVariable(String, String) - Method in class org.jmol.script.ScriptExpr
 
getStringParameter(String, boolean) - Method in class org.jmol.script.ScriptParam
 
getStrings(String, int, int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getStringUsing(Viewer, String, String) - Method in class org.jmol.modelset.Measurement
 
getStringX(String) - Static method in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
getStrucNo() - Method in class org.jmol.modelset.Atom
 
getStrucNo() - Method in class org.jmol.modelset.Group
 
getStrucNo() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getStructure() - Method in class org.jmol.modelset.Group
 
getStructure() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
getStructure() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
getStructure(String) - Method in class org.jmol.popup.PopupResource
 
getStructuredModels() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStructuredModels() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStructureID() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStructureID() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStructureId() - Method in class org.jmol.modelset.Atom
 
getStructureId() - Method in class org.jmol.modelset.Group
 
getStructureId() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getStructureId() - Method in class org.jmol.modelsetbio.Monomer
 
getStructureIterator(Object) - Method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
getStructureIterator(Object) - Method in class org.jmol.api.JmolAdapter
Get a StructureIterator.
getStructureList() - Method in class org.jmol.modelset.ModelSet
 
getStructureList() - Method in class org.jmol.viewer.GlobalSettings
 
getStructureList() - Method in class org.jmol.viewer.Viewer
 
getStructureMidPoint(int) - Method in class org.jmol.modelsetbio.ProteinStructure
 
getStructureState() - Method in class org.jmol.viewer.Viewer
 
getStructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getStructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getStuctureAsText(String, String[][], String[][]) - Method in class org.jmol.popup.PopupResource
 
getSubPattern(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
 
getSubstructureSet(String, Node[], int, BS, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSubstructureSet(String, Node[], int, BS, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
Returns a bitset matching the pattern within atoms.
getSubstructureSetArray(String, Node[], int, BS, BS, boolean, boolean) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSubstructureSetArray(String, Node[], int, BS, BS, boolean, boolean) - Method in class org.jmol.smiles.SmilesMatcher
Returns a vector of bitsets indicating which atoms match the pattern.
getSubstructureSets(String[], Node[], int, int, BS, Lst<BS>, Lst<BS>[]) - Method in interface org.jmol.api.SmilesMatcherInterface
 
getSubstructureSets(String[], Node[], int, int, BS, Lst<BS>, Lst<BS>[]) - Method in class org.jmol.smiles.SmilesMatcher
called by ForceFieldMMFF.setAtomTypes
getSubstructureType() - Method in class org.jmol.adapter.smarter.StructureIterator
 
getSubstructureType() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
getSubsystem(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getSubSystemUnitCell() - Method in interface org.jmol.api.JmolModulationSet
 
getSubSystemUnitCell() - Method in class org.jmol.util.ModulationSet
 
getSupported(String) - Method in class org.jmol.i18n.GT
 
getSupported(Language[], String) - Static method in class org.jmol.i18n.Language
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.AnimationWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.BackgroundColorWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.ConsoleWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.DownLoadWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
 
getSupportFileNames() - Method in class org.openscience.jmol.app.webexport.Widgets.Widget
The list of files returned by this function should contain the full path to each file.
getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
getSurfaceAtomIndex() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSurfaceData() - Method in class org.jmol.jvxl.readers.EfvetReader
 
getSurfaceData() - Method in class org.jmol.jvxl.readers.NffReader
 
getSurfaceData() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
 
getSurfaceData() - Method in class org.jmol.jvxl.readers.PmeshReader
 
getSurfaceData() - Method in class org.jmol.jvxl.readers.PolygonFileReader
 
getSurfaceDistance100() - Method in class org.jmol.modelset.Atom
 
getSurfaceDistance100(int) - Method in class org.jmol.modelset.AtomCollection
 
getSurfaceDistanceMax() - Method in class org.jmol.modelset.AtomCollection
 
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.IsoSolventReader
TEST: alternative EXACT position of fraction for spherical MarchingCubes FOR: ttest.xyz: 2 isosurface molecular test showing discontinuities C -2.70 0 0 C 2.75 0 0 RESULT: LINEAR (points slightly within R): $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.06620391572324] isosurfaceVolume = [41.639681683494324] NONLINEAR: $ isosurface resolution 5 volume area solvent 1.5 full isosurface1 created with cutoff=0.0; number of isosurfaces = 1 isosurfaceArea = [75.11873783245028] isosurfaceVolume = [41.727027252180655] revision 3/16/2014: isosurfaceArea = [75.13146821881998] isosurfaceVolume = [41.74598178064965] MSMS: msms -if ttest.xyzrn -of ttest -density 5 MSMS 2.6.1 started on Local PC Copyright M.F.
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSurfacePointAndFraction(float, boolean, float, float, T3, V3, int, int, int, int, int, float[], T3) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in interface org.jmol.jvxl.api.VertexDataServer
getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getSurfacePointIndexAndFraction(float, boolean, int, int, int, P3i, int, int, float, float, T3, V3, boolean, float[]) - Method in class org.jmol.shapesurface.Isosurface
 
getSurfaces() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getSurfaceSet() - Method in class org.jmol.jvxl.data.MeshData
 
getSurfaceSetForLevel(int) - Method in class org.jmol.jvxl.data.MeshData
 
getSurfaceSets() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
getSwingComponent(Object) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
getSwingComponent(Object) - Method in class org.jmol.popup.JSSwingPopupHelper
 
getSwingComponent(Object) - Method in interface org.jmol.popup.PopupHelper
 
getSym - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
 
getSymbol(String) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
getSymbolic() - Method in class org.jmol.adapter.readers.simple.InputReader
 
getSymbolic(String) - Method in class org.jmol.adapter.readers.simple.InputReader
 
getSymMatrices(int) - Method in class org.jmol.modelset.ModelSet
 
getSymmetry(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getSymmetry() - Method in class org.jmol.adapter.readers.cif.Subsystem
 
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getSymmetry() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
getSymmetry(Viewer, String) - Static method in class org.jmol.api.Interface
 
getSymmetry() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getSymmetryFromCode(String) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
getSymmetryFromCode(String) - Method in interface org.jmol.adapter.smarter.MSInterface
 
getSymmetryInfo(ModelSet, int, int, SymmetryInterface, String, int, P3, P3, String, int) - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryInfo(ModelSet, int, int, SymmetryInterface, String, int, P3, P3, String, int) - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryInfo(Symmetry, int, int, Symmetry, String, int, P3, P3, String, int, ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
 
getSymmetryInfoAsString() - Method in class org.jmol.modelset.ModelSet
 
getSymmetryInfoAtom(ModelSet, BS, String, int, P3, P3, String, int) - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryInfoAtom(ModelSet, BS, String, int, P3, P3, String, int) - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryInfoAtom(BS, String, int, P3, P3, String, int, ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
 
getSymmetryInfoStr() - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryInfoStr() - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryInfoString(ModelSet, int, int, P3, P3, String, String) - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryInfoString(ModelSet, int, int, P3, P3, String, String) - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryInfoString(Symmetry, int, int, P3, P3, String, String, ModelSet) - Method in class org.jmol.symmetry.SymmetryDesc
 
getSymmetryOperations() - Method in interface org.jmol.api.SymmetryInterface
 
getSymmetryOperations() - Method in class org.jmol.symmetry.Symmetry
 
getSymmetryOperatorList(boolean) - Method in class org.jmol.modelset.Atom
 
getSymmetryTranslation(int, int[], int) - Method in class org.jmol.modelset.Atom
Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom.
getSymOp() - Method in class org.jmol.modelset.Atom
 
getSymTemp(boolean) - Method in class org.jmol.modelset.ModelSet
 
getSyncMode() - Method in class org.jmol.viewer.StatusManager
 
getTabulatedPotential(Atom) - Method in class org.jmol.quantum.MepCalculation
 
getTaintedAtoms(byte) - Method in class org.jmol.modelset.AtomCollection
 
getTargetValence() - Method in class org.jmol.modelset.Atom
 
getTensor(Atom, String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
getTensor(Viewer, float[]) - Method in interface org.jmol.api.SymmetryInterface
 
getTensor(Viewer, float[]) - Method in class org.jmol.symmetry.Symmetry
 
getTensor(Viewer, float[]) - Method in class org.jmol.symmetry.UnitCell
 
getTensorInfo(String, String, BS) - Method in interface org.jmol.api.JmolNMRInterface
 
getTensorInfo(String, String, BS) - Method in class org.jmol.quantum.NMRCalculation
 
getTensorList(Lst<Object>) - Static method in class org.jmol.modelset.AtomCollection
 
getTensors() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getTensors() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getTensors() - Method in class org.jmol.modelset.Atom
 
getTerminatorAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
getTerminatorAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getTerminatorAtom() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
getTerminatorPoint() - Method in class org.jmol.modelsetbio.BioPolymer
 
getTestFlag(int) - Method in class org.jmol.viewer.Viewer
 
getText() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
getText() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
getText() - Method in class org.jmol.console.GenericConsole
 
getText() - Method in interface org.jmol.console.GenericTextArea
 
getText() - Method in class org.jmol.console.ScriptEditor
 
getText() - Method in class org.jmol.modelset.Text
 
getText() - Method in class org.jmol.popup.AwtSwingComponent
 
getText() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
getText() - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
getTextPixels(String, Font, Object, Object, int, int, int) - Static method in class org.jmol.awt.Image
 
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
 
getTextPixels(String, Font, Object, Object, int, int, int) - Static method in class org.jmol.awtjs.Image
 
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs.Platform
 
getTextPixels(String, Font, Object, int, int, int) - Static method in class org.jmol.awtjs2d.Image
 
getTextPixels(String, Font, Object, Object, int, int, int) - Method in class org.jmol.awtjs2d.Platform
 
getTextPosition() - Method in class org.jmol.util.GData
 
getTextState(Text) - Method in class org.jmol.viewer.StateCreator
 
getTextureName(short) - Method in class org.jmol.export._ObjExporter
Returns the name to be used for the texture associated with the given colix.
getTextWrapper - Static variable in class org.jmol.i18n.GT
 
getTextWrapper() - Static method in class org.jmol.i18n.GT
 
getThermalRadius(int) - Static method in class org.jmol.shapespecial.Ellipsoid
 
getThicknessMax() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getThisContext() - Method in interface org.jmol.api.JmolScriptEvaluator
 
getThisContext() - Method in class org.jmol.script.ScriptEval
 
getThread() - Method in interface org.jmol.api.MinimizerInterface
 
getThread() - Method in class org.jmol.minimize.Minimizer
 
getTimeDifference(int) - Method in class org.jmol.viewer.Gesture
 
getTimeFrom(String) - Static method in class org.jmol.util.Logger
 
getTimerMsg(String, int) - Static method in class org.jmol.util.Logger
 
getTlsGroups - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
getTok() - Method in interface org.jmol.api.JmolScriptFunction
 
getTok() - Method in class org.jmol.script.ScriptFunction
 
getToken(int) - Method in class org.jmol.script.ScriptParam
 
getToken() - Method in class org.jmol.script.ScriptTokenParser
gets the next token and sets global theToken and theValue
getToken(int) - Method in class org.jmol.scriptext.CmdExt
 
getTokenFromName(String) - Static method in class org.jmol.script.T
 
getTokens() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokens() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
getTokensFloat(String, float[], int) - Static method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
getTokensLike(String) - Static method in class org.jmol.script.T
 
getTokensType(Map<String, Object>, int) - Static method in class org.jmol.script.T
 
getTokFromName(String) - Static method in class org.jmol.script.T
 
getTop() - Method in class org.jmol.smiles.SmilesSearch
 
getToPlaneParameter() - Method in class org.jmol.jvxl.data.VolumeData
 
getTorsionAngleRadians(double[], double[], double[], double[], V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
getTorsionKey(int, int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getTorsions() - Method in class org.jmol.minimize.Minimizer
 
getTorsions(Atom[], int[][], float[][], int) - Static method in class org.jmol.scriptext.SmilesExt
 
getTrajectoryIndex(int) - Method in class org.jmol.modelset.ModelSet
 
getTrajectoryState() - Method in class org.jmol.viewer.JmolStateCreator
 
getTrajectoryState() - Method in class org.jmol.viewer.StateCreator
 
getTrajectoryState() - Method in class org.jmol.viewer.Viewer
 
getTrajectoryStep(P3[]) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
getTrajectoryStep(P3[], boolean) - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
getTransferData(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
 
getTransferData(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
getTransferDataFlavors() - Method in class org.jmol.awt.AwtClipboard
 
getTransferDataFlavors() - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
getTransformedVertexVectors() - Method in class org.jmol.util.GData
 
getTransformManager(Viewer, int, int, boolean) - Static method in class org.jmol.viewer.TransformManager
 
getTranslationScript() - Method in class org.jmol.viewer.TransformManager
 
getTranslationXPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslationYPercent() - Method in class org.jmol.viewer.TransformManager
 
getTranslucentFlag(float) - Static method in class org.jmol.util.C
 
getTranslucentLabel(short) - Static method in class org.jmol.shape.Shape
 
getTranslucentLevel(int) - Method in class org.jmol.script.ScriptEval
 
getTriad(T3) - Method in class org.jmol.export.___Exporter
 
getTriad(T3) - Method in class org.jmol.export._PovrayExporter
 
getTriad(int[]) - Method in class org.jmol.export._PovrayExporter
 
getTriangleData(T3, T3, T3) - Static method in class org.jmol.export.MeshData
Calculates the data (faces, vertices, normals) for a triangle.
getTriangleResource(String, T3, T3, T3) - Method in class org.jmol.export._IdtfExporter
 
getTriangles() - Method in class org.jmol.jvxl.readers.EfvetReader
 
getTrimmedLine() - Method in class org.jmol.g3d.LineRenderer
Cohen-Sutherland line clipping used to check visibility.
getTrueAtomCount() - Method in class org.jmol.modelset.Model
 
getType() - Method in interface org.jmol.api.JmolDialogInterface
 
getType(Atom) - Static method in enum org.jmol.c.HB
 
getType() - Method in class org.jmol.dialog.Dialog
 
getType() - Method in class org.jmol.modelsetbio.BioPolymer
 
getType(int) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
 
getType(String) - Static method in class org.jmol.util.Tensor
 
getUndeletedGroupAtomBits(BS) - Method in class org.jmol.viewer.Viewer
 
getUnescapedStringLiteral(boolean) - Method in class org.jmol.script.ScriptCompiler
lookingAtString returned true, and we need to unescape any t, r, n, ", ', x, u, or backslash after a backslash
getUniqueFloatDef(int, int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getUniqueID(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getUniqueID() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getUniqueID() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getUniqueID(int) - Method in interface org.jmol.api.PymolAtomReader
 
getUniqueID() - Method in class org.jmol.modelsetbio.Monomer
 
getUniquePoint(int, int, P3) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getUniqueTensorSet(BS) - Method in interface org.jmol.api.JmolNMRInterface
An attempt to find unique atoms using tensors.
getUniqueTensorSet(BS) - Method in class org.jmol.quantum.NMRCalculation
 
getUnitCell(T3[], boolean, String) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCell() - Method in class org.jmol.modelset.Atom
 
getUnitCell(int) - Method in class org.jmol.modelset.ModelSet
 
getUnitCell() - Method in class org.jmol.shape.Mesh
 
getUnitCell() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getUnitCell(T3[], boolean, String) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellAsArray(boolean) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellAsArray(boolean) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellAsArray(boolean) - Method in class org.jmol.util.SimpleUnitCell
 
getUnitCellForAtom(int) - Method in class org.jmol.modelset.ModelSet
 
getUnitCellInfo() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellInfo() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellInfo(int) - Method in class org.jmol.viewer.Viewer
 
getUnitCellInfoText() - Method in class org.jmol.viewer.Viewer
 
getUnitCellInfoType(int) - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellInfoType(int) - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellMultiplier() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellMultiplier() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellMultiplier() - Method in class org.jmol.symmetry.UnitCell
 
getUnitCellState() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellState() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellVectors() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellVectors() - Method in class org.jmol.symmetry.Symmetry
 
getUnitCellVectors() - Method in class org.jmol.symmetry.UnitCell
 
getUnitCellVertices() - Method in interface org.jmol.api.SymmetryInterface
 
getUnitCellVertices() - Method in class org.jmol.symmetry.Symmetry
 
getUnits() - Method in class org.jmol.minimize.forcefield.Calculations
 
getUnits() - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
 
getUnits() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
getUnitsymmetryInfo() - Method in class org.jmol.symmetry.Symmetry
 
getUnzippedReaderOrStreamFromName(String, byte[], boolean, boolean, boolean, boolean, Map<String, Object>) - Method in class org.jmol.viewer.FileManager
 
getUParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getURLContents(URL, byte[], String) - Static method in class org.jmol.awt.AwtFile
 
getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awt.Platform
 
getURLContents(URL, byte[], String) - Static method in class org.jmol.awtjs2d.JSFile
Note that the JS equivalent passes back a javajs.util.SB
getURLContents(URL, byte[], String, boolean) - Method in class org.jmol.awtjs2d.Platform
 
getURLContentsStatic(URL, byte[], String, boolean) - Static method in class org.jmol.awtjs2d.Platform
In case this needs to be performed directly, without interface
getUseMolecular() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
getUserDirectory() - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Returns a new File referenced by the property 'user.dir', or null if the property is not defined.
getUserFunctionResult(String, Lst<SV>, SV) - Method in class org.jmol.script.ScriptEval
 
getUserFunctionResult(String, Lst<SV>, SV) - Method in class org.jmol.script.ScriptExpr
 
getUserSettableType(String) - Static method in class org.jmol.modelset.AtomCollection
 
getUserVariable(String) - Method in class org.jmol.viewer.GlobalSettings
 
getUtil(String, Viewer, String) - Static method in class org.jmol.api.Interface
 
getV0abc(Object) - Method in interface org.jmol.api.SymmetryInterface
 
getV0abc(Object) - Method in class org.jmol.symmetry.Symmetry
Accepts a string, a 3x3 matrix, or a 4x4 matrix.
getV0abc(Object) - Method in class org.jmol.viewer.Viewer
convert string abc;offset or M3 or M4 to origin and three vectors -- a, b, c.
getV3() - Method in interface org.jmol.api.JmolModulationSet
 
getV3() - Method in class org.jmol.util.ModulationSet
 
getVal(MoveToThread.Slider) - Method in class org.jmol.thread.MoveToThread
 
getVal(float) - Method in class org.jmol.thread.MoveToThread.Slider
 
getValence() - Method in class org.jmol.modelset.Atom
 
getValence() - Method in class org.jmol.modelset.Bond
 
getValence() - Method in class org.jmol.smiles.SmilesAtom
 
getValence() - Method in class org.jmol.smiles.SmilesBond
 
getValence() - Method in interface org.jmol.util.Node
 
getValue(int) - Method in class org.jmol.adapter.readers.simple.InputReader
 
getValue(int, int, int, int) - Method in interface org.jmol.jvxl.api.VertexDataServer
for readers only
getValue(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
getValue(int, int, int) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
 
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getValue(int, int, int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getValue(double, boolean) - Method in class org.jmol.quantum.NciCalculation
 
getValue(int, int, int, int) - Method in class org.jmol.shapesurface.Isosurface
 
getValue(String, String) - Method in class org.jmol.util.GenericApplet
 
getValue(int, int, int, int, int, float[]) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
getValue(int, int, int) - Method in class org.openscience.jvxl.simplewriter.VoxelDataCreator
 
getValue2(int, int, int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getValueAB(float, float) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
getValueArray(int, int, int, int, float[]) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
getValueAt(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
getValueAtPoint(T3, boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
getValueAtPoint(P3) - Method in class org.jmol.quantum.MepCalculation
 
getValueAtPoint2(T3, BS) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
getValueLowerCase(String, String) - Method in class org.jmol.util.GenericApplet
 
getValues() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
getVanderwaalsMar(int, VDW) - Static method in class org.jmol.util.Elements
 
getVanderwaalsMar(int) - Method in class org.jmol.viewer.Viewer
 
getVanderwaalsMarType(int, VDW) - Method in class org.jmol.viewer.Viewer
 
getVanderwaalsRadiusFloat(Viewer, VDW) - Method in class org.jmol.modelset.Atom
 
getVariable(String) - Method in class org.jmol.script.ScriptContext
Context variables go up the stack until a function is found.
getVariable(Object) - Static method in class org.jmol.script.SV
 
getVariableAB(byte[]) - Static method in class org.jmol.script.SV
 
getVariableAD(double[]) - Static method in class org.jmol.script.SV
 
getVariableADD(double[][]) - Static method in class org.jmol.script.SV
 
getVariableAF(float[]) - Static method in class org.jmol.script.SV
 
getVariableAFF(float[][]) - Static method in class org.jmol.script.SV
 
getVariableAI(int[]) - Static method in class org.jmol.script.SV
 
getVariableAII(int[][]) - Static method in class org.jmol.script.SV
 
getVariableAP(T3[]) - Static method in class org.jmol.script.SV
 
getVariableAS(String[]) - Static method in class org.jmol.script.SV
 
getVariableASS(String[][]) - Static method in class org.jmol.script.SV
 
getVariableAV(SV[]) - Static method in class org.jmol.script.SV
 
getVariableList(Lst<?>) - Static method in class org.jmol.script.SV
 
getVariableList() - Method in class org.jmol.viewer.GlobalSettings
 
getVariableList(Map<String, SV>, int, boolean, boolean) - Static method in class org.jmol.viewer.StateManager
 
getVariableMap(Map<String, ?>) - Static method in class org.jmol.script.SV
 
getVariables(String) - Method in class org.jmol.viewer.PropertyManager
 
getVDW(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
getVDW(int) - Method in interface org.jmol.api.PymolAtomReader
 
getVdwClashRadius(ContactPair, double, double, double, double) - Static method in class org.jmol.shapesurface.Contact
well, heh, heh...
getVdwLabel() - Method in enum org.jmol.c.VDW
 
getVdwType(String) - Static method in enum org.jmol.c.VDW
 
getVdwType(VDW) - Method in class org.jmol.modelset.Atom
 
getVdwType2(String) - Static method in enum org.jmol.c.VDW
 
getVectorsAndOrigin() - Method in class org.jmol.jvxl.readers.MapFileReader
 
getVertex() - Method in class org.jmol.jvxl.readers.NffReader
 
getVertex(short, short) - Static method in class org.jmol.util.Geodesic
 
getVertexCount(int) - Static method in class org.jmol.util.Geodesic
 
getVertexIndexFromNumber(int) - Method in class org.jmol.shape.Mesh
 
getVertexList(DrawMesh, int, int) - Static method in class org.jmol.shapespecial.Draw
 
getVertexValues(boolean) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
getVertexVector(int) - Static method in class org.jmol.util.Geodesic
 
getVertexVectors() - Static method in class org.jmol.util.Geodesic
 
getVertexVectors() - Static method in class org.jmol.util.Normix
 
getVertices() - Method in class org.jmol.jvxl.readers.EfvetReader
 
getVertices(Mesh) - Method in class org.jmol.shape.MeshCollection
 
getVertices() - Method in class org.jmol.symmetry.UnitCell
 
getVertices() - Method in class org.jmol.util.MeshSurface
 
getVib() - Method in class org.jmol.adapter.smarter.AtomIterator
Note that atom.vib also serves to deliver specific data items.
getVib() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getVibration(boolean) - Method in interface org.jmol.api.JmolModulationSet
 
getVibration(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
getVibration(boolean) - Method in class org.jmol.util.ModulationSet
 
getVibrationCoord(char) - Method in class org.jmol.modelset.Atom
 
getVibrationCoord(int, char) - Method in class org.jmol.modelset.AtomCollection
 
getVibrationPoint(Vibration, T3, float) - Method in class org.jmol.viewer.TransformManager
 
getVibrationVector() - Method in class org.jmol.modelset.Atom
 
getViewerData() - Method in class org.jmol.popup.JmolGenericPopup
 
getViewpoint() - Method in class org.jmol.export._VrmlExporter
 
getViewScript(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
getViewState(TransformManager, SB) - Method in class org.jmol.viewer.StateCreator
 
getVisibleFramesBitSet() - Method in class org.jmol.api.JmolViewer
 
getVisibleFramesBitSet() - Method in class org.jmol.viewer.Viewer
 
getVisibleSet(boolean) - Method in class org.jmol.modelset.AtomCollection
 
getVisibleVBS() - Method in class org.jmol.shape.Mesh
 
getVisibleVertexBitSet() - Method in class org.jmol.shape.Mesh
 
getVisibleVertexBitSet() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
getVolume(Viewer, VDW) - Method in class org.jmol.modelset.Atom
 
getVolume() - Method in class org.jmol.util.ContactPair
 
getVolumetricVectorLengths() - Method in interface org.jmol.api.VolumeDataInterface
 
getVolumetricVectorLengths() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxel(int, int, int, int) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
getVoxelBitSet(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
getVoxelCounts() - Method in interface org.jmol.api.VolumeDataInterface
 
getVoxelCounts() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelData() - Method in interface org.jmol.api.VolumeDataInterface
 
getVoxelData() - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelDataAt(int) - Method in class org.jmol.jvxl.data.VolumeData
 
getVoxelValue(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
getVParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getWaterAtoms(BS) - Method in class org.jmol.modelset.AtomCollection
 
getWidth(Object) - Static method in class org.jmol.awt.Image
 
getWidth(Object) - Static method in class org.jmol.awtjs2d.Image
 
getWindow(Container) - Static method in class org.jmol.awt.Platform
 
getWindowBorder(String) - Method in class org.openscience.jmol.app.HistoryFile
 
getWindowPosition(String) - Method in class org.openscience.jmol.app.HistoryFile
 
getWindowSize(String) - Method in class org.openscience.jmol.app.HistoryFile
 
getWindowState(SB, int, int) - Method in class org.jmol.viewer.StateCreator
 
getWindowVisibility(String) - Method in class org.openscience.jmol.app.HistoryFile
 
getWingAtom() - Method in class org.jmol.modelsetbio.Monomer
 
getWingPoint(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
getWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
getWithinDistanceVector(Lst<Object[]>, float, P3, BS, boolean) - Method in class org.jmol.scriptext.IsoExt
 
getWord(String) - Method in class org.jmol.popup.PopupResource
 
getWordContents() - Method in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
getWordContents() - Method in class org.jmol.popup.MainPopupResourceBundle
 
getWordContents() - Method in class org.jmol.popup.PopupResource
 
getWorkingRadius(int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
getWorkingRadius(Atom, AtomData) - Method in class org.jmol.modelset.AtomCollection
 
getWrappedState(String, String[], Object, OC) - Method in class org.jmol.viewer.OutputManager
 
getWrappedStateScript() - Method in class org.jmol.viewer.Viewer
 
getX() - Method in class org.jmol.script.ScriptMathProcessor
 
getX(SmilesAtom, Node[], int, boolean, boolean) - Method in class org.jmol.smiles.SmilesSearch
 
getXmlAttrib(String, String) - Static method in class org.jmol.jvxl.readers.XmlReader
 
getXmlData(String, String, boolean, boolean) - Method in class org.jmol.jvxl.readers.XmlReader
 
getXmlPoint(String, String) - Method in class org.jmol.jvxl.readers.XmlReader
 
getXmlType(String) - Static method in class org.jmol.adapter.smarter.Resolver
 
getXOffset(int) - Static method in class org.jmol.viewer.JC
 
getXPlatformLook(JFileChooser) - Static method in class org.jmol.dialog.Dialog
 
getXSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
getXYZ() - Method in class org.jmol.adapter.smarter.AtomIterator
 
getXYZ() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
getXYZ(boolean) - Method in class org.jmol.symmetry.HallRotationTerm
 
getXyz(int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
getXyz(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
 
getXYZFromMatrix(M4, boolean, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getXYZFromRsVs(Matrix, Matrix, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
getYOffset(int) - Static method in class org.jmol.viewer.JC
 
getYzCount() - Method in class org.jmol.jvxl.data.VolumeData
 
getZapName() - Method in class org.jmol.viewer.Viewer
 
getZipDirectory(String, boolean, boolean) - Method in class org.jmol.viewer.FileManager
 
getZipDirectoryAsString(String) - Method in class org.jmol.script.ScriptManager
 
getZoom(int, int, BS, float) - Method in class org.jmol.script.ScriptEval
 
getZoomSetting() - Method in class org.jmol.viewer.TransformManager
 
getZParam(int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
getZshadeState(SB, TransformManager, boolean) - Method in class org.jmol.viewer.StateCreator
 
ghemicalMMLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GhemicalMMReader - Class in org.jmol.adapter.readers.simple
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
GhemicalMMReader() - Constructor for class org.jmol.adapter.readers.simple.GhemicalMMReader
 
ghostCheck - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
ghostOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
ghostPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
gibbsEnergy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
gibbsEnergy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
gibbsEntropy - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
gl_ambient - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
GL_LINE_LOOP - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_LINE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_LINES - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_POINTS - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_TRIANGLE_FAN - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_TRIANGLE_STRIP - Static variable in class org.jmol.shapecgo.CGOMesh
 
GL_TRIANGLES - Static variable in class org.jmol.shapecgo.CGOMesh
 
GLOBAL - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
GLOBAL_CONECT - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_DOMAINS - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_FRACTCOORD - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_ISPDB - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_SYMMETRY - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_UNITCELLS - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
GLOBAL_VALIDATIONS - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
globalBooleans - Static variable in class org.jmol.adapter.smarter.AtomSetCollection
 
globalDoApplySymmetry - Variable in class org.jmol.adapter.readers.xtal.AimsReader
 
globalSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
GlobalSettings - Class in org.jmol.viewer
 
GlobalSettings(Viewer, GlobalSettings, boolean) - Constructor for class org.jmol.viewer.GlobalSettings
 
globalSlabValue - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
globalStrucNo - Static variable in class org.jmol.modelsetbio.ProteinStructure
 
goButton - Variable in class org.openscience.chimetojmol.ChimePanel
 
goButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
GOLD - Static variable in class org.jmol.util.C
 
goPressed(String) - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
goPressed() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Save or else launch povray- ie do our thang!
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
gotoAndReadVoxelData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
gotocmd - Static variable in class org.jmol.script.T
 
gotoCommand(int, boolean, SimpleAttributeSet) - Method in class org.jmol.console.ScriptEditor
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
gotoData(int, int) - Method in class org.jmol.jvxl.readers.XsfReader
 
gotoParsedLine() - Method in class org.jmol.console.ScriptEditor
 
gotoPosition(int, int) - Method in class org.jmol.console.ScriptEditor
 
gotoTop() - Method in class org.jmol.console.ScriptEditor
 
grabPixels(Object, int, int, int[], int, int) - Static method in class org.jmol.awt.Image
 
grabPixels(Object, int, int, int[], int, int) - Method in class org.jmol.awt.Platform
 
grabPixels(Object, int, int) - Static method in class org.jmol.awtjs.Image
 
grabPixels(Object, int, int, int[], int, int) - Method in class org.jmol.awtjs.Platform
 
grabPixels(Object, int, int) - Static method in class org.jmol.awtjs2d.Image
 
grabPixels(Object, int, int, int[], int, int) - Method in class org.jmol.awtjs2d.Platform
 
grad - Variable in class org.jmol.quantum.NciCalculation
 
GRADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
gradient_max_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gradient_min_length - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gradient_min_slope - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gradient_normal_min_dot - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gradient_spacing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gradient_step_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gradient_symmetry - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gradients - Variable in class org.jmol.minimize.forcefield.Calculations
 
Graphics3D - Class in org.jmol.g3d
Provides high-level graphics primitives for 3D visualization for the software renderers.
Graphics3D() - Constructor for class org.jmol.g3d.Graphics3D
 
graphicsForMetrics - Variable in class org.jmol.util.GData
 
graphicsForTextOrImage - Variable in class org.jmol.g3d.Platform3D
 
GRAY - Static variable in class org.jmol.util.C
 
GRAY - Static variable in class org.jmol.util.ColorEncoder
 
GREEN - Static variable in class org.jmol.util.C
 
greyscalerendering - Static variable in class org.jmol.script.T
 
greyscaleRendering - Variable in class org.jmol.viewer.GlobalSettings
 
grid_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
grid_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
grid_slot - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
gridpoints - Static variable in class org.jmol.script.T
 
gRight - Variable in class org.jmol.util.GenericApplet
 
gRight - Variable in class org.jmol.viewer.Viewer
A graphics from a "slave" stereo display that has been synchronized with this this applet.
GromacsReader - Class in org.jmol.adapter.readers.more
 
GromacsReader() - Constructor for class org.jmol.adapter.readers.more.GromacsReader
 
gromacsWideFormat - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
gromacsWideFormat - Variable in class org.jmol.adapter.readers.pdb.PqrReader
 
group(String) - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
group - Variable in class org.jmol.modelset.Atom
 
Group - Class in org.jmol.modelset
 
Group() - Constructor for class org.jmol.modelset.Group
 
group - Static variable in class org.jmol.script.T
 
group1 - Variable in class org.jmol.modelset.Group
 
group1 - Static variable in class org.jmol.script.T
 
group3 - Variable in class org.jmol.adapter.smarter.Atom
 
group3Count - Static variable in class org.jmol.modelsetbio.Resolver
 
group3Counts - Variable in class org.jmol.modelset.ModelLoader
 
group3Counts - Variable in class org.jmol.popup.JmolGenericPopup
 
group3List - Variable in class org.jmol.popup.JmolGenericPopup
 
group3Lists - Variable in class org.jmol.modelset.ModelLoader
 
group3NameCount - Static variable in class org.jmol.modelsetbio.Resolver
 
group3Names - Static variable in class org.jmol.modelset.Group
 
group3Of - Variable in class org.jmol.modelset.ModelLoader
 
group3s - Variable in class org.jmol.adapter.readers.more.MdTopReader
 
group_arrow_prefix - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
group_auto_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
group_full_member_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
GROUP_PDB - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
groupCount - Variable in class org.jmol.modelset.Chain
 
groupCount - Variable in class org.jmol.modelset.Model
 
groupCount - Variable in class org.jmol.modelset.ModelLoader
 
groupID - Variable in class org.jmol.modelset.Group
 
groupID - Variable in class org.jmol.multitouch.ActionManagerMT
 
groupid - Static variable in class org.jmol.script.T
 
GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JC
 
GROUPID_ARGININE - Static variable in class org.jmol.viewer.JC
 
GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JC
 
GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JC
 
GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_ION_MAX - Static variable in class org.jmol.viewer.JC
 
GROUPID_ION_MIN - Static variable in class org.jmol.viewer.JC
 
GROUPID_LYSINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JC
 
GROUPID_PROLINE - Static variable in class org.jmol.viewer.JC
 
GROUPID_SOLVENT_MIN - Static variable in class org.jmol.viewer.JC
 
GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JC
 
GROUPID_WATER - Static variable in class org.jmol.viewer.JC
 
groupIndex - Variable in class org.jmol.modelset.Group
 
groupindex - Static variable in class org.jmol.script.T
 
groups - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
groups - Variable in class org.jmol.modelset.Chain
 
groups - Variable in class org.jmol.modelset.ModelLoader
 
growAtomArrays(int) - Method in class org.jmol.modelset.ModelSet
 
GS - Static variable in class org.jmol.quantum.QS
 
GT - Class in org.jmol.i18n
The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12 implementing translations in JavaScript
GT() - Constructor for class org.jmol.i18n.GT
 
GT(Viewer, String) - Constructor for class org.jmol.i18n.GT
 
gti(String, int) - Method in class org.jmol.popup.JmolGenericPopup
 
gto(String, Object) - Method in class org.jmol.popup.JmolGenericPopup
 
GTO_EXP - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
gui - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
GuiMap - Class in org.openscience.jmol.app.jmolpanel
 
GuiMap() - Constructor for class org.openscience.jmol.app.jmolpanel.GuiMap
 
guimap - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
guimap - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
gulpContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
GulpReader - Class in org.jmol.adapter.readers.xtal
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.
GulpReader() - Constructor for class org.jmol.adapter.readers.xtal.GulpReader
 
gxTemp - Variable in class org.jmol.quantum.NciCalculation
 
gxxTemp - Variable in class org.jmol.quantum.NciCalculation
 
gxyTemp - Variable in class org.jmol.quantum.NciCalculation
 
gxzTemp - Variable in class org.jmol.quantum.NciCalculation
 
gyTemp - Variable in class org.jmol.quantum.NciCalculation
 
gyyTemp - Variable in class org.jmol.quantum.NciCalculation
 
gyzTemp - Variable in class org.jmol.quantum.NciCalculation
 
gzTemp - Variable in class org.jmol.quantum.NciCalculation
 
gzzTemp - Variable in class org.jmol.quantum.NciCalculation
 

H

H3T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
H5T - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
h_bar_planck - Static variable in class org.jmol.quantum.NMRCalculation
 
h_bond_cone - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
h_bond_cutoff_center - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
h_bond_cutoff_edge - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
h_bond_exclusion - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
h_bond_from_proton - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
h_bond_max_angle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
h_bond_power_a - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
h_bond_power_b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
h_planck - Static variable in class org.jmol.quantum.NMRCalculation
 
half_bonds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
halfRoot5 - Static variable in class org.jmol.util.Geodesic
 
hAlignNames - Static variable in class org.jmol.viewer.JC
 
HallInfo - Class in org.jmol.symmetry
 
HallInfo(String) - Constructor for class org.jmol.symmetry.HallInfo
 
hallInfo - Variable in class org.jmol.symmetry.SpaceGroup
 
HallRotation - Class in org.jmol.symmetry
 
HallRotation(String, String) - Constructor for class org.jmol.symmetry.HallRotation
 
HallRotationTerm - Class in org.jmol.symmetry
 
HallRotationTerm(HallInfo, String, int, char) - Constructor for class org.jmol.symmetry.HallRotationTerm
 
hallRotationTerms - Static variable in class org.jmol.symmetry.HallRotation
 
hallSymbol - Variable in class org.jmol.symmetry.HallInfo
 
hallSymbol - Variable in class org.jmol.symmetry.SpaceGroup
 
HallTranslation - Class in org.jmol.symmetry
 
HallTranslation(char, P3i) - Constructor for class org.jmol.symmetry.HallTranslation
 
hallTranslationTerms - Static variable in class org.jmol.symmetry.HallTranslation
 
halo - Static variable in class org.jmol.script.T
 
Halos - Class in org.jmol.shape
 
Halos() - Constructor for class org.jmol.shape.Halos
 
HalosRenderer - Class in org.jmol.render
 
HalosRenderer() - Constructor for class org.jmol.render.HalosRenderer
 
halt - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
haltButton - Variable in class org.jmol.console.ScriptEditor
 
haltButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
haltExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
 
haltExecution() - Method in class org.jmol.script.ScriptEval
 
haltScriptExecution() - Method in class org.jmol.api.JmolViewer
 
haltScriptExecution() - Method in class org.jmol.viewer.Viewer
 
handleError() - Method in class org.jmol.script.ScriptCompiler
 
handleError(Error, boolean) - Method in class org.jmol.viewer.Viewer
 
handleEvent(Event) - Method in interface org.jmol.api.JmolAppletInterface
 
handleEvent(Event) - Method in class org.jmol.applet.AppletWrapper
 
handleEvent(Event) - Method in class org.jmol.util.GenericApplet
 
handleOutputToFile(Map<String, Object>, boolean) - Method in class org.jmol.viewer.OutputManager
general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
handleTlsMissingModels() - Method in class org.jmol.adapter.readers.pdb.PdbReader
for now, we just ignore TLS details if user has selected a specific model
has(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
HAS_CLIENT - Static variable in interface org.jmol.api.JmolGestureServerInterface
 
HAS_DRIVER - Static variable in interface org.jmol.api.JmolGestureServerInterface
 
HAS_MAXGRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
hasBfactorRange - Variable in class org.jmol.modelset.AtomCollection
 
hasBfactorRange - Variable in class org.jmol.shapebio.BioShape
 
hasColorData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
hasColorRange - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
hasContent() - Method in class org.jmol.g3d.Graphics3D
 
hasContent() - Method in class org.jmol.g3d.Platform3D
 
hasDatabasePrefix(String) - Static method in class org.jmol.viewer.Viewer
 
hasFocus(Object) - Static method in class org.jmol.awt.Display
 
hasFocus(Object) - Method in class org.jmol.awt.Platform
 
hasFocus(Object) - Static method in class org.jmol.awtjs2d.Display
 
hasFocus(Object) - Method in class org.jmol.awtjs2d.Platform
 
hasFocus() - Method in class org.jmol.viewer.Viewer
 
hasGridPoints - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
hash - Static variable in class org.jmol.script.T
 
hash_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
hashCode() - Method in class org.jmol.java.BS
Returns a hash code value for this bit set.
hashCode() - Method in class org.jmol.modelset.Atom
 
hashCode() - Method in class org.jmol.script.T
 
hasLocalArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
hasMoreElements() - Method in class org.jmol.bspt.CubeIterator
normal iterator predicate
hasNext() - Method in class org.jmol.adapter.smarter.AtomIterator
 
hasNext() - Method in class org.jmol.adapter.smarter.BondIterator
 
hasNext() - Method in class org.jmol.adapter.smarter.StructureIterator
 
hasNext() - Method in interface org.jmol.api.AtomIndexIterator
 
hasNext() - Method in interface org.jmol.api.JmolAdapterAtomIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapterBondIterator
 
hasNext() - Method in class org.jmol.api.JmolAdapterStructureIterator
 
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
hasNext() - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
 
hasNext() - Method in interface org.jmol.modelset.BondIterator
 
hasNext() - Method in class org.jmol.modelset.BondIteratorSelected
 
hasNext2() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
hasOAtom() - Method in class org.jmol.modelsetbio.AminoMonomer
 
hasOffset() - Method in class org.jmol.symmetry.UnitCell
 
hasPlane() - Method in class org.jmol.jvxl.data.VolumeData
 
hasRasmolHBonds - Variable in class org.jmol.modelset.Model
 
hasRnaO2Prime - Variable in class org.jmol.modelsetbio.NucleicMonomer
 
hasSerialArrayListFlavor(DataFlavor[]) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
hasStructure - Variable in class org.jmol.modelsetbio.BioPolymer
 
hasSymbol - Variable in class org.jmol.smiles.SmilesAtom
 
hasVibration() - Method in class org.jmol.modelset.Atom
 
hasWingPoints - Variable in class org.jmol.modelsetbio.BioPolymer
 
hAtomRadius - Variable in class org.jmol.atomdata.AtomData
 
hAtoms - Variable in class org.jmol.atomdata.AtomData
 
have(byte[], byte) - Static method in class org.jmol.modelsetbio.Monomer
 
haveAccess(Viewer.ACCESS) - Method in class org.jmol.viewer.Viewer
 
haveAnisou - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
haveAromatic - Variable in class org.jmol.adapter.readers.cif.CifReader
 
haveAt - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
haveAtomFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
haveAtomMods - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
haveAtoms - Variable in class org.jmol.shapespecial.Dipole
 
haveAtomSerials - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
haveAtomStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
 
haveAxis(int, V3) - Method in class org.jmol.symmetry.PointGroup
 
haveBFactors - Variable in class org.jmol.popup.JmolGenericPopup
 
haveBioModels - Variable in class org.jmol.modelset.ModelSet
 
haveBitSetVertices - Variable in class org.jmol.shapespecial.Polyhedra
 
haveBonds - Variable in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
haveBondStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
 
haveBorder - Variable in class org.openscience.jmol.app.JmolApp
 
haveBorder - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
haveBSClickable - Variable in class org.jmol.modelset.AtomCollection
 
haveBsDisplay - Variable in class org.jmol.render.MeshRenderer
 
haveBSVisible - Variable in class org.jmol.modelset.AtomCollection
 
haveCellWaveVector - Variable in class org.jmol.adapter.readers.cif.CifReader
 
haveCharges - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
haveCharges - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
haveCharges - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
haveCharges - Variable in class org.jmol.popup.JmolGenericPopup
 
haveCircle - Variable in class org.jmol.export._IdtfExporter
 
haveCoeffMap - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
haveComments - Variable in class org.jmol.script.ScriptCompiler
 
haveCommon(BS, BS) - Static method in class org.jmol.util.BSUtil
 
haveCone - Variable in class org.jmol.export._IdtfExporter
 
haveConsole - Variable in class org.openscience.jmol.app.JmolApp
 
haveContourData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
haveControlPointScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
 
haveCylinder - Variable in class org.jmol.export._IdtfExporter
 
haveCylinderIn - Variable in class org.jmol.export._IdtfExporter
 
haveDisplay - Variable in class org.jmol.viewer.Viewer
 
haveDisplay - Variable in class org.openscience.jmol.app.JmolApp
 
haveDisplay - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
haveDocumentAccess - Variable in class org.jmol.util.GenericApplet
 
haveDoubleBonds - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
haveEnergy - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
haveEnergy - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
haveFileSet() - Method in class org.jmol.viewer.Viewer
 
haveHeader - Variable in class org.jmol.adapter.readers.simple.MopacReader
 
haveHiddenBonds - Variable in class org.jmol.modelset.BondCollection
 
haveHoverCallback() - Method in class org.jmol.viewer.StatusManager
 
haveHsAlready - Variable in class org.jmol.modelsetbio.Resolver
 
haveInversionCenter - Variable in class org.jmol.symmetry.PointGroup
 
haveJDX - Variable in class org.jmol.viewer.Viewer
 
haveLine - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
 
haveM40Data - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
haveMacros - Variable in class org.jmol.export._PovrayExporter
 
haveMappedSerials - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
haveMeasurements - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
haveModel - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
haveModelKit() - Method in class org.jmol.modelset.ModelSet
 
haveModified - Variable in class org.jmol.modelset.MeasurementPending
 
haveMolecule - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
haveMultiTouchInput - Variable in class org.jmol.viewer.ActionManager
 
haveNboCharges - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
haveNboOrbitals - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
haveNotified - Variable in class org.jmol.thread.SpinThread
 
haveNotifiedError - Variable in class org.jmol.util.GenericApplet
 
haveNotifiedNaN - Variable in class org.jmol.viewer.TransformManager
 
haveNucleicLadder - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
haveOccupancy - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
haveOneProperty - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
haveParameters - Variable in class org.jmol.modelsetbio.BioPolymer
 
haveParameters() - Method in class org.jmol.modelsetbio.Monomer
 
havePartialChargeFilter - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
havePhonons - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
havePlanarContours - Variable in class org.jmol.shape.Mesh
 
havePlane - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
havePoints - Variable in class org.jmol.quantum.MOCalculation
 
havePoints - Variable in class org.jmol.quantum.NciCalculation
 
havePrimitiveMapping - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
haveQuads - Variable in class org.jmol.util.MeshSurface
 
haveReadColorData - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
haveReference - Variable in class org.jmol.thread.JmolThread
 
haveScenes - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
haveScenes - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
haveSelected - Variable in class org.jmol.smiles.SmilesSearch
 
haveSelection - Variable in class org.jmol.viewer.ActionManager
 
haveSequenceNumber(int) - Static method in class org.jmol.modelset.Group
 
haveSetAnisotropy - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
haveSetStructureList - Variable in class org.jmol.viewer.GlobalSettings
 
haveSpaceBeforeSquare - Variable in class org.jmol.script.ScriptMathProcessor
 
haveSphere - Variable in class org.jmol.export._IdtfExporter
 
haveStraightness - Variable in class org.jmol.modelset.AtomCollection
 
haveString - Variable in class org.jmol.script.ScriptTokenParser
 
haveSurfaceAtoms - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
haveTarget - Variable in class org.jmol.modelset.MeasurementPending
 
haveTranslations - Static variable in class org.jmol.dialog.Dialog
 
haveTranslucentObjects() - Method in interface org.jmol.api.JmolRendererInterface
 
haveTranslucentObjects() - Method in class org.jmol.export.Export3D
 
haveTranslucentObjects - Variable in class org.jmol.g3d.Graphics3D
 
haveTranslucentObjects() - Method in class org.jmol.g3d.Graphics3D
 
haveUnitCell - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
haveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
haveUnitCell() - Method in interface org.jmol.api.SymmetryInterface
 
haveUnitCell() - Method in class org.jmol.symmetry.Symmetry
 
haveUnitCells - Variable in class org.jmol.modelset.ModelSet
 
haveXyPoints - Variable in class org.jmol.shape.Mesh
 
HB - Enum in org.jmol.c
Enum for hydrogen bonding donor/acceptor type
HB() - Constructor for enum org.jmol.c.HB
 
HBond - Class in org.jmol.modelset
 
HBond(Atom, Atom, int, short, short, float) - Constructor for class org.jmol.modelset.HBond
 
hbond - Static variable in class org.jmol.script.T
 
hbondMin - Static variable in class org.jmol.modelset.ModelSet
 
hbondsangleminimum - Static variable in class org.jmol.script.T
 
hbondsAngleMinimum - Variable in class org.jmol.viewer.GlobalSettings
 
hbondsBackbone - Variable in class org.jmol.render.SticksRenderer
 
hbondsbackbone - Static variable in class org.jmol.script.T
 
hbondsBackbone - Variable in class org.jmol.viewer.GlobalSettings
 
hbondsdistancemaximum - Static variable in class org.jmol.script.T
 
hbondsDistanceMaximum - Variable in class org.jmol.viewer.GlobalSettings
 
hbondsrasmol - Static variable in class org.jmol.script.T
 
hbondsRasmol - Variable in class org.jmol.viewer.GlobalSettings
 
hbondsSolid - Variable in class org.jmol.render.SticksRenderer
 
hbondssolid - Static variable in class org.jmol.script.T
 
hbondsSolid - Variable in class org.jmol.viewer.GlobalSettings
 
HC - Static variable in class org.jmol.quantum.QS
 
hCount - Variable in class org.jmol.minimize.MinAtom
 
hDashes - Static variable in class org.jmol.render.FontLineShapeRenderer
 
header() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
header - Variable in class org.jmol.adapter.readers.xtal.MagresReader
 
header - Variable in class org.openscience.jmol.app.HistoryFile
The information written to the header of the history file.
HEADER_GAMESS_OCCUPANCIES - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
HEADER_GAMESS_ORIGINAL - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
HEADER_GAMESS_UK_MO - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
HEADER_NONE - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
headerContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
headless - Variable in class org.jmol.viewer.Viewer
determined by GraphicsEnvironment.isHeadless() from java -Djava.awt.headless=true disables command threading disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN , ANIMATION ON turns SPIN into just ROTATE
headlessImageParams - Variable in class org.jmol.viewer.Viewer
 
headOffsetVector - Variable in class org.jmol.renderspecial.VectorsRenderer
 
headScale - Variable in class org.jmol.renderspecial.VectorsRenderer
 
headWidthPixels - Variable in class org.jmol.renderspecial.DipolesRenderer
 
headWidthPixels - Variable in class org.jmol.renderspecial.VectorsRenderer
 
heavy_neighbor_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
heavyAtomIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
height - Variable in class org.jmol.export.Export3D
 
height - Variable in class org.jmol.g3d.SphereRenderer
 
height - Variable in class org.jmol.g3d.TextRenderer
 
height - Variable in class org.jmol.util.GData
 
height - Variable in class org.jmol.util.Rectangle
 
height - Variable in class org.jmol.viewer.TransformManager
 
height - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
heightOffscreen - Variable in class org.jmol.g3d.Platform3D
 
heightUnitVector - Variable in class org.jmol.modelsetbio.Sheet
 
Helix - Class in org.jmol.modelsetbio
 
Helix(AlphaPolymer, int, int, STR) - Constructor for class org.jmol.modelsetbio.Helix
 
helix - Static variable in class org.jmol.script.T
 
helix310 - Static variable in class org.jmol.script.T
 
HELIX_CLASS - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
helixalpha - Static variable in class org.jmol.script.T
 
helixpi - Static variable in class org.jmol.script.T
 
helixRockets - Variable in class org.jmol.renderbio.RocketsRenderer
 
helixstep - Static variable in class org.jmol.script.T
 
helixStep - Variable in class org.jmol.viewer.GlobalSettings
 
help - Static variable in class org.jmol.script.T
 
helpButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
helpButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
HelpDialog - Class in org.openscience.jmol.app.jmolpanel
 
HelpDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
 
HelpDialog(JFrame, String, boolean) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
 
HelpDialog(JFrame, URL) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog
If url is null, then the default help url is taken.
HelpDialog.PageLoader - Class in org.openscience.jmol.app.jmolpanel
temporary class that loads synchronously (although later than the request so that a cursor change can be done).
helper - Variable in class org.jmol.popup.GenericSwingPopup
 
helppath - Static variable in class org.jmol.script.T
 
helpPath - Variable in class org.jmol.viewer.GlobalSettings
 
hemisphereOnly - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
hermite3d - Variable in class org.jmol.export.Export3D
 
hermite3d - Variable in class org.jmol.g3d.Graphics3D
 
hermiteLevel - Variable in class org.jmol.renderbio.BioShapeRenderer
 
hermitelevel - Static variable in class org.jmol.script.T
 
hermiteLevel - Variable in class org.jmol.viewer.GlobalSettings
 
HermiteRenderer - Class in org.jmol.g3d
Implementation of hermite curves for drawing smoothed curves that pass through specified points.
HermiteRenderer() - Constructor for class org.jmol.g3d.HermiteRenderer
 
hess - Variable in class org.jmol.quantum.NciCalculation
 
het() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
hetatmData - Variable in class org.jmol.adapter.readers.cif.MMCifReader
optional nonloop format -- see 1jsa.cif
hetero - Static variable in class org.jmol.script.T
 
hetnam() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
hi - Variable in class org.jmol.util.ColorEncoder
 
hidden - Variable in class org.jmol.modelset.Object2d
 
hidden - Static variable in class org.jmol.script.T
 
hide - Static variable in class org.jmol.script.T
 
hide(ModelSet, BS, int, boolean) - Method in class org.jmol.viewer.SelectionManager
 
hide_long_bonds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
hide_underscore_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
hidenameinpopup - Static variable in class org.jmol.script.T
 
hideNameInPopup - Variable in class org.jmol.viewer.GlobalSettings
 
hidenavigationpoint - Static variable in class org.jmol.script.T
 
hideNavigationPoint - Variable in class org.jmol.viewer.GlobalSettings
 
hidenotselected - Static variable in class org.jmol.script.T
 
hideNotSelected - Variable in class org.jmol.viewer.SelectionManager
 
HIGH - Static variable in class org.jmol.util.ColorEncoder
 
highlight - Static variable in class org.jmol.script.T
 
highlight(BS) - Method in class org.jmol.viewer.Viewer
 
highlightBond(int, boolean) - Method in class org.jmol.viewer.Viewer
 
highresolution - Static variable in class org.jmol.script.T
 
highResolutionFlag - Variable in class org.jmol.viewer.GlobalSettings
 
history - Static variable in class org.jmol.script.T
 
historyButton - Variable in class org.jmol.console.GenericConsole
 
historyDisabled - Variable in class org.jmol.script.ScriptEval
 
HistoryFile - Class in org.openscience.jmol.app
The history file contains data from previous uses of Jmol.
HistoryFile(File, String) - Constructor for class org.openscience.jmol.app.HistoryFile
Creates a history file.
historyFile - Variable in class org.openscience.jmol.app.JmolApp
 
historyFile - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
historyFile - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
historyFile - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
historyFind(String, int) - Method in class org.jmol.viewer.Viewer
 
historylevel - Static variable in class org.jmol.script.T
 
histWinName - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
hkl - Static variable in class org.jmol.script.T
 
hklParameter(int) - Method in class org.jmol.script.ScriptParam
 
hmSymbol - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolAbbr - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolAbbrShort - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolAlternative - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolExt - Variable in class org.jmol.symmetry.SpaceGroup
 
hmSymbolFull - Variable in class org.jmol.symmetry.SpaceGroup
 
hNames - Variable in class org.jmol.modelsetbio.Resolver
 
hnmrPeaks - Variable in class org.jmol.popup.JmolGenericPopup
 
holdRepaint - Variable in class org.jmol.render.RepaintManager
 
homeAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
HomeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.HomeAction
 
homePosition() - Method in class org.jmol.api.JmolViewer
 
homePosition(boolean) - Method in class org.jmol.viewer.TransformManager
 
homePosition() - Method in class org.jmol.viewer.Viewer
 
homo - Static variable in class org.jmol.script.T
 
HOTPINK - Static variable in class org.jmol.util.C
 
hover - Static variable in class org.jmol.script.T
 
Hover - Class in org.jmol.shape
 
Hover() - Constructor for class org.jmol.shape.Hover
 
hoverable - Static variable in class org.jmol.viewer.ShapeManager
 
hoverActive - Variable in class org.jmol.viewer.ActionManager
 
hoverAtomIndex - Variable in class org.jmol.viewer.Viewer
 
hoverdelay - Static variable in class org.jmol.script.T
 
hoverDelay - Variable in class org.jmol.thread.HoverWatcherThread
 
hoverDelayMs - Variable in class org.jmol.viewer.GlobalSettings
 
hoverEnabled - Variable in class org.jmol.thread.JmolThread
 
hoverEnabled - Variable in class org.jmol.viewer.Viewer
 
hoverKey(int, int) - Method in class org.jmol.shapesurface.Isosurface
 
hoverlabel - Static variable in class org.jmol.script.T
 
hoverOff() - Method in class org.jmol.viewer.Viewer
 
hoverOn(int, boolean) - Method in class org.jmol.viewer.Viewer
 
hoverOnPt(int, int, String, String, T3) - Method in class org.jmol.viewer.Viewer
 
HoverRenderer - Class in org.jmol.render
 
HoverRenderer() - Constructor for class org.jmol.render.HoverRenderer
 
hoverText - Variable in class org.jmol.shape.Hover
 
hoverText - Variable in class org.jmol.viewer.Viewer
 
HoverWatcherThread - Class in org.jmol.thread
 
HoverWatcherThread(ActionManager, MouseState, MouseState, Viewer) - Constructor for class org.jmol.thread.HoverWatcherThread
 
hoverWatcherThread - Variable in class org.jmol.viewer.ActionManager
 
HS - Static variable in class org.jmol.quantum.QS
 
ht3 - Variable in class org.jmol.util.GData
 
htAtomicPotentials - Variable in class org.jmol.quantum.MepCalculation
 
htAtomMap - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htAtomMap - Variable in class org.jmol.modelset.ModelLoader
 
htAtomMods - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
htAudit - Variable in class org.jmol.adapter.readers.cif.CifReader
 
htBiomts - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
htBondMap - Variable in class org.jmol.modelsetbio.Resolver
 
htBonds - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
htBooleanParameterFlags - Variable in class org.jmol.viewer.GlobalSettings
 
htBridges - Variable in class org.jmol.dssx.DSSP
 
htCarveSets - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htCellTypes - Variable in class org.jmol.adapter.readers.cif.CifReader
 
htCheckbox - Variable in class org.jmol.popup.GenericSwingPopup
 
htDefinedAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htDefs - Variable in class org.jmol.export._IdtfExporter
 
htEdges - Variable in class org.jmol.adapter.readers.xtal.CgdReader
 
htEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
htElementMap - Static variable in class org.jmol.util.Elements
 
htElementsInCurrentGroup - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
htExponents - Variable in class org.jmol.adapter.readers.quantum.DgridReader
 
htFileCache - Variable in class org.jmol.script.ScriptContext
 
htFont3d - Static variable in class org.jmol.g3d.TextRenderer
 
htFont3dAntialias - Static variable in class org.jmol.g3d.TextRenderer
 
htFormul - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
htFuncMap - Variable in class org.jmol.adapter.readers.quantum.DgridReader
 
htGroup - Static variable in class org.jmol.modelset.Group
 
htGroup1 - Variable in class org.jmol.adapter.readers.cif.CifReader
 
htGroup1 - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
htGroup1 - Variable in class org.jmol.modelset.ModelLoader
 
htGroup1 - Static variable in class org.jmol.modelsetbio.NucleicPolymer
 
htGroupBonds - Variable in class org.jmol.modelsetbio.Resolver
 
htHetero - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
htHetero - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
htHiddenObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htLadders - Variable in class org.jmol.dssx.DSSP
 
htLanguages - Static variable in class org.jmol.i18n.GT
 
htMeasures - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htMeasures - Variable in class org.jmol.smiles.SmilesParser
 
htMenus - Variable in class org.jmol.popup.GenericSwingPopup
 
htMin - Variable in class org.jmol.modelset.MeasurementData
 
htMin - Variable in class org.jmol.shape.Measures
 
html - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
html - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
html5Applet - Variable in class org.jmol.export.JSExporter
 
html5Applet - Variable in class org.jmol.viewer.Viewer
 
htmlAppletTemplate - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
htmlName - Variable in class org.jmol.util.GenericApplet
 
htmlName - Variable in class org.jmol.viewer.Viewer
 
htmlPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
htModels - Variable in class org.jmol.shapesurface.MolecularOrbital
 
htModulation - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
htMolIds - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
htMOs - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
htNested - Variable in class org.jmol.smiles.SmilesSearch
 
htNodes - Variable in class org.jmol.export._IdtfExporter
 
htNonbooleanParameterValues - Variable in class org.jmol.viewer.GlobalSettings
 
htObjectAtoms - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htObjectGroups - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htObjects - Variable in class org.jmol.export.JSExporter
 
htObjects - Variable in class org.jmol.shape.MeshCollection
 
htObjectSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htPar - Variable in class org.jmol.dssx.AnnotationParser
 
htParams - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
htParams - Variable in class org.jmol.appletjs.Jmol
 
htParams - Variable in class org.jmol.io.DOMReader
 
htParams - Variable in class org.jmol.io.FileReader
 
htParams - Variable in class org.jmol.io.FilesReader
 
htPdbBondInfo - Static variable in class org.jmol.modelsetbio.Resolver
 
htPeaks - Variable in class org.jmol.modelset.ModelSet
 
htPropertyFlagsRemoved - Variable in class org.jmol.viewer.GlobalSettings
 
htPts - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
htRegistry - Static variable in class org.jmol.util.GenericApplet
 
htRings - Variable in class org.jmol.smiles.SmilesGenerator
 
htRingsSequence - Variable in class org.jmol.smiles.SmilesGenerator
 
htSites - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
htSites - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
htSources - Variable in class org.jmol.popup.AwtSwingPopupHelper
 
htSpacefill - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htSpecialAtoms - Static variable in class org.jmol.modelsetbio.Resolver
 
htSpheresRendered - Variable in class org.jmol.export._VrmlExporter
 
htSpheresRendered - Variable in class org.jmol.export.JSExporter
 
htStateSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
htSubsystems - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
htSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
htTemp - Variable in class org.jmol.dssx.AnnotationParser
 
htTiming - Static variable in class org.jmol.util.Logger
 
htUij - Variable in class org.jmol.util.ModulationSet
 
htUserFunctions - Variable in class org.jmol.script.ScriptTokenParser
 
htUserVariables - Variable in class org.jmol.viewer.GlobalSettings
 
htVertex - Static variable in class org.jmol.util.Geodesic
 
hType - Variable in class org.jmol.minimize.forcefield.AtomType
 
hydrogen - Static variable in class org.jmol.script.T
 
hydrogenAtomCount - Variable in class org.jmol.atomdata.AtomData
 
hydrogenAtomPsi(P3) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
hydrogenCount - Variable in class org.jmol.modelset.Model
 
hydrogensAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
hydrophobicities - Variable in class org.jmol.modelset.AtomCollection
 
hydrophobicities - Static variable in class org.jmol.util.Elements
 
hydrophobicity - Static variable in class org.jmol.script.T
 
hyperChemLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
HyperChemReader - Class in org.jmol.adapter.readers.simple
Support for .hin, HyperChem's native file format.
HyperChemReader() - Constructor for class org.jmol.adapter.readers.simple.HyperChemReader
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 

I

i(String, int) - Static method in class org.jmol.i18n.GT
 
i(int) - Static method in class org.jmol.script.T
 
i - Variable in class org.jmol.util.Point3fi
 
i0 - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
 
ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
ia - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
ia - Variable in class org.jmol.minimize.forcefield.Calculation
 
ia - Variable in class org.jmol.minimize.forcefield.Calculations
 
iA - Variable in class org.jmol.util.MeshSurface
 
iAddGridPoints - Variable in class org.jmol.jvxl.readers.Parameters
 
iAtom - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
iAtom - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
 
iatom - Variable in class org.jmol.adapter.smarter.AtomIterator
 
iAtom - Variable in class org.jmol.quantum.SlaterData
 
iatom0 - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
iAtomSurface - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
iAtomSurface - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
ib - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
ib - Variable in class org.jmol.minimize.forcefield.Calculation
 
ib - Variable in class org.jmol.minimize.forcefield.Calculations
 
iB - Variable in class org.jmol.util.MeshSurface
 
ibond - Variable in class org.jmol.adapter.smarter.BondIterator
 
iBond - Variable in class org.jmol.modelset.BondIteratorSelected
 
iBrace - Variable in class org.jmol.script.ScriptCompiler
 
ic - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
ic - Variable in class org.jmol.minimize.forcefield.Calculation
 
ic - Variable in class org.jmol.minimize.forcefield.Calculations
 
IC - Static variable in class org.jmol.quantum.QS
 
iC - Variable in class org.jmol.util.MeshSurface
 
iChain - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
 
iChain - Variable in class org.jmol.modelset.ModelLoader
 
ichBrace - Variable in class org.jmol.script.ScriptCompiler
 
ichComment - Variable in class org.jmol.script.ScriptTokenParser
 
ichCurrentCommand - Variable in class org.jmol.script.ScriptTokenParser
 
ichEnd - Variable in class org.jmol.script.ScriptTokenParser
 
ichToken - Variable in class org.jmol.script.ScriptTokenParser
 
iCommand - Variable in class org.jmol.script.ScriptTokenParser
 
iCommandError - Variable in class org.jmol.script.ScriptContext
 
iCommandError - Variable in class org.jmol.script.ScriptError
 
iCutout - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
id - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
id - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
ID - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
id - Variable in enum org.jmol.c.PAL
 
id - Variable in enum org.jmol.c.STR
 
id - Variable in class org.jmol.export._MayaExporter
 
id - Variable in class org.jmol.minimize.forcefield.Calculation
 
id - Variable in class org.jmol.minimize.forcefield.Calculations
 
id - Variable in class org.jmol.modelset.TickInfo
 
id - Variable in class org.jmol.script.ScriptContext
 
id - Static variable in class org.jmol.script.T
 
id - Variable in enum org.jmol.shapespecial.Draw.EnumDrawType
 
id - Variable in class org.jmol.shapespecial.Ellipsoid
 
id - Variable in class org.jmol.util.MeshCapper.CapVertex
for debugging
iD - Variable in class org.jmol.util.MeshSlicer
 
id - Variable in class org.jmol.util.ModulationSet
 
id - Variable in class org.jmol.util.Tensor
 
id - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
iData - Variable in class org.jmol.minimize.forcefield.Calculation
 
ident - Variable in class org.jmol.script.ScriptCompiler
 
ident - Variable in class org.jmol.script.ScriptFlowContext
 
identifier - Static variable in class org.jmol.script.T
 
identify - Static variable in class org.jmol.script.T
 
identLC - Variable in class org.jmol.script.ScriptCompiler
 
idle_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
idSpherical - Static variable in class org.jmol.quantum.QS
 
iE - Variable in class org.jmol.util.MeshSlicer
 
ifcmd - Static variable in class org.jmol.script.T
 
iFirstAtom - Variable in class org.jmol.modelset.MeasurementData
 
ifPt - Variable in class org.jmol.script.ScriptMathProcessor
 
ifStack - Variable in class org.jmol.script.ScriptMathProcessor
 
ignore - Static variable in class org.jmol.script.T
 
ignore_case - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ignore_pdb_segi - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ignoreApplicationBundle - Static variable in class org.jmol.i18n.GT
 
ignoreApplicationBundle() - Static method in class org.jmol.i18n.GT
 
ignoreError - Variable in class org.jmol.script.ScriptError
 
ignoreFileSpaceGroupName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreFileSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreFileUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ignoreMOs - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
ignoreStereochemistry - Variable in class org.jmol.smiles.SmilesSearch
 
ignoreSymmetry - Variable in class org.jmol.adapter.smarter.Atom
 
iGroup - Variable in class org.jmol.adapter.readers.xml.XmlXsdReader
 
ihalf - Variable in class org.jmol.util.ColorEncoder
 
iHaveBitSets - Variable in class org.jmol.shapesurface.Isosurface
 
iHaveCenterBitSet - Variable in class org.jmol.shapespecial.Polyhedra
 
iHaveDesiredModel - Variable in class org.jmol.adapter.readers.cif.CifReader
 
iHaveFractionalCoordinates - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveModelIndex - Variable in class org.jmol.shapesurface.Isosurface
 
iHaveModelStatement - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
iHaveQuotedString - Variable in class org.jmol.script.ScriptCompiler
 
iHaveSymmetryOperators - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHaveTwoEnds - Variable in class org.jmol.shapespecial.Dipoles
 
iHaveUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
iHideBackground - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
ijkToPoint3f(int, P3, int) - Static method in class org.jmol.util.SimpleUnitCell
Expanded cell notation: 111 - 1000 --> center 5,5,5; range 0 to 9 or -5 to +4 1000000 - 1999999 --> center 50,50,50; range 0 to 99 or -50 to +49 1000000000 - 1999999999 --> center 500, 500, 500; range 0 to 999 or -500 to +499
iList - Variable in class org.jmol.navigate.Navigator
 
image - Variable in class org.jmol.awt.AwtClipboard
The image to transfer into the clipboard.
Image - Class in org.jmol.awt
methods required by Jmol that access java.awt.Image private to org.jmol.awt
Image() - Constructor for class org.jmol.awt.Image
 
Image - Class in org.jmol.awtjs
methods required by Jmol that access java.awt.Image private to org.jmol.awt
Image() - Constructor for class org.jmol.awtjs.Image
 
Image - Class in org.jmol.awtjs2d
methods required by Jmol that access java.awt.Image private to org.jmol.awt
Image() - Constructor for class org.jmol.awtjs2d.Image
 
image - Variable in class org.jmol.modelset.Text
 
image - Static variable in class org.jmol.script.T
 
image_copy_always - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
image_dots_per_inch - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
IMAGE_OR_SCENE - Static variable in class org.jmol.viewer.JC
 
IMAGE_TYPES - Static variable in class org.jmol.viewer.JC
 
imageChoices - Variable in class org.jmol.dialog.Dialog
 
imageChoices - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
imageChooser - Static variable in class org.jmol.dialog.Dialog
 
imageExtensions - Variable in class org.jmol.dialog.Dialog
 
imageExtensions - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
imageFontScaling - Variable in class org.jmol.render.FontLineShapeRenderer
 
imageFontScaling - Variable in class org.jmol.render.MeshRenderer
 
imageFontScaling - Variable in class org.jmol.viewer.Viewer
 
ImageRenderer - Class in org.jmol.g3d
 
ImageRenderer() - Constructor for class org.jmol.g3d.ImageRenderer
 
imageScale - Variable in class org.jmol.modelset.Text
 
imageSizeChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Called when the ImageSize check box is modified
imageSizeHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeRatioBox - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeRatioCombo - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeTextHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeTextWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imageSizeWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
imagestate - Static variable in class org.jmol.script.T
 
imageState - Variable in class org.jmol.viewer.GlobalSettings
 
imageType - Variable in class org.jmol.dialog.Dialog
 
imageType - Variable in class org.jmol.viewer.StatusManager
 
imageType - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
imesh - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
imgHeight - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
imgWidth - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
iMo0 - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
iModel - Variable in class org.jmol.modelset.ModelLoader
 
iMolecule - Variable in class org.jmol.quantum.QMAtom
 
implicitHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
 
implicitString - Variable in class org.jmol.script.ScriptCompiler
 
implicitStringCommand - Static variable in class org.jmol.script.T
 
importData(JComponent, Transferable) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
in - Static variable in class org.jmol.script.T
 
IN_JMOL - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
inchi - Static variable in class org.jmol.script.T
 
inchikey - Static variable in class org.jmol.script.T
 
includeAllRelatedFrames(BS) - Method in class org.jmol.modelset.ModelSet
 
includes(int, int) - Static method in class org.jmol.viewer.binding.Binding
 
includeValueNaN - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
incompleteCmd - Variable in class org.jmol.console.GenericConsole
 
increment(int) - Method in class org.jmol.script.SV
 
increment - Static variable in class org.jmol.script.T
 
incrementLineCount(String) - Method in class org.jmol.script.ScriptCompiler
 
inDefinedStateBlock - Variable in class org.jmol.modelset.StateScript
 
INDENT - Static variable in class org.jmol.shapecgo.CGOMesh
 
index - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
index - Variable in class org.jmol.adapter.smarter.Atom
 
index - Variable in class org.jmol.bspt.Bspt
 
index - Variable in class org.jmol.minimize.MinAtom
 
index - Variable in class org.jmol.minimize.MinBond
 
index - Variable in class org.jmol.modelset.Chain
 
index - Variable in class org.jmol.modelset.Measurement
 
index - Variable in class org.jmol.quantum.QMAtom
 
index - Variable in class org.jmol.quantum.SlaterData
 
index - Variable in class org.jmol.script.SV
 
index - Variable in class org.jmol.shape.Mesh
 
index - Variable in class org.jmol.smiles.SmilesAtom
 
index - Variable in class org.jmol.smiles.SmilesMeasure
 
index - Variable in class org.jmol.symmetry.PointGroup.Operation
 
index - Variable in class org.jmol.symmetry.SpaceGroup
 
index - Variable in class org.jmol.symmetry.SymmetryOperation
 
index - Variable in class org.jmol.thread.SpinThread
 
index - Variable in class org.jmol.util.Edge
 
index - Variable in class org.jmol.viewer.MotionPoint
 
indexes - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Sequence of atom set indexes in current tree selection for a branch, or siblings for a leaf.
indexI - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
indexInModel - Variable in class org.jmol.util.JmolMolecule
 
indexLower(float, int) - Method in class org.jmol.jvxl.data.VolumeData
periodic grids should have val[0] == val[xMax] voxelCount: 1....2....3....4....5 xMax/index: 0....1....2....3....4....
indexUpper(float, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
indicatedModelIndex - Variable in class org.jmol.shapespecial.Draw
 
indices - Variable in class org.jmol.smiles.SmilesMeasure
 
iNested - Variable in class org.jmol.smiles.SmilesAtom
 
iNext - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
iNext - Variable in class org.jmol.renderbio.BioShapeRenderer
 
iNext2 - Variable in class org.jmol.renderbio.BioShapeRenderer
 
iNext3 - Variable in class org.jmol.renderbio.BioShapeRenderer
 
info - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
info - Variable in class org.jmol.atomdata.RadiusData
 
info - Variable in class org.jmol.modelsetbio.BasePair
 
info - Static variable in class org.jmol.script.T
 
info - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
info - Variable in class org.jmol.symmetry.PointGroup
 
info(String) - Method in class org.jmol.util.DefaultLogger
 
info(String) - Static method in class org.jmol.util.Logger
og* Writes a log at INFO level.
info(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at INFO level.
info - Variable in class org.openscience.jmol.app.JmolApp
 
INFO_A - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_ALPHA - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_B - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_BETA - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_C - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_DIMENSIONS - Static variable in class org.jmol.util.SimpleUnitCell
 
INFO_GAMMA - Static variable in class org.jmol.util.SimpleUnitCell
 
infoLabel - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
infoList - Static variable in class org.jmol.util.Tensor
 
infoStr - Variable in class org.jmol.symmetry.SymmetryInfo
 
inGreyscaleMode - Variable in class org.jmol.util.GData
 
INHERIT - Static variable in class org.jmol.util.ColorEncoder
 
INHERIT_ALL - Static variable in class org.jmol.util.C
 
INHERIT_COLOR - Static variable in class org.jmol.util.C
 
inInput - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
INIT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
init() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
init() - Method in class org.jmol.applet.AppletWrapper
 
init(int) - Method in class org.jmol.java.BS
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMepReader
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMlpReader
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoPlaneReader
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.SurfaceReader
implemented in SurfaceFileReader and
init(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
init(String, Viewer, Lst<Object>) - Method in class org.jmol.modelset.MeasurementData
 
init(String, Object, String, SC) - Method in class org.jmol.popup.AwtSwingComponent
 
init(Object) - Method in interface org.jmol.script.JmolCmdExtension
 
init(Object) - Method in interface org.jmol.script.JmolMathExtension
 
init(Object) - Method in interface org.jmol.script.JmolSmilesExtension
 
init(Object) - Method in class org.jmol.scriptext.CmdExt
 
init(Object) - Method in class org.jmol.scriptext.IsoExt
 
init(Object) - Method in class org.jmol.scriptext.MathExt
 
init(Object) - Method in class org.jmol.scriptext.SmilesExt
 
init(int, String, String, short, short, boolean) - Method in class org.jmol.shapespecial.Dipole
 
init(boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
INIT - Static variable in class org.jmol.thread.JmolThread
 
init(Object) - Method in class org.jmol.util.GenericApplet
 
init(float[]) - Method in class org.jmol.util.SimpleUnitCell
 
init(URL, String) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.ApbsReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.CastepDensityReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.CubeReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.EfvetReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JaguarReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JvxlReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.KinemageReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MapFileReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MrcBinaryReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MsmsReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.NffReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.ObjReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PltFormattedReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.Pmesh4Reader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PmeshReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.UhbdReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.VaspChgcarReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.XplorReader
 
init2(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.XsfReader
 
init2JXR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
init2MFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.MapFileReader
 
init2PFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PolygonFileReader
 
init2PR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.PmeshReader
 
init2SFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
init2VFR(SurfaceGenerator, BufferedReader) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
initADR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
initApplication() - Method in class org.jmol.util.GenericApplet
 
initCGO() - Method in class org.jmol.shapecgo.CGO
 
initDraw() - Method in class org.jmol.shapespecial.Draw
 
initEllipsoids(Object) - Method in class org.jmol.shapespecial.Ellipsoids
 
INITIAL_ATOMS - Static variable in class org.jmol.smiles.SmilesSearch
 
initialFile - Variable in class org.jmol.dialog.Dialog
 
initialize(AtomSetCollectionReader, int) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
initialize(BasisFunctionReader, String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
initialize() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initialize(AtomSetCollectionReader, int) - Method in interface org.jmol.adapter.smarter.MSInterface
 
initialize(int, P3[], BS) - Method in class org.jmol.bspt.Bspf
 
initialize(T3, float, boolean) - Method in class org.jmol.bspt.CubeIterator
initialize to return all points within the sphere defined by center and radius
initialize(Viewer, GenericPlatform) - Method in class org.jmol.g3d.Graphics3D
 
initialize() - Method in class org.jmol.jvxl.readers.Parameters
 
initialize(Bspf, BS, boolean, boolean, boolean, boolean) - Method in class org.jmol.modelset.AtomIteratorWithinModel
############## ITERATOR SHOULD BE RELEASED #################
initialize(Viewer, PopupResource, String) - Method in class org.jmol.popup.JmolGenericPopup
 
initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.MOCalculation
 
initialize(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
 
initialize - Static variable in class org.jmol.script.T
 
initialize(int, T3[], P4) - Method in class org.jmol.shape.Mesh
 
initialize() - Method in class org.jmol.shapebio.BioShapeCollection
 
initialize() - Method in class org.jmol.shapespecial.Dots
 
initialize(Viewer, GenericPlatform) - Method in class org.jmol.util.GData
 
initialize(Node[], int, int, BS, int, int) - Static method in class org.jmol.util.JmolMolecule
 
initialize(boolean) - Method in class org.jmol.viewer.Viewer
 
initialize(String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
initialize0(int, int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
 
initializeAnnotation(SV, int, int) - Method in interface org.jmol.api.JmolAnnotationParser
 
initializeAnnotation(SV, int, int) - Method in class org.jmol.dssx.AnnotationParser
We create a main list of mappings, where each mapping has _atoms and _path
initializeAtomBondModelCounts(int) - Method in class org.jmol.modelset.ModelLoader
 
initializeBonding() - Method in class org.jmol.modelset.ModelLoader
 
initializeBspf() - Method in class org.jmol.modelset.ModelSet
 
initializeBspt(int) - Method in class org.jmol.modelset.ModelSet
 
initializeCartesianToFractional() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeEigen() - Method in class org.jmol.quantum.NciCalculation
 
initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
 
initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.Export3D
 
initializeExporter(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
 
initializeExporter(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
initializeHydrogenAddition() - Method in interface org.jmol.api.JmolBioResolver
 
initializeHydrogenAddition() - Method in class org.jmol.modelsetbio.Resolver
 
initializeInfo(String, Map<String, Object>) - Method in class org.jmol.modelset.ModelLoader
 
initializeIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
initializeIsosurface() - Method in class org.jmol.shapesurface.Isosurface
 
initializeMapping() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
initializeMapping() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
initializeModel(boolean) - Method in class org.jmol.viewer.Viewer
 
initializeMSCIF() - Method in class org.jmol.adapter.readers.cif.CifReader
 
initializeOnePoint() - Method in class org.jmol.quantum.NciCalculation
 
initializeOnePoint() - Method in class org.jmol.quantum.QuantumCalculation
 
initializeOnePointQC() - Method in class org.jmol.quantum.QuantumCalculation
 
initializeOrientation(M3) - Method in interface org.jmol.api.SymmetryInterface
 
initializeOrientation(M3) - Method in class org.jmol.symmetry.Symmetry
 
initializeOutput(Viewer, double, Map<String, Object>) - Method in interface org.jmol.api.JmolRendererInterface
 
initializeOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.___Exporter
 
initializeOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._ObjExporter
 
initializeOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export._TachyonExporter
 
initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.export.Export3D
 
initializeOutput(Viewer, double, Map<String, Object>) - Method in class org.jmol.g3d.Graphics3D
 
initializePointers(int) - Method in class org.jmol.viewer.AnimationManager
 
initializePolymer(BioShape) - Method in class org.jmol.renderbio.BioShapeRenderer
 
initializeProperties() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
initializeReader() - Method in class org.jmol.adapter.readers.cif.CifReader
 
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.Mol3DReader
 
initializeReader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.MdTopReader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
initializeReader() - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
initializeReader() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
initializeReader() - Method in class org.jmol.adapter.readers.pdb.PqrReader
 
initializeReader() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GaussianWfnReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.OdysseyReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.SpartanReader
 
initializeReader() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.CubeReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.JmeReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.JSONReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
 
initializeReader() - Method in class org.jmol.adapter.readers.simple.MopacReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CgdReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.MagresReader
not sure how to work with symmetry here...
initializeReader() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspChgcarReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
initializeReader() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
initializeReader() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeShape(Viewer, ModelSet, int) - Method in class org.jmol.shape.Shape
 
initializeSurfaceData() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
initializeSymmetry() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeSymmetryOptions() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeTrajectoryFile() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
initializeUnitCellAndSymmetry() - Method in class org.jmol.modelset.ModelLoader
 
initializeVolumetricData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
initIFR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
initIMR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.IsoMepReader
 
initIsosurface(int) - Method in class org.jmol.scriptext.IsoExt
 
initModelSet() - Method in class org.jmol.shape.AtomShape
 
initModelSet() - Method in class org.jmol.shape.Measures
 
initModelSet() - Method in class org.jmol.shape.Object2dShape
 
initModelSet() - Method in class org.jmol.shape.Shape
 
initModelSet() - Method in class org.jmol.shapebio.BioShapeCollection
 
initModelSet() - Method in class org.jmol.shapespecial.Vectors
 
initModForStructure(int) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
initOptions() - Method in class org.jmol.applet.Jmol
 
initOptions() - Method in class org.jmol.appletjs.Jmol
 
initOptions() - Method in class org.jmol.util.GenericApplet
 
initOrientation(M3) - Method in class org.jmol.symmetry.UnitCell
 
initOutput(Viewer, double, GData, Map<String, Object>) - Method in class org.jmol.export.___Exporter
 
initPlanes() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
initRenderer() - Method in class org.jmol.render.AxesRenderer
 
initRenderer() - Method in class org.jmol.render.BbcageRenderer
 
initRenderer() - Method in class org.jmol.render.MeasuresRenderer
 
initRenderer() - Method in class org.jmol.render.ShapeRenderer
 
initRenderer() - Method in class org.jmol.render.UccageRenderer
 
initRenderer() - Method in class org.jmol.renderspecial.DotsRenderer
 
initShape() - Method in class org.jmol.shape.Axes
 
initShape() - Method in class org.jmol.shape.Bbcage
 
initShape() - Method in class org.jmol.shape.Echo
 
initShape() - Method in class org.jmol.shape.FontShape
 
initShape() - Method in class org.jmol.shape.Frank
 
initShape() - Method in class org.jmol.shape.Hover
 
initShape() - Method in class org.jmol.shape.Labels
 
initShape() - Method in class org.jmol.shape.Measures
 
initShape() - Method in class org.jmol.shape.MeshCollection
 
initShape() - Method in class org.jmol.shape.Shape
 
initShape() - Method in class org.jmol.shape.Sticks
 
initShape() - Method in class org.jmol.shape.Uccage
 
initShape() - Method in class org.jmol.shapebio.Backbone
 
initShape() - Method in class org.jmol.shapebio.Cartoon
 
initShape() - Method in class org.jmol.shapebio.MeshRibbon
 
initShape() - Method in class org.jmol.shapebio.Rockets
 
initShape() - Method in class org.jmol.shapebio.Trace
 
initShape() - Method in class org.jmol.shapespecial.Dots
 
initShape() - Method in class org.jmol.shapespecial.Draw
 
initShape() - Method in class org.jmol.shapespecial.Ellipsoids
 
initShape() - Method in class org.jmol.shapespecial.GeoSurface
 
initShape() - Method in class org.jmol.shapesurface.Contact
 
initShape() - Method in class org.jmol.shapesurface.Isosurface
 
initShape() - Method in class org.jmol.shapesurface.LcaoCartoon
 
initShape() - Method in class org.jmol.shapesurface.MolecularOrbital
 
initShape() - Method in class org.jmol.shapesurface.NBO
 
initShape() - Method in class org.jmol.shapesurface.Plot3D
 
initShape() - Method in class org.jmol.shapesurface.Pmesh
 
initSlice() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
initSR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
initState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
initState() - Method in class org.jmol.shape.Halos
 
initState() - Method in class org.jmol.shapesurface.Isosurface
 
initSubclass() - Method in class org.jmol.adapter.readers.cif.CifReader
 
initSubclass() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
initSwing(String, PopupResource, Object, boolean, boolean, boolean) - Method in class org.jmol.popup.GenericSwingPopup
 
initUnitcellVertices() - Method in class org.jmol.symmetry.UnitCell
 
initVariables() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
initVars() - Method in class org.jmol.export.__RayTracerExporter
 
initVDR(SurfaceGenerator) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
initWords(int) - Method in class org.jmol.java.BS
 
inline - Static variable in class org.jmol.script.T
 
inlineNewlineChar - Variable in class org.jmol.viewer.GlobalSettings
 
inMotion - Variable in class org.jmol.viewer.Viewer
 
inMovie - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
inNames - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
inPath - Variable in class org.jmol.awtjs2d.JsG2D
 
input - Variable in class org.jmol.console.GenericConsole
 
inputCode - Variable in class org.jmol.symmetry.HallRotationTerm
 
inputContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
inputFileName - Variable in class org.jmol.dialog.Dialog
 
inputFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
inputOnly - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
inputOnly - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
 
inputOnly - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
inputOnly - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
InputReader - Class in org.jmol.adapter.readers.simple
 
InputReader() - Constructor for class org.jmol.adapter.readers.simple.InputReader
 
InputScannerThread - Class in org.openscience.jmol.app
 
InputScannerThread(JmolViewer, boolean) - Constructor for class org.openscience.jmol.app.InputScannerThread
 
inputTabs - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
inRange(int, int, int) - Method in class org.jmol.viewer.MouseState
 
INS_CODE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
insert(SC, int) - Method in class org.jmol.popup.AwtSwingComponent
 
insertedCommand - Variable in class org.jmol.viewer.Viewer
 
insertion - Static variable in class org.jmol.script.T
 
INSERTION_CODE_MASK - Static variable in class org.jmol.modelset.Group
 
insertionCode - Variable in class org.jmol.adapter.smarter.Atom
 
insertString(int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
insideMaskTable - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
insideOut - Variable in class org.jmol.jvxl.data.JvxlData
 
insideOut - Variable in class org.jmol.jvxl.readers.Parameters
 
insideout - Static variable in class org.jmol.script.T
 
insideOut - Variable in class org.jmol.shape.Mesh
 
inSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
instance - Static variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
InstanceCellRenderer() - Constructor for class org.openscience.jmol.app.webexport.WebPanel.InstanceCellRenderer
 
instanceList - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
INT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
Int2IntHash - Class in org.jmol.util
 
Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
 
Int2IntHashEntry - Class in org.jmol.util
 
Int2IntHashEntry(int, int, Int2IntHashEntry) - Constructor for class org.jmol.util.Int2IntHashEntry
 
intAnimThread - Variable in class org.jmol.viewer.AnimationManager
 
intAsFloat - Variable in class org.jmol.modelset.LabelToken
 
intAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
intAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
integer - Static variable in class org.jmol.script.T
 
integerOutOfRange(int, int) - Method in class org.jmol.script.ScriptError
 
integrateSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
integration - Variable in class org.jmol.quantum.MOCalculation
 
intenseFraction - Variable in class org.jmol.util.Shader
 
INTERACTION_FACTOR - Static variable in class org.jmol.util.Tensor
 
interactionTensors - Variable in class org.jmol.adapter.readers.xtal.MagresReader
 
intercept(MarchingSquares.Triangle, int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
interestingAminoAtomIDs - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
interestingNucleicAtomIDs - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
Interface - Class in org.jmol.api
 
Interface() - Constructor for class org.jmol.api.Interface
 
interior - Static variable in class org.jmol.script.T
 
intermolecular - Static variable in class org.jmol.script.T
 
internal - Static variable in class org.jmol.script.T
 
internal_feedback - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
internal_gui - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
internal_gui_control_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
internal_gui_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
internal_gui_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
internal_prompt - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
internalRotationAngle - Variable in class org.jmol.viewer.TransformManager
 
internalRotationAxis - Variable in class org.jmol.viewer.TransformManager
 
internalRotationCenter - Variable in class org.jmol.viewer.TransformManager
 
internalSlab - Variable in class org.jmol.viewer.TransformManager
 
internalTranslation - Variable in class org.jmol.viewer.TransformManager
 
interpolate(int, int, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
 
interpolateFraction(T3, T3, float, float, float, int) - Method in class org.jmol.util.MeshSlicer
 
interpolatePoint(T3, T3, float, float, float, float, int) - Method in class org.jmol.util.MeshSlicer
 
interpolatePrecisely(int, int, int[][], float[][]) - Method in class org.jmol.g3d.CylinderRenderer
 
interpolateSphere(T3, T3, float, float, double, float, float, int) - Method in class org.jmol.util.MeshSlicer
 
interpolateX(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.CapVertex
Get interpolated x for the scan line intersection with an edge.
interrupt() - Method in interface org.jmol.api.JmolNavigatorInterface
 
interrupt() - Method in class org.jmol.thread.AnimationThread
 
interrupt() - Method in class org.jmol.thread.JmolThread
 
interrupt() - Method in class org.jmol.thread.MoveToThread
 
interruptQueueThreads() - Method in class org.jmol.script.ScriptManager
 
intersectID - Variable in class org.jmol.shapespecial.Draw
 
intersection - Variable in class org.jmol.jvxl.readers.Parameters
 
intersection - Static variable in class org.jmol.script.T
 
intersectPlane(P4, Lst<Object>, int) - Method in class org.jmol.modelset.ModelSet
 
intersectPlane(ModelSet, P4, float, int) - Method in class org.jmol.util.BoxInfo
returns a set of points defining the geometric object within the given plane that spans the unit cell within the given margins
intersectPlane(P4, Lst<Object>, int) - Method in class org.jmol.util.TriangleData
a generic cell - plane intersector -- used for finding the plane through a not static so as to allow JavaScript to not load it as core.
intersectPlane(P4, Lst<Object>, int) - Method in interface org.jmol.util.Triangulator
 
intersects(BS) - Method in class org.jmol.java.BS
Returns true if the specified BitSet has any bits set to true that are also set to true in this BitSet.
intlTableNumber - Variable in class org.jmol.symmetry.SpaceGroup
 
intlTableNumberExt - Variable in class org.jmol.symmetry.SpaceGroup
 
intlTableNumberFull - Variable in class org.jmol.symmetry.SpaceGroup
 
intparam - Static variable in class org.jmol.script.T
 
intParameter(int) - Method in class org.jmol.script.ScriptParam
 
intParameter(int) - Method in class org.jmol.scriptext.CmdExt
 
intParameterRange(int, int, int) - Method in class org.jmol.script.ScriptParam
 
intPeek() - Method in class org.jmol.script.ScriptTokenParser
 
intproperty - Static variable in class org.jmol.script.T
 
intramolecular - Variable in class org.jmol.modelset.MeasurementData
 
intramolecular - Static variable in class org.jmol.script.T
 
intramolecular - Variable in class org.jmol.shape.Measures
 
intThread - Variable in class org.jmol.thread.AnimationThread
 
intValue - Variable in class org.jmol.script.T
 
INVALID_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
invalidatedVertexCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
invalidateMesh - Variable in class org.jmol.renderbio.BioShapeRenderer
 
invalidatePolygons() - Method in class org.jmol.util.MeshSurface
 
invalidateSheets - Variable in class org.jmol.renderbio.BioShapeRenderer
 
invalidateSurfaceSet(int) - Method in class org.jmol.jvxl.data.MeshData
 
invalidateTriangles() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
invalidateTriangles() - Method in class org.jmol.shapesurface.Isosurface
 
invalidateVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
 
invalidControl - Variable in class org.jmol.modelsetbio.BioPolymer
 
invalidLead - Variable in class org.jmol.modelsetbio.BioPolymer
 
InvalidSmilesException - Exception in org.jmol.smiles
Exception thrown for invalid SMILES String
InvalidSmilesException(String) - Constructor for exception org.jmol.smiles.InvalidSmilesException
Constructs a InvalidSmilesException with a detail message.
invArg() - Method in class org.jmol.script.ScriptError
 
invArg() - Method in class org.jmol.scriptext.CmdExt
 
inverseMatrix - Variable in class org.jmol.jvxl.data.VolumeData
 
inverseNormixes - Static variable in class org.jmol.util.Normix
 
invertAtomCoordPlane(P4, BS) - Method in class org.jmol.viewer.Viewer
 
invertAtomCoordPt(P3, BS) - Method in class org.jmol.viewer.Viewer
 
invertInPlace(BS, int) - Static method in class org.jmol.util.BSUtil
inverts the bitset bits 0 through n-1, and returns a reference to the modified bitset
invertNormixes() - Method in class org.jmol.shape.Mesh
 
invertSelected(P3, P4, int, BS, BS) - Method in class org.jmol.modelset.ModelSet
 
invertSelected - Static variable in class org.jmol.script.T
 
invertSelected(P3, P4, int, BS) - Method in class org.jmol.viewer.Viewer
 
invertSelection() - Method in class org.jmol.viewer.SelectionManager
 
invMatrix - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
invPO() - Method in class org.jmol.scriptext.CmdExt
 
iObj - Variable in class org.jmol.export._IdtfExporter
 
iObj - Variable in class org.jmol.export.UseTable
 
iop - Variable in class org.jmol.util.ModulationSet
 
iopLast - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
iPlaneRaw - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
iPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
 
iProcess - Static variable in class org.jmol.script.ScriptEval
 
ipt - Variable in class org.jmol.util.MeshCapper.CapVertex
external reference
is(int) - Method in class org.jmol.modelset.Bond
 
IS - Static variable in class org.jmol.quantum.QS
 
is(MouseState) - Method in class org.jmol.viewer.MouseState
 
is2D - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
is2D - Variable in class org.jmol.modelset.ModelLoader
 
is4D - Variable in class org.jmol.viewer.TransformManager4D
 
IS_HETERO_FLAG - Static variable in class org.jmol.modelset.Atom
 
IS_POINTMAPPABLE - Static variable in class org.jmol.jvxl.readers.Parameters
 
IS_SILENT - Static variable in class org.jmol.jvxl.readers.Parameters
 
IS_SLABBABLE - Static variable in class org.jmol.jvxl.readers.Parameters
 
IS_SOLVENTTYPE - Static variable in class org.jmol.jvxl.readers.Parameters
 
isActive - Variable in class org.jmol.shape.AtomShape
 
isActive - Variable in class org.jmol.shapebio.BioShapeCollection
 
isActive() - Method in class org.jmol.shapespecial.Ellipsoids
 
isActiveLevel(int) - Static method in class org.jmol.util.Logger
Tells if a logging level is active.
isAdded(int) - Method in class org.jmol.modelset.Group
 
isAdjacentSp2(Atom) - Method in class org.jmol.modelset.AtomCollection
 
isAligned(P3, P3, P3) - Method in class org.jmol.shapespecial.Polyhedra
 
isAll - Variable in class org.jmol.modelset.MeasurementData
 
isAll - Variable in class org.jmol.renderspecial.PolyhedraRenderer
 
isAll - Variable in class org.jmol.shape.Object2dShape
 
isAllQ - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
isAlphaMonomer() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isAltKeyReleased - Variable in class org.jmol.viewer.ActionManager
 
isAltLoc(String) - Method in class org.jmol.modelset.Atom
 
isAmide - Variable in class org.jmol.minimize.MinBond
 
isAminoMonomer() - Method in class org.jmol.modelsetbio.AminoMonomer
 
isAngstroms - Variable in class org.jmol.adapter.readers.simple.CubeReader
 
isAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
 
isAngstroms - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
isAnisotropic - Variable in class org.jmol.jvxl.readers.Parameters
 
isAnisotropic - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isAntialiased() - Method in interface org.jmol.api.JmolGraphicsInterface
 
isAntialiased() - Method in class org.jmol.export.Export3D
is full scene / oversampling antialiasing in effect
isAntialiased - Variable in class org.jmol.render.HalosRenderer
 
isAntialiased - Variable in class org.jmol.render.SticksRenderer
 
isAntialiased() - Method in class org.jmol.util.GData
is full scene / oversampling antialiasing in effect
isAntiparallel - Variable in class org.jmol.dssx.Bridge
 
isAppend - Variable in class org.jmol.io.FileReader
 
isAppend - Variable in class org.jmol.io.FilesReader
 
isAppendSelected() - Method in class org.jmol.dialog.FilePreview
 
isApplet - Variable in class org.jmol.popup.GenericSwingPopup
 
isApplet - Variable in class org.jmol.viewer.Viewer
 
isApprox(V3d, V3d, double) - Static method in class org.jmol.minimize.Util
 
isArc - Variable in class org.jmol.shapespecial.Draw
 
isArchive - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
isAromatic - Variable in class org.jmol.minimize.MinBond
 
isAromatic() - Method in class org.jmol.modelset.Bond
 
isaromatic - Static variable in class org.jmol.script.T
 
isAromatic - Variable in class org.jmol.smiles.SmilesAtom
 
isAromatic() - Method in class org.jmol.smiles.SmilesAtom
 
isAromaticBond(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
isAromaticRing(BS, BS, BS, int) - Static method in class org.jmol.smiles.SmilesAromatic
 
isArray(Object) - Static method in class org.jmol.script.SV
Must be updated if getVariable is updated!
isArrayItem - Variable in class org.jmol.script.ScriptMathProcessor
 
isArrayParameter(int) - Method in class org.jmol.script.ScriptParam
 
isArrow - Variable in class org.jmol.shapespecial.Draw
 
isAssignment - Variable in class org.jmol.script.ScriptMathProcessor
 
isAtEnd() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
isAtomAssignable(int) - Method in class org.jmol.modelset.ModelSet
 
isAtomHidden(int) - Method in class org.jmol.modelset.AtomCollection
 
isAtomNameMatch(Atom, String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
 
isAtomPDB(int) - Method in class org.jmol.modelset.ModelSet
 
isAtomSelected(int) - Method in class org.jmol.viewer.SelectionManager
 
isAV(Object) - Static method in class org.jmol.util.Escape
 
isBarb - Variable in class org.jmol.shapespecial.Draw
 
isBarb - Variable in class org.jmol.shapespecial.DrawMesh
 
isBbcageDefault - Variable in class org.jmol.modelset.ModelSet
 
isBCSfile - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
 
isBiColor - Variable in enum org.jmol.c.STER
 
isBiColor() - Method in enum org.jmol.c.STER
 
isBicolorMap - Variable in class org.jmol.jvxl.data.JvxlData
 
isBicolorMap - Variable in class org.jmol.jvxl.readers.Parameters
 
isBicolorMap - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
isBilbao - Variable in class org.jmol.symmetry.SpaceGroup
 
isBinary - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isBinary - Variable in class org.jmol.jvxl.readers.PmeshReader
 
isBio() - Method in interface org.jmol.api.SymmetryInterface
 
isBio - Variable in class org.jmol.symmetry.SpaceGroup
 
isBio - Variable in class org.jmol.symmetry.Symmetry
 
isBio() - Method in class org.jmol.symmetry.Symmetry
 
isBio - Variable in class org.jmol.symmetry.SymmetryOperation
 
isBioAtom - Variable in class org.jmol.smiles.SmilesAtom
 
isBioModel - Variable in class org.jmol.modelset.Model
 
isbiomol - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
isBiomolecule - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
isBioSequence - Variable in class org.jmol.smiles.SmilesParser
 
isBioShape - Variable in class org.jmol.shape.Shape
 
isBond - Variable in class org.jmol.shapespecial.Dipoles
 
isBondDipole(int) - Method in class org.jmol.shapespecial.Dipoles
 
isBonded(Atom) - Method in class org.jmol.modelset.Atom
 
isBondedCorrectly(int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
 
isBondedCorrectlyRange(int, int, int, byte[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
 
isBondSet - Variable in class org.jmol.script.ScriptParam
 
isBondType() - Method in class org.jmol.shapespecial.Dipole
 
isBondType(char, boolean, boolean) - Static method in class org.jmol.smiles.SmilesBond
 
isBondType1(AtomType, AtomType) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
isBound(int, int) - Method in class org.jmol.viewer.binding.Binding
 
isBound(int, int) - Method in class org.jmol.viewer.Viewer
 
isBreakableContext(int) - Static method in class org.jmol.script.ScriptCompiler
 
isBXSF - Variable in class org.jmol.jvxl.readers.XsfReader
 
isCA2(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isCarbohydrate() - Method in class org.jmol.modelset.Atom
 
isCarbohydrate() - Method in class org.jmol.modelset.Group
 
isCarbohydrate() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isCarbohydrate - Variable in class org.jmol.renderbio.BioShapeRenderer
 
isCartesian - Variable in class org.jmol.export.___Exporter
 
isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
 
isCartesianExport - Variable in class org.jmol.render.SticksRenderer
 
isCartoonsSelected() - Method in class org.jmol.dialog.FilePreview
 
isCavity - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
isCavity - Variable in class org.jmol.jvxl.readers.Parameters
 
isCell - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
isCellEditable(int, int) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
isCenteringOp - Variable in class org.jmol.symmetry.SymmetryOperation
 
isCenterParameter(int) - Method in class org.jmol.script.ScriptParam
 
isCentrosymmetric - Variable in class org.jmol.symmetry.HallInfo
 
isCheckOnly - Variable in class org.jmol.script.ScriptCompiler
 
isCircle - Variable in class org.jmol.shapespecial.Draw
 
isClickable() - Method in class org.jmol.modelset.Atom
 
isClipped(int, int, int) - Method in class org.jmol.export.Export3D
 
isClipped(int, int) - Method in class org.jmol.export.Export3D
 
isClipped(int, int) - Method in class org.jmol.util.GData
 
isClipped3(int, int, int) - Method in class org.jmol.util.GData
 
isClippedXY(int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
 
isClippedXY(int, int, int) - Method in class org.jmol.export.Export3D
 
isClippedXY(int, int, int) - Method in class org.jmol.util.GData
 
isClippedZ(int) - Method in class org.jmol.util.GData
 
isClosedFace - Variable in class org.jmol.jvxl.readers.PmeshReader
 
isCmdf - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
isCmdLine_C_Option - Variable in class org.jmol.script.ScriptEval
 
isCmdLine_c_or_C_Option - Variable in class org.jmol.script.ScriptEval
 
isColixColorInherited(short) - Static method in class org.jmol.util.C
 
isColixLastAvailable(short) - Static method in class org.jmol.util.C
 
isColixTranslucent(short) - Static method in class org.jmol.util.C
 
isCollapsed - Variable in class org.jmol.shapespecial.Polyhedra
 
isColorExplicit - Variable in class org.jmol.shapesurface.Isosurface
 
isColorIndex - Variable in class org.jmol.util.ColorEncoder
 
isColorParam(int) - Method in class org.jmol.script.ScriptParam
 
isColorReversed - Variable in class org.jmol.jvxl.data.JvxlData
 
isColorReversed - Variable in class org.jmol.jvxl.readers.Parameters
 
isColorSolid - Variable in class org.jmol.util.MeshSurface
 
isCommaAsOrAllowed - Variable in class org.jmol.script.ScriptTokenParser
 
isCommandDisplayable(int) - Method in class org.jmol.script.ScriptEval
provides support for the script editor
isCommensurate - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
isComment - Variable in class org.jmol.script.ScriptCompiler
 
isComplete - Variable in class org.jmol.script.ScriptContext
 
isCompoundDocument - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
isConcatenated - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isConnect() - Method in class org.jmol.modelset.StateScript
 
isConnected(Atom[], int) - Method in class org.jmol.modelset.Measurement
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.AminoMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.Monomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isConnectedAfter(Monomer) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isConnectedPrevious() - Method in class org.jmol.modelset.Group
 
isConnectedPrevious() - Method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
isConnectedPrevious() - Method in class org.jmol.modelsetbio.Monomer
 
isConnectStateBug - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
isContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
 
isContoured - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isContoured - Variable in class org.jmol.jvxl.data.JvxlData
 
isContoured - Variable in class org.jmol.jvxl.readers.Parameters
 
isCore - Variable in class org.jmol.quantum.SlaterData
 
isCourseGrained - Variable in class org.jmol.adapter.readers.cif.CifReader
 
isCourseGrained - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
isCovalent() - Method in class org.jmol.modelset.Bond
 
isCovalent() - Method in class org.jmol.smiles.SmilesBond
 
isCovalent() - Method in class org.jmol.util.Edge
 
isCovalentlyBonded(Atom) - Method in class org.jmol.modelset.Atom
 
iscroll - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
isCrossed - Variable in class org.jmol.shapespecial.Draw
 
isCrossLinked(BNode) - Method in class org.jmol.modelset.Atom
 
isCrossLinked(Group) - Method in class org.jmol.modelset.Group
 
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.Monomer
 
isCrossLinked(Group) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isCrossLinked(BNode) - Method in class org.jmol.smiles.SmilesAtom
 
isCrossLinked(BNode) - Method in interface org.jmol.util.BNode
 
isCursorOnTopOf(int, int, int, Atom) - Method in class org.jmol.modelset.Atom
 
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.AtomCollection
used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability
isCursorOnTopOf(Atom, int, int, int, Atom) - Method in class org.jmol.modelset.Group
 
isCurve - Variable in class org.jmol.shapespecial.Draw
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.data.JvxlData
 
isCutoffAbsolute - Variable in class org.jmol.jvxl.readers.Parameters
 
isCylinder - Variable in class org.jmol.shapespecial.Draw
 
isDatabaseCode(char) - Static method in class org.jmol.viewer.Viewer
 
isDataFlavorSupported(DataFlavor) - Method in class org.jmol.awt.AwtClipboard
 
isDataFlavorSupported(DataFlavor) - Method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler.ArrayListTransferable
 
isDataFrame - Variable in class org.jmol.renderbio.BackboneRenderer
 
isDataOnly - Variable in class org.openscience.jmol.app.JmolApp
 
isDecimal(SV) - Method in class org.jmol.script.ScriptMathProcessor
 
isDefaultColorRasmol - Variable in class org.jmol.viewer.ColorManager
 
isDeleted() - Method in class org.jmol.modelset.Atom
 
isDeleted() - Method in class org.jmol.smiles.SmilesAtom
 
isDeleted() - Method in interface org.jmol.util.BNode
 
isDiaxial(Node, Node, Node, Node, VTemp, float) - Static method in class org.jmol.smiles.SmilesSearch
 
isDirectedTowardsCamera(short) - Method in class org.jmol.util.GData
 
isDirectory() - Method in class org.jmol.awtjs2d.JSFile
 
isDisplayWithinNot - Variable in class org.jmol.shape.MeshCollection
 
isDna() - Method in class org.jmol.modelset.Atom
 
isDna - Variable in class org.jmol.modelset.Chain
 
isDna() - Method in class org.jmol.modelset.Group
 
isDna() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isDna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isDna() - Method in class org.jmol.smiles.SmilesAtom
 
isDna() - Method in interface org.jmol.util.BNode
 
isDone - Variable in class org.jmol.thread.SpinThread
 
isDotDot - Variable in class org.jmol.script.ScriptCompiler
 
isDrawType(String, int, float) - Method in class org.jmol.symmetry.PointGroup
 
isDssrSet - Variable in class org.jmol.modelsetbio.NucleicPolymer
 
isE_fr_energy - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
isE_wo_entrp - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
isEccentric - Variable in class org.jmol.jvxl.readers.Parameters
 
isEccentric - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isEcho - Static variable in class org.jmol.modelset.Text
 
isElectronDensityCalc - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
isElement(int, int) - Static method in class org.jmol.util.Elements
 
isEmbeddedExpression - Variable in class org.jmol.script.ScriptTokenParser
 
isEmpty() - Method in class org.jmol.java.BS
Returns true if this BitSet contains no bits that are set to true.
isEnabled() - Method in interface org.jmol.api.JmolModulationSet
 
isEnabled() - Method in class org.jmol.popup.AwtSwingComponent
 
isEnabled() - Method in class org.jmol.util.ModulationSet
 
isEndOfCommand - Variable in class org.jmol.script.ScriptCompiler
 
isEqual(PointGroup) - Method in class org.jmol.symmetry.PointGroup
 
isEquiv(Tensor) - Method in class org.jmol.util.Tensor
 
isError - Variable in exception org.jmol.script.ScriptException
 
isError() - Method in class org.jmol.script.ScriptTokenParser
 
isError - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
iSet - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
isExact - Variable in class org.jmol.render.LabelsRenderer
 
isExecuting() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isExecuting() - Method in class org.jmol.script.ScriptEval
 
isExport - Variable in class org.jmol.render.ShapeRenderer
 
isExpressionNext() - Method in class org.jmol.script.ScriptTokenParser
 
isFinalized - Variable in class org.jmol.adapter.readers.cif.Subsystem
 
isFinalized - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isFinalized - Variable in class org.jmol.symmetry.SymmetryOperation
 
isFinite(double) - Static method in class org.jmol.minimize.Util
 
isFirst - Variable in class org.jmol.smiles.SmilesAtom
 
isFirst - Variable in class org.jmol.thread.AnimationThread
 
isFixed - Variable in class org.jmol.shape.MeshCollection
 
isFixed - Variable in class org.jmol.shapespecial.DrawMesh
 
isFlatSp2Ring(Node[], BS, BS, float) - Static method in class org.jmol.smiles.SmilesAromatic
3D-SEARCH aromaticity test.
isFloatInfo(String) - Static method in class org.jmol.util.Tensor
 
isFloatParameter(int) - Method in class org.jmol.script.ScriptParam
 
isFloatParameter(int) - Method in class org.jmol.scriptext.CmdExt
 
isFractional - Variable in class org.jmol.adapter.readers.xtal.AimsReader
 
isFront(P3, P3, P3) - Static method in class org.jmol.g3d.HermiteRenderer
 
isFullSceneAntialiasingEnabled - Variable in class org.jmol.g3d.Graphics3D
 
isFullyLit() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isFullyLit - Variable in class org.jmol.shapespecial.Polyhedron
 
isFunction - Variable in class org.jmol.script.ScriptContext
 
isFunction(String) - Method in class org.jmol.viewer.Viewer
 
isGesture - Variable in class org.jmol.thread.SpinThread
 
isGhostPass - Variable in class org.jmol.render.MeshRenderer
 
isGreaterOnly - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
isGuanine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isHbonded(int, int, int, int, int[][][][]) - Method in class org.jmol.dssx.DSSP
 
isHeader - Variable in class org.jmol.adapter.readers.simple.InputReader
 
isHeader(String) - Method in class org.jmol.dssx.AnnotationParser
 
isHeadless() - Method in class org.jmol.awt.Platform
 
isHeadless() - Method in class org.jmol.awtjs2d.Platform
 
isHelix() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isHelix(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
 
isHelix() - Method in class org.jmol.modelsetbio.Monomer
 
isHetero - Variable in class org.jmol.adapter.smarter.Atom
 
isHetero(String) - Method in interface org.jmol.api.JmolBioResolver
 
isHetero() - Method in class org.jmol.modelset.Atom
 
isHetero() - Method in class org.jmol.modelset.Group
 
isHetero(String) - Method in class org.jmol.modelsetbio.Resolver
MMCif, Gromacs, MdTop, Mol2 readers only
isHidden - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
isHidden - Variable in class org.jmol.modelset.Measurement
 
isHighRes - Variable in class org.jmol.renderbio.BioShapeRenderer
 
isHover - Variable in class org.jmol.shape.Object2dShape
 
iShowNormals - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
iShowSolid - Variable in class org.jmol.renderspecial.DotsRenderer
 
isHydrogen() - Method in class org.jmol.modelset.Bond
 
isHydrogen() - Method in class org.jmol.smiles.SmilesBond
 
isHydrogen() - Method in class org.jmol.util.Edge
 
isIDcmd(int) - Static method in class org.jmol.script.T
commands that allow implicit ID as first parameter
isImproper - Variable in class org.jmol.symmetry.HallRotationTerm
 
isInDisplayRange(int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
 
isInDisplayRange(int, int) - Method in class org.jmol.export.Export3D
 
isInDisplayRange(int, int) - Method in class org.jmol.util.GData
 
isInitializedIndex(int) - Method in class org.jmol.bspt.Bspf
 
isInLatticeCell(int, P3, P3, boolean) - Method in class org.jmol.modelset.ModelSet
 
isInPosition(V3, float) - Method in class org.jmol.viewer.TransformManager
 
isInRange(Atom, Atom, float, float, boolean, boolean, boolean) - Method in class org.jmol.modelset.BondCollection
 
isInRange(RadiusData, float) - Method in class org.jmol.modelset.Measurement
 
isInSelectionSubset(int) - Method in class org.jmol.viewer.SelectionManager
 
isInside - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isInside(float, float, boolean) - Static method in class org.jmol.jvxl.calc.MarchingCubes
 
isInsideOut() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
isInSymmetryRange(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
isInt(float) - Static method in class org.jmol.adapter.readers.xtal.CastepReader
 
isIntramolecular(Atom[], int) - Method in class org.jmol.modelset.Measurement
 
isInvalid - Variable in class org.jmol.g3d.TextRenderer
 
isInvertible(MinAtom) - Static method in class org.jmol.minimize.forcefield.CalculationsMMFF
 
isInvertible(int) - Static method in class org.jmol.minimize.forcefield.CalculationsUFF
 
isIsotropic - Variable in class org.jmol.util.Tensor
 
isJmolDataFrame - Variable in class org.jmol.modelset.Model
 
isJmolDataFrame() - Method in class org.jmol.viewer.Viewer
 
isJmolDataFrameForAtom(Atom) - Method in class org.jmol.modelset.ModelSet
 
isJmolDataFrameForModel(int) - Method in class org.jmol.modelset.ModelSet
 
isJmolVariable(String) - Method in class org.jmol.viewer.GlobalSettings
 
isJmolZformat - Variable in class org.jmol.adapter.readers.simple.InputReader
 
isJNLP - Variable in class org.jmol.util.GenericApplet
 
isJNLP - Variable in class org.jmol.viewer.Viewer
 
isJPEG - Variable in class org.jmol.dialog.Dialog.QualityListener
 
isJS - Variable in class org.jmol.popup.GenericSwingPopup
 
isJS - Variable in class org.jmol.script.ScriptEval
 
isJS - Variable in class org.jmol.thread.JmolThread
 
isJS - Variable in class org.jmol.util.GenericApplet
 
isJS - Variable in class org.jmol.viewer.Viewer
 
isJSThread - Variable in class org.jmol.script.ScriptContext
 
isJvxl - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isJvxlPrecisionColor - Variable in class org.jmol.jvxl.data.JvxlData
 
iskiosk - Static variable in class org.jmol.script.T
 
isKiosk - Variable in class org.jmol.viewer.Viewer
 
isKiosk() - Method in class org.jmol.viewer.Viewer
 
isKiosk - Variable in class org.openscience.jmol.app.JmolApp
 
isKnownPDBGroup(String) - Method in interface org.jmol.api.JmolBioResolver
 
isKnownPDBGroup(String) - Method in class org.jmol.modelsetbio.Resolver
 
isLabelOrHover - Variable in class org.jmol.modelset.Object2d
 
isLabelPropertyTok(int) - Static method in class org.jmol.modelset.LabelToken
 
isLastFrame - Variable in class org.jmol.popup.JmolGenericPopup
 
isLastModel(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
after reading a model, Q: Is this the last model?
isLeadAtom() - Method in class org.jmol.modelset.Atom
 
isLeadAtom(int) - Method in class org.jmol.modelset.Group
 
isLeadAtom(int) - Method in class org.jmol.modelsetbio.Monomer
 
isLeadAtom - Variable in class org.jmol.smiles.SmilesAtom
 
isLeadAtom() - Method in class org.jmol.smiles.SmilesAtom
 
isLeadAtom() - Method in interface org.jmol.util.BNode
 
isLegacyModelType - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
isLegendre - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
isLigandBondBug - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
isLike(SV, SV) - Static method in class org.jmol.script.SV
a LIKE "x" a is a string and equals x a LIKE "*x" a is a string and ends with x a LIKE "x*" a is a string and starts with x a LIKE "*x*" a is a string and contains x
isLine - Variable in class org.jmol.shapespecial.Draw
 
isLinear(int) - Method in class org.jmol.minimize.forcefield.Calculations
 
isLinear(int) - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
 
isLinear(MinAtom) - Static method in class org.jmol.minimize.MinAtom
 
isLinear(P3[]) - Method in class org.jmol.symmetry.PointGroup
 
isLineContinuation(int, boolean) - Method in class org.jmol.script.ScriptCompiler
 
isLoadOption(int) - Method in class org.jmol.script.ScriptEval
 
isLonePair - Variable in class org.jmol.shapesurface.LcaoCartoon
 
isLongMode - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isM3D - Variable in class org.jmol.adapter.readers.simple.AlchemyReader
 
isMac - Static variable in class org.jmol.dialog.Dialog
 
isMagCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
 
isMapped - Variable in class org.jmol.jvxl.readers.Parameters
 
isMathExpressionCommand - Variable in class org.jmol.script.ScriptTokenParser
 
isMenuItem(Object) - Method in class org.jmol.console.GenericConsole
 
isMenuItem(Object) - Method in class org.jmol.console.JmolConsole
 
isMenuItem(Object) - Method in class org.jmol.consolejs.AppletConsole
 
isMerged - Variable in class org.jmol.util.MeshSurface
 
isMesh - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
isMesh - Variable in class org.jmol.shapebio.Strands
 
isMin(Map<String, Integer>) - Method in class org.jmol.modelset.Measurement
 
isMixed(Matrix) - Method in class org.jmol.adapter.readers.cif.Subsystem
 
isMMCIF - Variable in class org.jmol.adapter.readers.cif.CifReader
 
isModelKit - Variable in class org.jmol.modelset.Model
 
isModelkit() - Method in class org.jmol.modelset.Model
 
isModelPDB(int) - Method in class org.jmol.viewer.Viewer
 
isModified() - Method in class org.jmol.script.SV
 
isModulated(int) - Method in class org.jmol.modelset.AtomCollection
 
isModulated - Variable in class org.jmol.util.Tensor
 
isMolecular - Variable in class org.jmol.adapter.readers.cif.CifReader
 
isMolecular - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isMolecular - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
isMolecular - Variable in class org.jmol.shapesurface.LcaoCartoon
 
isMonomerSelected(int) - Method in class org.jmol.modelsetbio.BioPolymer
 
isMopac - Variable in class org.jmol.adapter.readers.simple.InputReader
 
isMouseDown - Variable in class org.jmol.awt.Mouse
 
isMouseDown - Variable in class org.jmol.awtjs2d.Mouse
 
isMove - Variable in class org.jmol.thread.MoveToThread
 
isMovie - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
isMovie - Variable in class org.jmol.viewer.AnimationManager
 
isMTClient() - Method in class org.jmol.viewer.ActionManager
 
isMTServer() - Method in class org.jmol.viewer.ActionManager
 
isMultiCell - Variable in class org.jmol.symmetry.SymmetryInfo
 
isMultiConfiguration - Variable in class org.jmol.popup.JmolGenericPopup
 
isMultiFrame - Variable in class org.jmol.popup.JmolGenericPopup
 
isMultiModel - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
isMultiTouch - Variable in class org.jmol.viewer.ActionManager
 
isMultiTouchClient - Variable in class org.jmol.viewer.ActionManager
 
isMultiTouchServer - Variable in class org.jmol.viewer.ActionManager
 
isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
 
isNav - Variable in class org.jmol.thread.SpinThread
 
isNavigating() - Method in class org.jmol.viewer.TransformManager
 
isNavigationMode - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
isNavTo - Variable in class org.jmol.navigate.Navigator
 
isNci - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
isNear(double, double) - Static method in class org.jmol.minimize.Util
 
isNear3(double, double, double) - Static method in class org.jmol.minimize.Util
 
isNearPlane(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
 
isNearZero(double) - Static method in class org.jmol.minimize.Util
 
isNearZero2(double, double) - Static method in class org.jmol.minimize.Util
 
isNegligible(double, double) - Static method in class org.jmol.minimize.Util
 
isNegligible3(double, double, double) - Static method in class org.jmol.minimize.Util
 
isNewChain - Variable in class org.jmol.modelset.ModelLoader
 
isNewFormat - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
isNewSet - Variable in class org.jmol.script.ScriptTokenParser
 
isNext(String) - Method in class org.jmol.jvxl.readers.XmlReader
 
isNonzero() - Method in class org.jmol.util.ModulationSet
 
isNonzero() - Method in class org.jmol.util.Vibration
 
isNot - Variable in class org.jmol.smiles.SmilesBond
 
isNot - Variable in class org.jmol.smiles.SmilesMeasure
 
isNotCentroid(P3, int, int[], boolean) - Method in class org.jmol.symmetry.Symmetry
 
isNotInRange(float) - Method in class org.jmol.viewer.AnimationManager
 
isNucleic() - Method in class org.jmol.modelset.Atom
 
isNucleic() - Method in class org.jmol.modelset.Group
 
isNucleic() - Method in class org.jmol.modelsetbio.BioPolymer
 
isNucleic() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isNucleic - Variable in class org.jmol.renderbio.BioShapeRenderer
 
isNucleic() - Method in class org.jmol.smiles.SmilesAtom
 
isNucleic() - Method in interface org.jmol.util.BNode
 
isNucleicMonomer() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
IsoExt - Class in org.jmol.scriptext
 
IsoExt() - Constructor for class org.jmol.scriptext.IsoExt
 
IsoFxyReader - Class in org.jmol.jvxl.readers
 
IsoFxyReader() - Constructor for class org.jmol.jvxl.readers.IsoFxyReader
 
IsoFxyzReader - Class in org.jmol.jvxl.readers
 
IsoFxyzReader() - Constructor for class org.jmol.jvxl.readers.IsoFxyzReader
 
IsoIntersectReader - Class in org.jmol.jvxl.readers
 
IsoIntersectReader() - Constructor for class org.jmol.jvxl.readers.IsoIntersectReader
 
IsoMepReader - Class in org.jmol.jvxl.readers
 
IsoMepReader() - Constructor for class org.jmol.jvxl.readers.IsoMepReader
 
isomesh_auto_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
isomeshes - Variable in class org.jmol.shapesurface.Isosurface
 
IsoMlpReader - Class in org.jmol.jvxl.readers
 
IsoMlpReader() - Constructor for class org.jmol.jvxl.readers.IsoMlpReader
 
IsoMOReader - Class in org.jmol.jvxl.readers
 
IsoMOReader() - Constructor for class org.jmol.jvxl.readers.IsoMOReader
 
isOn - Variable in class org.jmol.shapespecial.Ellipsoid
 
isOn - Variable in class org.jmol.util.CommandHistory
 
isOpFunc(T) - Static method in class org.jmol.script.ScriptMathProcessor
 
IsoPlaneReader - Class in org.jmol.jvxl.readers
 
IsoPlaneReader() - Constructor for class org.jmol.jvxl.readers.IsoPlaneReader
 
isoPointIndexPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isOrderH(int) - Static method in class org.jmol.modelset.Bond
 
IsoShapeReader - Class in org.jmol.jvxl.readers
 
IsoShapeReader() - Constructor for class org.jmol.jvxl.readers.IsoShapeReader
 
IsoSolventReader - Class in org.jmol.jvxl.readers
 
IsoSolventReader() - Constructor for class org.jmol.jvxl.readers.IsoSolventReader
 
IsoSolventReader.Edge - Class in org.jmol.jvxl.readers
 
IsoSolventReader.Face - Class in org.jmol.jvxl.readers
 
isosurface - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
isosurface - Static variable in class org.jmol.script.T
 
isosurface(int) - Method in class org.jmol.scriptext.IsoExt
 
Isosurface - Class in org.jmol.shapesurface
 
Isosurface() - Constructor for class org.jmol.shapesurface.Isosurface
 
isosurfacekey - Static variable in class org.jmol.script.T
 
isosurfaceKey - Variable in class org.jmol.viewer.GlobalSettings
 
IsosurfaceMesh - Class in org.jmol.shapesurface
 
IsosurfaceMesh(Viewer, String, short, int) - Constructor for class org.jmol.shapesurface.IsosurfaceMesh
 
isosurfacepropertysmoothing - Static variable in class org.jmol.script.T
 
isosurfacePropertySmoothing - Variable in class org.jmol.viewer.GlobalSettings
 
isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.T
 
isosurfacePropertySmoothingPower - Variable in class org.jmol.viewer.GlobalSettings
 
IsosurfaceRenderer - Class in org.jmol.rendersurface
 
IsosurfaceRenderer() - Constructor for class org.jmol.rendersurface.IsosurfaceRenderer
 
isotopeData - Variable in class org.jmol.quantum.NMRCalculation
isotopeData keyed by nnnSym, for example: 1H, 19F, etc.; and also by element name itself: H, F, etc., for default
isotropy() - Method in class org.jmol.util.Tensor
isotropy = average of eigenvalues
isOutput - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
isOutputFile - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
isPaletteVariable(byte) - Static method in enum org.jmol.c.PAL
 
isParallel(V3, V3) - Method in class org.jmol.symmetry.PointGroup
 
isParallel - Variable in class org.jmol.viewer.Viewer
 
isParallel() - Method in class org.jmol.viewer.Viewer
 
isPartial() - Method in class org.jmol.modelset.Bond
 
isPass2 - Variable in class org.jmol.render.SticksRenderer
 
isPass2 - Variable in class org.jmol.renderbio.BioShapeRenderer
 
isPass2 - Variable in class org.jmol.util.GData
 
isPathGuide - Variable in class org.jmol.navigate.Navigator
 
isPaused() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isPaused() - Method in class org.jmol.script.ScriptEval
 
isPaused - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
isPauseDelay - Variable in class org.jmol.script.ScriptDelayThread
 
isPDB - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
isPDB - Variable in class org.jmol.popup.JmolGenericPopup
 
isPdbWithMultipleBonds - Variable in class org.jmol.modelset.Model
 
isPeriodic() - Method in interface org.jmol.api.SymmetryInterface
 
isPeriodic - Variable in class org.jmol.jvxl.data.VolumeData
 
isPeriodic - Variable in class org.jmol.jvxl.readers.Parameters
 
isPeriodic - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isPeriodic() - Method in class org.jmol.symmetry.Symmetry
 
isPeriodic() - Method in class org.jmol.symmetry.SymmetryInfo
 
isPerpendicular - Variable in class org.jmol.shapespecial.Draw
 
isPerpendicular(V3, V3) - Method in class org.jmol.symmetry.PointGroup
 
isPhaseColored - Variable in class org.jmol.shapesurface.Isosurface
 
isPhonon - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
isPhosphorusMonomer() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPickable(IsosurfaceMesh, BS) - Method in class org.jmol.shapesurface.Isosurface
 
isPickAtomAssignCharge - Variable in class org.jmol.viewer.ActionManager
 
isPlanar(P3, P3, P3, P3) - Method in class org.jmol.shapespecial.Polyhedra
 
isPlanarMapping - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
isPlane - Variable in class org.jmol.shapespecial.Draw
 
isPocket - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
isPoint3f(int) - Method in class org.jmol.script.ScriptParam
 
isPolygonDisplayable(int) - Method in class org.jmol.render.MeshRenderer
 
isPolygonDisplayable(int) - Method in class org.jmol.renderspecial.DrawRenderer
 
isPolygonDisplayable(Mesh, int) - Static method in class org.jmol.shapespecial.Draw
 
isPolymer - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isPolymer - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
isPolymer() - Method in interface org.jmol.api.SymmetryInterface
 
isPolymer - Variable in class org.jmol.render.CageRenderer
 
isPolymer() - Method in class org.jmol.symmetry.Symmetry
 
isPolymer() - Method in class org.jmol.util.SimpleUnitCell
 
isPositiveOnly - Variable in class org.jmol.jvxl.readers.Parameters
 
isPossibleHBond(HB, HB) - Static method in enum org.jmol.c.HB
 
isPQR - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
isPreliminary - Variable in class org.jmol.minimize.forcefield.Calculations
 
isPreviewOnly - Variable in class org.jmol.viewer.Viewer
 
isPrimitive - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isPrimitive - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
isPrintOnly - Variable in class org.jmol.viewer.Viewer
 
isPrintOnly - Variable in class org.openscience.jmol.app.JmolApp
 
isProgressive - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isPromolecular - Variable in class org.jmol.quantum.NciCalculation
 
isProperties - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isProtein() - Method in enum org.jmol.c.STR
 
isProtein() - Method in class org.jmol.modelset.Atom
 
isProtein() - Method in class org.jmol.modelset.Group
 
isProtein() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isProtein() - Method in class org.jmol.smiles.SmilesAtom
 
isProtein() - Method in interface org.jmol.util.BNode
 
isPurine() - Method in class org.jmol.modelset.Atom
 
isPurine() - Method in class org.jmol.modelset.Group
 
isPurine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isPurine - Variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPurine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPurine() - Method in class org.jmol.smiles.SmilesAtom
 
isPurine() - Method in interface org.jmol.util.BNode
 
isPyMOLsession - Variable in class org.jmol.modelset.ModelLoader
 
isPymolStyle() - Method in class org.jmol.modelset.Bond
 
isPyrimidine() - Method in class org.jmol.modelset.Atom
 
isPyrimidine() - Method in class org.jmol.modelset.Group
 
isPyrimidine() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isPyrimidine - Variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPyrimidine() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isPyrimidine() - Method in class org.jmol.smiles.SmilesAtom
 
isPyrimidine() - Method in interface org.jmol.util.BNode
 
isQ - Variable in class org.jmol.util.ModulationSet
 
isQuantumBasisSupported(char) - Static method in class org.jmol.quantum.QS
 
isQueueProcessing() - Method in interface org.jmol.api.JmolScriptManager
 
isQueueProcessing() - Method in class org.jmol.script.ScriptManager
 
isQuiet - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isRadical - Variable in class org.jmol.shapesurface.LcaoCartoon
 
isRawType(int) - Static method in class org.jmol.script.SV
 
isReadableAsString(String) - Static method in class org.jmol.viewer.PropertyManager
 
isReducedDensity - Variable in class org.jmol.quantum.NciCalculation
 
isRenderScalable() - Method in class org.jmol.shapespecial.DrawMesh
 
isRepaintPending() - Method in interface org.jmol.api.JmolRepaintManager
 
isRepaintPending() - Method in class org.jmol.render.RepaintManager
 
isRepaintPending() - Method in class org.jmol.viewer.Viewer
 
isReset - Variable in class org.jmol.thread.JmolThread
 
isReversed - Variable in class org.jmol.shapespecial.Draw
 
isReversed - Variable in class org.jmol.util.ColorEncoder
 
isrhombohedral - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
 
isRingBond(SB, int, int) - Static method in class org.jmol.smiles.SmilesSearch
 
isRingCheck - Variable in class org.jmol.smiles.SmilesSearch
 
isRna() - Method in class org.jmol.modelset.Atom
 
isRna - Variable in class org.jmol.modelset.Chain
 
isRna() - Method in class org.jmol.modelset.Group
 
isRna() - Method in class org.jmol.modelsetbio.BioPolymer
 
isRna() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
isRna() - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
isRna() - Method in class org.jmol.smiles.SmilesAtom
 
isRna() - Method in interface org.jmol.util.BNode
 
isRockets - Variable in class org.jmol.renderbio.RocketRenderer
 
isRockets - Variable in class org.jmol.renderbio.RocketsRenderer
 
isRotated45 - Variable in class org.jmol.shapespecial.Draw
 
isRotateMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
isRubberBandSelect(int) - Method in class org.jmol.viewer.ActionManager
 
isSameAs(UnitCell) - Method in class org.jmol.symmetry.UnitCell
 
isSameAtoms(Dipole, String) - Method in class org.jmol.shapespecial.Dipoles
 
isScalar(SV) - Static method in class org.jmol.script.SV
 
isScaled - Variable in class org.jmol.shape.Labels
 
isScaledAlready - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
isScaleSet - Variable in class org.jmol.shapespecial.DrawMesh
 
isScaleSet - Variable in class org.jmol.util.BoxInfo
 
isScriptExecuting() - Method in class org.jmol.api.JmolViewer
 
isScriptExecuting() - Method in class org.jmol.viewer.Viewer
 
isScriptQueued() - Method in interface org.jmol.api.JmolScriptManager
 
isScriptQueued - Variable in class org.jmol.script.ScriptManager
 
isScriptQueued() - Method in class org.jmol.script.ScriptManager
 
isScriptQueued() - Method in class org.jmol.viewer.Viewer
 
isScriptType(String) - Static method in class org.jmol.viewer.JC
 
isSelectAction(int) - Method in class org.jmol.viewer.ActionManager
 
isSelected() - Method in interface org.jmol.api.JmolAbstractButton
 
isSelected() - Method in class org.jmol.console.JmolLabel
 
isSelected(BS) - Method in class org.jmol.modelset.Group
 
isSelected() - Method in class org.jmol.popup.AwtSwingComponent
 
isSelected(BS, int) - Method in class org.jmol.util.Tensor
 
isSelected(int) - Method in class org.jmol.viewer.SelectionManager
 
isSequential - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isSerial - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
isServer() - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
isServer - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
isServer() - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
isSet - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
isSetBrace - Variable in class org.jmol.script.ScriptTokenParser
 
isSetOrDefine - Variable in class org.jmol.script.ScriptTokenParser
 
isShapeSecondary(int) - Static method in class org.jmol.viewer.JC
 
isSheet() - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isSheet(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
 
isSheet() - Method in class org.jmol.modelsetbio.Monomer
 
isShifted - Variable in class org.jmol.awtjs2d.JsG2D
 
isShowCommand - Variable in class org.jmol.script.ScriptCompiler
 
isShowScriptOutput - Variable in class org.jmol.script.ScriptCompiler
 
isSigned - Variable in class org.jmol.applet.AppletWrapper
 
isSigned() - Method in class org.jmol.applet.AppletWrapper
 
isSigned - Variable in class org.jmol.applet.WrappedAppletLoader
 
isSigned - Variable in class org.jmol.popup.GenericSwingPopup
 
isSigned - Variable in class org.jmol.util.GenericApplet
 
isSignedApplet - Variable in class org.jmol.viewer.Viewer
 
isSignedAppletLocal - Variable in class org.jmol.viewer.Viewer
 
isSilent - Variable in class org.jmol.jvxl.readers.Parameters
 
isSilent - Variable in class org.jmol.minimize.Minimizer
 
isSilent - Variable in class org.jmol.script.ScriptCompiler
 
isSilent - Variable in class org.jmol.smiles.SmilesSearch
 
isSilent - Variable in class org.jmol.viewer.Viewer
 
isSilent - Variable in class org.openscience.jmol.app.InputScannerThread
 
isSilent - Variable in class org.openscience.jmol.app.JmolApp
 
isSingleThreaded() - Method in class org.jmol.awt.Platform
 
isSingleThreaded() - Method in class org.jmol.awtjs2d.Platform
 
isSingleThreaded - Variable in class org.jmol.viewer.Viewer
 
isSlab - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isSlab - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
isSlab() - Method in interface org.jmol.api.SymmetryInterface
 
isSlab - Variable in class org.jmol.render.CageRenderer
 
isSlab() - Method in class org.jmol.symmetry.Symmetry
 
isSlab() - Method in class org.jmol.util.SimpleUnitCell
 
isSlabbable - Variable in class org.jmol.jvxl.data.JvxlData
 
isSlabEnabled - Variable in class org.jmol.export.__RayTracerExporter
 
isSmarts - Variable in class org.jmol.smiles.SmilesParser
 
isSmarts - Variable in class org.jmol.smiles.SmilesSearch
 
isSmilesFind - Variable in class org.jmol.smiles.SmilesSearch
 
isSpaceOrTab(char) - Static method in class org.jmol.script.ScriptCompiler
 
isSpartanArchive(String) - Method in class org.jmol.adapter.readers.quantum.SpartanReader
 
isSpecialAssignment - Variable in class org.jmol.script.ScriptMathProcessor
 
isSpinFixed - Variable in class org.jmol.viewer.TransformManager
 
isSpinInternal - Variable in class org.jmol.viewer.TransformManager
 
isSpinSelected - Variable in class org.jmol.viewer.TransformManager
 
isSquared - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isSquared - Variable in class org.jmol.jvxl.data.VolumeData
 
isSquared - Variable in class org.jmol.jvxl.readers.Parameters
 
isSquaredLinear - Variable in class org.jmol.jvxl.readers.Parameters
 
isSquaredLinear - Variable in class org.jmol.quantum.MOCalculation
 
isSSG - Variable in class org.jmol.symmetry.SpaceGroup
 
isStateScript - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
isStateScript() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isStateScript - Variable in class org.jmol.script.ScriptContext
 
isStateScript - Variable in class org.jmol.script.ScriptEval
 
isStateScript() - Method in class org.jmol.script.ScriptEval
 
isStateScript - Variable in class org.jmol.script.ScriptTokenParser
 
isStaticFunction(String) - Static method in class org.jmol.viewer.Viewer
 
isStep - Variable in class org.jmol.navigate.Navigator
 
isStepping() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isStepping() - Method in class org.jmol.script.ScriptEval
 
isStereo() - Method in class org.jmol.modelset.Bond
 
isStereoDouble() - Method in class org.jmol.viewer.Viewer
 
isStereoSlave - Variable in class org.jmol.util.GenericApplet
 
isStereoSlave - Variable in class org.jmol.viewer.Viewer
A flag to indicate that THIS is the right-side panel of a pair of synced applets running a left-right stereo display (that would be piped into a dual-image polarized projector system such as GeoWall).
isStopped() - Method in interface org.jmol.api.JmolScriptEvaluator
 
isStopped() - Method in class org.jmol.script.ScriptEval
 
isStringArray(String) - Static method in class org.jmol.util.Escape
 
isSubsystem - Variable in class org.jmol.util.ModulationSet
 
isSupercell() - Method in interface org.jmol.api.SymmetryInterface
 
isSupercell() - Method in class org.jmol.symmetry.Symmetry
 
isSupercell() - Method in class org.jmol.util.SimpleUnitCell
 
isSurface - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
isSurface - Variable in class org.jmol.shapespecial.Dots
 
isSurfacePoint - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
isSymmetry - Variable in class org.jmol.popup.JmolGenericPopup
 
isSynced - Variable in class org.jmol.viewer.StatusManager
 
isSyntaxAndFileCheck - Variable in class org.jmol.viewer.Viewer
 
isSyntaxCheck - Variable in class org.jmol.viewer.Viewer
 
isTainted() - Method in class org.jmol.modelset.Measurement
 
isTainted - Variable in class org.jmol.popup.GenericSwingPopup
 
isTainted(BS[], int, byte) - Static method in class org.jmol.viewer.StateCreator
 
isTainted - Variable in class org.jmol.viewer.Viewer
 
iStep - Variable in class org.jmol.navigate.Navigator
 
iStep - Variable in class org.jmol.thread.MoveToThread
 
isTerminator(int) - Method in class org.jmol.script.ScriptTokenParser
we allow : and % to have null values
isToken(int) - Method in class org.jmol.script.ScriptTokenParser
 
isTraceAlpha - Variable in class org.jmol.renderbio.BioShapeRenderer
 
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
isTrajectory - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
isTrajectory - Variable in class org.jmol.modelset.Measurement
 
isTrajectory - Variable in class org.jmol.modelset.Model
 
isTrajectory - Variable in class org.jmol.modelset.ModelLoader
 
isTrajectory(int) - Method in class org.jmol.modelset.ModelSet
 
isTrajectoryMeasurement(int[]) - Method in class org.jmol.modelset.ModelSet
 
isTrajectorySubFrame(int) - Method in class org.jmol.modelset.ModelSet
 
isTranslucent() - Method in class org.jmol.modelset.Atom
 
isTranslucent - Variable in class org.jmol.render.MeshRenderer
 
isTranslucent - Variable in class org.jmol.util.ColorEncoder
 
isTranslucentInherit - Variable in class org.jmol.render.MeshRenderer
 
isTriangleSet - Variable in class org.jmol.util.MeshSurface
 
istructure - Variable in class org.jmol.adapter.smarter.StructureIterator
 
isTruncated - Variable in class org.jmol.jvxl.data.JvxlData
 
isTryCatch - Variable in class org.jmol.script.ScriptContext
 
isTS - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
isTurn(float, float) - Method in class org.jmol.modelsetbio.AminoPolymer
 
isTwoSided - Variable in class org.jmol.shape.Mesh
 
isTypeSet - Variable in class org.jmol.adapter.readers.quantum.GamessReader
 
isUnitCell - Variable in class org.jmol.popup.JmolGenericPopup
 
isUnmodulated - Variable in class org.jmol.util.Tensor
 
isUpdating - Variable in class org.jmol.applet.Jmol
 
isUserAction(int) - Method in class org.jmol.viewer.binding.Binding
 
isUserFunction(String) - Method in class org.jmol.script.ScriptTokenParser
 
isUserToken - Variable in class org.jmol.script.ScriptCompiler
 
isUserValue - Variable in class org.jmol.shapespecial.Dipole
 
isUserValue - Variable in class org.jmol.shapespecial.Dipoles
 
isValid - Variable in class org.jmol.bspt.Bspf
 
isValid - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
isValid() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
isValid - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
isValid - Variable in class org.jmol.modelset.Measurement
 
isValid() - Method in class org.jmol.modelset.Measurement
 
isValid() - Method in class org.jmol.modelset.StateScript
 
isValid - Variable in class org.jmol.shape.Mesh
 
isValid - Variable in class org.jmol.shapespecial.Dipole
 
isValid - Variable in class org.jmol.shapespecial.Draw
 
isValid - Variable in class org.jmol.shapespecial.Ellipsoid
 
isValid - Variable in class org.jmol.shapespecial.Polyhedron
 
isValid(float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
isValidElementSymbolNoCaseSecondChar(String) - Static method in class org.jmol.adapter.readers.xtal.ShelxReader
 
isValidSym1(char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidSym2(char, char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidSymChar1(char) - Static method in class org.jmol.adapter.smarter.Atom
 
isValidSymNoCase(char, char) - Static method in class org.jmol.adapter.smarter.Atom
 
isVariable(String) - Method in class org.jmol.script.ScriptFunction
 
isVariableType(Object) - Static method in class org.jmol.script.SV
Must be updated if getVariable is updated!
isVdw - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
isVector - Variable in class org.jmol.shapespecial.Draw
 
isVector - Variable in class org.jmol.shapespecial.DrawMesh
 
isVersion3 - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
isVersion5 - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
isVertices - Variable in class org.jmol.shapespecial.Draw
 
isVibration - Variable in class org.jmol.popup.JmolGenericPopup
 
isVibrationOn() - Method in class org.jmol.viewer.TransformManager
 
isVisible() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
isVisible(int) - Method in class org.jmol.modelset.Atom
 
isVisible - Variable in class org.jmol.modelset.Measurement
 
isVisible - Variable in class org.jmol.shape.Bbcage
 
isVisibleForMe(Atom) - Method in class org.jmol.render.ShapeRenderer
 
isWebGL - Variable in class org.jmol.export.___Exporter
 
isWebGL - Variable in class org.jmol.export.Export3D
 
isWebGL - Variable in class org.jmol.popup.GenericSwingPopup
 
isWebGL - Variable in class org.jmol.viewer.Viewer
 
isWindowCentered() - Method in class org.jmol.viewer.TransformManager
 
isWithin(int) - Method in class org.jmol.modelsetbio.ProteinStructure
 
isWithin(P3) - Method in class org.jmol.util.BoxInfo
 
isWithinCell(int, P3, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
isWithinFourBonds(Atom, Atom) - Method in class org.jmol.shapesurface.Contact
 
isWithinNot - Variable in class org.jmol.shapesurface.Isosurface
 
isWithinRadius(T3) - Method in class org.jmol.bspt.CubeIterator
checks one Point3f for distance
isWithinStructure(STR) - Method in class org.jmol.modelset.Atom
 
isWithinStructure(STR) - Method in class org.jmol.modelset.Group
 
isWithinStructure(STR) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
isXLowToHigh - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
isXLowToHigh - Variable in class org.jmol.jvxl.data.JvxlData
 
isXLowToHigh - Variable in class org.jmol.jvxl.readers.Parameters
 
isXLowToHigh - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
isXmlFile - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
isXYZ - Variable in class org.jmol.modelset.ModelSet
 
isZapped - Variable in class org.jmol.popup.JmolGenericPopup
 
isZeroBased - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
isZoomArea(int) - Method in class org.jmol.viewer.ActionManager
 
itemMax - Variable in class org.jmol.popup.JmolGenericPopup
 
itemStateChanged(ItemEvent) - Method in class org.jmol.dialog.Dialog.ExportChoiceListener
 
itemStateChanged(ItemEvent) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
itemStateChanged(ItemEvent) - Method in class org.jmol.popup.JSSwingPopupHelper
 
itemStateChanged(ItemEvent) - Method in class org.openscience.chimetojmol.ChimePanel
 
itemStateChanged(ItemEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
iter - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
iter - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
iterateOverAllNewAtoms(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
iterateOverAllNewBonds(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
iterateOverAllNewModels(JmolAdapter, Object) - Method in class org.jmol.modelset.ModelLoader
 
iterateOverAllNewStructures(JmolAdapter, Object) - Method in interface org.jmol.api.JmolBioResolver
 
iterateOverAllNewStructures(JmolAdapter, Object) - Method in class org.jmol.modelsetbio.Resolver
Pull in all spans of helix, etc.
iToken - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
 
iToken - Variable in class org.jmol.jvxl.readers.PmeshReader
 
iToken - Variable in class org.jmol.script.ScriptContext
 
iToken - Variable in class org.jmol.script.ScriptParam
 
itokenInfix - Variable in class org.jmol.script.ScriptTokenParser
 
iType - Variable in class org.jmol.util.Tensor
 
iVal - Variable in class org.jmol.minimize.forcefield.FFParam
 
ival(int, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
iValue(T) - Static method in class org.jmol.script.SV
 

J

J_FACTOR - Static variable in class org.jmol.quantum.NMRCalculation
 
jaguarLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
JaguarReader - Class in org.jmol.adapter.readers.quantum
Jaguar reader tested for the two samples files in CVS.
JaguarReader() - Constructor for class org.jmol.adapter.readers.quantum.JaguarReader
 
JaguarReader - Class in org.jmol.jvxl.readers
 
JaguarReader() - Constructor for class org.jmol.jvxl.readers.JaguarReader
 
JANA_FWV_Q1_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
JANA_FWV_Q2_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
JANA_FWV_Q3_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
JANA_OCC_ABS_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
JANA_OCC_ABS_O_0 - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
JanaReader - Class in org.jmol.adapter.readers.xtal
A reader for Jana M50+M40 file pairs.
JanaReader() - Constructor for class org.jmol.adapter.readers.xtal.JanaReader
 
janaStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
javaname - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
javascript - Static variable in class org.jmol.script.T
 
jbr - Variable in class org.jmol.modelset.ModelLoader
 
jbr - Variable in class org.jmol.viewer.Viewer
 
jc - Variable in class org.jmol.popup.AwtSwingComponent
 
JC - Class in org.jmol.viewer
 
JC() - Constructor for class org.jmol.viewer.JC
 
JcampdxReader - Class in org.jmol.adapter.readers.more
A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS= acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ...
JcampdxReader() - Constructor for class org.jmol.adapter.readers.more.JcampdxReader
 
jcampdxStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
jcd - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
JDXMOLParser - Class in org.jmol.jsv
Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.
JDXMOLParser() - Constructor for class org.jmol.jsv.JDXMOLParser
 
jm - Variable in class org.jmol.popup.AwtSwingComponent
 
jmb - Variable in class org.jmol.viewer.FileManager
 
JmeReader - Class in org.jmol.adapter.readers.simple
 
JmeReader() - Constructor for class org.jmol.adapter.readers.simple.JmeReader
 
jmi - Variable in class org.jmol.popup.AwtSwingComponent
 
Jmol - Class in org.jmol.applet
 
Jmol() - Constructor for class org.jmol.applet.Jmol
 
Jmol - Class in org.jmol.appletjs
Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
Jmol(Map<String, Object>) - Constructor for class org.jmol.appletjs.Jmol
cannot ignore super because it involves preparing fields
jmol - Static variable in class org.jmol.script.T
 
JMOL - Static variable in class org.jmol.util.ColorEncoder
 
Jmol - Class in org.openscience.jmol.app
 
Jmol(JmolApp, Splash, JFrame, Jmol, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.Jmol
 
jmol - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
jmol - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
JMOL_DIAMETER - Static variable in class org.jmol.shapecgo.CGOMesh
 
JmolAbstractButton - Interface in org.jmol.api
 
JmolAdapter - Class in org.jmol.api
The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering.
JmolAdapter() - Constructor for class org.jmol.api.JmolAdapter
 
JmolAdapterAtomIterator - Interface in org.jmol.api
 
JmolAdapterBondIterator - Class in org.jmol.api
 
JmolAdapterBondIterator() - Constructor for class org.jmol.api.JmolAdapterBondIterator
 
JmolAdapterStructureIterator - Class in org.jmol.api
 
JmolAdapterStructureIterator() - Constructor for class org.jmol.api.JmolAdapterStructureIterator
 
JmolAnnotationParser - Interface in org.jmol.api
 
JmolApp - Class in org.openscience.jmol.app
 
JmolApp() - Constructor for class org.openscience.jmol.app.JmolApp
 
JmolApp(String[]) - Constructor for class org.openscience.jmol.app.JmolApp
standard Jmol application entry point
jmolApp - Variable in class org.openscience.jmol.app.JmolData
 
jmolApp - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
JmolApp.OptSort - Class in org.openscience.jmol.app
 
JmolAppAPI - Interface in org.jmol.api
 
JmolAppConsoleInterface - Interface in org.jmol.api
 
JmolAppletInterface - Interface in org.jmol.api
This is the API of methods that are available to JavaScript via LiveConnect to the Jmol applet.
JmolAsyncException - Exception in org.jmol.viewer
 
JmolAsyncException(String) - Constructor for exception org.jmol.viewer.JmolAsyncException
 
jmolAtomCount - Variable in class org.jmol.smiles.SmilesSearch
 
jmolAtoms - Variable in class org.jmol.smiles.SmilesSearch
 
JmolAwtPopup - Class in org.jmol.popup
 
JmolAwtPopup() - Constructor for class org.jmol.popup.JmolAwtPopup
 
JmolBinary - Class in org.jmol.io
 
JmolBinary(FileManager) - Constructor for class org.jmol.io.JmolBinary
 
jmolBinding - Variable in class org.jmol.viewer.ActionManager
 
JmolBinding - Class in org.jmol.viewer.binding
 
JmolBinding() - Constructor for class org.jmol.viewer.binding.JmolBinding
 
JmolBioResolver - Interface in org.jmol.api
 
JmolButton - Class in org.jmol.console
 
JmolButton(String) - Constructor for class org.jmol.console.JmolButton
 
JmolButton(ImageIcon) - Constructor for class org.jmol.console.JmolButton
 
JmolCallbackListener - Interface in org.jmol.api
 
JmolCmdExtension - Interface in org.jmol.script
 
JmolConsole - Class in org.jmol.console
 
JmolConsole() - Constructor for class org.jmol.console.JmolConsole
 
jmolConsole - Variable in class org.jmol.console.ScriptEditor
 
JmolConsole.FileChecker - Class in org.jmol.console
 
jmolData - Variable in class org.jmol.modelset.Model
 
jmolData - Variable in class org.jmol.modelset.ModelLoader
 
JmolData - Class in org.openscience.jmol.app
 
JmolData(JmolApp) - Constructor for class org.openscience.jmol.app.JmolData
 
JmolDataManager - Interface in org.jmol.api
 
jmolDefaultProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
jmolDefaults - Static variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
jmolDefaultsButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
JmolDialogInterface - Interface in org.jmol.api
 
JmolDomReaderInterface - Interface in org.jmol.api
 
JmolEnvCalc - Interface in org.jmol.api
 
JmolFilesReaderInterface - Interface in org.jmol.api
 
JmolFrame - Interface in org.jmol.awt
 
jmolFrameType - Variable in class org.jmol.modelset.Model
 
JmolGenericPopup - Class in org.jmol.popup
A generic popup class that is then instantiated for a given platform and context as one of: org.jmol.popup.JmolPopup (via org.jmol.popup.SwingPopup) org.jmol.modelkit.ModelKitPopup (via org.jmol.popup.SwingPopup) org.jmol.awtjs2d.JSmolPopup (via org.jmol.awtjs2d.JSPopup) org.jmol.awtjs2d.JSModelKitPopup (via org.jmol.awtjs2d.JSPopup)
JmolGenericPopup() - Constructor for class org.jmol.popup.JmolGenericPopup
 
JmolGestureServerInterface - Interface in org.jmol.api
 
JmolGraphicsInterface - Interface in org.jmol.api
 
jmolIndex - Variable in class org.jmol.smiles.SmilesAtom
 
JmolInstance - Class in org.openscience.jmol.app.webexport
 
JmolInstance(JmolViewer, String, int, int, int) - Constructor for class org.openscience.jmol.app.webexport.JmolInstance
 
jmolJarPath() - Method in class org.openscience.jmol.app.webexport.WebPanel
Returns a string version of the path to Jmol.jar (including the trailing Jmol.jar) decoded using the system default text encoding (usually UTF-8).
jmolJarURL() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
JmolJDXMOLParser - Interface in org.jmol.api
 
JmolJDXMOLReader - Interface in org.jmol.api
 
JmolJniClientAdapter - Class in org.jmol.multitouch.jni
 
JmolJniClientAdapter() - Constructor for class org.jmol.multitouch.jni.JmolJniClientAdapter
 
JmolJSpecView - Interface in org.jmol.api
 
JmolJSPopup - Class in org.jmol.awtjs2d
 
JmolJSPopup() - Constructor for class org.jmol.awtjs2d.JmolJSPopup
The main popup window for the applet -- as JavaScript
JmolLabel - Class in org.jmol.console
 
JmolLabel(String, int) - Constructor for class org.jmol.console.JmolLabel
 
JmolMathExtension - Interface in org.jmol.script
 
JmolMeasurementClient - Interface in org.jmol.api
 
JmolModulationSet - Interface in org.jmol.api
 
JmolMolecule - Class in org.jmol.util
an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings
JmolMolecule() - Constructor for class org.jmol.util.JmolMolecule
 
JmolMovieCreatorInterface - Interface in org.jmol.api
 
JmolMultiTouchAdapter - Interface in org.jmol.multitouch
 
JmolMultiTouchClient - Interface in org.jmol.multitouch
 
JmolMultiTouchClientAdapter - Class in org.jmol.multitouch
 
JmolMultiTouchClientAdapter() - Constructor for class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
jmolName - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
JmolNavigatorInterface - Interface in org.jmol.api
 
JmolNMRInterface - Interface in org.jmol.api
 
JmolObject - Class in org.jmol.adapter.readers.pymol
a class to store rendering information prior to finishing file loading, specifically designed for reading PyMOL PSE files.
JmolObject(int, String, BS, Object) - Constructor for class org.jmol.adapter.readers.pymol.JmolObject
 
jmolObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
jmolPanel - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
JmolPanel - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel(JmolApp, Splash, JFrame, JmolPanel, int, int, Map<String, Object>, Point) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel
 
JmolPanel.AboutAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ActionChangedListener - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.AnimButton - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.AppCloser - Class in org.openscience.jmol.app.jmolpanel
To shutdown when run as an application.
JmolPanel.AtomSetChooserAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.CloseAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ConsoleAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.CopyImageAction - Class in org.openscience.jmol.app.jmolpanel
An Action to copy the current image into the clipboard.
JmolPanel.CopyScriptAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.CreditsAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ExecuteScriptAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ExitAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ExportAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.GaussianAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.NBOAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.NewAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.NewwinAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenMolAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenPdbAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.OpenUrlAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.PasteClipboardAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.PovrayAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.PrintAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.RecentFilesAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ResizeAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ScriptEditorAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ScriptWindowAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.SurfaceToolAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ToWebAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.UguideAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.ViewMeasurementTableAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.WhatsNewAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolPanel.WriteAction - Class in org.openscience.jmol.app.jmolpanel
 
JmolParallelProcessor - Interface in org.jmol.api
 
JmolPatternMatcher - Interface in org.jmol.api
 
JmolPdfCreatorInterface - Interface in org.jmol.api
 
jmolpopup - Variable in class org.jmol.viewer.Viewer
 
jmolPosition - Variable in class org.openscience.jmol.app.JmolApp
 
JmolPropertyManager - Interface in org.jmol.api
 
jmolRenderer - Variable in class org.jmol.export.___Exporter
 
JmolRendererInterface - Interface in org.jmol.api
 
JmolRepaintManager - Interface in org.jmol.api
 
JmolResourceHandler - Class in org.openscience.jmol.app.jmolpanel
Provides access to resources (for example, strings and images).
JmolResourceHandler() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
JmolSceneGenerator - Interface in org.jmol.api
 
jmolScriptCallback(CBK) - Method in class org.jmol.viewer.StatusManager
 
jmolScriptCallbacks - Variable in class org.jmol.viewer.StatusManager
 
JmolScriptEditorInterface - Interface in org.jmol.api
 
JmolScriptEvaluator - Interface in org.jmol.api
 
JmolScriptFunction - Interface in org.jmol.api
 
JmolScriptManager - Interface in org.jmol.api
 
JmolSelectionListener - Interface in org.jmol.api
listen to atom selections in a Jmol Viewer
JmolSmilesExtension - Interface in org.jmol.script
 
JmolSparshClientAdapter - Class in org.jmol.multitouch.sparshui
 
JmolSparshClientAdapter() - Constructor for class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
JmolStateCreator - Class in org.jmol.viewer
 
JmolStateCreator() - Constructor for class org.jmol.viewer.JmolStateCreator
 
JmolStatusListener - Interface in org.jmol.api
 
JmolSyncInterface - Interface in org.jmol.api
 
jmolTest() - Method in class org.jmol.viewer.Viewer
 
JmolThread - Class in org.jmol.thread
 
JmolThread() - Constructor for class org.jmol.thread.JmolThread
 
JmolToggleButton - Class in org.jmol.console
 
JmolToggleButton(ImageIcon) - Constructor for class org.jmol.console.JmolToggleButton
 
JmolTouchSimulatorInterface - Interface in org.jmol.api
 
JmolUtil - Class in org.jmol.io
 
JmolUtil() - Constructor for class org.jmol.io.JmolUtil
 
JmolViewer - Class in org.jmol.api
JmolViewer is the main API for the Viewer class.
JmolViewer() - Constructor for class org.jmol.api.JmolViewer
 
JmolXmlHandler - Interface in org.jmol.adapter.readers.xml
 
JmolZipUtilities - Interface in org.jmol.api
 
join - Static variable in class org.jmol.script.T
 
JPEG_CONTINUE_STRING - Static variable in class org.jmol.io.JmolBinary
 
JPEG_EXTENSIONS - Static variable in class org.jmol.viewer.JC
 
jpiDispose() - Method in class org.jmol.popup.JmolGenericPopup
 
jpiGetMenuAsObject() - Method in class org.jmol.popup.JmolGenericPopup
 
jpiGetMenuAsString(String) - Method in class org.jmol.popup.GenericSwingPopup
 
jpiInitialize(PlatformViewer, String) - Method in class org.jmol.awtjs2d.JmolJSPopup
 
jpiInitialize(PlatformViewer, String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
jpiInitialize(PlatformViewer, String) - Method in class org.jmol.modelkit.ModelKitPopup
 
jpiInitialize(PlatformViewer, String) - Method in class org.jmol.popup.JmolAwtPopup
 
jpiShow(int, int) - Method in class org.jmol.popup.JmolGenericPopup
 
jpiUpdateComputedMenus() - Method in class org.jmol.popup.JmolGenericPopup
 
jsc - Variable in class org.jmol.viewer.Viewer
 
jsConsole - Variable in class org.jmol.consolejs.AppletConsole
 
jsCylinder(Object, String, boolean, P3, P3, Object[]) - Method in class org.jmol.export.JSExporter
 
jsDocumentBase - Static variable in class org.jmol.viewer.Viewer
 
jsEndExport(Object) - Method in class org.jmol.export.JSExporter
 
jsEval(String) - Method in class org.jmol.viewer.StatusManager
 
jsEval(String) - Method in class org.jmol.viewer.Viewer
 
JSExporter - Class in org.jmol.export
A class to output WebGL graphics.
JSExporter() - Constructor for class org.jmol.export.JSExporter
 
jsExporter3D - Variable in class org.jmol.viewer.Viewer
 
JSFile - Class in org.jmol.awtjs2d
A class that mimics java.io.File We allow access to
JSFile(String) - Constructor for class org.jmol.awtjs2d.JSFile
 
JSFont - Class in org.jmol.awtjs
methods required by Jmol that access java.awt.Font private to org.jmol.awtjs
JSFont() - Constructor for class org.jmol.awtjs.JSFont
 
JSFont - Class in org.jmol.awtjs2d
methods required by Jmol that access java.awt.Font private to org.jmol.awtjs2d
JSFont() - Constructor for class org.jmol.awtjs2d.JSFont
 
JsG2D - Class in org.jmol.awtjs2d
generic 2D drawing methods -- JavaScript version
JsG2D() - Constructor for class org.jmol.awtjs2d.JsG2D
 
jsInitExport(Object) - Method in class org.jmol.export.JSExporter
 
jsl - Variable in class org.jmol.viewer.StatusManager
 
JSModelKitPopup - Class in org.jmol.awtjs2d
 
JSModelKitPopup() - Constructor for class org.jmol.awtjs2d.JSModelKitPopup
 
jsObjectCall(Object[], String, Object[]) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
jsObjectGetMember(Object[], String) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
jsoDocument - Variable in class org.jmol.applet.Jmol
 
json - Static variable in class org.jmol.script.T
 
JsonNioClient - Interface in org.openscience.jmol.app.jsonkiosk
a client of a JsonNioService -- just needs notices of the service shutting down or indicating that a banner needs to be changed.
JsonNioServer - Interface in org.openscience.jmol.app.jsonkiosk
 
JsonNioServerThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
 
JsonNioService - Class in org.openscience.jmol.app.jsonkiosk
 
JsonNioService() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
JsonNioService.JsonNioServerThread - Class in org.openscience.jmol.app.jsonkiosk
 
JsonNioService.JsonNioThread - Class in org.openscience.jmol.app.jsonkiosk
 
JsonNioService.JSONObject - Class in org.openscience.jmol.app.jsonkiosk
 
JsonNioThread() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioThread
 
JSONObject() - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
JSONObject(String) - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
JSONObject(Map<String, Object>) - Constructor for class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
JSONReader - Class in org.jmol.adapter.readers.simple
 
JSONReader() - Constructor for class org.jmol.adapter.readers.simple.JSONReader
 
jsonStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
jsParams - Variable in class org.jmol.viewer.Viewer
 
JSpecView - Class in org.jmol.jsv
 
JSpecView() - Constructor for class org.jmol.jsv.JSpecView
 
jSpecViewForceNew - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
jSpecViewFrame - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
jsSphere(Object, String, boolean, P3, Object[]) - Method in class org.jmol.export.JSExporter
 
jsSurface(Object, T3[], T3[], int[][], int, int, int, BS, int, int, int[], int[]) - Method in class org.jmol.export.JSExporter
 
JSSwingPopupHelper - Class in org.jmol.popup
For menus, popup-related awt/swing class references are in this file.
JSSwingPopupHelper(GenericMenuInterface) - Constructor for class org.jmol.popup.JSSwingPopupHelper
 
jsTriangle(Object, int, T3, T3, T3) - Method in class org.jmol.export.JSExporter
 
jsv - Variable in class org.jmol.viewer.Viewer
 
JSV_NOT - Static variable in class org.jmol.viewer.JC
 
JSV_SELECT - Static variable in class org.jmol.viewer.JC
 
JSV_SEND_H1SIMULATE - Static variable in class org.jmol.viewer.JC
 
JSV_SEND_JDXMOL - Static variable in class org.jmol.viewer.JC
 
JSV_SETPEAKS - Static variable in class org.jmol.viewer.JC
 
JSV_STRUCTURE - Static variable in class org.jmol.viewer.JC
 
JSVInterface - Interface in org.jmol.api
and interface for JSpecView for the Jmol application
junk - Variable in class org.jmol.thread.JmolThread
 
justifymeasurements - Static variable in class org.jmol.script.T
 
justifyMeasurements - Variable in class org.jmol.viewer.GlobalSettings
 
justOneModel - Variable in class org.jmol.modelset.MeasurementData
 
justTransferFile(File, File, InputStream) - Method in class org.openscience.chimetojmol.ChimePanel
 
Jvxl - Class in org.openscience.jvxl
 
Jvxl() - Constructor for class org.openscience.jvxl.Jvxl
 
JVXL_VERSION - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
JVXL_VERSION1 - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
JVXL_VERSION_XML - Static variable in class org.jmol.jvxl.data.JvxlCoder
 
jvxlAppendCharacter2(float, float, float, int, int, SB, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlAppendCommandState(SB, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlAppendEncodedNumber(SB, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
JvxlCoder - Class in org.jmol.jvxl.data
 
JvxlCoder() - Constructor for class org.jmol.jvxl.data.JvxlCoder
 
jvxlColorData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlColorDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlColorEncodingRead - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlCompressString(String, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlCreateColorData(JvxlData, float[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlCreateHeader(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
Creates a two-line header for the XJVXL file.
jvxlCreateHeaderWithoutTitleOrAtoms(VolumeData, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlCutoff - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
JvxlData - Class in org.jmol.jvxl.data
 
JvxlData() - Constructor for class org.jmol.jvxl.data.JvxlData
 
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
jvxlData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlData - Variable in class org.jmol.shapesurface.Isosurface
 
jvxlData - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIs2dContour - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIsColorDensity - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlDataIsColorMapped - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDataIsPrecisionColor - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlDecodeBitSet(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlDecodeBitSetRange(String, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlDecodeContourData(JvxlData, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlDecodeTriangleData(String, String, String) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
decode triangle data found within element as created with jvxlEncodeTriangleData (see above)
jvxlDecodeVertexData(String, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
decode vertex data found within element as created by jvxlEncodeVertexData (see above)
jvxlDecompressString(String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEdgeData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlEdgeDataRead - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlEncodeBitSet(BS) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEncodeBitSet0(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEncodeBitSetBuffer(BS, int, SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlEncodeContourData(Lst<Object>[], SB) - Static method in class org.jmol.jvxl.data.JvxlCoder
contour data are appended to a string buffer in the form of a triangle bitset data triangle bitset data triangle bitset data ...
jvxlExcluded - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFileHeaderBuffer - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlFileMessage - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFileTitle - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlFractionAsCharacter(float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlFractionAsCharacterRange(float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlFractionFromCharacter(int, int, int, float) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlFractionFromCharacter2(int, int, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetData(VoxelDataCreator, Parameters, VolumeData, String[], Lst<P3>, float[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
jvxlGetFile(VolumeData, JvxlData, String[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetFile(JvxlData, MeshData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetFileXml(JvxlData, MeshData, String[], String, boolean, int, String, String) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetInfo(JvxlData) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetInfoData(JvxlData, boolean) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlGetNextFraction(int, int, float) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlNSurfaceInts - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlParseEncodedInt(String, int, int, int[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlPlane - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlReadDefinitionLine(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
JvxlReader - Class in org.jmol.jvxl.readers
 
JvxlReader() - Constructor for class org.jmol.jvxl.readers.JvxlReader
 
jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlReadFractionData(String, int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
"edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge.
jvxlReadSurfaceInfo() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlSetColorRanges(float, float, float, float, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlSetCompressionRatio(SB, JvxlData, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlSkipData(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
jvxlSkipDataBlock(int, boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
jvxlSurfaceData - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlUpdateInfo(String[], long) - Method in class org.jmol.jvxl.data.JvxlData
 
jvxlUpdateInfo() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
jvxlValueAsCharacter(float, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlValueFromCharacter2(int, int, float, float, int, int) - Static method in class org.jmol.jvxl.data.JvxlCoder
 
jvxlVolumeDataXml - Variable in class org.jmol.jvxl.data.JvxlData
 
jvxlVoxelBitSet - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
JvxlWrite - Class in org.openscience.jvxl.simplewriter
 
JvxlWrite() - Constructor for class org.openscience.jvxl.simplewriter.JvxlWrite
 
JvxlXmlReader - Class in org.jmol.jvxl.readers
 
JvxlXmlReader() - Constructor for class org.jmol.jvxl.readers.JvxlXmlReader
 
jzt - Variable in class org.jmol.viewer.Viewer
 
jzu - Variable in class org.jmol.io.JmolBinary
 

K

ka - Variable in class org.jmol.minimize.MinAngle
 
kb - Variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
 
kb - Variable in class org.jmol.minimize.forcefield.UFFDistanceCalc
 
KCAL22 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL332 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL44 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL6 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL644 - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
KCAL_TO_KJ - Static variable in class org.jmol.minimize.forcefield.Calculations
 
keep_alive - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
keepChars - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
keepCharsList - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
keepRunning - Variable in class org.jmol.applet.TickerThread
 
keepRunning - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
key - Variable in class org.jmol.adapter.readers.cif.CifReader
 
key - Variable in class org.jmol.console.KeyJCheckBox
 
key - Variable in class org.jmol.console.KeyJCheckBoxMenuItem
 
key - Variable in class org.jmol.console.KeyJMenu
 
key - Variable in class org.jmol.console.KeyJMenuItem
 
key - Variable in class org.jmol.console.KeyJRadioButtonMenuItem
 
key - Variable in class org.jmol.minimize.forcefield.Calculation
 
key - Variable in class org.jmol.minimize.MinObject
 
key - Variable in class org.jmol.modelset.LabelToken
 
key - Variable in class org.jmol.script.FileLoadThread
 
key - Variable in class org.jmol.util.Int2IntHashEntry
 
KEY_BNDK - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
KEY_LIST - Static variable in class org.jmol.shapecgo.CGO
 
KEY_OOP - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
KEY_PBCI - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
KEY_SBDEF - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
KEY_VDW - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
keyBuffer - Variable in class org.jmol.awt.Mouse
 
keyBuffer - Variable in class org.jmol.awtjs2d.Mouse
 
KeyJCheckBox - Class in org.jmol.console
 
KeyJCheckBox(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBox
 
KeyJCheckBoxMenuItem - Class in org.jmol.console
 
KeyJCheckBoxMenuItem(String, String, Map<String, Object>, boolean) - Constructor for class org.jmol.console.KeyJCheckBoxMenuItem
 
KeyJMenu - Class in org.jmol.console
 
KeyJMenu(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenu
 
KeyJMenuItem - Class in org.jmol.console
 
KeyJMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJMenuItem
 
KeyJRadioButtonMenuItem - Class in org.jmol.console
 
KeyJRadioButtonMenuItem(String, String, Map<String, Object>) - Constructor for class org.jmol.console.KeyJRadioButtonMenuItem
 
keyMap - Variable in class org.jmol.shapecgo.CGO
 
keyPressed(KeyEvent) - Method in class org.jmol.awt.Mouse
 
keyPressed(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
 
keyPressed(int, int) - Method in class org.jmol.viewer.ActionManager
called by MouseManager.keyPressed
keyProcessing - Variable in class org.jmol.viewer.ActionManager
 
keyReleased(KeyEvent) - Method in class org.jmol.awt.Mouse
 
keyReleased(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
 
keyReleased(int) - Method in class org.jmol.viewer.ActionManager
 
keys - Static variable in class org.jmol.script.T
 
keyTyped(KeyEvent) - Method in class org.jmol.awt.Mouse
 
keyTyped(KeyEvent) - Method in class org.jmol.awtjs2d.Mouse
 
keyTyped(int, int) - Method in class org.jmol.viewer.ActionManager
 
keyword - Variable in class org.jmol.export.UseTable
 
keyword - Static variable in class org.jmol.script.T
 
keyXy - Variable in class org.jmol.shapesurface.Isosurface
 
kind - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
KinemageReader - Class in org.jmol.jvxl.readers
 
KinemageReader() - Constructor for class org.jmol.jvxl.readers.KinemageReader
 
kinEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
kioskFrame - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
KioskFrame - Class in org.openscience.jmol.app.jsonkiosk
A borderless rectangle, like the applet, that contains the application for use in kiosk-style displays, as for example projected on the wall as in http://molecularPlayground.org
KioskFrame(int, int, int, int, JPanel) - Constructor for class org.openscience.jmol.app.jsonkiosk.KioskFrame
 
KNOWN_TYPES - Static variable in class org.jmol.util.Tensor
 
knownGroupID(String) - Static method in class org.jmol.modelsetbio.Resolver
 
kvec - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
 

L

LABEL - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
label - Static variable in class org.jmol.script.T
 
label1 - Variable in class org.jmol.console.GenericConsole
 
LABEL_ALIGN_FLAGS - Static variable in class org.jmol.viewer.JC
 
label_anchor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
label_angle_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
label_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
LABEL_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
LABEL_DEFAULT_X_OFFSET - Static variable in class org.jmol.viewer.JC
 
LABEL_DEFAULT_Y_OFFSET - Static variable in class org.jmol.viewer.JC
 
label_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
label_dihedral_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
label_distance_digits - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
LABEL_EXACT_OFFSET_FLAG - Static variable in class org.jmol.viewer.JC
 
LABEL_FLAG_OFFSET - Static variable in class org.jmol.viewer.JC
 
LABEL_FLAGS - Static variable in class org.jmol.viewer.JC
 
label_font_id - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
LABEL_FRONT_FLAG - Static variable in class org.jmol.viewer.JC
 
LABEL_GROUP_FLAG - Static variable in class org.jmol.viewer.JC
 
LABEL_MAXIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
LABEL_MINIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
label_outline_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
LABEL_POINTER_FLAGS - Static variable in class org.jmol.viewer.JC
 
label_position - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
LABEL_SCALE_FLAG - Static variable in class org.jmol.viewer.JC
 
label_shadow_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
label_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
LABEL_ZPOS_FLAGS - Static variable in class org.jmol.viewer.JC
 
labelBoxes - Variable in class org.jmol.shape.Labels
 
labelColix - Variable in class org.jmol.modelset.Measurement
 
labelColix - Variable in class org.jmol.render.LabelsRenderer
 
labelColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
labeler - Variable in class org.jmol.modelset.AtomCollection
 
labelFontId - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
labelFormat - Variable in class org.jmol.shape.Hover
 
labelMode - Variable in class org.jmol.viewer.ActionManager
 
labelPosition - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
labelPosition0 - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
labels - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
labels - Variable in class org.jmol.console.GenericConsole
 
labels - Variable in class org.jmol.dssx.DSSP
 
labels - Variable in class org.jmol.jvxl.readers.MrcBinaryReader
 
labels - Variable in class org.jmol.shape.Axes
 
Labels - Class in org.jmol.shape
 
Labels() - Constructor for class org.jmol.shape.Labels
 
labels - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
 
labelSize - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
LabelsRenderer - Class in org.jmol.render
 
LabelsRenderer() - Constructor for class org.jmol.render.LabelsRenderer
 
labelsXn - Static variable in class org.jmol.symmetry.SymmetryOperation
 
labelsXnSub - Static variable in class org.jmol.symmetry.SymmetryOperation
 
labelsXYZ - Static variable in class org.jmol.symmetry.SymmetryOperation
 
LabelToken - Class in org.jmol.modelset
 
LabelToken() - Constructor for class org.jmol.modelset.LabelToken
 
labelTokenIds - Static variable in class org.jmol.modelset.LabelToken
 
labelTokenParams - Static variable in class org.jmol.modelset.LabelToken
 
ladder - Variable in class org.jmol.dssx.Bridge
 
ladderOnly - Variable in class org.jmol.renderbio.NucleicRenderer
 
language - Variable in class org.jmol.i18n.GT
 
Language - Class in org.jmol.i18n
 
Language(String, String, String, boolean) - Constructor for class org.jmol.i18n.Language
 
language - Variable in class org.jmol.i18n.Language
 
language - Static variable in class org.jmol.script.T
 
language - Variable in class org.jmol.util.GenericApplet
 
language - Static variable in class org.openscience.jmol.app.jmolpanel.GuiMap
 
languageList - Static variable in class org.jmol.i18n.GT
 
languagetranslation - Static variable in class org.jmol.script.T
 
last - Static variable in class org.jmol.script.T
 
LAST - Static variable in class org.jmol.util.MeshCapper
 
LAST_AVAILABLE_COLIX - Static variable in class org.jmol.util.C
 
lastAltLoc - Variable in class org.jmol.adapter.readers.cif.CifReader
 
lastAltLoc - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
lastAssignedString - Variable in class org.jmol.script.ScriptMathProcessor
 
lastAtom - Variable in class org.jmol.jvxl.readers.KinemageReader
 
lastAtomIndex - Variable in class org.jmol.modelset.Group
 
lastChainAtom - Variable in class org.jmol.smiles.SmilesSearch
 
lastColix - Variable in class org.jmol.util.MeshSurface
 
lastColor - Variable in class org.jmol.util.MeshSurface
 
lastConnections - Variable in class org.jmol.viewer.StateManager
 
lastContext - Variable in class org.jmol.viewer.StateManager
 
lastCoordinates - Variable in class org.jmol.viewer.StateManager
 
lastData - Variable in class org.jmol.viewer.Viewer
 
lastDisorderAssembly - Variable in class org.jmol.adapter.readers.cif.CifReader
 
lastError - Static variable in exception org.jmol.smiles.InvalidSmilesException
 
lastFlowCommand - Variable in class org.jmol.script.ScriptTokenParser
 
lastFrameDelay - Variable in class org.jmol.viewer.AnimationManager
 
lastFrameDelayMs - Variable in class org.jmol.viewer.AnimationManager
 
lastFrameIndex - Variable in class org.jmol.viewer.AnimationManager
 
lastFramePainted - Variable in class org.jmol.viewer.AnimationManager
 
lastFullPathName - Variable in class org.jmol.viewer.FileManager
 
lastGroup - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
lastIndex - Variable in class org.jmol.modelset.MeasurementPending
 
lastInfo - Static variable in class org.jmol.symmetry.SpaceGroup
 
lastInsertion - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
lastLogTime - Variable in class org.jmol.multitouch.ActionManagerMT
 
lastMark - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
lastMoData - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
lastModel - Variable in class org.jmol.jsv.JDXMOLParser
 
lastModelIndex - Variable in class org.jmol.atomdata.AtomData
 
lastModelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
lastModelPainted - Variable in class org.jmol.viewer.AnimationManager
 
lastMotionEventNumber - Variable in class org.jmol.applet.Jmol
 
lastMotionEventNumber - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
lastName - Variable in class org.jmol.adapter.readers.xtal.CgdReader
 
lastNameAsGiven - Variable in class org.jmol.viewer.FileManager
 
lastOpened - Static variable in class org.jmol.console.ScriptEditor
 
lastOrientation - Variable in class org.jmol.viewer.StateManager
 
lastQPt - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
lastRawColor - Variable in class org.jmol.g3d.Graphics3D
 
lastRepaintTime - Variable in class org.jmol.thread.JmolThread
 
lastScene - Variable in class org.jmol.viewer.StateManager
 
lastSelected - Variable in class org.jmol.viewer.StateManager
 
lastSequenceNumber - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
lastSetH - Variable in class org.jmol.modelsetbio.Resolver
 
lastShape - Variable in class org.jmol.viewer.StateManager
 
lastSourceSerial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
lastSpaceGroupName - Variable in class org.jmol.adapter.readers.cif.CifReader
 
lastState - Variable in class org.jmol.viewer.StateManager
 
lastTargetSerial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
lastText - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
lastToken - Variable in class org.jmol.script.ScriptTokenParser
 
latestMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
LATT - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
lattice - Static variable in class org.jmol.script.T
 
lattice - Variable in class org.jmol.shape.Mesh
 
LATTICE_VECTOR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
latticeCells - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
latticeCells - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
latticeCode - Variable in class org.jmol.adapter.readers.xtal.Wien2kReader
 
latticeCode - Variable in class org.jmol.symmetry.HallInfo
 
latticeExtension - Variable in class org.jmol.symmetry.HallInfo
 
latticeOffset - Variable in class org.jmol.render.MeshRenderer
 
latticeOnly - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
latticeOp - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
latticeOp - Variable in class org.jmol.symmetry.SpaceGroup
 
latticeParameter - Variable in class org.jmol.symmetry.SpaceGroup
 
latticeTranslationData - Static variable in class org.jmol.symmetry.HallTranslation
 
latticeType - Variable in class org.jmol.adapter.readers.cif.CifReader
 
latticeVectorPtr - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
lattvecs - Variable in class org.jmol.adapter.readers.cif.CifReader
 
lattvecs - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
layoutWindow(String) - Method in class org.jmol.console.AppletConsole
 
layoutWindow(String) - Method in class org.jmol.console.GenericConsole
 
layoutWindow(Container) - Method in class org.jmol.console.ScriptEditor
 
layoutWindow(String) - Method in class org.jmol.consolejs.AppletConsole
 
layoutWindow(Container) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
layoutWindow(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
lcaocartoon - Static variable in class org.jmol.script.T
 
lcaoCartoon() - Method in class org.jmol.scriptext.IsoExt
 
LcaoCartoon - Class in org.jmol.shapesurface
 
LcaoCartoon() - Constructor for class org.jmol.shapesurface.LcaoCartoon
 
LcaoCartoonRenderer - Class in org.jmol.rendersurface
 
LcaoCartoonRenderer() - Constructor for class org.jmol.rendersurface.LcaoCartoonRenderer
 
lcaoColorNeg - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoColorPos - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoDir - Variable in class org.jmol.shapesurface.Isosurface
 
lcaoID - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoScale - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoTranslucent - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoTranslucentLevel - Variable in class org.jmol.shapesurface.LcaoCartoon
 
lcaoType - Variable in class org.jmol.jvxl.readers.Parameters
 
leadatom - Static variable in class org.jmol.script.T
 
leadAtomIndex - Variable in class org.jmol.modelset.Group
 
leadAtomIndices - Variable in class org.jmol.modelsetbio.BioPolymer
 
leadAtomIndices - Variable in class org.jmol.renderbio.BioShapeRenderer
 
leadAtomIndices - Variable in class org.jmol.shapebio.BioShape
 
LEADER_CHAR_MAX - Static variable in class org.jmol.adapter.smarter.Resolver
 
leadMidpoints - Variable in class org.jmol.modelsetbio.BioPolymer
 
leadPoints - Variable in class org.jmol.modelsetbio.BioPolymer
 
leaf - Variable in class org.jmol.bspt.CubeIterator
 
Leaf - Class in org.jmol.bspt
A leaf of Point3f objects in the bsp tree
Leaf(Bspt, Leaf, int) - Constructor for class org.jmol.bspt.Leaf
 
leafCountMax - Static variable in class org.jmol.bspt.Bspt
 
leafIndex - Variable in class org.jmol.bspt.CubeIterator
 
left - Static variable in class org.jmol.script.T
 
left - Variable in class org.jmol.util.Modulation
 
LEFT - Static variable in class org.jmol.viewer.binding.Binding
 
LEFT_CLICKED - Variable in class org.jmol.viewer.ActionManager
 
LEFT_DRAGGED - Variable in class org.jmol.viewer.ActionManager
 
leftAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
leftbrace - Static variable in class org.jmol.script.T
 
leftdivide - Static variable in class org.jmol.script.T
 
leftOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
leftparen - Static variable in class org.jmol.script.T
 
leftPlane - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
leftsquare - Static variable in class org.jmol.script.T
 
LEG_DISP_AXIS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_DISP_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_DISP_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_DISP_ORDER - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_OCC_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_OCC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_OCC_ORDER - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_U_COEF - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_U_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_U_ORDER - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
LEG_U_TENS - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
legacy_mouse_zoom - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
legacy_vdw_radii - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
legacyautobonding - Static variable in class org.jmol.script.T
 
legacyAutoBonding - Variable in class org.jmol.viewer.GlobalSettings
 
legacyhaddition - Static variable in class org.jmol.script.T
 
legacyHAddition - Variable in class org.jmol.viewer.GlobalSettings
 
legacyjavafloat - Static variable in class org.jmol.script.T
 
legacyJavaFloat - Variable in class org.jmol.viewer.GlobalSettings
 
legendre - Static variable in class org.jmol.util.Modulation
 
legendres - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
length() - Method in class org.jmol.awtjs2d.JSFile
 
length() - Method in class org.jmol.java.BS
Returns the "logical size" of this BitSet: the index of the highest set bit in the BitSet plus one.
length - Static variable in class org.jmol.script.T
 
length - Variable in class org.jmol.shapespecial.Draw
 
length - Variable in class org.openscience.jvxl.MonitorInputStream
 
lengths - Variable in class org.jmol.shapespecial.Ellipsoid
 
lengthsFreeEnum - Variable in class org.jmol.util.TempArray
 
lengthsFreePoints - Variable in class org.jmol.util.TempArray
 
lengthsFreeScreens - Variable in class org.jmol.util.TempArray
 
lengthUnitFactors - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
 
lengthUnitIds - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
 
lenLine - Variable in class org.jmol.adapter.readers.more.MdCrdReader
 
LEVEL_DEBUG - Static variable in class org.jmol.util.Logger
 
LEVEL_DEBUGHIGH - Static variable in class org.jmol.util.Logger
 
LEVEL_ERROR - Static variable in class org.jmol.util.Logger
 
LEVEL_FATAL - Static variable in class org.jmol.util.Logger
 
LEVEL_INFO - Static variable in class org.jmol.util.Logger
 
LEVEL_MAX - Static variable in class org.jmol.util.Logger
 
LEVEL_WARN - Static variable in class org.jmol.util.Logger
 
ligandModels - Variable in class org.jmol.viewer.Viewer
 
ligandModelSet - Variable in class org.jmol.viewer.Viewer
 
light - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
light2 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
light3 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
light4 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
light5 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
light6 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
light7 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
light8 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
light9 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
light_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
lighting - Variable in class org.jmol.export._TachyonExporter
 
lighting - Static variable in class org.jmol.script.T
 
lighting - Variable in class org.jmol.shape.Mesh
 
lighting - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
lightSource - Variable in class org.jmol.export.___Exporter
 
lightSource - Variable in class org.jmol.util.Shader
 
LIME - Static variable in class org.jmol.util.C
 
line - Variable in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
line - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
line - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
line - Variable in class org.jmol.dssx.AnnotationParser
 
line - Variable in class org.jmol.jsv.JDXMOLParser
 
line - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
line - Variable in class org.jmol.jvxl.readers.XmlReader
 
line - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
line - Static variable in class org.jmol.script.T
 
line3d - Variable in class org.jmol.g3d.CylinderRenderer
 
line3d - Variable in class org.jmol.g3d.Graphics3D
 
line_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
line_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
line_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
line_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
line_stick_helper - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
line_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
line_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
linearCombination - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
linearCombination - Variable in class org.jmol.quantum.MOCalculation
 
linearOffsets - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
linearRotTrans - Variable in class org.jmol.symmetry.SymmetryOperation
 
linearSearch() - Method in class org.jmol.minimize.forcefield.ForceField
 
linearTolerance - Variable in class org.jmol.symmetry.PointGroup
 
lineBits - Variable in class org.jmol.g3d.LineRenderer
 
lineBuffer - Variable in class org.jmol.adapter.readers.simple.InputReader
 
lineCache - Variable in class org.jmol.g3d.LineRenderer
 
lineCurrent - Variable in class org.jmol.script.ScriptTokenParser
 
linedata - Static variable in class org.jmol.script.T
 
lineData - Variable in class org.jmol.shape.Mesh
 
lineData - Variable in class org.jmol.shapespecial.Draw
 
lineEnd - Variable in class org.jmol.script.ScriptContext
 
lineEnd - Variable in class org.jmol.script.ScriptEval
 
lineHeight - Variable in class org.jmol.modelset.Text
 
lineheight - Variable in class org.jmol.render.UccageRenderer
 
lineIndices - Variable in class org.jmol.script.ScriptCompiler
 
lineIndices - Variable in class org.jmol.script.ScriptContext
 
lineIndices - Variable in class org.jmol.script.ScriptEval
 
lineIndices - Variable in class org.jmol.script.ScriptFunction
 
lineLength - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
lineNumbers - Variable in class org.jmol.script.ScriptCompiler
 
lineNumbers - Variable in class org.jmol.script.ScriptContext
 
lineNumbers - Variable in class org.jmol.script.ScriptEval
 
lineNumbers - Variable in class org.jmol.script.ScriptFunction
 
lineOptions - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
 
linePt - Variable in class org.jmol.jvxl.readers.XplorReader
 
LineRenderer - Class in org.jmol.g3d
 
LineRenderer(Graphics3D) - Constructor for class org.jmol.g3d.LineRenderer
 
lines - Variable in class org.jmol.modelset.Text
 
lines - Static variable in class org.jmol.script.T
 
lineStart - Variable in class org.jmol.script.ScriptFlowContext
 
lineStartsWithRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
lineTo(Object, int, int) - Method in interface org.jmol.api.GenericGraphics
 
lineTo(Object, int, int) - Method in class org.jmol.awt.AwtG2D
 
lineTo(Object, int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
lineTypeX - Variable in class org.jmol.g3d.LineRenderer
 
LINEWIDTH - Static variable in class org.jmol.shapecgo.CGOMesh
 
lineWidthMad - Variable in class org.jmol.export.___Exporter
 
link - Static variable in class org.jmol.script.T
 
link(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper.CapVertex
Link this vertex with v or remove it from the chain.
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.AboutDialog
Opens a web page in an external browser
linkActivated(URL) - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
Follows the reference in an link.
linkedMesh - Variable in class org.jmol.shape.Mesh
 
linkedMesh - Variable in class org.jmol.shape.MeshCollection
 
list - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
list - Variable in class org.jmol.minimize.forcefield.MMFFOOPCalc
 
list - Static variable in class org.jmol.script.T
 
listAt(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
listAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
listBS(BS) - Method in class org.jmol.script.ScriptExpr
 
listCommands - Variable in class org.jmol.script.ScriptEval
 
listCommands - Variable in class org.jmol.viewer.Viewer
 
listeners - Variable in class org.jmol.viewer.SelectionManager
 
listf - Static variable in class org.jmol.script.T
 
listIsosurface(int) - Method in class org.jmol.scriptext.CmdExt
 
listLabel - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
listParameter(int, int, int) - Method in class org.jmol.script.ScriptParam
 
listSavedStates() - Method in class org.jmol.viewer.StateManager
 
listToMap(Lst<Object>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
return a map of lists of the type: [ [name1,...], [name2,...], ...]
listToSettings(Lst<Object>, Map<Integer, Lst<Object>>) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
lltoken - Variable in class org.jmol.script.ScriptCompiler
 
lnLength - Variable in class org.jmol.script.ScriptCompiler
 
lo - Variable in class org.jmol.util.ColorEncoder
 
load - Static variable in class org.jmol.script.T
 
load() - Method in class org.openscience.jmol.app.HistoryFile
Loads properties from the history file.
LOAD_ATOM_DATA_TYPES - Static variable in class org.jmol.viewer.JC
 
loadArea1() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
loadArea2(String) - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
loadAtomDataAndReturnError(Object, int) - Method in class org.jmol.viewer.Viewer
or just apply the data to the current model set
loadatomdatatolerance - Static variable in class org.jmol.script.T
 
loadAtomDataTolerance - Variable in class org.jmol.viewer.GlobalSettings
 
loadButton - Variable in class org.jmol.console.GenericConsole
 
loadButton - Variable in class org.jmol.console.ScriptEditor
 
loadCoordinates(String, boolean, boolean) - Method in class org.jmol.modelset.AtomCollection
 
loadDefaultShapes(ModelSet) - Method in class org.jmol.viewer.ShapeManager
 
loadDOMNode(Object) - Method in interface org.jmol.api.JmolAppletInterface
 
loadDOMNode(Object) - Method in class org.jmol.util.GenericApplet
 
loader - Variable in class org.jmol.jsv.JDXMOLParser
 
loadFile(String, int, int) - Method in class org.jmol.awt.FileDropper
 
loadFileAsync(String, String, int, boolean) - Method in class org.jmol.script.ScriptEval
Allows asynchronous file loading from the LOAD or SCRIPT command.
loadFileResourceAsync(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
loadFileResourceAsync(String) - Method in class org.jmol.script.ScriptEval
load a static file asynchronously
loadFiles(List<File>) - Method in class org.jmol.awt.FileDropper
 
loadformat - Static variable in class org.jmol.script.T
 
loadFormat - Variable in class org.jmol.viewer.GlobalSettings
 
loadGeometries - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
loadImage(Object, String) - Method in class org.jmol.viewer.FileManager
 
loadImageData(Object, String, String, ScriptContext) - Method in class org.jmol.viewer.Viewer
NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java.
loading - Variable in class org.jmol.util.GenericApplet
 
loadInline(String) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated. 
loadInline(String[]) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated. 
loadInline(String, String) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated. 
loadInline(String[], String) - Method in interface org.jmol.api.JmolAppletInterface
Deprecated. 
loadInline(String) - Method in class org.jmol.api.JmolViewer
 
loadInline(String, char) - Method in class org.jmol.api.JmolViewer
 
loadInline(String[]) - Method in class org.jmol.api.JmolViewer
 
loadInline(String[], boolean) - Method in class org.jmol.api.JmolViewer
 
loadInline(List<Object>, boolean) - Method in class org.jmol.api.JmolViewer
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE
loadInline(String) - Method in class org.jmol.util.GenericApplet
Deprecated. 
loadInline(String, String) - Method in class org.jmol.util.GenericApplet
Deprecated. 
loadInline(String[]) - Method in class org.jmol.util.GenericApplet
Deprecated. 
loadInline(String[], String) - Method in class org.jmol.util.GenericApplet
Deprecated. 
loadInline(String) - Method in class org.jmol.viewer.Viewer
from Applet and external applications only
loadInline(String, char) - Method in class org.jmol.viewer.Viewer
external apps only
loadInline(String[]) - Method in class org.jmol.viewer.Viewer
external apps only
loadInline(String[], boolean) - Method in class org.jmol.viewer.Viewer
external apps and applet only
loadInline(List<Object>, boolean) - Method in class org.jmol.viewer.Viewer
External applications only; does not preserve state -- intentionally!
loadInlineAppend(String, boolean) - Method in class org.jmol.api.JmolViewer
 
loadInlineAppend(String, boolean) - Method in class org.jmol.viewer.Viewer
used by applet and console
loadInlineArray(String[], String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
 
loadInlineArray(String[], String, boolean) - Method in class org.jmol.util.GenericApplet
 
loadInlineScript(String, char, boolean, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
used by loadInline and openFileFull
loadInlineScriptRepaint(String, char, boolean) - Method in class org.jmol.viewer.Viewer
 
loadInlineString(String, String, boolean) - Method in interface org.jmol.api.JmolAppletInterface
 
loadInlineString(String, String, boolean) - Method in class org.jmol.util.GenericApplet
 
loadligandformat - Static variable in class org.jmol.script.T
 
loadLigandFormat - Variable in class org.jmol.viewer.GlobalSettings
 
loadModel() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
loadModelFromFile(String, String, String[], Object, boolean, Map<String, Object>, SB, SB, int, boolean) - Method in class org.jmol.viewer.Viewer
Used by the ScriptEvaluator LOAD command to open one or more files.
loadModelFromFileRepaint(String, String, String[], Object) - Method in class org.jmol.viewer.Viewer
for JmolSimpleViewer -- external applications only (and no-script JavaScript)
loadNote - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
loadScript - Variable in class org.jmol.modelset.Model
 
loadShape(int) - Method in class org.jmol.viewer.ShapeManager
 
loadState - Variable in class org.jmol.modelset.Model
 
loadVibrations - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
lobe - Static variable in class org.jmol.script.T
 
localAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
localAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
localArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
localArrayListType - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
localFunctions - Variable in class org.jmol.viewer.Viewer
 
localize(boolean, Properties) - Method in class org.jmol.popup.PopupResource
 
localSpaceGroupName - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
lock - Variable in class org.jmol.script.ScriptParallelProcessor
 
log(String) - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
log(String) - Method in interface org.jmol.atomdata.AtomDataServer
 
log(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
log(String) - Method in class org.jmol.minimize.forcefield.ForceField
 
log - Static variable in class org.jmol.script.T
 
log(PrintStream, int, String, Throwable) - Method in class org.jmol.util.DefaultLogger
Method to output a log.
log(String) - Method in class org.jmol.viewer.Viewer
 
log(String) - Method in class org.openscience.chimetojmol.ChimePanel
 
log(String) - Static method in class org.openscience.jmol.app.webexport.LogPanel
 
log_box_selections - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
log_conformations - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
logArea - Variable in class org.openscience.chimetojmol.ChimePanel
 
logArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
 
logcommands - Static variable in class org.jmol.script.T
 
logCommands - Variable in class org.jmol.viewer.GlobalSettings
 
logCompression - Variable in class org.jmol.jvxl.readers.Parameters
 
logCube - Variable in class org.jmol.jvxl.readers.Parameters
 
logData - Variable in class org.jmol.minimize.forcefield.Calculations
 
logDebugScript(T[], int) - Method in class org.jmol.script.ScriptEval
 
logEvent(String, P3) - Method in class org.jmol.multitouch.ActionManagerMT
 
logfile - Static variable in class org.jmol.script.T
 
logFileName - Variable in class org.jmol.viewer.Viewer
 
logFilePath - Variable in class org.jmol.viewer.Viewer
 
Logger - Class in org.jmol.util
Logger mechanism.
Logger() - Constructor for class org.jmol.util.Logger
 
LoggerInterface - Interface in org.jmol.util
Interface used for the logging mechanism.
loggestures - Static variable in class org.jmol.script.T
 
logGestures - Variable in class org.jmol.viewer.GlobalSettings
 
logging - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
logging - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
logging - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
logging - Variable in class org.jmol.minimize.forcefield.Calculations
 
loggingEnabled - Variable in class org.jmol.minimize.forcefield.Calculations
 
loglevel - Static variable in class org.jmol.script.T
 
logLevel() - Static method in class org.jmol.util.Logger
Indicates if the level is logged.
logLoadInfo(String) - Method in class org.jmol.script.ScriptEval
 
logMessages - Variable in class org.jmol.jvxl.readers.Parameters
 
logMessages - Variable in class org.jmol.script.ScriptTokenParser
 
LogPanel - Class in org.openscience.jmol.app.webexport
 
LogPanel() - Constructor for class org.openscience.jmol.app.webexport.LogPanel
 
logScrollPane - Variable in class org.openscience.chimetojmol.ChimePanel
 
logToFile(String) - Method in class org.jmol.viewer.OutputManager
 
lonepair - Static variable in class org.jmol.script.T
 
LONG_BINGET - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
LONG_BINPUT - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
lookForSyncID() - Method in class org.jmol.script.ScriptCompiler
Check for a set of characters that does not start with double quote or at-sign and terminates with #, }, or an end of line.
lookingAtBitset() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtComment() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtDecimal() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtEndOfLine() - Method in class org.jmol.script.ScriptCompiler
Look for end of script or a new line.
lookingAtExponential() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtImpliedString(boolean, boolean, boolean) - Method in class org.jmol.script.ScriptCompiler
An "implied string" is a parameter that is not quoted but because of its position in a command is implied to be a string.
lookingAtInteger() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtLeadingWhitespace() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtLoadFormat(boolean) - Method in class org.jmol.script.ScriptCompiler
 
lookingAtLookupToken(int) - Method in class org.jmol.script.ScriptCompiler
 
lookingAtMathContinuation(int) - Method in class org.jmol.script.ScriptCompiler
 
lookingAtMatrix() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtObjectID() - Method in class org.jmol.script.ScriptCompiler
Look for a valid $...
lookingAtSeqcode() - Method in class org.jmol.script.ScriptCompiler
 
lookingAtSetBraceSyntax() - Method in class org.jmol.script.ScriptCompiler
look for '{' at the start of a command, allowing for syntaxes {xxx}.yyy = ...
lookingAtString(boolean) - Method in class org.jmol.script.ScriptCompiler
look for a quoted string, possibly allowing single quotes.
lookingAtTerminator() - Method in class org.jmol.script.ScriptCompiler
Look for valid terminating semicolon -- one not within for(), for example.
lookup(String) - Static method in class org.jmol.symmetry.HallRotation
 
lookupCode - Variable in class org.jmol.symmetry.HallRotationTerm
 
lookupIdentifierValue(String) - Method in class org.jmol.script.ScriptEval
 
lookupIdentifierValue(String) - Method in class org.jmol.script.ScriptExpr
 
lookupInterpolatedVoxelValue(T3, boolean) - Method in interface org.jmol.api.VolumeDataInterface
 
lookupInterpolatedVoxelValue(T3, boolean) - Method in class org.jmol.jvxl.data.VolumeData
 
lookupSpecialAtomID(String) - Method in interface org.jmol.api.JmolBioResolver
 
lookupSpecialAtomID(String) - Method in class org.jmol.modelsetbio.Resolver
 
lookupValue(String, boolean) - Method in class org.jmol.script.ScriptEval
 
loop - Static variable in class org.jmol.script.T
 
LoopedStreams - Class in org.openscience.jmol.app.jmolpanel
 
LoopedStreams() - Constructor for class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
LOW - Static variable in class org.jmol.util.ColorEncoder
 
lowdenCharges - Variable in class org.jmol.adapter.readers.quantum.GamessUSReader
 
lp - Static variable in class org.jmol.script.T
 
lstDipoles - Variable in class org.jmol.shapespecial.Dipole
 
lstRegions - Variable in class org.jmol.util.MeshCapper
dynamic region processing.
ltoken - Variable in class org.jmol.script.ScriptCompiler
 
ltokenPostfix - Variable in class org.jmol.script.ScriptTokenParser
 
lumo - Static variable in class org.jmol.script.T
 
lumoEnergy - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
 

M

m - Variable in class org.jmol.export._IdtfExporter
 
m - Variable in class org.jmol.render.MeasuresRenderer
 
m - Variable in class org.jmol.util.MeshSlicer
 
m2_rotate - Variable in class org.jmol.viewer.TransformManager4D
 
m3_toScreen - Variable in class org.jmol.viewer.TransformManager4D
 
m3dStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
m4 - Variable in class org.jmol.thread.SpinThread
 
m4 - Variable in class org.jmol.viewer.TransformManager4D
 
MAC_COMMAND - Static variable in class org.jmol.viewer.binding.Binding
 
mad - Variable in class org.jmol.modelset.Bond
 
mad - Variable in class org.jmol.modelset.Measurement
 
mad - Variable in class org.jmol.modelset.MeasurementData
 
mad - Variable in class org.jmol.render.ShapeRenderer
 
mad - Variable in class org.jmol.renderbio.RocketRenderer
 
mad - Variable in class org.jmol.shape.AtomShape
 
mad - Variable in class org.jmol.shape.FontLineShape
 
mad - Variable in class org.jmol.shapespecial.Dipole
 
mad - Variable in class org.jmol.viewer.Connection
 
mad0 - Variable in class org.jmol.render.MeasuresRenderer
 
MAD_GLOBAL - Static variable in class org.jmol.modelset.Atom
 
madAtom - Variable in class org.jmol.modelset.Atom
 
madBeg - Variable in class org.jmol.render.ShapeRenderer
 
madDnaRna - Variable in class org.jmol.shapebio.BioShapeCollection
 
madEnd - Variable in class org.jmol.render.ShapeRenderer
 
madHelixSheet - Variable in class org.jmol.shapebio.BioShapeCollection
 
madMid - Variable in class org.jmol.render.ShapeRenderer
 
madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JC
 
madOn - Variable in class org.jmol.shapebio.BioShapeCollection
 
mads - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
mads - Variable in class org.jmol.renderbio.BioShapeRenderer
 
mads - Variable in class org.jmol.shape.AtomShape
 
madTurnRandom - Variable in class org.jmol.shapebio.BioShapeCollection
 
mag2d - Variable in class org.jmol.render.SticksRenderer
 
magCenterings - Variable in class org.jmol.adapter.readers.cif.CifReader
 
MAGENTA - Static variable in class org.jmol.util.C
 
MAGNETIC_SUSCEPTIBILITY_FACTOR - Static variable in class org.jmol.util.Tensor
 
magneticshielding - Static variable in class org.jmol.script.T
 
MAGNETOGYRIC_RATIO - Static variable in class org.jmol.quantum.NMRCalculation
 
magOp - Variable in class org.jmol.symmetry.SymmetryOperation
 
magresFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MagresReader - Class in org.jmol.adapter.readers.xtal
 
MagresReader() - Constructor for class org.jmol.adapter.readers.xtal.MagresReader
 
magresUnits - Variable in class org.jmol.adapter.readers.xtal.MagresReader
 
MAIN - Static variable in class org.jmol.thread.JmolThread
 
main(String[]) - Static method in class org.openscience.chimetojmol.ChimeToJmol
 
main(String[]) - Static method in class org.openscience.jmol.app.Jmol
 
main(String[]) - Static method in class org.openscience.jmol.app.JmolData
 
main(String[]) - Static method in class org.openscience.jvxl.Jvxl
 
main(String[]) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
MainPopupResourceBundle - Class in org.jmol.popup
 
MainPopupResourceBundle(String, Properties) - Constructor for class org.jmol.popup.MainPopupResourceBundle
 
makeBonds(String[][], boolean) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
 
makeColorScheme(String, int[], boolean) - Method in class org.jmol.util.ColorEncoder
 
makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.modelset.ModelSet
 
makeConnections(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.viewer.Viewer
 
makeConnections2(float, float, int, int, BS, BS, BS, boolean, boolean, float) - Method in class org.jmol.modelset.ModelSet
 
makePlane(float, float, float, P4) - Static method in class org.openscience.jmol.app.surfacetool.Slice
 
makePoints - Variable in class org.jmol.shapespecial.Draw
 
manager - Variable in class org.jmol.awt.Mouse
 
manager - Variable in class org.jmol.awtjs2d.Mouse
 
manifest - Static variable in class org.jmol.script.T
 
mantissa(float) - Method in class org.jmol.jvxl.data.VolumeData
 
map(Object, String, String, Map<String, Object>) - Static method in class org.jmol.console.GenericConsole
 
map - Variable in class org.jmol.quantum.MOCalculation
 
map - Variable in class org.jmol.viewer.PropertyManager
 
map - Variable in class org.openscience.jmol.app.jmolpanel.GuiMap
 
map_auto_expand_sym - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mapAtomResIDs(Map<String, Integer>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
Map all atom and residue unit ids to atom indexes
mapc - Variable in class org.jmol.jvxl.readers.MapFileReader
 
MapFileReader - Class in org.jmol.jvxl.readers
 
MapFileReader() - Constructor for class org.jmol.jvxl.readers.MapFileReader
 
mapGet(String) - Method in class org.jmol.script.SV
 
mapGroups(Map<String, String>) - Method in class org.jmol.dssx.AnnotationParser
 
mapLattice - Variable in class org.jmol.jvxl.data.JvxlData
 
mapLattice - Variable in class org.jmol.jvxl.readers.Parameters
 
mapObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
mapPartialCharge(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mappedDataMax - Variable in class org.jmol.jvxl.data.JvxlData
 
mappedDataMax - Variable in class org.jmol.jvxl.readers.Parameters
 
mappedDataMin - Variable in class org.jmol.jvxl.data.JvxlData
 
mappedDataMin - Variable in class org.jmol.jvxl.readers.Parameters
 
mappingPlane - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
mappingPlane - Variable in class org.jmol.jvxl.data.VolumeData
 
mappingPlaneNormalMag - Variable in class org.jmol.jvxl.data.VolumeData
 
mapproperty - Static variable in class org.jmol.script.T
 
mapProperty() - Method in class org.jmol.scriptext.CmdExt
 
mapPut(String, SV) - Method in class org.jmol.script.SV
 
mapr - Variable in class org.jmol.jvxl.readers.MapFileReader
 
maps - Variable in class org.jmol.jvxl.readers.MapFileReader
 
mapSurface() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
mapT - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
mapValue(String) - Method in class org.jmol.script.SV
 
mapWidth - Variable in class org.jmol.g3d.TextRenderer
 
mar - Variable in class org.jmol.render.StarsRenderer
 
marBond - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
MarchingCubes - Class in org.jmol.jvxl.calc
 
MarchingCubes() - Constructor for class org.jmol.jvxl.calc.MarchingCubes
 
MarchingCubes(VertexDataServer, VolumeData, Parameters, BS) - Constructor for class org.jmol.jvxl.calc.MarchingCubes
 
marchingCubes - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MarchingSquares - Class in org.jmol.jvxl.calc
 
MarchingSquares(VertexDataServer, VolumeData, P4, float[], int, int, boolean) - Constructor for class org.jmol.jvxl.calc.MarchingSquares
 
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
marchingSquares - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MarchingSquares.ContourVertex - Class in org.jmol.jvxl.calc
 
MarchingSquares.Triangle - Class in org.jmol.jvxl.calc
 
margin - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
margin - Variable in class org.jmol.util.BoxInfo
 
MARK - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
mark(int) - Method in class org.openscience.jvxl.MonitorInputStream
 
markCount - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
markFaceVoxels(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
markLines(String, char) - Static method in class org.jmol.util.Parser
 
markPlaneVoxels(P3, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
markPosition - Variable in class org.openscience.jvxl.MonitorInputStream
 
marks - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
markSphereVoxels(float, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
markToroidVoxels() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
MAROON - Static variable in class org.jmol.util.C
 
mass - Static variable in class org.jmol.script.T
 
mat - Variable in class org.jmol.g3d.SphereRenderer
 
mat - Variable in class org.jmol.renderbio.BioShapeRenderer
 
mat - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
mat4 - Variable in class org.jmol.modelset.ModelSet
 
mat4 - Variable in class org.jmol.util.MeshSurface
 
mat4t - Variable in class org.jmol.modelset.ModelSet
 
match(String, Node[], int, BS, BS, boolean, boolean, boolean, int) - Method in class org.jmol.smiles.SmilesMatcher
 
matchAllAtoms - Variable in class org.jmol.smiles.SmilesSearch
 
matchingAtom - Variable in class org.jmol.smiles.SmilesAtom
 
matchingBond - Variable in class org.jmol.smiles.SmilesBond
 
matEllipsoidToScreen - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
mathExpressionCommand - Static variable in class org.jmol.script.T
 
mathExt - Variable in class org.jmol.script.ScriptEval
 
MathExt - Class in org.jmol.scriptext
 
MathExt() - Constructor for class org.jmol.scriptext.MathExt
 
mathfunc - Static variable in class org.jmol.script.T
 
mathop - Static variable in class org.jmol.script.T
 
mathproperty - Static variable in class org.jmol.script.T
 
matInv - Variable in class org.jmol.modelset.ModelSet
 
matR - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
matrix3f - Static variable in class org.jmol.script.T
 
matrix4f - Static variable in class org.jmol.script.T
 
matrix_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
matrixCartesianToFractional - Variable in class org.jmol.util.SimpleUnitCell
 
matrixCtoFANoOffset - Variable in class org.jmol.util.SimpleUnitCell
 
matrixEnd - Variable in class org.jmol.thread.MoveToThread
 
matrixFractionalToCartesian - Variable in class org.jmol.util.SimpleUnitCell
 
matrixFtoCNoOffset - Variable in class org.jmol.util.SimpleUnitCell
 
matrixRotate - Variable in class org.jmol.viewer.TransformManager
 
matrixStart - Variable in class org.jmol.thread.MoveToThread
 
matrixStartInv - Variable in class org.jmol.thread.MoveToThread
 
matrixStep - Variable in class org.jmol.thread.MoveToThread
 
matrixStereo - Variable in class org.jmol.viewer.TransformManager
 
matrixT - Variable in class org.jmol.render.MeasuresRenderer
 
matrixTemp - Variable in class org.jmol.viewer.TransformManager
 
matrixTemp3 - Variable in class org.jmol.viewer.TransformManager
 
matrixTemp4 - Variable in class org.jmol.viewer.TransformManager
 
matrixTest - Variable in class org.jmol.viewer.TransformManager
 
matrixToScript(Object) - Static method in class org.jmol.util.Escape
 
matrixTransform - Variable in class org.jmol.viewer.TransformManager
 
matrixTransformInv - Variable in class org.jmol.viewer.TransformManager
 
matRot - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
matScreenToCartesian - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
matScreenToEllipsoid - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
matSupercell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
matTemp - Variable in class org.jmol.modelset.ModelSet
 
matUnitCellOrientation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
max - Static variable in class org.jmol.script.T
 
max - Variable in class org.jmol.smiles.SmilesMeasure
 
MAX_ACTION_UNDO - Static variable in class org.jmol.viewer.StateCreator
 
MAX_ADJACENT_PHOSPHORUS_DISTANCE - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
MAX_BOND_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shape.Sticks
 
MAX_BONDS_LENGTH_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
 
MAX_DOUBLE_CLICK_MILLIS - Static variable in class org.jmol.viewer.ActionManager
 
MAX_FILES - Static variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
MAX_LEVEL - Static variable in class org.jmol.shapespecial.Dots
 
MAX_NUM_TO_CACHE - Static variable in class org.jmol.modelset.BondCollection
 
MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapespecial.Draw
 
MAX_OBJECT_CLICK_DISTANCE_SQUARED - Static variable in class org.jmol.shapesurface.Isosurface
 
max_squarable_double - Static variable in class org.jmol.minimize.Util
 
max_threads - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
MAX_TREE_DEPTH - Static variable in class org.jmol.bspt.Bspt
 
max_triangles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
max_ups - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
MAX_VERTICES - Static variable in class org.jmol.shapespecial.Polyhedra
 
maxAxis - Static variable in class org.jmol.symmetry.PointGroup
 
maxBondingRadius - Variable in class org.jmol.modelset.AtomCollection
 
maxBondWarned - Variable in class org.jmol.modelset.ModelSet
 
maxColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
 
maxData - Variable in class org.jmol.shapesurface.Contact
 
maxDistance - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
maxElement - Variable in class org.jmol.symmetry.PointGroup
 
maxGrid - Variable in class org.jmol.jvxl.data.VolumeData
 
maxGrid - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
maxHbondAlphaDistance - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
maxHbondAlphaDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
MAXID - Static variable in class org.jmol.quantum.QS
 
MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JC
 
MAXIMUM_CLICK_TIME - Static variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
MAXIMUM_QUEUE_LENGTH - Static variable in class org.jmol.viewer.StatusManager
 
MAXIMUM_ZOOM_PERCENTAGE - Static variable in class org.jmol.viewer.TransformManager
 
MAXIMUM_ZOOM_PERSPECTIVE_DEPTH - Static variable in class org.jmol.viewer.TransformManager
 
maximumSize - Variable in class org.jmol.viewer.Viewer
 
maxLeft - Variable in class org.jmol.bspt.Node
 
maxLevel - Static variable in class org.jmol.util.Geodesic
 
maxOddSizeSphere - Static variable in class org.jmol.g3d.SphereRenderer
 
maxr - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
maxRadius - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
maxRight - Variable in class org.jmol.bspt.Node
 
maxRS - Variable in class org.jmol.jvxl.readers.AtomDataReader
maximun (atom radius + solvent radius)
maxSerial - Variable in class org.jmol.adapter.readers.cif.CifReader
 
maxSerial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
maxSerial - Variable in class org.jmol.modelsetbio.Resolver
 
maxSet - Variable in class org.jmol.jvxl.readers.Parameters
 
maxset - Static variable in class org.jmol.script.T
 
maxSize - Variable in class org.jmol.util.CommandHistory
 
maxSphereCache - Static variable in class org.jmol.util.Shader
 
maxSphereDiameter - Static variable in class org.jmol.g3d.SphereRenderer
 
maxSphereDiameter2 - Static variable in class org.jmol.g3d.SphereRenderer
 
MAXUNDO - Static variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
maxVanderwaalsRadius - Variable in class org.jmol.modelset.AtomCollection
 
maxVectorLength - Variable in class org.jmol.jvxl.data.VolumeData
 
maxX - Variable in class org.jmol.g3d.SphereRenderer
 
maxXYZ - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
maxXYZ0 - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
maxXYZ0 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
maxY - Variable in class org.jmol.g3d.SphereRenderer
 
maxZ - Variable in class org.jmol.g3d.SphereRenderer
 
maybeGetBaseRing5Points(P3[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
mayScript - Variable in class org.jmol.util.GenericApplet
 
mc - Variable in class org.jmol.modelset.ModelSet
model count
MdCrdReader - Class in org.jmol.adapter.readers.more
Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command
MdCrdReader() - Constructor for class org.jmol.adapter.readers.more.MdCrdReader
 
mDeriv - Variable in class org.jmol.g3d.SphereRenderer
 
mDeriv - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
mdlLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
mDsimulation - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
mdTopLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MdTopReader - Class in org.jmol.adapter.readers.more
A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file
MdTopReader() - Constructor for class org.jmol.adapter.readers.more.MdTopReader
 
MEAS_DIGITS - Static variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
measure - Static variable in class org.jmol.script.T
 
measure() - Method in class org.jmol.scriptext.CmdExt
 
MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JC
 
measureallmodels - Static variable in class org.jmol.script.T
 
measureAllModels - Variable in class org.jmol.shape.Measures
 
measureAllModels - Variable in class org.jmol.viewer.GlobalSettings
 
measureDistanceUnits - Variable in class org.jmol.viewer.GlobalSettings
 
Measurement - Class in org.jmol.modelset
 
Measurement() - Constructor for class org.jmol.modelset.Measurement
 
measurementCount - Variable in class org.jmol.shape.Measures
 
MeasurementData - Class in org.jmol.modelset
 
MeasurementData() - Constructor for class org.jmol.modelset.MeasurementData
 
measurementHeaders - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
measurementlabels - Static variable in class org.jmol.script.T
 
measurementLabels - Variable in class org.jmol.viewer.GlobalSettings
 
MeasurementListWindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementListWindowListener
 
measurementnumbers - Static variable in class org.jmol.script.T
 
MeasurementPending - Class in org.jmol.modelset
 
MeasurementPending() - Constructor for class org.jmol.modelset.MeasurementPending
 
measurementQueued - Variable in class org.jmol.viewer.ActionManager
 
measurements - Variable in class org.jmol.modelset.MeasurementData
 
measurements - Static variable in class org.jmol.script.T
 
measurements - Variable in class org.jmol.shape.Measures
 
measurementsAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
measurementStrings - Variable in class org.jmol.modelset.MeasurementData
 
measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
MeasurementTable - Class in org.openscience.jmol.app.jmolpanel
 
MeasurementTable(Viewer, JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable
Constructor
measurementTable - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
MeasurementTable.MeasurementListWindowListener - Class in org.openscience.jmol.app.jmolpanel
 
MeasurementTable.MeasurementTableModel - Class in org.openscience.jmol.app.jmolpanel
 
measurementTableModel - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
MeasurementTableModel() - Constructor for class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementTableModel
 
measurementunits - Static variable in class org.jmol.script.T
 
Measures - Class in org.jmol.shape
 
Measures() - Constructor for class org.jmol.shape.Measures
 
measures - Variable in class org.jmol.smiles.SmilesSearch
 
measuresEnabled - Variable in class org.jmol.viewer.ActionManager
 
MeasuresRenderer - Class in org.jmol.render
 
MeasuresRenderer() - Constructor for class org.jmol.render.MeasuresRenderer
 
mediaTracker - Variable in class org.jmol.applet.AppletWrapper
 
mem - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
memBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
memo - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
MEMORY_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
menu - Static variable in class org.jmol.script.T
 
MENU_NAME - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
MENU_NAME - Static variable in class org.jmol.popup.MainPopupResourceBundle
 
menuAddButtonGroup(SC) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
menuAddButtonGroup(SC) - Method in class org.jmol.popup.JSSwingPopupHelper
 
menuAddButtonGroup(SC) - Method in interface org.jmol.popup.PopupHelper
 
menuAddItem(SC, SC) - Method in class org.jmol.popup.GenericSwingPopup
 
menuAddSeparator(SC) - Method in class org.jmol.popup.GenericSwingPopup
 
menuAddSubMenu(SC, SC) - Method in class org.jmol.popup.GenericSwingPopup
 
menubar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
menuCheckBoxCallback(SC) - Method in class org.jmol.popup.GenericSwingPopup
 
menuClearListeners(SC) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
menuClearListeners(SC) - Method in class org.jmol.popup.JSSwingPopupHelper
 
menuClearListeners(SC) - Method in interface org.jmol.popup.PopupHelper
 
menuClickCallback(SC, String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
menuClickCallback(SC, String) - Method in class org.jmol.modelkit.ModelKitPopup
 
menuClickCallback(SC, String) - Method in class org.jmol.popup.GenericSwingPopup
 
menuContents - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
menuContents - Static variable in class org.jmol.popup.MainPopupResourceBundle
 
menuCreateCheckboxItem(SC, String, String, String, boolean, boolean) - Method in class org.jmol.popup.GenericSwingPopup
 
menuCreateItem(SC, String, String, String) - Method in class org.jmol.popup.GenericSwingPopup
 
menuCreatePopup(String, Object) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
menuCreatePopup(String, Object) - Method in class org.jmol.popup.JSSwingPopupHelper
 
menuCreatePopup(String, Object) - Method in interface org.jmol.popup.PopupHelper
 
menuEnable(SC, boolean) - Method in class org.jmol.popup.GenericSwingPopup
 
menuEnabled() - Method in class org.jmol.viewer.Viewer
 
menuFile - Variable in class org.openscience.jmol.app.JmolApp
 
menuFocusCallback(String, String, boolean) - Method in class org.jmol.awtjs2d.JmolJSPopup
 
menuFocusCallback(String, String, boolean) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
menuFocusCallback(String, String, boolean) - Method in class org.jmol.modelkit.ModelKitPopup
 
menuFocusCallback(String, String, boolean) - Method in class org.jmol.popup.JmolAwtPopup
 
menuGetAsText(SB, int, SC, String) - Method in class org.jmol.popup.GenericSwingPopup
 
menuGetId(SC) - Method in class org.jmol.popup.GenericSwingPopup
 
menuGetListPosition(SC) - Method in class org.jmol.popup.GenericSwingPopup
 
menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
menuInsertSubMenu(SC, SC, int) - Method in class org.jmol.popup.JSSwingPopupHelper
 
menuInsertSubMenu(SC, SC, int) - Method in interface org.jmol.popup.PopupHelper
 
MENUITEM_HEIGHT - Static variable in class org.jmol.popup.JmolGenericPopup
 
menuItems - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
menuMap - Variable in class org.jmol.console.GenericConsole
 
menuName - Variable in class org.jmol.popup.GenericSwingPopup
 
menuNewSubMenu(String, String) - Method in class org.jmol.popup.GenericSwingPopup
 
menuRemoveAll(SC, int) - Method in class org.jmol.popup.GenericSwingPopup
 
menuSetAutoscrolls(SC) - Method in class org.jmol.popup.GenericSwingPopup
 
menuSetCheckBoxOption(SC, String, String) - Method in class org.jmol.awtjs2d.JmolJSPopup
 
menuSetCheckBoxOption(SC, String, String) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
menuSetCheckBoxOption(SC, String, String) - Method in class org.jmol.modelkit.ModelKitPopup
 
menuSetCheckBoxOption(SC, String, String) - Method in class org.jmol.popup.GenericSwingPopup
 
menuSetCheckBoxOption(SC, String, String) - Method in class org.jmol.popup.JmolAwtPopup
 
menuSetCheckBoxValue(SC) - Method in class org.jmol.popup.GenericSwingPopup
 
menuSetLabel(SC, String) - Method in class org.jmol.popup.GenericSwingPopup
 
menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JmolJSPopup
 
menuShowPopup(SC, int, int) - Method in class org.jmol.awtjs2d.JSModelKitPopup
 
menuShowPopup(SC, int, int) - Method in class org.jmol.modelkit.ModelKitPopup
 
menuShowPopup(SC, int, int) - Method in class org.jmol.popup.GenericSwingPopup
 
menuShowPopup(SC, int, int) - Method in class org.jmol.popup.JmolAwtPopup
 
menuStructure - Variable in class org.jmol.api.JmolViewer
 
menuText - Variable in class org.jmol.popup.JmolGenericPopup
 
mep - Static variable in class org.jmol.script.T
 
mep_calcType - Variable in class org.jmol.jvxl.readers.Parameters
 
mep_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
mep_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
 
MEP_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
mep_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
mepCalc - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
MepCalculation - Class in org.jmol.quantum
 
MepCalculation() - Constructor for class org.jmol.quantum.MepCalculation
 
MepCalculationInterface - Interface in org.jmol.api
 
mepList - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
mepType - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
merge(Shape) - Method in class org.jmol.shape.MeshCollection
called by ParallelProcessor at completion
merge(Shape) - Method in class org.jmol.shape.Shape
 
merge(Shape) - Method in class org.jmol.shapesurface.Isosurface
 
merge(MeshData) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
merge(Shape) - Method in class org.jmol.shapesurface.LcaoCartoon
 
merge(Shape) - Method in class org.jmol.shapesurface.MolecularOrbital
 
mergeAssociatedNormalCount - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
mergeAtomArrays(AtomCollection) - Method in class org.jmol.modelset.AtomCollection
 
mergeBufferPixel(int[], int, int, int) - Static method in class org.jmol.g3d.Graphics3D
 
mergeGroups - Variable in class org.jmol.modelset.ModelLoader
 
mergeGroups() - Method in class org.jmol.modelset.ModelLoader
 
mergeMesh(MeshData) - Method in class org.jmol.shapesurface.Contact
 
mergeModelArrays(ModelSet) - Method in class org.jmol.modelset.ModelSet
initial transfer of model data from old to new model set.
mergeModelSet - Variable in class org.jmol.modelset.ModelLoader
 
mergePolygonCount0 - Variable in class org.jmol.util.MeshSurface
 
mergePolygons(MeshSurface, int, int, int[][]) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
mergeResults(Lst<ShapeManager>) - Method in class org.jmol.script.ScriptParallelProcessor
 
mergeSets(int, int) - Method in class org.jmol.jvxl.data.MeshData
 
mergeShapes(Shape[]) - Method in class org.jmol.viewer.ShapeManager
 
mergeTrajectories(AtomSetCollection) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
mergeTrajectories(boolean) - Method in class org.jmol.modelset.ModelSet
 
mergeVertexCount0 - Variable in class org.jmol.util.MeshSurface
 
merging - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
merging - Variable in class org.jmol.modelset.ModelLoader
 
mesh - Variable in class org.jmol.render.MeshRenderer
 
mesh - Static variable in class org.jmol.script.T
 
Mesh - Class in org.jmol.shape
 
Mesh() - Constructor for class org.jmol.shape.Mesh
always use Mesh().mesh1(thisID, colix, index)
mesh1(Viewer, String, short, int) - Method in class org.jmol.shape.Mesh
 
mesh_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_carve_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_carve_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_carve_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_clear_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_clear_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_clear_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_grid_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_negative_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_negative_visible - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_normals - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_skip - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_type - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mesh_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
MeshCapper - Class in org.jmol.util
A class to properly cap a convoluted, closed slice of an isosurface inspired by: Computational Geometry: Algorithms and Applications Mark de Berg, Marc van Kreveld, Mark Overmars, and Otfried Schwarzkopf Springer-Verlag, Berlin Heidelberg 1997 Chapter 3.
MeshCapper() - Constructor for class org.jmol.util.MeshCapper
 
MeshCapper.CapVertex - Class in org.jmol.util
A class to provide linked vertices for MeshCapper
meshColix - Variable in class org.jmol.shape.Mesh
 
meshColix - Variable in class org.jmol.shapesurface.Isosurface
 
MeshCollection - Class in org.jmol.shape
 
MeshCollection() - Constructor for class org.jmol.shape.MeshCollection
 
meshColor - Variable in class org.jmol.jvxl.data.JvxlData
 
meshColor - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
meshCount - Variable in class org.jmol.shape.MeshCollection
 
MeshData - Class in org.jmol.export
Class to generate mesh data (faces, vertices, and normals) for several kinds of generic meshes.
MeshData() - Constructor for class org.jmol.export.MeshData
 
MeshData - Class in org.jmol.jvxl.data
 
MeshData() - Constructor for class org.jmol.jvxl.data.MeshData
 
meshData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
meshData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
MeshData.SortSet - Class in org.jmol.jvxl.data
 
MeshData.SSet - Class in org.jmol.jvxl.data
 
MeshDataServer - Interface in org.jmol.jvxl.api
 
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
meshDataServer - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
meshes - Variable in class org.jmol.renderbio.BioShapeRenderer
 
meshes - Variable in class org.jmol.shape.MeshCollection
 
meshes - Variable in class org.jmol.shapebio.BioShape
 
meshOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
meshReady - Variable in class org.jmol.renderbio.BioShapeRenderer
 
meshReady - Variable in class org.jmol.shapebio.BioShape
 
MeshRenderer - Class in org.jmol.render
 
MeshRenderer() - Constructor for class org.jmol.render.MeshRenderer
 
meshRibbon - Static variable in class org.jmol.script.T
 
MeshRibbon - Class in org.jmol.shapebio
 
MeshRibbon() - Constructor for class org.jmol.shapebio.MeshRibbon
 
MeshRibbonRenderer - Class in org.jmol.renderbio
 
MeshRibbonRenderer() - Constructor for class org.jmol.renderbio.MeshRibbonRenderer
 
meshScale - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
meshscale - Static variable in class org.jmol.script.T
 
meshScale - Variable in class org.jmol.viewer.GlobalSettings
 
meshSlabValue - Variable in class org.jmol.render.MeshRenderer
 
MeshSlicer - Class in org.jmol.util
 
MeshSlicer() - Constructor for class org.jmol.util.MeshSlicer
 
MeshSurface - Class in org.jmol.util
 
MeshSurface() - Constructor for class org.jmol.util.MeshSurface
 
meshTranslucency - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
meshType - Variable in class org.jmol.util.MeshSurface
 
meshWidth - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
message - Variable in class org.jmol.dssx.AnnotationParser
 
message - Variable in exception org.jmol.script.ScriptException
 
message - Static variable in class org.jmol.script.T
 
messageQueue - Variable in class org.jmol.viewer.StatusManager
 
messagestylechime - Static variable in class org.jmol.script.T
 
messageStyleChime - Variable in class org.jmol.viewer.GlobalSettings
 
meth - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
methBox - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
METHOD_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mf - Variable in class org.jmol.util.JmolMolecule
 
mi - Variable in class org.jmol.util.Point3fi
model index
middle - Static variable in class org.jmol.script.T
 
MIDDLE - Static variable in class org.jmol.viewer.binding.Binding
 
middle - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
millis - Variable in class org.jmol.script.ScriptDelayThread
 
min - Static variable in class org.jmol.script.T
 
min - Variable in class org.jmol.smiles.SmilesMeasure
 
MIN_AXIS_LEN - Static variable in class org.jmol.shape.Axes
 
MIN_COEF - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
MIN_DELAY_MS - Static variable in class org.jmol.viewer.MouseState
 
MIN_MESH_RENDER_SIZE - Static variable in class org.jmol.renderbio.BioShapeRenderer
 
min_mesh_spacing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
MIN_RESNO - Static variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
min_squarable_double - Static variable in class org.jmol.minimize.Util
 
MinAngle - Class in org.jmol.minimize
 
MinAngle(int[]) - Constructor for class org.jmol.minimize.MinAngle
 
minAngles - Variable in class org.jmol.minimize.forcefield.Calculations
 
minAngles - Variable in class org.jmol.minimize.forcefield.ForceField
 
minAngles - Variable in class org.jmol.minimize.Minimizer
 
minArray - Variable in class org.jmol.modelset.MeasurementData
 
MinAtom - Class in org.jmol.minimize
 
MinAtom(int, Atom, double[], int) - Constructor for class org.jmol.minimize.MinAtom
 
minAtomCount - Variable in class org.jmol.minimize.forcefield.ForceField
 
minAtoms - Variable in class org.jmol.minimize.forcefield.Calculations
 
minAtoms - Variable in class org.jmol.minimize.forcefield.ForceField
 
minAtoms - Variable in class org.jmol.minimize.Minimizer
 
MinBond - Class in org.jmol.minimize
 
MinBond(int, int, int, int, int, int, Integer) - Constructor for class org.jmol.minimize.MinBond
 
minBondCount - Variable in class org.jmol.minimize.forcefield.ForceField
 
minbonddistance - Static variable in class org.jmol.script.T
 
minBondDistance - Variable in class org.jmol.viewer.GlobalSettings
 
minBondDistance - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
minBonds - Variable in class org.jmol.minimize.forcefield.Calculations
 
minBonds - Variable in class org.jmol.minimize.forcefield.ForceField
 
minBonds - Variable in class org.jmol.minimize.Minimizer
 
minColorIndex - Variable in class org.jmol.jvxl.data.JvxlData
 
minData - Variable in class org.jmol.shapesurface.Contact
 
minDistanceForPlanarity - Static variable in class org.jmol.shapespecial.Polyhedra
 
minGrid - Variable in class org.jmol.jvxl.data.VolumeData
 
miniLogArea - Static variable in class org.openscience.jmol.app.webexport.LogPanel
 
MINIMIZATION_ATOM_MAX - Static variable in class org.jmol.viewer.JC
 
minimizationcriterion - Static variable in class org.jmol.script.T
 
minimizationCriterion - Variable in class org.jmol.viewer.GlobalSettings
 
minimizationOn() - Method in interface org.jmol.api.MinimizerInterface
 
minimizationOn - Variable in class org.jmol.minimize.Minimizer
 
minimizationOn() - Method in class org.jmol.minimize.Minimizer
 
minimizationrefresh - Static variable in class org.jmol.script.T
 
minimizationRefresh - Variable in class org.jmol.viewer.GlobalSettings
 
minimizationsilent - Static variable in class org.jmol.script.T
 
minimizationSilent - Variable in class org.jmol.viewer.GlobalSettings
 
minimizationsteps - Static variable in class org.jmol.script.T
 
minimizationSteps - Variable in class org.jmol.viewer.GlobalSettings
 
MinimizationThread - Class in org.jmol.minimize
 
MinimizationThread() - Constructor for class org.jmol.minimize.MinimizationThread
 
minimizationThread - Variable in class org.jmol.minimize.Minimizer
 
minimize(int, double, BS, BS, boolean, boolean, String) - Method in interface org.jmol.api.MinimizerInterface
 
minimize(int, double, BS, BS, boolean, boolean, String) - Method in class org.jmol.minimize.Minimizer
 
minimize - Static variable in class org.jmol.script.T
 
minimize() - Method in class org.jmol.scriptext.CmdExt
 
minimize(boolean) - Method in class org.jmol.viewer.ActionManager
 
minimize(JmolScriptEvaluator, int, float, BS, BS, float, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
MINIMIZE_FIXED_RANGE - Static variable in class org.jmol.viewer.JC
 
minimizer - Variable in class org.jmol.minimize.forcefield.ForceField
 
minimizer - Variable in class org.jmol.minimize.MinimizationThread
 
Minimizer - Class in org.jmol.minimize
 
Minimizer() - Constructor for class org.jmol.minimize.Minimizer
 
minimizer - Variable in class org.jmol.viewer.Viewer
 
MinimizerInterface - Interface in org.jmol.api
 
minimizeWithoutThread() - Method in class org.jmol.minimize.Minimizer
 
MINIMUM_ELAPSED_SECONDS - Static variable in class org.jmol.applet.AppletWrapper
 
minimumHbondDistance2 - Static variable in class org.jmol.modelsetbio.AminoPolymer
 
MININUM_GESTURE_DELAY_MILLISECONDS - Static variable in class org.jmol.viewer.ActionManager
 
minLeft - Variable in class org.jmol.bspt.Node
 
minMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
minmaxmask - Static variable in class org.jmol.script.T
 
MinObject - Class in org.jmol.minimize
 
MinObject() - Constructor for class org.jmol.minimize.MinObject
 
minpixelselradius - Static variable in class org.jmol.script.T
 
minPixelSelRadius - Variable in class org.jmol.viewer.GlobalSettings
 
MinPosition - Class in org.jmol.minimize
not implemented -- would be a force toward a given position in space
MinPosition(int[], double[]) - Constructor for class org.jmol.minimize.MinPosition
 
minPositions - Variable in class org.jmol.minimize.forcefield.Calculations
 
minPositions - Variable in class org.jmol.minimize.forcefield.ForceField
 
minPositions - Variable in class org.jmol.minimize.Minimizer
 
minPtsPerAng - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
minRight - Variable in class org.jmol.bspt.Node
 
minScreenDimension - Variable in class org.jmol.export.__RayTracerExporter
 
minSet - Variable in class org.jmol.jvxl.readers.Parameters
 
minset - Static variable in class org.jmol.script.T
 
minSyncRepeatMs - Variable in class org.jmol.viewer.StatusManager
 
minToPlaneDistance - Variable in class org.jmol.jvxl.data.VolumeData
 
MinTorsion - Class in org.jmol.minimize
 
MinTorsion(int[]) - Constructor for class org.jmol.minimize.MinTorsion
 
minTorsions - Variable in class org.jmol.minimize.forcefield.Calculations
 
minTorsions - Variable in class org.jmol.minimize.forcefield.ForceField
 
minTorsions - Variable in class org.jmol.minimize.Minimizer
 
minus - Static variable in class org.jmol.script.T
 
minusMinus - Static variable in class org.jmol.script.T
 
minX - Variable in class org.jmol.g3d.SphereRenderer
 
minXYZ - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
minXYZ0 - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
minXYZ0 - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
minY - Variable in class org.jmol.g3d.SphereRenderer
 
minZ - Variable in class org.jmol.g3d.SphereRenderer
 
minZ - Variable in class org.jmol.render.LabelsRenderer
 
misc - Static variable in class org.jmol.script.T
 
missingHydrogenCount - Variable in class org.jmol.smiles.SmilesAtom
 
ml - Variable in class org.jmol.modelsetbio.Resolver
 
mlp - Static variable in class org.jmol.script.T
 
MlpCalculation - Class in org.jmol.quantum
 
MlpCalculation() - Constructor for class org.jmol.quantum.MlpCalculation
 
mltb - Variable in class org.jmol.minimize.forcefield.AtomType
 
mm - Variable in class org.jmol.viewer.Viewer
 
mmcifLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MMCifReader - Class in org.jmol.adapter.readers.cif
 
MMCifReader() - Constructor for class org.jmol.adapter.readers.cif.MMCifReader
 
MMCifValidationParser - Class in org.jmol.adapter.readers.cif
 
MMCifValidationParser() - Constructor for class org.jmol.adapter.readers.cif.MMCifValidationParser
 
mmff - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
MMFFAngleCalc - Class in org.jmol.minimize.forcefield
 
MMFFAngleCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFAngleCalc
 
MMFFDistanceCalc - Class in org.jmol.minimize.forcefield
 
MMFFDistanceCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFDistanceCalc
 
MMFFESCalc - Class in org.jmol.minimize.forcefield
 
MMFFESCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFESCalc
 
MMFFOOPCalc - Class in org.jmol.minimize.forcefield
 
MMFFOOPCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFOOPCalc
 
MMFFSBCalc - Class in org.jmol.minimize.forcefield
 
MMFFSBCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFSBCalc
 
MMFFTorsionCalc - Class in org.jmol.minimize.forcefield
 
MMFFTorsionCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFTorsionCalc
 
MMFFVDWCalc - Class in org.jmol.minimize.forcefield
 
MMFFVDWCalc() - Constructor for class org.jmol.minimize.forcefield.MMFFVDWCalc
 
mmType - Variable in class org.jmol.minimize.forcefield.AtomType
 
mo - Static variable in class org.jmol.script.T
 
mo(boolean, int) - Method in class org.jmol.scriptext.IsoExt
 
MO_MAX_GRID - Static variable in class org.jmol.jvxl.readers.Parameters
 
MO_OCC - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
MOCalculation - Class in org.jmol.quantum
 
MOCalculation() - Constructor for class org.jmol.quantum.MOCalculation
 
MOCalculationInterface - Interface in org.jmol.api
 
moCoeff - Variable in class org.jmol.quantum.MOCalculation
 
moCoefficients - Variable in class org.jmol.quantum.MOCalculation
 
moColorNeg - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moColorPos - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moCombo(Lst<Object[]>) - Method in class org.jmol.scriptext.IsoExt
 
moCount - Variable in class org.jmol.adapter.readers.quantum.JaguarReader
 
moCount - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
moCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
moCutoff - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moData - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
moData - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
moData - Variable in class org.jmol.jvxl.readers.Parameters
 
modAverage - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modAxes - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modAxes - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
modCell - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modCoord - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modCount - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modDebug - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modDim - Variable in class org.jmol.adapter.readers.cif.CifReader
 
modDim - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modDim - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
modDim - Variable in class org.jmol.symmetry.SpaceGroup
 
modDim - Variable in class org.jmol.symmetry.SymmetryOperation
 
modDim - Variable in class org.jmol.util.Vibration
modDim will be > 0 for modulation
mode - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
mode - Variable in class org.jmol.jvxl.readers.MapFileReader
 
mode - Static variable in class org.jmol.script.T
 
mode - Variable in class org.jmol.viewer.TransformManager
 
MODE_3D - Static variable in class org.jmol.viewer.TransformManager4D
 
MODE_4D_WX - Static variable in class org.jmol.viewer.TransformManager4D
 
MODE_4D_WY - Static variable in class org.jmol.viewer.TransformManager4D
 
MODE_4D_WZ - Static variable in class org.jmol.viewer.TransformManager4D
 
MODE_ARRAY - Static variable in class org.jmol.smiles.SmilesMatcher
 
MODE_BITSET - Static variable in class org.jmol.smiles.SmilesMatcher
 
MODE_CUBE - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
MODE_ELLIPTICAL - Static variable in class org.jmol.renderbio.BioShapeRenderer
 
MODE_FILL_COORDS - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_MODEL - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_MOLECULES - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_MULTIMODEL - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FILL_RADII - Static variable in class org.jmol.atomdata.AtomData
 
MODE_FLAT - Static variable in class org.jmol.renderbio.BioShapeRenderer
 
MODE_GET_ATTACHED_HYDROGENS - Static variable in class org.jmol.atomdata.AtomData
 
MODE_GET_COLOR_INDEXES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_GET_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_HEX - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
 
MODE_HYBRID36 - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
 
MODE_JVXL - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
MODE_MAP - Static variable in class org.jmol.smiles.SmilesMatcher
 
MODE_MASK - Static variable in class org.jmol.viewer.binding.Binding
 
MODE_NAVIGATION - Static variable in class org.jmol.viewer.TransformManager
 
MODE_NONELLIPTICAL - Static variable in class org.jmol.renderbio.BioShapeRenderer
 
MODE_PDB - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
 
MODE_PERSPECTIVE_PYMOL - Static variable in class org.jmol.viewer.TransformManager
 
MODE_PLANES - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
MODE_PUT_SETS - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_PUT_VERTICES - Static variable in class org.jmol.jvxl.data.MeshData
 
MODE_STANDARD - Static variable in class org.jmol.viewer.TransformManager
 
MODE_TUBE - Static variable in class org.jmol.renderbio.BioShapeRenderer
 
moDebug - Variable in class org.jmol.shapesurface.MolecularOrbital
 
model(int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
model - Variable in class org.jmol.modelset.Chain
 
Model - Class in org.jmol.modelset
 
Model() - Constructor for class org.jmol.modelset.Model
 
model - Variable in class org.jmol.modelset.ModelLoader
 
model - Variable in class org.jmol.modelsetbio.BioPolymer
 
model - Static variable in class org.jmol.script.T
 
MODEL_CURRENT - Static variable in class org.jmol.viewer.AnimationManager
 
MODEL_NO - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
modelAdapter - Variable in class org.jmol.viewer.Viewer
 
modelAdapter - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
modelAtomCount - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
modelbased - Static variable in class org.jmol.script.T
 
modelCenterOffset - Variable in class org.jmol.viewer.TransformManager
 
modelCount - Variable in class org.jmol.popup.JmolGenericPopup
 
modelField - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
modelFilename - Variable in class org.openscience.jmol.app.JmolApp
 
modelFileNumberFromFloat(float) - Static method in class org.jmol.modelset.ModelSet
 
modelFileNumbers - Variable in class org.jmol.modelset.ModelSet
 
modelFlags - Variable in class org.jmol.shapespecial.DrawMesh
 
modelHasVibrationVectors(int) - Method in class org.jmol.viewer.Viewer
 
modelIdList - Variable in class org.jmol.jsv.JDXMOLParser
 
modelIndex - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
modelIndex - Variable in class org.jmol.atomdata.AtomData
 
modelIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
modelIndex - Variable in class org.jmol.jvxl.readers.Parameters
 
modelIndex - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
modelIndex - Variable in class org.jmol.modelset.Model
 
modelIndex - Variable in class org.jmol.modelset.Object2d
 
modelIndex - Variable in class org.jmol.modelset.StateScript
 
modelIndex - Variable in class org.jmol.popup.JmolGenericPopup
 
modelindex - Static variable in class org.jmol.script.T
 
modelIndex - Variable in class org.jmol.shape.Mesh
 
modelIndex - Variable in class org.jmol.shape.MeshCollection
 
modelIndex - Variable in class org.jmol.shapebio.BioShape
 
modelIndex - Variable in class org.jmol.shapespecial.Dipole
 
modelIndex - Variable in class org.jmol.shapespecial.Ellipsoid
 
modelIndex - Variable in class org.jmol.shapespecial.Polyhedron
 
modelIndex - Variable in class org.jmol.util.JmolMolecule
 
modelIndex - Variable in class org.jmol.util.Tensor
 
modelIndexForFrame(int) - Method in class org.jmol.viewer.AnimationManager
 
modelInfo - Variable in class org.jmol.popup.JmolGenericPopup
 
modelInfo - Variable in class org.jmol.shapespecial.Draw
 
MODELKIT_ZAP_STRING - Static variable in class org.jmol.viewer.JC
 
MODELKIT_ZAP_TITLE - Static variable in class org.jmol.viewer.JC
 
modelkitmode - Static variable in class org.jmol.script.T
 
modelKitMode - Variable in class org.jmol.viewer.GlobalSettings
 
ModelKitPopup - Class in org.jmol.modelkit
 
ModelKitPopup() - Constructor for class org.jmol.modelkit.ModelKitPopup
 
modelkitPopup - Variable in class org.jmol.viewer.Viewer
 
ModelKitPopupResourceBundle - Class in org.jmol.modelkit
 
ModelKitPopupResourceBundle(String, Properties) - Constructor for class org.jmol.modelkit.ModelKitPopupResourceBundle
 
ModelLoader - Class in org.jmol.modelset
 
ModelLoader(Viewer, String, SB, Object, ModelSet, BS) - Constructor for class org.jmol.modelset.ModelLoader
 
ModelManager - Class in org.jmol.viewer
 
ModelManager(Viewer) - Constructor for class org.jmol.viewer.ModelManager
 
modelMap - Variable in class org.jmol.adapter.readers.cif.CifReader
 
modelMolecule - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
modelName - Variable in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
modelName - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
modelName - Variable in class org.jmol.atomdata.AtomData
 
modelNames - Variable in class org.jmol.modelset.ModelSet
 
modelNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
modelNumberParameter(int) - Method in class org.jmol.script.ScriptParam
 
modelNumbers - Variable in class org.jmol.modelset.ModelSet
 
modelNumbersForAtomLabel - Variable in class org.jmol.modelset.ModelSet
 
modelPanel - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
modelRadius - Variable in class org.jmol.viewer.TransformManager
 
modelRadiusPixels - Variable in class org.jmol.viewer.TransformManager
 
models - Variable in class org.jmol.export._IdtfExporter
 
ModelSet - Class in org.jmol.modelset
 
ModelSet(Viewer, String) - Constructor for class org.jmol.modelset.ModelSet
 
modelSet - Variable in class org.jmol.viewer.ModelManager
 
modelSetFileName - Variable in class org.jmol.popup.JmolGenericPopup
 
modelSetHasVibrationVectors() - Method in class org.jmol.modelset.AtomCollection
 
modelSetInfo - Variable in class org.jmol.popup.JmolGenericPopup
 
modelSetName - Variable in class org.jmol.modelset.ModelSet
 
modelSetName - Variable in class org.jmol.popup.JmolGenericPopup
 
modelSetPathName - Variable in class org.jmol.viewer.ModelManager
 
modelSetProperties - Variable in class org.jmol.modelset.ModelSet
 
modelSetRoot - Variable in class org.jmol.popup.JmolGenericPopup
 
modelSetTypeName - Variable in class org.jmol.modelset.ModelSet
 
modelsOf(BS, BS) - Method in class org.jmol.modelset.ModelSet
 
modelStartEnd - Variable in class org.jmol.adapter.smarter.Structure
 
modelVisibilityFlags - Variable in class org.jmol.shapebio.BioShape
 
modelZeroBased - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
modeMultipleBond - Variable in class org.jmol.render.SticksRenderer
 
modeMultipleBond - Variable in class org.jmol.viewer.GlobalSettings
 
modificationMode - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
modifiers - Variable in class org.jmol.export._IdtfExporter
 
modifiers - Variable in class org.jmol.viewer.MouseState
 
modifiersWhenPressed10 - Variable in class org.jmol.awt.Mouse
 
modifiersWhenPressed10 - Variable in class org.jmol.awtjs2d.Mouse
 
modify - Static variable in class org.jmol.script.T
 
modifyorcreate - Static variable in class org.jmol.script.T
 
modifySend(int, int, int, String) - Method in class org.jmol.viewer.StatusManager
 
modLast - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modMatrices - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modMatrices - Variable in class org.jmol.adapter.readers.cif.Subsystem
 
modo - Static variable in class org.jmol.script.T
 
moDots - Variable in class org.jmol.shapesurface.MolecularOrbital
 
modPack - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
mods - Variable in class org.jmol.util.ModulationSet
 
modScale - Variable in class org.jmol.util.Vibration
 
modSelected - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modt1 - Static variable in class org.jmol.script.T
 
modt2 - Static variable in class org.jmol.script.T
 
modt3 - Static variable in class org.jmol.script.T
 
modTemp - Variable in class org.jmol.util.ModulationSet
 
modTUV - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modType - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modulateAtom(Atom) - Method in class org.jmol.adapter.readers.cif.MSRdr
The displacement will be set as the atom vibration vector; the string buffer will be appended with the t value for a given unit cell.
modulated - Variable in class org.jmol.adapter.readers.cif.CifReader
 
modulating - Variable in class org.jmol.render.MeasuresRenderer
 
modulation - Static variable in class org.jmol.script.T
 
modulation() - Method in class org.jmol.scriptext.CmdExt
Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).
Modulation - Class in org.jmol.util
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals, including Fourier series, Crenel functions, and sawtooth functions
Modulation(char, char, double[], String, double[]) - Constructor for class org.jmol.util.Modulation
Each atomic modulation involves a fractional coordinate wave vector q, a Fourier power n, a modulation axis (x, y, or, z), and specified parameters that depend upon the type of function.
modulationFields - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
modulationOn - Variable in class org.jmol.modelset.ModelLoader
 
modulationscale - Static variable in class org.jmol.script.T
 
modulationScale - Variable in class org.jmol.viewer.GlobalSettings
 
ModulationSet - Class in org.jmol.util
A class to group a set of modulations for an atom as a "vibration" Extends V3 so that it will be a displacement, and its value will be an occupancy
ModulationSet() - Constructor for class org.jmol.util.ModulationSet
 
modulationTUV - Variable in class org.jmol.modelset.ModelLoader
 
MODULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
moduleNestingLevel - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
modVib - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
modx - Static variable in class org.jmol.script.T
 
modxyz - Static variable in class org.jmol.script.T
 
mody - Static variable in class org.jmol.script.T
 
modz - Static variable in class org.jmol.script.T
 
moe_separate_chains - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
MOEnergySorter() - Constructor for class org.jmol.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter
 
moFactor - Variable in class org.jmol.quantum.MOCalculation
 
moFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
moFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
moFill - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moFrontOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
 
MOInfo() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
 
moIsPositiveOnly - Variable in class org.jmol.shapesurface.MolecularOrbital
 
Mol2Reader - Class in org.jmol.adapter.readers.more
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
Mol2Reader() - Constructor for class org.jmol.adapter.readers.more.Mol2Reader
 
mol2Records - Static variable in class org.jmol.adapter.smarter.Resolver
 
Mol3DReader - Class in org.jmol.adapter.readers.molxyz
3D only
Mol3DReader() - Constructor for class org.jmol.adapter.readers.molxyz.Mol3DReader
 
molAtoms - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
moldenFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MoldenReader - Class in org.jmol.adapter.readers.quantum
A molecular structure and orbital reader for MolDen files.
MoldenReader() - Constructor for class org.jmol.adapter.readers.quantum.MoldenReader
 
molecular - Static variable in class org.jmol.script.T
 
MolecularOrbital - Class in org.jmol.shapesurface
 
MolecularOrbital() - Constructor for class org.jmol.shapesurface.MolecularOrbital
 
MolecularOrbitalRenderer - Class in org.jmol.rendersurface
 
MolecularOrbitalRenderer() - Constructor for class org.jmol.rendersurface.MolecularOrbitalRenderer
 
molecularType - Variable in class org.jmol.adapter.readers.cif.CifReader
 
MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
MOLECULE - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
molecule - Static variable in class org.jmol.script.T
 
MOLECULE_ATOM - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_ATOM_SCALAR - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND_ARRAY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_BOND_BUILTIN - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
MOLECULE_FORMULA - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
moleculeCount - Variable in class org.jmol.modelset.BondCollection
 
moleculeCount - Variable in class org.jmol.modelset.Model
 
moleculeIndex - Variable in class org.jmol.util.JmolMolecule
 
moleculeNames - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
moleculeNesting - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
molecules - Variable in class org.jmol.modelset.BondCollection
 
Molecules - Class in org.openscience.jmol.app.webexport
 
Molecules() - Constructor for class org.openscience.jmol.app.webexport.Molecules
 
moleculeXml - Variable in class org.jmol.jvxl.data.JvxlData
 
molHasTLS - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
moLinearCombination - Variable in class org.jmol.shapesurface.Isosurface
 
moLinearCombination - Variable in class org.jmol.shapesurface.MolecularOrbital
 
molName - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
MolReader - Class in org.jmol.adapter.readers.molxyz
A reader for MDLI mol and sdf files.
MolReader() - Constructor for class org.jmol.adapter.readers.molxyz.MolReader
 
molTtypes - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
MOMENT_LABEL - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
MOMENT_PRELIM_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
MOMENT_PRELIM_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
MOMENT_PRELIM_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
MOMENT_X - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
MOMENT_Y - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
MOMENT_Z - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
moMesh - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moModelSet - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
 
moMonteCarloCount - Variable in class org.jmol.shapesurface.MolecularOrbital
 
monitorenergy - Static variable in class org.jmol.script.T
 
monitorEnergy - Variable in class org.jmol.viewer.GlobalSettings
 
MonitorInputStream - Class in org.openscience.jvxl
 
MonitorInputStream(InputStream, int) - Constructor for class org.openscience.jvxl.MonitorInputStream
 
Monomer - Class in org.jmol.modelsetbio
 
Monomer() - Constructor for class org.jmol.modelsetbio.Monomer
 
monomer - Static variable in class org.jmol.script.T
 
monomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
 
monomerCount - Variable in class org.jmol.renderbio.BioShapeRenderer
 
monomerCount - Variable in class org.jmol.shape.AtomShape
 
monomerIndex - Variable in class org.jmol.modelsetbio.Monomer
 
monomerIndexFirst - Variable in class org.jmol.modelsetbio.ProteinStructure
 
monomerIndexLast - Variable in class org.jmol.modelsetbio.ProteinStructure
 
monomers - Variable in class org.jmol.modelsetbio.BioPolymer
 
monomers - Variable in class org.jmol.renderbio.BioShapeRenderer
 
monomers - Variable in class org.jmol.shapebio.BioShape
 
monteCarloCount - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
moNumber - Variable in class org.jmol.shapesurface.Isosurface
 
moNumber - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moOffset(int) - Method in class org.jmol.scriptext.IsoExt
 
mopacArchiveContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MopacArchiveReader - Class in org.jmol.adapter.readers.simple
Mopac Archive reader -- presumes "zMatrix" is really Cartesians use FILTER "NOCENTER" to NOT center atoms in unit cell use CENTROID for complete molecules with centroids within unit cell use PACKED CENTROID for complete molecules with any atoms within unit cell
MopacArchiveReader() - Constructor for class org.jmol.adapter.readers.simple.MopacArchiveReader
 
mopacContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
MopacGraphfReader - Class in org.jmol.adapter.readers.quantum
Reads Mopac 2007 GRAPHF output files
MopacGraphfReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
MopacReader - Class in org.jmol.adapter.readers.simple
Reads Mopac 93, 6, 7, 2002, or 2009 output files
MopacReader() - Constructor for class org.jmol.adapter.readers.simple.MopacReader
 
MopacSlaterReader - Class in org.jmol.adapter.readers.quantum
 
MopacSlaterReader() - Constructor for class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
mopacVersion - Variable in class org.jmol.adapter.readers.simple.MopacReader
 
moPlane - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moRandomSeed - Variable in class org.jmol.shapesurface.MolecularOrbital
 
MOReader - Class in org.jmol.adapter.readers.quantum
General methods for reading molecular orbital data, including embedded output from the NBO program.
MOReader() - Constructor for class org.jmol.adapter.readers.quantum.MOReader
 
moreColors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
moreInfo - Variable in class org.jmol.symmetry.UnitCell
 
moResolution - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moreTokens() - Method in class org.jmol.script.ScriptTokenParser
 
moreUnitCellInfo - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
morph - Static variable in class org.jmol.script.T
 
morph(float) - Method in class org.jmol.viewer.AnimationManager
 
morphCount - Variable in class org.jmol.viewer.AnimationManager
 
morphTrajectories(int, int, float) - Method in class org.jmol.modelset.ModelSet
 
mos - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
mos - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
mosaicPreviewChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Called when the MosaicPreview check box is modified
mosaicPreviewCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
mosaicPreviewComboEnd - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
mosaicPreviewComboStart - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
mosaicPreviewEnd - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
mosaicPreviewStart - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
moScale - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moSlab - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moSlabValue - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moSquareData - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moSquareLinear - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moSymmetry - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
 
motion_bias - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
motion_hand - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
motion_linear - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
motion_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
motion_simple - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
motionDisabled - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
motionEventNumber - Variable in class org.jmol.viewer.Viewer
 
MotionPoint - Class in org.jmol.viewer
 
MotionPoint() - Constructor for class org.jmol.viewer.MotionPoint
 
moTitleFormat - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moTranslucency - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moTranslucentLevel - Variable in class org.jmol.shapesurface.MolecularOrbital
 
moTypes - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
Mouse - Class in org.jmol.awt
formerly org.jmol.viewer.MouseManager14 methods required by Jmol that access java.awt.event private to org.jmol.awt
Mouse(double, PlatformViewer, Object) - Constructor for class org.jmol.awt.Mouse
Mouse is the listener for all events.
Mouse - Class in org.jmol.awtjs2d
JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now) J2SRequireImport is needed because we want to allow JavaScript access to java.awt.Event constant names
Mouse(double, PlatformViewer, Object) - Constructor for class org.jmol.awtjs2d.Mouse
 
mouse - Static variable in class org.jmol.script.T
 
mouse - Variable in class org.jmol.viewer.Viewer
either org.jmol.awt.Mouse or org.jmol.awtjs2d.Mouse
mouse_grid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mouse_limit - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
MOUSE_NONE - Static variable in class org.jmol.viewer.JC
 
mouse_restart_movie_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mouse_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mouse_selection_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mouse_wheel_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mouse_z_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.multitouch.ActionManagerMT
 
mouseAction(int, long, int, int, int, int) - Method in class org.jmol.viewer.ActionManager
 
mouseClicked(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseClicked(long, int, int, int, int) - Method in class org.jmol.awt.Mouse
 
mouseClicked(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseClicked(MouseEvent) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mouseClicked(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseDown - Variable in class org.jmol.multitouch.ActionManagerMT
 
mousedragfactor - Static variable in class org.jmol.script.T
 
mouseDragFactor - Variable in class org.jmol.viewer.ActionManager
 
mouseDragged(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
mouseDragged(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseDragged(long, int, int, int) - Method in class org.jmol.awt.Mouse
 
mouseDragged(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseEntered(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseEntered(long, int, int) - Method in class org.jmol.awt.Mouse
 
mouseEntered(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseEntered(MouseEvent) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mouseEntered(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseEnterExit(long, int, int, boolean) - Method in class org.jmol.viewer.ActionManager
 
mouseExited(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseExited(long, int, int) - Method in class org.jmol.awt.Mouse
 
mouseExited(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseExited(MouseEvent) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mouseExited(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseMode - Variable in class org.jmol.viewer.TransformManager4D
 
mouseMoved(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseMoved(long, int, int, int) - Method in class org.jmol.awt.Mouse
 
mouseMoved(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseMoved(int, int) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
mouseMoved(int, int) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
mousePressed(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
mousePressed(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mousePressed(long, int, int, int, boolean) - Method in class org.jmol.awt.Mouse
 
mousePressed(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mousePressed(MouseEvent) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mousePressed(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseReleased(long, int, int) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
mouseReleased(MouseEvent) - Method in class org.jmol.awt.Mouse
 
mouseReleased(long, int, int, int) - Method in class org.jmol.awt.Mouse
 
mouseReleased(MouseEvent) - Method in class org.jmol.awtjs2d.Mouse
 
mouseReleased(MouseEvent) - Method in class org.jmol.popup.AwtSwingPopupHelper
 
mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mouseReleased(MouseEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
mouseScript(String) - Method in class org.jmol.viewer.JmolStateCreator
 
mouseScript(String) - Method in class org.jmol.viewer.StateCreator
 
MouseState - Class in org.jmol.viewer
 
MouseState(String) - Constructor for class org.jmol.viewer.MouseState
 
mouseWheel(long, int, int) - Method in class org.jmol.awt.Mouse
 
mousewheelfactor - Static variable in class org.jmol.script.T
 
mouseWheelFactor - Variable in class org.jmol.viewer.ActionManager
 
mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awt.Mouse
 
mouseWheelMoved(MouseWheelEvent) - Method in class org.jmol.awtjs2d.Mouse
 
movableX - Variable in class org.jmol.modelset.Object2d
 
movableXPercent - Variable in class org.jmol.modelset.Object2d
 
movableY - Variable in class org.jmol.modelset.Object2d
 
movableYPercent - Variable in class org.jmol.modelset.Object2d
 
movableZ - Variable in class org.jmol.modelset.Object2d
 
movableZPercent - Variable in class org.jmol.modelset.Object2d
 
MOVE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
move - Static variable in class org.jmol.script.T
 
move(JmolScriptEvaluator, V3, float, V3, float, float, int) - Method in class org.jmol.viewer.TransformManager
 
move(JmolScriptEvaluator, V3, float, V3, float, float, int) - Method in class org.jmol.viewer.Viewer
 
move2D(int, int, int) - Method in class org.jmol.shape.Labels
 
move2D(DrawMesh, int[], int, int, int, boolean) - Method in class org.jmol.shapespecial.Draw
 
moveAtoms(M4, M3, M3, V3, BS, P3, boolean, boolean) - Method in class org.jmol.modelset.ModelSet
 
moveAtoms(M4, M3, M3, V3, P3, boolean, BS, boolean) - Method in class org.jmol.viewer.Viewer
 
moveAtomWithHydrogens(int, int, int, int, BS) - Method in class org.jmol.viewer.Viewer
 
moved(long, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
 
moved - Variable in class org.jmol.thread.HoverWatcherThread
 
moved - Variable in class org.jmol.viewer.ActionManager
 
movepict(String) - Method in class org.openscience.jmol.app.webexport.JmolInstance
 
moveRotationCenter(P3, boolean) - Method in class org.jmol.viewer.TransformManager
 
moveSelected(int, int, int, int, int, BS, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
moveto - Static variable in class org.jmol.script.T
 
moveTo(JmolScriptEvaluator, float, P3, T3, float, M3, float, float, float, float, P3, float, float, float, float, float, float) - Method in class org.jmol.viewer.TransformManager
 
moveTo(JmolScriptEvaluator, float, P3, V3, float, M3, float, float, float, float, P3, float, float, float, float, float, float) - Method in class org.jmol.viewer.Viewer
 
MoveToAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.MoveToAction
 
moveToPyMOL(JmolScriptEvaluator, float, float[]) - Method in class org.jmol.viewer.TransformManager
 
moveToText - Variable in class org.jmol.modelset.Orientation
 
MoveToThread - Class in org.jmol.thread
 
MoveToThread() - Constructor for class org.jmol.thread.MoveToThread
 
movetoThread - Variable in class org.jmol.viewer.TransformManager
 
MoveToThread.Slider - Class in org.jmol.thread
 
movetoTime - Variable in class org.openscience.jmol.app.webexport.Test
 
moveUpdate(float) - Method in class org.jmol.viewer.Viewer
 
movie - Static variable in class org.jmol.script.T
 
movie_animate_by_frame - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movie_auto_interpolate - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movie_auto_store - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movie_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movie_fps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movie_loop - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movie_panel - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movie_panel_row_height - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movie_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movie_rock - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
movingSelected - Variable in class org.jmol.viewer.Viewer
 
mp - Variable in class org.jmol.viewer.ActionManager
 
mPending - Variable in class org.jmol.shape.Measures
 
mpr - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
mpts - Variable in class org.jmol.render.MeasuresRenderer
modulation points, which must be refreshed based on phase of the vibration; keyed on atom index.
mr - Variable in class org.jmol.adapter.readers.cif.CifReader
 
mr - Variable in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
mrc - Static variable in class org.jmol.script.T
 
MrcBinaryReader - Class in org.jmol.jvxl.readers
 
MrcBinaryReader() - Constructor for class org.jmol.jvxl.readers.MrcBinaryReader
 
ms - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ms - Variable in class org.jmol.modelset.Measurement
 
ms - Variable in class org.jmol.modelset.MeasurementData
 
ms - Variable in class org.jmol.modelset.Model
 
ms - Variable in class org.jmol.modelset.ModelLoader
 
ms - Variable in class org.jmol.modelsetbio.Resolver
 
ms - Variable in class org.jmol.render.ShapeRenderer
 
ms - Variable in class org.jmol.shape.Shape
 
ms - Variable in class org.jmol.viewer.ShapeManager
 
ms - Variable in class org.jmol.viewer.Viewer
 
MSCifRdr - Class in org.jmol.adapter.readers.cif
 
MSCifRdr() - Constructor for class org.jmol.adapter.readers.cif.MSCifRdr
 
msg - Variable in class org.jmol.jvxl.data.JvxlData
 
msInfo - Variable in class org.jmol.modelset.ModelSet
 
MSInterface - Interface in org.jmol.adapter.smarter
Modulated Structure Reader Interface
msms - Static variable in class org.jmol.script.T
 
MsmsReader - Class in org.jmol.jvxl.readers
 
MsmsReader() - Constructor for class org.jmol.jvxl.readers.MsmsReader
 
MSRdr - Class in org.jmol.adapter.readers.cif
generalized modulated structure reader class for CIF and Jana -- includes Fourier, Crenel, Sawtooth; displacement, occupancy, and Uij -- handles up to 6 modulation wave vectors -- commensurate and incommensurate, including composites -- not handling _cell_commen_t_section_1
MSRdr() - Constructor for class org.jmol.adapter.readers.cif.MSRdr
 
msRdr - Variable in class org.jmol.adapter.readers.cif.Subsystem
 
mTemp - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
mTemp - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
mtlout - Variable in class org.jmol.export._ObjExporter
BufferedWriter for the .mtl file.
mu - Variable in class org.jmol.modelsetbio.Monomer
 
mul - Static variable in class org.jmol.script.T
 
mul3 - Static variable in class org.jmol.script.T
 
mult - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
MULTI_POINT_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JC
 
MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JC
 
MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JC
 
MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JC
 
multiModel - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
multipleBondRadiusFactor - Variable in class org.jmol.render.SticksRenderer
 
multiplebondradiusfactor - Static variable in class org.jmol.script.T
 
multipleBondRadiusFactor - Variable in class org.jmol.viewer.GlobalSettings
 
multipleBondSpacing - Variable in class org.jmol.render.SticksRenderer
 
multiplebondspacing - Static variable in class org.jmol.script.T
 
multipleBondSpacing - Variable in class org.jmol.viewer.GlobalSettings
 
multiplex - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
multiplier - Variable in class org.jmol.navigate.Navigator
 
multiprocessor - Static variable in class org.jmol.script.T
 
multiProcessor - Variable in class org.jmol.viewer.GlobalSettings
 
multiTouch - Variable in class org.jmol.viewer.Viewer
 
multSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
mustBeConnected - Variable in class org.jmol.modelset.MeasurementData
 
mustBeConnected - Variable in class org.jmol.shape.Measures
 
mustFinalizeModelSet - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
mustNotBeConnected - Variable in class org.jmol.modelset.MeasurementData
 
mustNotBeConnected - Variable in class org.jmol.shape.Measures
 
mustRender - Variable in class org.jmol.viewer.Viewer
 
mustResumeEval - Variable in class org.jmol.script.ScriptContext
 
mustResumeEval - Variable in class org.jmol.script.ScriptEval
 
mxyz - Variable in class org.jmol.util.ModulationSet
 
myAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
myAtoms - Variable in class org.jmol.util.ContactPair
 
myAttributes - Variable in class org.jmol.adapter.readers.xml.XmlMagResReader
 
myAttributes - Variable in class org.jmol.adapter.readers.xml.XmlMolproReader
 
myAttributes - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
myAttributes - Variable in class org.jmol.adapter.readers.xml.XmlQEReader
 
myAttributes - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
myBsA - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
myBsB - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
myColorPt - Variable in class org.jmol.shapesurface.LcaoCartoon
 
myColorPt - Variable in class org.jmol.shapesurface.MolecularOrbital
 
myDir - Variable in class org.openscience.chimetojmol.ChimePanel
 
myFps - Variable in class org.jmol.thread.SpinThread
 
myIndex - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
myLabels - Variable in class org.jmol.symmetry.SymmetryOperation
 
myMask - Variable in class org.jmol.shape.Sticks
 
myName - Variable in class org.jmol.script.SV
 
myName - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
mySlabValue - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
myStatusListener - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
myType - Variable in class org.jmol.shape.FontShape
 
myType - Variable in class org.jmol.shape.MeshCollection
 
MyUndoableEditListener() - Constructor for class org.jmol.console.ScriptEditor.EditorDocument.MyUndoableEditListener
 
myVisibilityFlag - Static variable in class org.jmol.modelset.Bond
 
myVisibilityFlag - Variable in class org.jmol.render.ShapeRenderer
 
myX - Variable in class org.jmol.quantum.QMAtom
 
myX2 - Variable in class org.jmol.quantum.QMAtom
 
myY - Variable in class org.jmol.quantum.QMAtom
 
myY2 - Variable in class org.jmol.quantum.QMAtom
 
myZ - Variable in class org.jmol.quantum.QMAtom
 
myZ2 - Variable in class org.jmol.quantum.QMAtom
 

N

n - Variable in class org.jmol.jvxl.data.MeshData.SSet
 
N - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
n(int, int) - Static method in class org.jmol.script.T
 
N1 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N3 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N7 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
N9 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
na - Variable in class org.jmol.jvxl.readers.MapFileReader
 
na - Variable in class org.jmol.util.SimpleUnitCell
 
nada - Static variable in class org.jmol.script.T
 
nAltLocs - Variable in class org.jmol.modelset.Model
 
name - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
name - Variable in class org.jmol.adapter.readers.xml.XmlVaspReader
 
name - Variable in class org.jmol.awtjs2d.JSFile
 
name - Variable in enum org.jmol.c.PAL
 
name - Variable in enum org.jmol.c.STER
 
name - Variable in class org.jmol.export._MayaExporter
 
name - Variable in class org.jmol.minimize.forcefield.ForceField
 
name - Variable in class org.jmol.script.ScriptFunction
 
name - Static variable in class org.jmol.script.T
 
name - Variable in enum org.jmol.shapespecial.Draw.EnumDrawType
 
name - Variable in class org.jmol.symmetry.PointGroup
 
name - Variable in class org.jmol.symmetry.SpaceGroup
 
name - Variable in class org.jmol.symmetry.UnitCell
 
name - Variable in class org.jmol.thread.JmolThread
 
name - Variable in enum org.jmol.util.Edge.EnumBondOrder
 
name - Variable in class org.jmol.viewer.binding.Binding
 
name - Variable in class org.jmol.viewer.MouseState
 
name - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
name - Variable in class org.openscience.jmol.app.webexport.Widgets.Widget
 
name0 - Variable in class org.jmol.script.ContextToken
 
NAME_HALL - Static variable in class org.jmol.symmetry.SpaceGroup
 
NAME_HM - Static variable in class org.jmol.symmetry.SpaceGroup
 
nameAsGiven - Variable in class org.jmol.viewer.FileManager
 
nameAsGivenIn - Variable in class org.jmol.io.FileReader
 
namedSets - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
 
nameList - Static variable in enum org.jmol.c.CBK
 
nameOf(int) - Static method in class org.jmol.script.T
note: nameOf is a very inefficient mechanism for getting the name of a token.
nameRequired - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
names - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
names - Variable in class org.jmol.script.ScriptFunction
 
namesAsGivenIn - Variable in class org.jmol.io.FilesReader
 
naNoH - Static variable in class org.jmol.modelsetbio.Resolver
 
nativeLanguage - Variable in class org.jmol.i18n.Language
 
nAtom - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
 
nAtoms - Variable in class org.jmol.adapter.readers.cif.CifReader
 
nAtoms - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
nAtoms - Variable in class org.jmol.adapter.readers.more.MdTopReader
 
nAtoms - Variable in class org.jmol.adapter.readers.more.Mol2Reader
 
nAtoms - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
nAtoms - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
 
nAtoms - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
nAtoms - Variable in class org.jmol.symmetry.PointGroup
 
nAtoms0 - Variable in class org.jmol.adapter.readers.cif.CifReader
 
nAtomsOr - Variable in class org.jmol.smiles.SmilesAtom
 
naturalIsotopeMasses - Static variable in class org.jmol.util.Elements
 
naturalIsotopes - Static variable in class org.jmol.util.Elements
 
nav - Variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_IGNORE - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_NEWXY - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_NEWXYZ - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_NEWZ - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_NONE - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_RESET - Static variable in class org.jmol.viewer.TransformManager
 
NAV_MODE_ZOOMED - Static variable in class org.jmol.viewer.TransformManager
 
navCenter - Variable in class org.jmol.modelset.Orientation
 
navCenter - Variable in class org.jmol.thread.MoveToThread
 
navDepth - Variable in class org.jmol.modelset.Orientation
 
navDepth - Variable in class org.jmol.thread.MoveToThread
 
navfps - Static variable in class org.jmol.script.T
 
navFps - Variable in class org.jmol.viewer.TransformManager
 
navigate(float, P3[][], P3[], float[], int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navigate(float, P3[][], P3[], float[], int, int) - Method in class org.jmol.navigate.Navigator
 
navigate - Static variable in class org.jmol.script.T
 
navigate() - Method in class org.jmol.scriptext.CmdExt
 
navigate(int, int) - Method in class org.jmol.viewer.Viewer
 
navigateAxis(V3, float) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navigateAxis(V3, float) - Method in class org.jmol.navigate.Navigator
 
navigateAxis(V3, float) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
navigateAxis(V3, float) - Method in class org.jmol.viewer.Viewer
 
navigateKey(int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navigateKey(int, int) - Method in class org.jmol.navigate.Navigator
 
navigateKey(int, int) - Method in class org.jmol.viewer.TransformManager
entry point for keyboard-based navigation
navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.navigate.Navigator
 
navigateList(JmolScriptEvaluator, Lst<Object[]>) - Method in class org.jmol.viewer.TransformManager
 
navigatePt(P3) - Method in class org.jmol.viewer.Viewer
 
navigatesurface - Static variable in class org.jmol.script.T
 
navigateTo(float, V3, float, P3, float, float, float) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navigateTo(float, V3, float, P3, float, float, float) - Method in class org.jmol.navigate.Navigator
 
navigating - Variable in class org.jmol.viewer.TransformManager
 
navigationCenter - Variable in class org.jmol.viewer.TransformManager
 
navigationdepth - Static variable in class org.jmol.script.T
 
navigationDepthPercent - Variable in class org.jmol.viewer.TransformManager
 
navigationList - Variable in class org.jmol.navigate.Navigator
 
navigationMode - Variable in class org.jmol.modelset.Orientation
 
navigationmode - Static variable in class org.jmol.script.T
 
navigationMode - Variable in class org.jmol.viewer.GlobalSettings
 
navigationOffset - Variable in class org.jmol.viewer.TransformManager
 
navigationperiodic - Static variable in class org.jmol.script.T
 
navigationPeriodic - Variable in class org.jmol.viewer.GlobalSettings
 
navigationShiftXY - Variable in class org.jmol.viewer.TransformManager
 
navigationslab - Static variable in class org.jmol.script.T
 
navigationSlabOffset - Variable in class org.jmol.viewer.TransformManager
 
navigationspeed - Static variable in class org.jmol.script.T
 
navigationSpeed - Variable in class org.jmol.viewer.GlobalSettings
 
Navigator - Class in org.jmol.navigate
Navigator is a user input mechanism that utilizes the keypad to drive through the model.
Navigator() - Constructor for class org.jmol.navigate.Navigator
 
navInterrupt() - Method in class org.jmol.viewer.TransformManager
 
navMinMax - Variable in class org.jmol.viewer.ShapeManager
 
navMode - Variable in class org.jmol.viewer.TransformManager
 
navOn - Variable in class org.jmol.viewer.TransformManager
 
navTranslatePercent(float, float) - Method in class org.jmol.viewer.Viewer
 
navTranslatePercentOrTo(float, float, float) - Method in interface org.jmol.api.JmolNavigatorInterface
 
navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.navigate.Navigator
 
navTranslatePercentOrTo(float, float, float) - Method in class org.jmol.viewer.TransformManager
seconds < 0 means "to (x,y)"; >= 0 mean "to (x%, y%)"
navx - Static variable in class org.jmol.script.T
 
navX - Variable in class org.jmol.viewer.TransformManager
 
navy - Static variable in class org.jmol.script.T
 
NAVY - Static variable in class org.jmol.util.C
 
navY - Variable in class org.jmol.viewer.TransformManager
 
navz - Static variable in class org.jmol.script.T
 
navZ - Variable in class org.jmol.viewer.TransformManager
 
nAxes - Variable in class org.jmol.symmetry.PointGroup
 
nb - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nb - Variable in class org.jmol.util.SimpleUnitCell
 
nb_spheres_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
nb_spheres_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
nb_spheres_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
nBackbonesDisplayed - Variable in class org.jmol.modelset.Atom
 
nBalls - Variable in class org.jmol.export._MayaExporter
 
nBasis - Variable in class org.jmol.adapter.readers.quantum.QchemReader
 
nBasisFunctions - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
nBF - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
nBits - Variable in class org.jmol.g3d.LineRenderer
 
nBlock - Variable in class org.jmol.jvxl.readers.XplorReader
 
nbo - Static variable in class org.jmol.script.T
 
NBO - Class in org.jmol.shapesurface
 
NBO() - Constructor for class org.jmol.shapesurface.NBO
 
nboAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
NBOAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NBOAction
 
nboDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
NBODialog - Class in org.openscience.jmol.app.jmolpanel
A dialog for interacting with NBO-Server (experimental)
NBODialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.NBODialog
Creates a dialog for getting info related to output frames in nbo format.
nBonds - Variable in class org.jmol.minimize.MinAtom
 
nBondsDisplayed - Variable in class org.jmol.modelset.Atom
 
nBondsOr - Variable in class org.jmol.smiles.SmilesBond
 
nboPathButton - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
NBORenderer - Class in org.jmol.rendersurface
 
NBORenderer() - Constructor for class org.jmol.rendersurface.NBORenderer
 
nboType - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
nboType - Variable in class org.jmol.shapesurface.MolecularOrbital
 
nBrickX - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
nBrickY - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
nBytes - Variable in class org.jmol.jvxl.data.JvxlData
 
nBytes - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nc - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nc - Variable in class org.jmol.util.SimpleUnitCell
 
nCharNewLine(int) - Method in class org.jmol.script.ScriptCompiler
Check for line ending at this point in script.
nci - Static variable in class org.jmol.script.T
 
NciCalculation - Class in org.jmol.quantum
 
NciCalculation() - Constructor for class org.jmol.quantum.NciCalculation
 
nCoef - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
nCoefficients - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
nContourMax - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
nContourMax - Static variable in class org.jmol.jvxl.readers.Parameters
 
nContours - Variable in class org.jmol.jvxl.data.JvxlData
 
nContours - Variable in class org.jmol.jvxl.readers.Parameters
 
nContourSegments - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
nCyl - Variable in class org.jmol.export._MayaExporter
 
nData - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nDataPoints - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nDegrees - Variable in class org.jmol.thread.SpinThread
 
NDIM - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
ndim() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
nDir - Variable in class org.openscience.chimetojmol.ChimePanel
 
nDots - Variable in class org.jmol.jvxl.readers.KinemageReader
 
ndots - Static variable in class org.jmol.render.FontLineShapeRenderer
 
ne - Variable in class org.jmol.adapter.readers.quantum.QchemReader.MOInfo
 
nearbyAtomCount - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
nEdges - Variable in class org.jmol.jvxl.data.JvxlData
 
needAromatic - Variable in class org.jmol.smiles.SmilesSearch
 
needRightParen - Variable in class org.jmol.script.ScriptCompiler
 
needRingData - Variable in class org.jmol.smiles.SmilesSearch
 
needRingMemberships - Variable in class org.jmol.smiles.SmilesSearch
 
needSelections() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
needToCompleteInitialization - Variable in class org.jmol.applet.AppletWrapper
 
needToFill - Variable in class org.jmol.g3d.HermiteRenderer
 
needTranslucent - Variable in class org.jmol.render.MeshRenderer
 
negativeAtomCount - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
negCorner - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
neighbor_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
neighborCenters - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborCount - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborIndices - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborPlusProbeRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborRadii2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
neighborVertexesArrays - Static variable in class org.jmol.util.Geodesic
 
neighborVertexesArrays - Static variable in class org.jmol.util.Normix
 
neighborVertexesIcosahedron - Static variable in class org.jmol.util.Geodesic
 
nElements - Variable in class org.jmol.util.JmolMolecule
 
nError - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
nestedBond - Variable in class org.jmol.smiles.SmilesSearch
 
newA(float[], boolean) - Static method in class org.jmol.symmetry.UnitCell
 
newA(float[]) - Static method in class org.jmol.util.SimpleUnitCell
 
newAction(int, String, String) - Static method in class org.jmol.viewer.ActionManager
 
newAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
NewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
NewAction(String) - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
newAndSetBit(int) - Static method in class org.jmol.util.BSUtil
 
newAntialiasing - Variable in class org.jmol.util.GData
 
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
newAtomSet(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
newAtomSet() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
newAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newAtomSet(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
newAtomSetClear(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newBinaryDocument() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
newBinding(Viewer, String) - Static method in class org.jmol.viewer.binding.Binding
 
newBitSet2(int, int) - Static method in class org.jmol.util.BSUtil
 
newBS(BS, int[]) - Static method in class org.jmol.modelset.BondSet
 
newBufferedImage(Object, int, int) - Static method in class org.jmol.awt.Image
 
newBufferedImage(int, int) - Static method in class org.jmol.awt.Image
 
newBufferedImage(Object, int, int) - Method in class org.jmol.awt.Platform
 
newBufferedImage(Object, int, int) - Static method in class org.jmol.awtjs.Image
 
newBufferedImage(int, int) - Static method in class org.jmol.awtjs.Image
 
newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs.Platform
 
newBufferedImage(Object, int, int) - Method in class org.jmol.awtjs2d.Platform
 
newChain - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
newCloneAtom(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
newCmd(int, Object) - Static method in class org.jmol.script.ContextToken
 
newContext(boolean) - Static method in class org.jmol.script.ContextToken
 
newContextVariable(String) - Method in class org.jmol.script.ScriptCompiler
 
newDataReader(Viewer, Object) - Static method in class org.jmol.viewer.FileManager
 
newEcho(Viewer, Font, String, short, int, int, float) - Static method in class org.jmol.modelset.Text
 
newFile(String) - Method in class org.jmol.awt.Platform
 
newFile(String) - Static method in class org.jmol.awtjs2d.JSFile
 
newFile(String) - Method in class org.jmol.awtjs2d.Platform
 
newFilesReader(String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.FileManager
 
newFont(String, boolean, boolean, float) - Static method in class org.jmol.awt.AwtFont
 
newFont(String, boolean, boolean, float) - Method in class org.jmol.awt.Platform
 
newFont(String, boolean, boolean, float) - Static method in class org.jmol.awtjs.JSFont
 
newFont(String, boolean, boolean, float) - Method in class org.jmol.awtjs.Platform
 
newFont(String, boolean, boolean, float, String) - Static method in class org.jmol.awtjs2d.JSFont
 
newFont(String, boolean, boolean, float) - Method in class org.jmol.awtjs2d.Platform
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in interface org.jmol.api.GenericGraphics
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awt.AwtG2D
 
newGrayScaleImage(Object, Object, int, int, int[]) - Method in class org.jmol.awtjs2d.JsG2D
 
newI(int) - Static method in class org.jmol.script.SV
 
newI(int) - Static method in class org.jmol.util.Rgb16
 
newJButton(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJCheckBox(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJCheckBoxMenuItem(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJMenu(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newJRadioButtonMenuItem(String) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
newLabel(Viewer, Font, String, short, short, int, float, float[]) - Static method in class org.jmol.modelset.Text
 
newLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
newList(String) - Method in class org.jmol.dssx.AnnotationParser
 
newMeasurementData(String, Lst<Object>) - Method in class org.jmol.viewer.Viewer
 
newMenuItem(SC, SC, String, String, String) - Method in class org.jmol.popup.GenericSwingPopup
 
newMesh(boolean, T3[], int, int[][], T3[], int) - Static method in class org.jmol.util.MeshSurface
 
newModel(int) - Method in class org.jmol.adapter.readers.cif.CifReader
 
newN(int) - Static method in class org.jmol.java.BS
Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range 0 through nbits-1.
newNavigationCenter() - Method in class org.jmol.navigate.Navigator
We do not want the fixed navigation offset to change, but we need a new model-based equivalent position.
newOffScreenImage(int, int) - Method in class org.jmol.awt.Platform
 
newOffScreenImage(int, int) - Method in class org.jmol.awtjs.Platform
 
newOffScreenImage(int, int) - Method in class org.jmol.awtjs2d.Platform
 
newP(T3[], boolean) - Static method in class org.jmol.symmetry.UnitCell
 
newPoint(int, P3, P3, int, int, int) - Method in class org.jmol.symmetry.SpaceGroup
 
newPoint(P3, P3, int, int, int) - Method in class org.jmol.symmetry.SymmetryOperation
 
newReader(String) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
newReaderBr(String, BufferedReader) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
newRegion(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
Add a new region to the list of regions.
newS(String) - Static method in class org.jmol.script.SV
 
newScale - Variable in class org.jmol.shapespecial.Draw
 
newScriptEvaluator() - Method in class org.jmol.script.ScriptManager
 
newScriptParallelProcessor(String, int) - Static method in class org.jmol.script.ScriptCompiler
 
newSet() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
newSg() - Method in class org.jmol.shapesurface.Isosurface
 
newSlider(float, float) - Method in class org.jmol.thread.MoveToThread
 
newSpaceGroupPoint(int, P3, P3, int, int, int) - Method in interface org.jmol.api.SymmetryInterface
 
newSpaceGroupPoint(int, P3, P3, int, int, int) - Method in class org.jmol.symmetry.Symmetry
 
newSurface(int, ContactPair, BS, BS, RadiusData, float[], Object, boolean, VolumeData, float) - Method in class org.jmol.shapesurface.Contact
 
newSV(int, int, Object) - Static method in class org.jmol.script.SV
 
newT(T) - Static method in class org.jmol.script.SV
 
newTensorType(V3[], float[], String, String) - Method in class org.jmol.util.Tensor
common processing of eigenvectors.
newTextLabel(String, float[], int, int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
newV(int, Object) - Static method in class org.jmol.script.SV
 
newVertex(P3, V3, float) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
newVertexBitSet() - Static method in class org.jmol.util.Normix
 
newVoxelDataCube() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
newwinAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
NewwinAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.NewwinAction
 
newWindowHeight - Variable in class org.jmol.util.GData
 
newWindowWidth - Variable in class org.jmol.util.GData
 
next - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
next() - Method in interface org.jmol.api.AtomIndexIterator
 
next - Variable in class org.jmol.dssx.AnnotationParser
 
next - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
next() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
next() - Method in interface org.jmol.modelset.BondIterator
 
next() - Method in class org.jmol.modelset.BondIteratorSelected
 
next - Static variable in class org.jmol.script.T
 
next - Variable in class org.jmol.util.Int2IntHashEntry
 
next - Variable in class org.jmol.util.MeshCapper.CapVertex
 
NEXT - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
nextAtomSet() - Method in class org.jmol.adapter.readers.cif.CifReader
 
nextClearBit(int) - Method in class org.jmol.java.BS
Returns the index of the first bit that is set to false that occurs on or after the specified starting index.
nextCommand - Variable in class org.jmol.util.CommandHistory
Position of the next command.
nextElement() - Method in class org.jmol.bspt.CubeIterator
normal iterator method
nextFileName(String, int) - Method in class org.jmol.console.GenericConsole
 
nextFileName(String, int) - Method in class org.jmol.console.JmolConsole
 
nextFileName(String, int) - Method in class org.jmol.consolejs.AppletConsole
 
nextIndex() - Method in interface org.jmol.modelset.BondIterator
 
nextIndex() - Method in class org.jmol.modelset.BondIteratorSelected
 
nextList(int, P3) - Method in class org.jmol.navigate.Navigator
 
nextMeasure(int, int, Measurement, int) - Method in class org.jmol.modelset.MeasurementData
iterator for measurements
nextRandom8Bit() - Method in class org.jmol.util.Shader
Implements RANDU algorithm for random noise in lighting/shading.
nextSetBit(int) - Method in class org.jmol.java.BS
Returns the index of the first bit that is set to true that occurs on or after the specified starting index.
nextToken() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
 
nextToken() - Method in class org.jmol.jvxl.readers.PmeshReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.MrcBinaryReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.UhbdReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.VaspChgcarReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
nextVoxel() - Method in class org.jmol.jvxl.readers.XplorReader
 
nFaces - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
nFast - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
NffReader - Class in org.jmol.jvxl.readers
 
NffReader() - Constructor for class org.jmol.jvxl.readers.NffReader
 
nFilePoints - Variable in class org.jmol.jvxl.readers.CastepDensityReader
 
nFiles - Variable in class org.openscience.chimetojmol.ChimePanel
 
nFiltered - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
nFrankList - Variable in class org.jmol.popup.JmolGenericPopup
 
nFree - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
nGaussians - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
nGaussians - Variable in class org.jmol.quantum.MOCalculation
 
nhChecked - Variable in class org.jmol.modelsetbio.AminoMonomer
 
nHits - Variable in class org.jmol.navigate.Navigator
 
nihResolverFormat - Variable in class org.jmol.viewer.GlobalSettings
 
nImage - Variable in class org.jmol.export.___Exporter
 
nIn - Variable in class org.jmol.util.Shader
 
nInsertions - Variable in class org.jmol.modelset.Model
 
nInvalid - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
nioClosed(JsonNioServer) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
nioClosed(JsonNioServer) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
 
nioRunContent(JsonNioServer) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
nioRunContent(JsonNioServer) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
 
nitrogenHydrogenPoint - Variable in class org.jmol.modelsetbio.AlphaMonomer
 
nLatticeTypes - Static variable in class org.jmol.symmetry.HallTranslation
 
nLatticeVectors - Variable in class org.jmol.adapter.readers.xtal.AimsReader
 
nLCAO - Variable in class org.jmol.shapesurface.Isosurface
 
nList - Variable in class org.jmol.shapecgo.CGOMesh
 
nMatrixElements - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
nModels - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
nModels - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
nMolecular - Variable in class org.jmol.adapter.readers.cif.CifReader
 
nMolecules - Variable in class org.jmol.quantum.NciCalculation
 
nmr - Static variable in class org.jmol.script.T
 
NMR_DC - Static variable in class org.jmol.modelset.Measurement
 
NMR_JC - Static variable in class org.jmol.modelset.Measurement
 
NMR_NOT - Static variable in class org.jmol.modelset.Measurement
 
NMRCalculation - Class in org.jmol.quantum
 
NMRCalculation() - Constructor for class org.jmol.quantum.NMRCalculation
 
nmrCalculation - Variable in class org.jmol.viewer.Viewer
 
nmrpredictformat - Static variable in class org.jmol.script.T
 
nmrPredictFormat - Variable in class org.jmol.viewer.GlobalSettings
 
nmrType(String) - Static method in class org.jmol.modelset.Measurement
 
nmrurlformat - Static variable in class org.jmol.script.T
 
nmrUrlFormat - Variable in class org.jmol.viewer.GlobalSettings
 
nMtlBytes - Variable in class org.jmol.export._ObjExporter
Bytes written to the .mtl file.
nNested - Variable in class org.jmol.smiles.SmilesSearch
 
NO_ANISOTROPY - Static variable in class org.jmol.jvxl.readers.Parameters
 
no_idle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
NO_VALUE - Static variable in class org.jmol.quantum.NciCalculation
 
noArgs - Static variable in class org.jmol.script.T
 
noAromatic - Variable in class org.jmol.smiles.SmilesSearch
 
noAtoms - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
 
noAutoBond - Variable in class org.jmol.modelset.ModelLoader
 
NOBASIS_LIST - Static variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
noBondSym - Variable in class org.jmol.adapter.readers.xtal.CgdReader
 
nocontourlines - Static variable in class org.jmol.script.T
 
noCopy(int, int) - Method in class org.jmol.script.ScriptExpr
 
noCross - Variable in class org.jmol.renderspecial.DipolesRenderer
 
nocross - Static variable in class org.jmol.script.T
 
noCross - Variable in class org.jmol.shapespecial.Dipole
 
Node - Class in org.jmol.bspt
Nodes of the bspt.
Node(Bspt, int, Leaf) - Constructor for class org.jmol.bspt.Node
 
Node - Interface in org.jmol.util
 
nodebug - Static variable in class org.jmol.script.T
 
nodes - Variable in class org.jmol.util.JmolMolecule
 
nodes - Variable in class org.jmol.viewer.Gesture
 
nodots - Static variable in class org.jmol.script.T
 
noedges - Static variable in class org.jmol.script.T
 
noFaceSpheres - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
nofill - Static variable in class org.jmol.script.T
 
noGraphicsAllowed - Variable in class org.jmol.viewer.Viewer
 
nohead - Static variable in class org.jmol.script.T
 
noHead - Variable in class org.jmol.shapespecial.Draw
 
noHead - Variable in class org.jmol.shapespecial.DrawMesh
 
NOHISTORYATALL_FLAG - Static variable in class org.jmol.util.CommandHistory
 
NOHISTORYLINE_FLAG - Static variable in class org.jmol.util.CommandHistory
 
noload - Static variable in class org.jmol.script.T
 
nomesh - Static variable in class org.jmol.script.T
 
nonbonded_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
nonbonded_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
nonbonded_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
nonbonded_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
nonbondedSize - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
nonbondedTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
NONE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
NONE - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
NONE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
none - Static variable in class org.jmol.script.T
 
nonequivalent - Static variable in class org.jmol.script.T
 
noneSelected - Variable in class org.jmol.viewer.SelectionManager
 
nonhydrogenDegree - Variable in class org.jmol.smiles.SmilesAtom
 
NONPOLY_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
NONPOLY_ENTITY_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
NONPOLY_NAME - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
nonpolyFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
noplane - Static variable in class org.jmol.script.T
 
nOps - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
nOps - Variable in class org.jmol.symmetry.PointGroup
 
nOrbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
nOrbitals0 - Variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
norm - Variable in class org.jmol.renderbio.BioShapeRenderer
 
norm - Variable in class org.jmol.util.MeshSlicer
 
normal - Static variable in class org.jmol.script.T
 
NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
 
NORMAL_MODE - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
normal_workaround - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
normalCount - Variable in class org.jmol.util.MeshSurface
 
normalize_ccp4_maps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
normalize_grd_maps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
normalize_o_maps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
normalizeShell(int) - Method in class org.jmol.quantum.MOCalculation
 
normalizeTranslation(M4) - Static method in class org.jmol.symmetry.SymmetryOperation
 
normalizeTwelfths(float, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
normalizeUV - Variable in class org.jmol.export._ObjExporter
Whether to normalize UV texture coordinates.
normalOrAxis - Variable in class org.jmol.symmetry.PointGroup.Operation
 
normals - Variable in class org.jmol.util.MeshSurface
 
normalsTemp - Variable in class org.jmol.util.MeshSurface
 
normAnglePanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
normDispl - Variable in class org.jmol.adapter.readers.xtal.BilbaoReader
 
normix - Variable in class org.jmol.rendercgo.CGORenderer
 
Normix - Class in org.jmol.util
Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
Normix() - Constructor for class org.jmol.util.Normix
 
normix0 - Variable in class org.jmol.rendercgo.CGORenderer
 
normix1 - Variable in class org.jmol.rendercgo.CGORenderer
 
normix2 - Variable in class org.jmol.rendercgo.CGORenderer
 
NORMIX_GEODESIC_LEVEL - Static variable in class org.jmol.util.Normix
 
NORMIX_NULL - Static variable in class org.jmol.util.Normix
 
normixCount - Static variable in class org.jmol.util.GData
 
normixCount - Variable in class org.jmol.util.MeshSurface
 
normixCount - Static variable in class org.jmol.util.Normix
 
normixes - Variable in class org.jmol.render.MeshRenderer
 
normixes - Variable in class org.jmol.shape.Mesh
 
normixes - Variable in class org.jmol.shapespecial.Polyhedron
 
normixesT - Variable in class org.jmol.shapespecial.Polyhedra
 
norml - Variable in class org.jmol.renderbio.BioShapeRenderer
 
noSymmetryCount - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
not - Variable in class org.jmol.smiles.SmilesAtom
 
notBondedIndex - Variable in class org.jmol.smiles.SmilesAtom
 
notCrossLinked - Variable in class org.jmol.smiles.SmilesAtom
 
note - Variable in class org.jmol.modelset.MeasurementData
 
NOTE_SCRIPT_FILE - Static variable in class org.jmol.viewer.JC
 
notfrontonly - Static variable in class org.jmol.script.T
 
notHelixOrSheet(int) - Method in class org.jmol.modelsetbio.Sheet
 
notifyAtomPicked(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyCallback(CBK, Object[]) - Method in interface org.jmol.api.JmolCallbackListener
 
notifyCallback(CBK, Object[]) - Method in class org.jmol.console.GenericConsole
 
notifyCallback(CBK, Object[]) - Method in class org.jmol.util.GenericApplet
 
notifyCallback(CBK, Object[]) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyContext(ScriptContext, Object[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
notifyContext(ScriptContext, Object[]) - Method in class org.jmol.console.ScriptEditor
 
notifyEnabled(CBK) - Method in interface org.jmol.api.JmolCallbackListener
 
notifyEnabled(CBK) - Method in class org.jmol.console.GenericConsole
 
notifyEnabled(CBK) - Method in class org.jmol.util.GenericApplet
 
notifyEnabled(CBK) - Method in class org.jmol.viewer.StatusManager
 
notifyEnabled(CBK) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyEndOfRendering() - Method in class org.jmol.awt.Platform
 
notifyEndOfRendering() - Method in class org.jmol.awtjs2d.Platform
 
notifyEndOfRendering() - Method in class org.jmol.g3d.Platform3D
 
notifyError(String, String, String) - Method in class org.jmol.viewer.StatusManager
 
notifyError(String, String, String) - Method in class org.jmol.viewer.Viewer
 
notifyFileLoaded(String, String, String, String, Boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifyFileOpen(String, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
notifyFileOpen(String) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
" (*)" appended to a file name indicates that this file was loaded asynchronously
notifyMinimizationStatus(String, Integer, Float, Float, String) - Method in class org.jmol.viewer.StatusManager
 
notifyMinimizationStatus() - Method in class org.jmol.viewer.Viewer
 
notifyMouseClicked(int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
notifyResumeStatus() - Method in interface org.jmol.api.JmolScriptEvaluator
 
notifyResumeStatus() - Method in class org.jmol.script.ScriptEval
 
notifyScriptStart() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
notifyScriptStart() - Method in class org.jmol.console.ScriptEditor
 
notifyScriptTermination() - Method in interface org.jmol.api.JmolScriptEditorInterface
 
notifyScriptTermination() - Method in class org.jmol.console.ScriptEditor
 
notifyStatusReady(boolean) - Method in class org.jmol.api.JmolViewer
 
notifyStatusReady(boolean) - Method in class org.jmol.viewer.Viewer
 
notifyStructureModified(int, int, int) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
notifySurfaceGenerationCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
notifySurfaceGenerationCompleted() - Method in class org.jmol.shapesurface.Isosurface
 
notifySurfaceMappingCompleted() - Method in interface org.jmol.jvxl.api.MeshDataServer
 
notifySurfaceMappingCompleted() - Method in class org.jmol.shapesurface.Isosurface
 
notifySync(String, String) - Method in class org.jmol.util.GenericApplet
 
notifyViewerRepaintDone() - Method in class org.jmol.api.JmolViewer
 
notifyViewerRepaintDone() - Method in class org.jmol.viewer.Viewer
 
notInCentroid(ModelSet, BS, int[]) - Method in interface org.jmol.api.SymmetryInterface
 
notInCentroid(ModelSet, BS, int[]) - Method in class org.jmol.symmetry.Symmetry
 
notionalUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
notionalUnitCell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
notionalUnitcell - Variable in class org.jmol.util.SimpleUnitCell
 
notionalUnitcellTags - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
NotPDB - Variable in class org.jmol.popup.JmolGenericPopup
 
notriangles - Static variable in class org.jmol.script.T
 
nOut - Variable in class org.jmol.util.Shader
 
noValuesAtAll - Variable in class org.jmol.quantum.NciCalculation
 
now - Static variable in class org.jmol.script.T
 
noZapped - Variable in class org.jmol.popup.JmolGenericPopup
 
NP - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
nPairs - Variable in class org.jmol.smiles.SmilesGenerator
 
nParameters - Variable in class org.jmol.script.ScriptFunction
 
nPeaks - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
nPoints - Variable in class org.jmol.jvxl.data.VolumeData
 
nPoints - Variable in class org.jmol.shapespecial.Draw
 
nPoints - Variable in class org.jmol.smiles.SmilesMeasure
 
nPointsX - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsX - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nPointsY - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsY - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nPointsZ - Variable in class org.jmol.jvxl.data.JvxlData
 
nPointsZ - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
nPolygons - Variable in class org.jmol.jvxl.readers.NffReader
 
nPolygons - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
 
nPolygons - Variable in class org.jmol.jvxl.readers.PmeshReader
 
npqd - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
nPrimitives - Variable in class org.jmol.smiles.SmilesAtom
 
nPrimitives - Variable in class org.jmol.smiles.SmilesBond
 
nProcessors - Static variable in class org.jmol.viewer.Viewer
 
nRead - Variable in class org.jmol.jvxl.readers.XplorReader
 
nRegions - Variable in class org.jmol.util.MeshCapper
informational only
nRes - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
nRes - Variable in class org.jmol.modelsetbio.ProteinStructure
 
nRotations - Variable in class org.jmol.symmetry.HallInfo
 
nSemiSkip - Variable in class org.jmol.script.ScriptCompiler
 
nSets - Variable in class org.jmol.util.MeshSurface
 
nSFO - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
nSkip - Variable in class org.jmol.jvxl.readers.CastepDensityReader
 
nSkipX - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nSkipY - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nSkipZ - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nSlaters - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
nSPDF - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
nSurfaceAtoms - Variable in class org.jmol.modelset.AtomCollection
 
nSurfaceInts - Variable in class org.jmol.jvxl.data.JvxlData
 
nSurfaces - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
nTab - Variable in class org.jmol.console.GenericConsole
 
nTest - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
nText - Variable in class org.jmol.export.___Exporter
 
nTokens - Variable in class org.jmol.script.ScriptTokenParser
 
nTriangles - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
nTriangles - Variable in class org.jmol.jvxl.readers.PolygonFileReader
 
nTriangles - Variable in class org.jmol.util.MeshCapper
informational only
nTries - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
nType - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
 
nuclearCharges - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
nucleic - Static variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
nucleic - Static variable in class org.jmol.script.T
 
NucleicMonomer - Class in org.jmol.modelsetbio
 
NucleicMonomer() - Constructor for class org.jmol.modelsetbio.NucleicMonomer
 
NucleicPolymer - Class in org.jmol.modelsetbio
 
NucleicPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.NucleicPolymer
 
nucleicRenderer - Variable in class org.jmol.renderbio.CartoonRenderer
 
NucleicRenderer - Class in org.jmol.renderbio
extends CartoonRenderer for nucleics
NucleicRenderer() - Constructor for class org.jmol.renderbio.NucleicRenderer
 
nucleus - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
nullGroup - Variable in class org.jmol.modelset.ModelLoader
 
nullModelSetName - Variable in class org.jmol.popup.JmolGenericPopup
 
nullObj - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
nullShadeIndex - Static variable in class org.jmol.g3d.Graphics3D
 
nullToken - Static variable in class org.jmol.shape.Labels
 
number - Variable in enum org.jmol.util.Edge.EnumBondOrder
 
numberOutOfRange(float, float) - Method in class org.jmol.script.ScriptError
 
numCached - Variable in class org.jmol.modelset.BondCollection
 
numSet - Variable in class org.jmol.modelset.MeasurementPending
 
numWindows - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
nUnique - Static variable in class org.jmol.symmetry.PointGroup
 
nUNK - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
nUnnamed - Variable in class org.jmol.shape.MeshCollection
 
nValue(T) - Static method in class org.jmol.script.SV
 
nVertexColors - Variable in class org.jmol.jvxl.data.JvxlData
 
nVertices - Variable in class org.jmol.jvxl.readers.PolygonFileReader
 
nVertices - Variable in class org.jmol.shapespecial.Polyhedra
 
nVib - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
nVibrations - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
nvidia_bugs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
nwchemContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
nwChemMode - Variable in class org.jmol.quantum.MOCalculation
 
NWChemReader - Class in org.jmol.adapter.readers.quantum
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
NWChemReader() - Constructor for class org.jmol.adapter.readers.quantum.NWChemReader
 
nWidgets - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
nx - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nX - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
 
nX - Variable in class org.jmol.quantum.QuantumCalculation
 
nXX - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
nxyzStart - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nY - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
ny - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nY - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
 
nY - Variable in class org.jmol.quantum.QuantumCalculation
 
nZ - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
nz - Variable in class org.jmol.jvxl.readers.MapFileReader
 
nZ - Variable in class org.jmol.quantum.QuantumCalculation
 

O

o(String, Object) - Static method in class org.jmol.i18n.GT
 
O - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
o(int, Object) - Static method in class org.jmol.script.T
 
O1P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O2 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O2P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O2Pr - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O3P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O4 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O4P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O5P - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
O6 - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
OBJ - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
obj - Static variable in class org.jmol.script.T
 
OBJ_AXIS1 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_AXIS2 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_AXIS3 - Static variable in class org.jmol.viewer.StateManager
 
OBJ_BACKGROUND - Static variable in class org.jmol.viewer.StateManager
 
OBJ_BOUNDBOX - Static variable in class org.jmol.viewer.StateManager
 
OBJ_FRANK - Static variable in class org.jmol.viewer.StateManager
 
OBJ_MAX - Static variable in class org.jmol.viewer.StateManager
 
OBJ_UNITCELL - Static variable in class org.jmol.viewer.StateManager
 
objCls1 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
objCls2 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
objColors - Variable in class org.jmol.viewer.GlobalSettings
 
object - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
object - Static variable in class org.jmol.script.T
 
Object2d - Class in org.jmol.modelset
 
Object2d() - Constructor for class org.jmol.modelset.Object2d
 
Object2dShape - Class in org.jmol.shape
 
Object2dShape() - Constructor for class org.jmol.shape.Object2dShape
 
OBJECT_ALIGNMENT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_CALCULATOR - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_CALLBACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_CGO - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_GADGET - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_GROUP - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_MAPDATA - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_MAPDATA - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
OBJECT_MAPMESH - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_MAPMESH - Static variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
OBJECT_MEASURE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_MOLECULE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_SELECTION - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_SLICE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OBJECT_SURFACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
objectHidden - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
objectInfo - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
objectJmolName - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
objectName - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
objectName - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
objectNameID - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
objectNameID - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
objectNameList - Static variable in class org.jmol.viewer.StateManager
 
objectNameParameter(int) - Method in class org.jmol.script.ScriptParam
 
objectOf(DefaultListModel<?>, Object) - Static method in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
objects - Variable in class org.jmol.shape.Object2dShape
 
objectSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
objectsPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
objectType - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
objFileRootName - Variable in class org.jmol.export._ObjExporter
Path of the OBJ file without the extension.
objID1 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
objID2 - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
objMad - Variable in class org.jmol.viewer.GlobalSettings
 
ObjReader - Class in org.jmol.jvxl.readers
 
ObjReader() - Constructor for class org.jmol.jvxl.readers.ObjReader
 
objStateOn - Variable in class org.jmol.viewer.GlobalSettings
 
OCC_CRENEL_C - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
OCC_CRENEL_W - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
OCC_SPECIAL_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
occluded - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
occludedObjects - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
occupancies - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
occupancies - Variable in class org.jmol.modelset.AtomCollection
 
OCCUPANCY - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
occupancy - Static variable in class org.jmol.script.T
 
octants - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
OdysseyReader - Class in org.jmol.adapter.readers.quantum
 
OdysseyReader() - Constructor for class org.jmol.adapter.readers.quantum.OdysseyReader
 
off - Static variable in class org.jmol.script.T
 
officialRelease - Static variable in class org.jmol.viewer.JC
 
offscreen_rendering_for_antialiasing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
offscreen_rendering_multiplier - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
offscreenImage - Variable in class org.jmol.g3d.Platform3D
 
offset(int, int) - Method in class org.jmol.adapter.readers.pymol.JmolObject
offset is carried out in ModelLoader when the "script" is processed to move the bits to skip the base atom index.
offset - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
offset - Variable in class org.jmol.render.LabelsRenderer
 
offset - Variable in class org.jmol.render.UccageRenderer
 
offset - Variable in class org.jmol.renderspecial.DipolesRenderer
 
offset - Static variable in class org.jmol.script.T
 
offset - Variable in class org.jmol.shapespecial.Draw
 
offset(V3) - Method in class org.jmol.shapespecial.DrawMesh
 
offset(BS, int, int) - Static method in class org.jmol.util.BSUtil
offset the bitset in place by the specified number of bits starting at a given position
offset - Variable in class org.jmol.util.MeshSurface
 
offsetAfterPrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
offsetAngstroms - Variable in class org.jmol.shapespecial.Dipole
 
offsetCenter(P3) - Method in class org.jmol.jvxl.data.VolumeData
 
offsetObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
offsetPbufBeginLine - Variable in class org.jmol.g3d.SphereRenderer
 
offsetPercent - Variable in class org.jmol.shapespecial.Dipole
 
offsetPt - Variable in class org.jmol.shapespecial.Dipole
 
offsets - Variable in class org.jmol.modelsetbio.Monomer
 
offsets - Variable in class org.jmol.shape.Labels
 
offsetSide - Variable in class org.jmol.renderspecial.DipolesRenderer
 
offsetside - Static variable in class org.jmol.script.T
 
offsetSide - Variable in class org.jmol.shapespecial.Dipole
 
offsetT - Variable in class org.jmol.render.UccageRenderer
 
offsetX - Variable in class org.jmol.modelset.Object2d
 
offsetY - Variable in class org.jmol.modelset.Object2d
 
OK - Static variable in interface org.jmol.api.JmolGestureServerInterface
 
OK - Static variable in class org.jmol.script.ScriptCompiler
 
ok - Variable in class org.jmol.util.MeshCapper.CapVertex
unique vertex test
ok() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
OK2 - Static variable in class org.jmol.script.ScriptCompiler
 
okButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
okButton - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
OKPressed() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog
 
oldDir - Variable in class org.openscience.chimetojmol.ChimePanel
 
oldType - Variable in class org.jmol.util.ContactPair
 
OLIVE - Static variable in class org.jmol.util.C
 
omega - Variable in class org.jmol.modelsetbio.Monomer
 
omega - Static variable in class org.jmol.script.T
 
on - Static variable in class org.jmol.script.T
 
once - Static variable in class org.jmol.script.T
 
ONE_OVER_D - Static variable in class org.jmol.quantum.MepCalculation
 
ONE_OVER_ONE_PLUS_D - Static variable in class org.jmol.quantum.MepCalculation
 
oneFifth - Static variable in class org.jmol.util.Geodesic
 
onePerLine - Variable in class org.jmol.jvxl.readers.PmeshReader
 
oneTenth - Static variable in class org.jmol.util.Geodesic
 
only - Static variable in class org.jmol.script.T
 
onlySelectedDots - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
oopCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
oopCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
oops(Exception) - Method in class org.jmol.minimize.MinimizationThread
 
oops(Exception) - Method in class org.jmol.navigate.Navigator
 
oops(Exception) - Method in class org.jmol.thread.JmolThread
 
opacity - Variable in class org.jmol.awt.AwtColor
 
opacityFractionalFromArgb(int) - Static method in class org.jmol.export.___Exporter
 
opacityFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
 
opAnd - Static variable in class org.jmol.script.T
 
opAND - Static variable in class org.jmol.script.T
 
opaque - Static variable in class org.jmol.script.T
 
opaque_background - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
OPAQUE_MASK - Static variable in class org.jmol.util.C
 
openAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
OpenAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenAction
 
openBufferedReader(String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
 
openBufferedReader(String, BufferedReader, Map<String, Object>) - Method in class org.jmol.api.JmolAdapter
 
openBufferedReader(String, String, BufferedReader) - Method in class org.jmol.api.JmolAdapter
 
openButton - Variable in class org.jmol.console.ScriptEditor
 
openChooser - Static variable in class org.jmol.dialog.Dialog
 
openDOM(Object) - Method in class org.jmol.api.JmolViewer
 
openDOM(Object) - Method in class org.jmol.viewer.Viewer
applet DOM method -- does not preserve state
openExportChannel(double, String, boolean) - Method in class org.jmol.viewer.Viewer
 
openFile(String) - Method in class org.jmol.api.JmolViewer
 
openFile(String) - Method in class org.jmol.appletjs.Jmol
 
openFile(String) - Method in class org.jmol.viewer.Viewer
for JmolSimpleViewer -- external applications only (and no-script JavaScript)
openFile() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
openFileAsync(String, int) - Method in interface org.jmol.api.JmolScriptManager
 
openFileAsync(String) - Method in class org.jmol.api.JmolViewer
 
openFileAsync(String, int) - Method in class org.jmol.script.ScriptManager
From file dropping.
openFileAsyncSpecial(String, int) - Method in class org.jmol.api.JmolViewer
 
openFileAsyncSpecial(String, int) - Method in class org.jmol.appletjs.Jmol
 
openFileAsyncSpecial(String, int) - Method in class org.jmol.viewer.Viewer
opens a file as a model, a script, or a surface via the creation of a script that is queued \t at the beginning disallows script option - used by JmolFileDropper and JmolPanel file-open actions - sets up a script to load the file.
openFileFull(String, boolean, Map<String, Object>, SB) - Method in class org.jmol.viewer.Viewer
does NOT repaint
openFilePreview - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
openFiles(String[]) - Method in class org.jmol.api.JmolViewer
 
openFiles(String[]) - Method in class org.jmol.viewer.Viewer
for JmolSimpleViewer -- external applications only
openmolAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
OpenMolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenMolAction
 
openOutputChannel(double, String, boolean, boolean) - Method in class org.jmol.viewer.OutputManager
 
openOutputChannel(double, String, boolean, boolean) - Method in class org.jmol.viewer.OutputManagerAwt
 
openOutputChannel(double, String, boolean, boolean) - Method in class org.jmol.viewer.OutputManagerJS
 
openpdbAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
OpenPdbAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenPdbAction
 
openPreview - Variable in class org.jmol.dialog.Dialog
 
openReader(String, String, Reader) - Method in class org.jmol.api.JmolViewer
Opens the file and creates the model set, given the reader.
openReader(String, String, Reader) - Method in class org.jmol.viewer.Viewer
Opens the file, given an already-created reader.
openStringInline(String) - Method in class org.jmol.api.JmolViewer
 
openStringInline(String) - Method in class org.jmol.viewer.Viewer
only used by file dropper.
openStringInlineParamsAppend(String, Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.
openStringsInlineParamsAppend(String[], Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
opens multiple files inline; does NOT repaint
openurlAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
OpenUrlAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
opEQ - Static variable in class org.jmol.script.T
 
OPER_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
OPER_XYZ - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
operate() - Method in class org.jmol.script.ScriptMathProcessor
 
Operation() - Constructor for class org.jmol.symmetry.PointGroup.Operation
 
Operation(V3, int) - Constructor for class org.jmol.symmetry.PointGroup.Operation
 
Operation(V3) - Constructor for class org.jmol.symmetry.PointGroup.Operation
 
OPERATION_IMPROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
 
OPERATION_INVERSION_CENTER - Static variable in class org.jmol.symmetry.PointGroup
 
OPERATION_PLANE - Static variable in class org.jmol.symmetry.PointGroup
 
OPERATION_PROPER_AXIS - Static variable in class org.jmol.symmetry.PointGroup
 
operationCount - Variable in class org.jmol.symmetry.SpaceGroup
 
operations - Variable in class org.jmol.symmetry.SpaceGroup
 
operFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
opGE - Static variable in class org.jmol.script.T
 
opGT - Static variable in class org.jmol.script.T
 
opId - Variable in class org.jmol.symmetry.SymmetryOperation
 
opIf - Static variable in class org.jmol.script.T
 
opLE - Static variable in class org.jmol.script.T
 
opLIKE - Static variable in class org.jmol.script.T
 
opLT - Static variable in class org.jmol.script.T
 
opNE - Static variable in class org.jmol.script.T
 
opNot - Static variable in class org.jmol.script.T
 
opOr - Static variable in class org.jmol.script.T
 
oPt - Variable in class org.jmol.script.ScriptMathProcessor
 
OPT_ARCS - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
OPT_ARROWS - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
OPT_AXES - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
OPT_BALL - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
OPT_COUNT - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
OPT_DOTS - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
OPT_FILL - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
OPT_WIREFRAME - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
options - Static variable in class org.jmol.script.T
 
options - Variable in class org.jmol.shapespecial.Ellipsoid
 
opToggle - Static variable in class org.jmol.script.T
 
opTokenFor(int) - Method in class org.jmol.scriptext.MathExt
 
optOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
optParameterAsString(int) - Method in class org.jmol.script.ScriptParam
 
OPTS - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
optsField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
OptSort() - Constructor for class org.openscience.jmol.app.JmolApp.OptSort
 
opXor - Static variable in class org.jmol.script.T
 
or(BS) - Method in class org.jmol.java.BS
Performs a logical OR of this bit set with the bit set argument.
ORANGE - Static variable in class org.jmol.util.C
 
orbital - Static variable in class org.jmol.script.T
 
orbitalData - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
orbitalInfo - Variable in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
orbitals - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
orbitals - Variable in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
Orbitals - Class in org.openscience.jmol.app.webexport
 
Orbitals() - Constructor for class org.openscience.jmol.app.webexport.Orbitals
 
OrbitalSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.OrbitalSorter
 
orbitalsRead - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
orbitalType - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
order - Variable in class org.jmol.adapter.smarter.Bond
 
order - Variable in class org.jmol.minimize.MinBond
 
order - Variable in class org.jmol.symmetry.HallRotationTerm
 
order - Variable in class org.jmol.symmetry.PointGroup.Operation
 
order - Variable in class org.jmol.util.Edge
 
order - Variable in class org.jmol.util.Modulation
 
order - Variable in class org.jmol.viewer.Connection
 
ORDER_AROMATIC - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_AROMATIC_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_AROMATIC_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_DOUBLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_COVALENT_TRIPLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_HBOND - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL01 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL12 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL23 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PARTIAL32 - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PYMOL_MULT - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_PYMOL_SINGLE - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_STEREO_FAR - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_STEREO_NEAR - Static variable in class org.jmol.api.JmolAdapter
 
ORDER_UNSPECIFIED - Static variable in class org.jmol.api.JmolAdapter
 
org.jmol.adapter.readers.cif - package org.jmol.adapter.readers.cif
 
org.jmol.adapter.readers.molxyz - package org.jmol.adapter.readers.molxyz
 
org.jmol.adapter.readers.more - package org.jmol.adapter.readers.more
 
org.jmol.adapter.readers.pdb - package org.jmol.adapter.readers.pdb
 
org.jmol.adapter.readers.pymol - package org.jmol.adapter.readers.pymol
 
org.jmol.adapter.readers.quantum - package org.jmol.adapter.readers.quantum
 
org.jmol.adapter.readers.simple - package org.jmol.adapter.readers.simple
 
org.jmol.adapter.readers.xml - package org.jmol.adapter.readers.xml
 
org.jmol.adapter.readers.xtal - package org.jmol.adapter.readers.xtal
 
org.jmol.adapter.smarter - package org.jmol.adapter.smarter
 
org.jmol.api - package org.jmol.api
 
org.jmol.applet - package org.jmol.applet
 
org.jmol.appletjs - package org.jmol.appletjs
 
org.jmol.atomdata - package org.jmol.atomdata
 
org.jmol.awt - package org.jmol.awt
 
org.jmol.awtjs - package org.jmol.awtjs
 
org.jmol.awtjs2d - package org.jmol.awtjs2d
 
org.jmol.bspt - package org.jmol.bspt
Provides Binary Space Partitioning Functionality to spacially separate data structures in n-dimensions
org.jmol.c - package org.jmol.c
 
org.jmol.console - package org.jmol.console
 
org.jmol.consolejs - package org.jmol.consolejs
 
org.jmol.dialog - package org.jmol.dialog
 
org.jmol.dssx - package org.jmol.dssx
 
org.jmol.export - package org.jmol.export
 
org.jmol.g3d - package org.jmol.g3d
Provides a software implementation of complete 3D graphics engine for rendering molecules and associated shapes.
org.jmol.geodesic - package org.jmol.geodesic
 
org.jmol.i18n - package org.jmol.i18n
 
org.jmol.image - package org.jmol.image
 
org.jmol.io - package org.jmol.io
 
org.jmol.java - package org.jmol.java
 
org.jmol.jsv - package org.jmol.jsv
 
org.jmol.jvxl.api - package org.jmol.jvxl.api
 
org.jmol.jvxl.calc - package org.jmol.jvxl.calc
 
org.jmol.jvxl.data - package org.jmol.jvxl.data
 
org.jmol.jvxl.readers - package org.jmol.jvxl.readers
 
org.jmol.minimize - package org.jmol.minimize
 
org.jmol.minimize.forcefield - package org.jmol.minimize.forcefield
 
org.jmol.modelkit - package org.jmol.modelkit
 
org.jmol.modelset - package org.jmol.modelset
 
org.jmol.modelsetbio - package org.jmol.modelsetbio
 
org.jmol.multitouch - package org.jmol.multitouch
 
org.jmol.multitouch.jni - package org.jmol.multitouch.jni
 
org.jmol.multitouch.sparshui - package org.jmol.multitouch.sparshui
 
org.jmol.navigate - package org.jmol.navigate
 
org.jmol.popup - package org.jmol.popup
 
org.jmol.quantum - package org.jmol.quantum
 
org.jmol.render - package org.jmol.render
 
org.jmol.renderbio - package org.jmol.renderbio
 
org.jmol.rendercgo - package org.jmol.rendercgo
 
org.jmol.renderspecial - package org.jmol.renderspecial
 
org.jmol.rendersurface - package org.jmol.rendersurface
 
org.jmol.script - package org.jmol.script
 
org.jmol.scriptext - package org.jmol.scriptext
 
org.jmol.shape - package org.jmol.shape
 
org.jmol.shapebio - package org.jmol.shapebio
 
org.jmol.shapecgo - package org.jmol.shapecgo
 
org.jmol.shapespecial - package org.jmol.shapespecial
 
org.jmol.shapesurface - package org.jmol.shapesurface
 
org.jmol.smiles - package org.jmol.smiles
org.jmol.symmetry - package org.jmol.symmetry
 
org.jmol.thread - package org.jmol.thread
 
org.jmol.util - package org.jmol.util
 
org.jmol.viewer - package org.jmol.viewer
 
org.jmol.viewer.binding - package org.jmol.viewer.binding
 
org.openscience.chimetojmol - package org.openscience.chimetojmol
 
org.openscience.jmol.app - package org.openscience.jmol.app
 
org.openscience.jmol.app.jmolpanel - package org.openscience.jmol.app.jmolpanel
 
org.openscience.jmol.app.jmolpanel.console - package org.openscience.jmol.app.jmolpanel.console
 
org.openscience.jmol.app.jsonkiosk - package org.openscience.jmol.app.jsonkiosk
 
org.openscience.jmol.app.surfacetool - package org.openscience.jmol.app.surfacetool
 
org.openscience.jmol.app.webexport - package org.openscience.jmol.app.webexport
 
org.openscience.jvxl - package org.openscience.jvxl
 
org.openscience.jvxl.simplewriter - package org.openscience.jvxl.simplewriter
 
orientation - Variable in class org.jmol.modelset.Model
 
Orientation - Class in org.jmol.modelset
 
Orientation(Viewer, boolean, float[]) - Constructor for class org.jmol.modelset.Orientation
 
orientation - Static variable in class org.jmol.script.T
 
origin - Variable in class org.jmol.jvxl.data.VolumeData
 
origin - Variable in class org.jmol.jvxl.readers.MapFileReader
 
origin - Variable in class org.jmol.jvxl.readers.Parameters
 
origin - Static variable in class org.jmol.script.T
 
origin - Variable in class org.jmol.shapespecial.Dipole
 
originalSystemProperties - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
originBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
originPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
originPoint - Variable in class org.jmol.shape.Axes
 
originScreen - Variable in class org.jmol.render.AxesRenderer
 
ortho - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
oStack - Variable in class org.jmol.script.ScriptMathProcessor
 
OT - Static variable in class org.jmol.modelsetbio.AminoMonomer
 
otherAtoms - Variable in class org.jmol.shapespecial.Polyhedra
 
out - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
out - Variable in class org.jmol.export.___Exporter
 
out - Variable in class org.jmol.jvxl.readers.SurfaceFileReader
 
out - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
out - Static variable in class org.jmol.script.T
 
output(String) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
output - Variable in class org.jmol.console.GenericConsole
 
output(String) - Method in class org.jmol.console.ScriptEditor
 
output(String) - Method in class org.jmol.export.___Exporter
 
output(T3) - Method in class org.jmol.export.___Exporter
 
output(T3) - Method in class org.jmol.export._IdtfExporter
 
output(T3, SB, boolean) - Method in class org.jmol.export._IdtfExporter
 
output(T3) - Method in class org.jmol.export._MayaExporter
 
output(T3) - Method in class org.jmol.export._ObjExporter
 
output(T3) - Method in class org.jmol.export._PovrayExporter
 
output(T3) - Method in class org.jmol.export._TachyonExporter
 
output(T3) - Method in class org.jmol.export._VrmlExporter
 
output(T3) - Method in class org.jmol.export.JSExporter
 
output(String) - Method in class org.jmol.util.GenericApplet
 
outputAlphaCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputAppearance(short, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputAppearance(short, boolean) - Method in class org.jmol.export._X3dExporter
 
outputBeforePrompt(String, SimpleAttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
outputBuffer - Variable in class org.jmol.script.ScriptContext
 
outputBuffer - Variable in class org.jmol.script.ScriptEval
 
outputBuffer - Variable in class org.jmol.util.GenericApplet
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
 
outputCircle(P3, P3, short, float) - Method in class org.jmol.export._IdtfExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
 
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
 
outputCircle(int, int, int, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export._X3dExporter
 
outputCircle(P3, P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
 
outputCircle1(P3, P3, short, float) - Method in class org.jmol.export._ObjExporter
Local implementation of outputCircle.
outputColorIndices(int[][], int, BS, int, Map<Short, Integer>, short[], short[]) - Method in class org.jmol.export._VrmlExporter
 
outputColors(Lst<Short>) - Method in class org.jmol.export._VrmlExporter
 
outputComment(String) - Method in class org.jmol.export.___Exporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export.__CartesianExporter
 
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export._IdtfExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export._MayaExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export._ObjExporter
 
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
 
outputCone(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export._VrmlExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export._X3dExporter
 
outputCone(P3, P3, float, short) - Method in class org.jmol.export.JSExporter
 
outputCone1(P3, P3, float, short) - Method in class org.jmol.export._ObjExporter
Local implementation of outputCone.
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
 
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export.__RayTracerExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._IdtfExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._MayaExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._ObjExporter
 
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._PovrayExporter
 
outputCylinder(P3, P3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export._X3dExporter
 
outputCylinder(P3, P3, P3, short, byte, float, P3, P3, boolean) - Method in class org.jmol.export.JSExporter
 
outputCylinder1(P3, P3, P3, short, byte, float, P3, P3) - Method in class org.jmol.export._ObjExporter
Local implementation of outputCylinder.
outputCylinderChildScaled(P3, P3, short, byte, float) - Method in class org.jmol.export._VrmlExporter
 
outputCylinderChildScaled(P3, P3, short, byte, float) - Method in class org.jmol.export._X3dExporter
 
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export.__RayTracerExporter
 
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._PovrayExporter
 
outputCylinderConical(P3, P3, float, float, short) - Method in class org.jmol.export._TachyonExporter
 
outputDocument - Variable in class org.jmol.console.AppletConsole.GenericTextPane
 
outputEcho(String) - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
outputEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
outputEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
outputEllipse(P3, P3, P3, P3, short) - Method in class org.jmol.export._IdtfExporter
 
outputEllipse1(P3, P3, P3, P3, short) - Method in class org.jmol.export._ObjExporter
Local implementation of outputEllipse.
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.__CartesianExporter
 
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export.__RayTracerExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._IdtfExporter
 
outputEllipsoid(P3, M4, short) - Method in class org.jmol.export._IdtfExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._MayaExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._ObjExporter
 
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._PovrayExporter
 
outputEllipsoid(P3, float, double[], short) - Method in class org.jmol.export._TachyonExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._VrmlExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export._X3dExporter
 
outputEllipsoid(P3, P3[], short) - Method in class org.jmol.export.JSExporter
 
outputEllipsoid1(P3, float, float, float, A4, short) - Method in class org.jmol.export._ObjExporter
Local implementation of outputEllipsoid.
outputError(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
outputError(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
outputErrorForeground(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
outputErrorForeground(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
outputExtension - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputFace(int[], int[], int) - Method in class org.jmol.export.__CartesianExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._IdtfExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._MayaExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._ObjExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export._VrmlExporter
 
outputFace(int[], int[], int) - Method in class org.jmol.export.JSExporter
 
outputFace1(int[], int[], int[]) - Method in class org.jmol.export._ObjExporter
Local implementation of outputFace used for no texture coordinates.
outputFace2(int[], int, int[], int[]) - Method in class org.jmol.export._ObjExporter
Local implementation of outputFace used with texture coordinates.
outputFileName - Variable in class org.jmol.dialog.Dialog
 
outputFileType - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputFooter() - Method in class org.jmol.export.___Exporter
 
outputFooter() - Method in class org.jmol.export._IdtfExporter
 
outputFooter() - Method in class org.jmol.export._TachyonExporter
 
outputFooter() - Method in class org.jmol.export._VrmlExporter
 
outputFooter() - Method in class org.jmol.export._X3dExporter
 
outputFooter() - Method in class org.jmol.export.JSExporter
 
outputFormatChanged() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Called when the OutputFormat check box is modified
outputFormatCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputFormatCombo - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputHeader() - Method in class org.jmol.export.___Exporter
 
outputHeader() - Method in class org.jmol.export._IdtfExporter
 
outputHeader() - Method in class org.jmol.export._MayaExporter
 
outputHeader() - Method in class org.jmol.export._ObjExporter
 
outputHeader() - Method in class org.jmol.export._PovrayExporter
 
outputHeader() - Method in class org.jmol.export._TachyonExporter
 
outputHeader() - Method in class org.jmol.export._VrmlExporter
 
outputHeader() - Method in class org.jmol.export._X3dExporter
 
outputHeader() - Method in class org.jmol.export.JSExporter
 
outputHeight - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outputIndices(int[][], int[], int, BS, int) - Method in class org.jmol.export.__CartesianExporter
 
outputJmolPerspective() - Method in class org.jmol.export.___Exporter
 
outputList(T3[], int, M4, String, BS) - Method in class org.jmol.export._ObjExporter
create the v or vn list
OutputManager - Class in org.jmol.viewer
 
OutputManager() - Constructor for class org.jmol.viewer.OutputManager
 
outputManager - Variable in class org.jmol.viewer.Viewer
 
OutputManagerAwt - Class in org.jmol.viewer
 
OutputManagerAwt() - Constructor for class org.jmol.viewer.OutputManagerAwt
 
OutputManagerJS - Class in org.jmol.viewer
 
OutputManagerJS() - Constructor for class org.jmol.viewer.OutputManagerJS
 
outputMsg(String) - Method in class org.jmol.console.GenericConsole
 
outputMtl(String) - Method in class org.jmol.export._ObjExporter
Write to the .mtl file and keep track of the bytes written.
outputNodes() - Method in class org.jmol.export._IdtfExporter
 
outputNormals(Lst<String>) - Method in class org.jmol.export._VrmlExporter
 
outputQuaternionFrame(P3, P3, P3, P3, float, String, String) - Method in class org.jmol.export._VrmlExporter
 
outputRing(int, int, int, V3, float, short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.__CartesianExporter
 
outputSphere(float, float, float, float, short) - Method in class org.jmol.export.__RayTracerExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._IdtfExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._MayaExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._ObjExporter
 
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._PovrayExporter
 
outputSphere(float, float, float, float, short) - Method in class org.jmol.export._TachyonExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export._VrmlExporter
 
outputSphere(P3, float, short, boolean) - Method in class org.jmol.export.JSExporter
 
outputSphereChildUnscaled(P3, float, short) - Method in class org.jmol.export._VrmlExporter
 
outputSphereChildUnscaled(P3, float, short) - Method in class org.jmol.export._X3dExporter
 
outputStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
outputStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.___Exporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._IdtfExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._MayaExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._PovrayExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._TachyonExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._VrmlExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export._X3dExporter
 
outputSurface(T3[], T3[], short[], int[][], short[], int, int, int, BS, int, short, Lst<Short>, Map<Short, Integer>, P3) - Method in class org.jmol.export.JSExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export.__CartesianExporter
 
outputTextPixel(int, int, int, int) - Method in class org.jmol.export.__RayTracerExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._IdtfExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._MayaExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._ObjExporter
 
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._PovrayExporter
 
outputTextPixel(int, int, int, int) - Method in class org.jmol.export._TachyonExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._VrmlExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export._X3dExporter
 
outputTextPixel(P3, int) - Method in class org.jmol.export.JSExporter
 
outputTexture(short, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputTexture(int, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputTexture2(String, String, boolean) - Method in class org.jmol.export._TachyonExporter
 
outputTextureCode() - Method in class org.jmol.export._TachyonExporter
 
outputToFile(Map<String, Object>) - Method in class org.jmol.api.JmolViewer
 
outputToFile(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
 
outputToFile(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
outputTransRot(P3, P3, int, int, int) - Method in class org.jmol.export._VrmlExporter
 
outputTransRot(P3, P3, int, int, int, String, String) - Method in class org.jmol.export._VrmlExporter
 
outputTransRot(P3, P3, int, int, int) - Method in class org.jmol.export._X3dExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.__CartesianExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.__RayTracerExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._IdtfExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._MayaExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._ObjExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._PovrayExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._TachyonExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._VrmlExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export._X3dExporter
 
outputTriangle(T3, T3, T3, short) - Method in class org.jmol.export.JSExporter
 
outputTriangle(int, int, int) - Method in class org.jmol.util.MeshCapper
Export triangle to MeshSlicer
outputTriangle1(T3, T3, T3, short) - Method in class org.jmol.export._ObjExporter
Local implementation of outputCylinder.
outputVertex(T3, T3) - Method in class org.jmol.export.___Exporter
 
outputVertex(T3, T3) - Method in class org.jmol.export.__RayTracerExporter
 
outputVertices(T3[], int, T3) - Method in class org.jmol.export.___Exporter
 
outputWidth - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
outSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
oValue(SV) - Static method in class org.jmol.script.SV
 
overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
overlay_lines - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 

P

p - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
P - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
P - Static variable in class org.jmol.quantum.QS
 
p - Variable in class org.jmol.render.MeasuresRenderer
 
p0 - Variable in class org.jmol.g3d.Pixelator
 
p0 - Variable in class org.jmol.quantum.NciCalculation
 
p1 - Variable in class org.jmol.quantum.NciCalculation
 
p1 - Variable in class org.jmol.render.SticksRenderer
 
p2 - Variable in class org.jmol.quantum.NciCalculation
 
p2 - Variable in class org.jmol.render.SticksRenderer
 
p2nLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
P2nReader - Class in org.jmol.adapter.readers.pdb
P2N file reader.
P2nReader() - Constructor for class org.jmol.adapter.readers.pdb.P2nReader
 
p4 - Variable in class org.jmol.viewer.TransformManager4D
 
P_CHECK - Static variable in class org.jmol.util.MeshSurface
 
P_CONTOUR - Static variable in class org.jmol.util.MeshSurface
 
P_EXPLICIT_COLOR - Static variable in class org.jmol.util.MeshSurface
 
P_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
P_LIST - Static variable in class org.jmol.adapter.readers.quantum.MOReader
 
packageReadable(String, String, String) - Static method in class org.jmol.util.Escape
 
packageReadableSb(String, String, SB) - Static method in class org.jmol.util.Escape
 
packed - Static variable in class org.jmol.script.T
 
packingError - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
packingError - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
pageAuthorName - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
pageAuthorName - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
PageLoader(URL, Cursor) - Constructor for class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
 
pages - Variable in class org.openscience.chimetojmol.ChimePanel
 
pageUpBuffer - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
paint(Graphics) - Method in class org.jmol.applet.AppletWrapper
 
paint(Graphics) - Method in class org.jmol.applet.Jmol
 
paint(Graphics) - Method in interface org.jmol.applet.WrappedApplet
 
paint(Graphics) - Method in class org.jmol.dialog.FilePreview.FPPanel
 
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
paint(Graphics) - Method in class org.openscience.jmol.app.jmolpanel.Splash
 
pairSearch(Lst<Object[]>, Calculation, Lst<Object[]>, Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
 
PAL - Enum in org.jmol.c
Enum for animation mode.
PAL(String, int) - Constructor for enum org.jmol.c.PAL
 
PALETTE_ALTLOC - Static variable in enum org.jmol.c.PAL
 
PALETTE_AMINO - Static variable in enum org.jmol.c.PAL
 
PALETTE_CHAIN - Static variable in enum org.jmol.c.PAL
 
PALETTE_CPK - Static variable in enum org.jmol.c.PAL
 
PALETTE_ENERGY - Static variable in enum org.jmol.c.PAL
 
PALETTE_FIXEDTEMP - Static variable in enum org.jmol.c.PAL
 
PALETTE_FORMAL_CHARGE - Static variable in enum org.jmol.c.PAL
 
PALETTE_GROUP - Static variable in enum org.jmol.c.PAL
 
PALETTE_INSERTION - Static variable in enum org.jmol.c.PAL
 
PALETTE_JMOL - Static variable in enum org.jmol.c.PAL
 
PALETTE_MOLECULE - Static variable in enum org.jmol.c.PAL
 
PALETTE_MONOMER - Static variable in enum org.jmol.c.PAL
 
PALETTE_NONE - Static variable in enum org.jmol.c.PAL
 
PALETTE_PARTIAL_CHARGE - Static variable in enum org.jmol.c.PAL
 
PALETTE_POLYMER - Static variable in enum org.jmol.c.PAL
 
PALETTE_PROPERTY - Static variable in enum org.jmol.c.PAL
 
PALETTE_RASMOL - Static variable in enum org.jmol.c.PAL
 
PALETTE_SHAPELY - Static variable in enum org.jmol.c.PAL
 
PALETTE_STRAIGHTNESS - Static variable in enum org.jmol.c.PAL
 
PALETTE_STRUCTURE - Static variable in enum org.jmol.c.PAL
 
PALETTE_SURFACE - Static variable in enum org.jmol.c.PAL
 
PALETTE_TEMP - Static variable in enum org.jmol.c.PAL
 
PALETTE_TYPE - Static variable in enum org.jmol.c.PAL
 
PALETTE_VARIABLE - Static variable in enum org.jmol.c.PAL
 
PALETTE_VOLATILE - Static variable in enum org.jmol.c.PAL
 
paletteBW - Variable in class org.jmol.util.ColorEncoder
 
paletteFriendly - Variable in class org.jmol.util.ColorEncoder
 
paletteID - Variable in class org.jmol.modelset.Atom
 
paletteIDs - Variable in class org.jmol.shape.AtomShape
 
paletteWB - Variable in class org.jmol.util.ColorEncoder
 
palindrome - Static variable in class org.jmol.script.T
 
panel() - Method in class org.openscience.jmol.app.webexport.Test
 
panelIndex - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
panelName - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
PAR_D - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_HARD - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_R - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_RADIUS - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_THETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_U - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_V - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_X - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_XI - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_Z - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
PAR_ZETA - Static variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
parA - Variable in class org.jmol.minimize.forcefield.Calculations
 
parallel - Static variable in class org.jmol.script.T
 
parallelProcessor - Variable in class org.jmol.script.ScriptContext
 
parallelProcessor - Variable in class org.jmol.script.ScriptEval
 
parallelProcessor - Variable in class org.jmol.script.ScriptProcessRunnable
 
paramAsStr(int) - Method in class org.jmol.script.ScriptParam
 
paramAsStr(int) - Method in class org.jmol.scriptext.CmdExt
 
parameterExpression(int, int, String, boolean, boolean, int, boolean, Map<String, SV>, String, boolean) - Method in class org.jmol.script.ScriptExpr
This is the primary driver of the RPN (reverse Polish notation) expression processor.
parameterExpressionBoolean(int, int) - Method in class org.jmol.script.ScriptExpr
 
parameterExpressionList(int, int, boolean) - Method in class org.jmol.script.ScriptExpr
 
parameterExpressionList(int, int, boolean) - Method in class org.jmol.script.ScriptParam
 
parameterExpressionSelect(Map<String, SV>, T[]) - Method in class org.jmol.script.ScriptExpr
 
parameterExpressionString(int, int) - Method in class org.jmol.script.ScriptExpr
 
parameterExpressionToken(int) - Method in class org.jmol.script.ScriptExpr
 
parameterIndex(String) - Static method in class org.jmol.adapter.readers.xtal.GulpReader
 
Parameters - Class in org.jmol.jvxl.readers
 
Parameters() - Constructor for class org.jmol.jvxl.readers.Parameters
 
parameters - Variable in class org.jmol.jvxl.readers.Parameters
 
parameters - Static variable in class org.jmol.script.T
 
params - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
params - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
params - Variable in class org.jmol.util.Modulation
 
paramTypes - Static variable in class org.jmol.script.T
 
parB - Variable in class org.jmol.minimize.forcefield.Calculations
 
parBorU - Variable in class org.jmol.util.Tensor
 
parC - Variable in class org.jmol.minimize.forcefield.Calculations
 
parenCount - Variable in class org.jmol.script.ScriptCompiler
 
parenCount - Variable in class org.jmol.script.ScriptMathProcessor
 
parent - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
parent - Variable in class org.jmol.adapter.readers.xml.XmlReader
 
parent - Variable in class org.jmol.popup.AwtSwingComponent
 
parent - Variable in class org.jmol.script.ScriptFlowContext
 
parent - Variable in class org.jmol.smiles.SmilesAtom
 
parentContext - Variable in class org.jmol.script.ScriptContext
 
parse(String) - Method in class org.jmol.smiles.SmilesParser
Parses a SMILES String
parseAtom(SmilesSearch, SmilesAtom, String, SmilesAtom, SmilesBond, boolean, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
Parses an atom definition
parseAtomTokens(Atom, String) - Method in class org.jmol.adapter.readers.simple.InputReader
 
parseBond(SmilesSearch, SmilesBond, String, SmilesBond, SmilesAtom, boolean, boolean) - Method in class org.jmol.smiles.SmilesParser
 
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
parseBondToken(String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
parseCommandLine(String[]) - Method in class org.openscience.jmol.app.JmolApp
 
parseCommandParameter() - Method in class org.jmol.script.ScriptCompiler
 
parseDataArray(String, boolean) - Method in class org.jmol.scriptext.CmdExt
 
parsedContext - Variable in class org.jmol.console.ScriptEditor
 
parsedData - Variable in class org.jmol.console.ScriptEditor
 
parseFloat(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
parseFloat() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloat() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseFloatArray(float[], String, String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseFloatArrayBsData(String[], BS, float[]) - Static method in class org.jmol.util.Parser
 
parseFloatArrayFromMatchAndField(String, BS, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
the major lifter here.
parseFloatArrayStr(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseFloatRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloatRange(String, int, int) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseFloatStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseFloatStr(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseInt(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
parseInt() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseInt() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseIntAt(String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseIntNext(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseIntRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseIntStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseIntStr(String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
parseKnownToken() - Method in class org.jmol.script.ScriptCompiler
 
parseLattRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseLineParameters(String[], byte[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
parseLoopParameters(String[]) - Method in class org.jmol.adapter.readers.cif.CifReader
sets up arrays and variables for tokenizer.getData()
parseLoopParametersFor(String, String[]) - Method in class org.jmol.adapter.readers.cif.CifReader
 
parseM40Floats() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
parseMeasure(SmilesSearch, String, SmilesAtom) - Method in class org.jmol.smiles.SmilesParser
 
parseNested(SmilesSearch, String, String) - Method in class org.jmol.smiles.SmilesParser
 
parser - Variable in class org.jmol.adapter.readers.cif.CifReader
 
Parser - Class in org.jmol.util
 
Parser() - Constructor for class org.jmol.util.Parser
 
parseRing(SmilesSearch, int, SmilesAtom, SmilesBond) - Method in class org.jmol.smiles.SmilesParser
Parses a ring definition
parseScript(String) - Method in class org.jmol.console.ScriptEditor
 
parseSfacCoefficients(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseSfacElementSymbols(String[]) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseSfacRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseSmiles(SmilesSearch, String, SmilesAtom, boolean) - Method in class org.jmol.smiles.SmilesParser
Parses a part of a SMILES String
parseStringInfestedFloatArray(String, BS, float[]) - Static method in class org.jmol.util.Parser
parses a "dirty" string for floats.
parseSymmRecord() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
parseToken() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTokenNext(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTokenRange(String, int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseTokenStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
parseVariableLength(String) - Method in class org.jmol.smiles.SmilesParser
 
parseVariables(String) - Method in class org.jmol.smiles.SmilesParser
 
parseXML(XmlReader, Object, BufferedReader) - Method in interface org.jmol.adapter.readers.xml.JmolXmlHandler
 
parseXML(XmlReader, Object, BufferedReader) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
parseXML() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JC
 
PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JC
 
partialCharge - Variable in class org.jmol.adapter.smarter.Atom
 
partialCharge - Variable in class org.jmol.minimize.MinAtom
 
partialcharge - Static variable in class org.jmol.script.T
 
partialCharges - Variable in class org.jmol.adapter.readers.simple.AmpacReader
 
partialCharges - Variable in class org.jmol.minimize.Minimizer
 
partialCharges - Variable in class org.jmol.modelset.AtomCollection
 
partialdots - Static variable in class org.jmol.script.T
 
partialDots - Variable in class org.jmol.viewer.GlobalSettings
 
PARTICLE_CHAIN - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
 
PARTICLE_NONE - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
 
PARTICLE_SYMOP - Static variable in class org.jmol.adapter.smarter.XtalSymmetry
 
particleradius - Static variable in class org.jmol.script.T
 
particleRadius - Variable in class org.jmol.viewer.GlobalSettings
 
pass2Flag01 - Variable in class org.jmol.g3d.Graphics3D
 
pasteClipboardAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PasteClipboardAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PasteClipboardAction
 
pasteClipboardActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
path - Variable in class org.jmol.awt.AwtG2D
 
path() - Method in class org.jmol.script.ScriptFlowContext
 
path - Static variable in class org.jmol.script.T
 
PATH_KEY - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
AtomSetCollectionReader.readData() will close any BufferedReader
PATH_SEPARATOR - Static variable in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
PathButton - Variable in class org.openscience.jmol.app.webexport.Test
 
pathforallfiles - Static variable in class org.jmol.script.T
 
pathForAllFiles - Variable in class org.jmol.viewer.FileManager
 
pattern - Variable in class org.jmol.smiles.SmilesSearch
 
patternAtoms - Variable in class org.jmol.smiles.SmilesSearch
 
PatternMatcher - Class in org.jmol.util
 
PatternMatcher() - Constructor for class org.jmol.util.PatternMatcher
 
pause - Static variable in class org.jmol.script.T
 
PAUSE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
PAUSE_DELAY - Static variable in class org.jmol.script.ScriptDelayThread
 
pauseAnimation() - Method in class org.jmol.viewer.AnimationManager
 
pauseButton - Variable in class org.jmol.console.ScriptEditor
 
pauseExecution(boolean) - Method in interface org.jmol.api.JmolScriptEvaluator
 
pauseExecution(boolean) - Method in class org.jmol.script.ScriptEval
 
pauseScript(boolean) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
pauseScriptExecution() - Method in class org.jmol.viewer.Viewer
 
pb - Variable in class org.jmol.g3d.Pixelator
 
pBotLeft - Variable in class org.jmol.g3d.HermiteRenderer
 
pBotRight - Variable in class org.jmol.g3d.HermiteRenderer
 
pbuf - Variable in class org.jmol.g3d.Graphics3D
 
pBuffer - Variable in class org.jmol.g3d.Platform3D
 
pBufferT - Variable in class org.jmol.g3d.Platform3D
 
pbufT - Variable in class org.jmol.g3d.Graphics3D
 
pButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
pc - Variable in class org.jmol.script.ScriptContext
 
pc - Variable in class org.jmol.script.ScriptEval
 
pc - Variable in class org.jmol.util.MeshSurface
polygon count
pc0 - Variable in class org.jmol.script.ScriptContext
 
pcEnd - Variable in class org.jmol.script.ScriptContext
 
pcEnd - Variable in class org.jmol.script.ScriptEval
 
PCHRG - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
pcl - Variable in class org.jmol.awt.FileDropper
 
pcResume - Variable in class org.jmol.script.ScriptEval
 
pcs - Variable in class org.jmol.util.MeshSurface
polygon color index "colix" array
pcs - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
pdb - Static variable in class org.jmol.script.T
 
PDB_ANNOTATIONS - Static variable in class org.jmol.viewer.JC
 
pdb_conect_all - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_discrete_chains - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_echo_tags - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_formal_charges - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_hetatm_guess_valences - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_hetatm_sort - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_honor_model_number - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_ignore_conect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_insertions_go_first - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_insure_orthogonal - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_literal_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_no_end_record - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_reformat_names_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_retain_ids - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_standard_order - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_truncate_residue_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_unbond_cations - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdb_use_ter_records - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pdbaddhydrogens - Static variable in class org.jmol.script.T
 
pdbAddHydrogens - Variable in class org.jmol.viewer.GlobalSettings
 
pdbAtomForH - Static variable in class org.jmol.dssx.AnnotationParser
 
pdbBondInfo - Static variable in class org.jmol.modelsetbio.Resolver
pdbBondInfo describes in a compact way what the hydrogen atom names are for each standard amino acid.
pdbCartoonChecked - Static variable in class org.jmol.dialog.FilePreview
 
pdbgetheader - Static variable in class org.jmol.script.T
 
pdbGetHeader - Variable in class org.jmol.viewer.GlobalSettings
 
pdbHeader - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
pdbheader - Static variable in class org.jmol.script.T
 
pdbHydrogenCount - Static variable in class org.jmol.modelsetbio.Resolver
 
pdbLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
PDBOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
PdbReader - Class in org.jmol.adapter.readers.pdb
PDB file reader.
PdbReader() - Constructor for class org.jmol.adapter.readers.pdb.PdbReader
 
pdbRecords - Static variable in class org.jmol.modelsetbio.BioModel
 
pdbsequential - Static variable in class org.jmol.script.T
 
pdbSequential - Variable in class org.jmol.viewer.GlobalSettings
 
peakData - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
peakFilePath - Variable in class org.jmol.jsv.JDXMOLParser
 
peakIndex - Variable in class org.jmol.jsv.JDXMOLParser
 
peek() - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
per - Static variable in class org.jmol.script.T
 
percent - Static variable in class org.jmol.script.T
 
percent - Variable in class org.jmol.shapespecial.Ellipsoid
 
percentToPixels(char, float) - Method in class org.jmol.viewer.TransformManager
 
percentvdwatom - Static variable in class org.jmol.script.T
 
percentVdwAtom - Variable in class org.jmol.viewer.GlobalSettings
 
percentVdwAtom - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
period - Static variable in class org.jmol.script.T
 
PERIOD_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for the vibration period in seconds.
PERIOD_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Precision of the vibration period slider in seconds.
PERIOD_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Initial value for the vibration period in seconds.
periodicOriginXyz - Variable in class org.jmol.symmetry.SymmetryInfo
 
PeriodicVolumeFileReader - Class in org.jmol.jvxl.readers
 
PeriodicVolumeFileReader() - Constructor for class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
periodSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
perpendicular - Static variable in class org.jmol.script.T
 
perper - Static variable in class org.jmol.script.T
 
perspectiveAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
perspectivedepth - Static variable in class org.jmol.script.T
 
perspectiveDepth - Variable in class org.jmol.viewer.TransformManager
 
perspectiveDepth - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
perspectiveFactor - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
perspectivemodel - Static variable in class org.jmol.script.T
 
perspectiveModel - Variable in class org.jmol.viewer.TransformManager
 
perspectiveOffset - Variable in class org.jmol.viewer.TransformManager
 
perspectiveShiftXY - Variable in class org.jmol.viewer.TransformManager
 
pfaatBinding - Variable in class org.jmol.viewer.ActionManager
 
PfaatBinding - Class in org.jmol.viewer.binding
 
PfaatBinding() - Constructor for class org.jmol.viewer.binding.PfaatBinding
 
pfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
pFF - Variable in class org.jmol.minimize.Minimizer
 
phase - Variable in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
phase - Static variable in class org.jmol.script.T
 
phi - Variable in class org.jmol.modelsetbio.Monomer
 
phi - Static variable in class org.jmol.script.T
 
phong - Variable in class org.jmol.export._TachyonExporter
 
phongexponent - Static variable in class org.jmol.script.T
 
phongExponent - Variable in class org.jmol.util.Shader
 
PhosphorusMonomer - Class in org.jmol.modelsetbio
 
PhosphorusMonomer() - Constructor for class org.jmol.modelsetbio.PhosphorusMonomer
 
phosphorusOffsets - Static variable in class org.jmol.modelsetbio.PhosphorusMonomer
 
PhosphorusPolymer - Class in org.jmol.modelsetbio
 
PhosphorusPolymer(Monomer[]) - Constructor for class org.jmol.modelsetbio.PhosphorusPolymer
 
PI_OVER_2 - Static variable in class org.jmol.minimize.forcefield.Calculations
 
PICK_COLOR - Static variable in class org.jmol.shapecgo.CGOMesh
 
pickable - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pickAtomAssignType - Variable in class org.jmol.viewer.ActionManager
 
pickBondAssignType - Variable in class org.jmol.viewer.ActionManager
 
pickedAtom - Variable in class org.jmol.shape.Labels
 
pickedMesh - Variable in class org.jmol.shape.MeshCollection
 
pickedModel - Variable in class org.jmol.shape.MeshCollection
 
pickedOffset - Variable in class org.jmol.shape.Labels
 
pickedPt - Variable in class org.jmol.shape.MeshCollection
 
pickedVertex - Variable in class org.jmol.shape.MeshCollection
 
pickedX - Variable in class org.jmol.shape.Labels
 
pickedY - Variable in class org.jmol.shape.Labels
 
picking - Static variable in class org.jmol.script.T
 
PICKING_ASSIGN_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_ASSIGN_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_CENTER - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_CONNECT - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DELETE_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DELETE_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_LIGAND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MINIMIZE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MINIMIZE_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAG_SELECTED - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_DRAW - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_IDENTIFY - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_IDENTIFY_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_INVERT_STEREO - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_LABEL - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_ANGLE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_DISTANCE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_SEQUENCE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_MEASURE_TORSION - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_NAVIGATE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_OFF - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_ROTATE_BOND - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_ATOM - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_CHAIN - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_ELEMENT - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_GROUP - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_MODEL - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_MOLECULE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_POLYMER - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_SITE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SELECT_STRUCTURE - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SPIN - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_STRUTS - Static variable in class org.jmol.viewer.ActionManager
 
PICKING_SYMMETRY - Static variable in class org.jmol.viewer.ActionManager
 
pickingModeNames - Static variable in class org.jmol.viewer.ActionManager
 
pickingspinrate - Static variable in class org.jmol.script.T
 
pickingSpinRate - Variable in class org.jmol.viewer.GlobalSettings
 
pickingstyle - Static variable in class org.jmol.script.T
 
pickingStyle - Variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_MEASURE_OFF - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_MEASURE_ON - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_CHIME - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_DRAG - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_JMOL - Static variable in class org.jmol.viewer.ActionManager
picking styles
PICKINGSTYLE_SELECT_PFAAT - Static variable in class org.jmol.viewer.ActionManager
 
PICKINGSTYLE_SELECT_RASMOL - Static variable in class org.jmol.viewer.ActionManager
 
pickingStyleMeasure - Variable in class org.jmol.viewer.ActionManager
 
pickingStyleNames - Static variable in class org.jmol.viewer.ActionManager
 
pickingStyleSelect - Variable in class org.jmol.viewer.ActionManager
 
picklabel - Static variable in class org.jmol.script.T
 
pickLabel - Variable in class org.jmol.viewer.GlobalSettings
 
PickleReader - Class in org.jmol.adapter.readers.pymol
generic Python Pickle file reader only utilizing records needed for PyMOL.
PickleReader(GenericBinaryDocument, Viewer) - Constructor for class org.jmol.adapter.readers.pymol.PickleReader
 
pictFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
pictIsScratchFile - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
pid - Variable in class org.jmol.shapespecial.Ellipsoid
 
pidOf(Object) - Static method in enum org.jmol.c.PAL
 
pilp - Variable in class org.jmol.minimize.forcefield.AtomType
 
PINK - Static variable in class org.jmol.util.C
 
pipedIS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
pipedOS - Variable in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
pis - Variable in class org.jmol.util.MeshSurface
polygon indexes
piUnitsX - Variable in class org.jmol.jsv.JDXMOLParser
 
piUnitsY - Variable in class org.jmol.jsv.JDXMOLParser
 
pixel - Variable in class org.jmol.g3d.Graphics3D
 
pixel0 - Variable in class org.jmol.g3d.Graphics3D
 
Pixelator - Class in org.jmol.g3d
 
Pixelator(Graphics3D) - Constructor for class org.jmol.g3d.Pixelator
 
PixelatorScreened - Class in org.jmol.g3d
A class to create a "screened" translucent effect by discarding pixels in a checkerboard fashion.
PixelatorScreened(Graphics3D, Pixelator) - Constructor for class org.jmol.g3d.PixelatorScreened
 
PixelatorShaded - Class in org.jmol.g3d
A class to do Z Shading of pixels.
PixelatorShaded(Graphics3D) - Constructor for class org.jmol.g3d.PixelatorShaded
 
PixelatorT - Class in org.jmol.g3d
Handle pixels in Pass 2 - Translucency
PixelatorT(Graphics3D) - Constructor for class org.jmol.g3d.PixelatorT
 
pixelScale - Variable in class org.jmol.thread.MoveToThread
 
pixelScreened - Variable in class org.jmol.g3d.Graphics3D
 
pixelShaded - Variable in class org.jmol.g3d.Graphics3D
 
pixelSize - Variable in class org.jmol.export._ObjExporter
The size of a pixel based on some assumptions about screen size
pixelT0 - Variable in class org.jmol.g3d.Graphics3D
 
plane - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
plane - Variable in class org.jmol.modelsetbio.Resolver
 
plane - Static variable in class org.jmol.script.T
 
plane - Variable in class org.jmol.shapespecial.Draw
 
plane1 - Variable in class org.jmol.adapter.readers.simple.InputReader
 
plane2 - Variable in class org.jmol.adapter.readers.simple.InputReader
 
plane_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
plane_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
planeCenter - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
planeCount - Variable in class org.jmol.jvxl.readers.UhbdReader
 
planeParameter(int) - Method in class org.jmol.script.ScriptParam
 
planeRadius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
planes - Variable in class org.jmol.shapespecial.Polyhedron
 
planeShade - Variable in class org.jmol.g3d.SphereRenderer
 
planeShades - Variable in class org.jmol.g3d.SphereRenderer
 
planesT - Variable in class org.jmol.shapespecial.Polyhedra
 
planeU - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
planeV - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
planeValue(T) - Method in class org.jmol.script.ScriptMathProcessor
 
Platform - Class in org.jmol.awt
 
Platform() - Constructor for class org.jmol.awt.Platform
 
Platform - Class in org.jmol.awtjs
WebGL interface
Platform() - Constructor for class org.jmol.awtjs.Platform
 
Platform - Class in org.jmol.awtjs2d
JavaScript 2D canvas version requires Ajax-based URL stream processing.
Platform() - Constructor for class org.jmol.awtjs2d.Platform
 
platform - Variable in class org.jmol.g3d.Graphics3D
 
Platform3D - Class in org.jmol.g3d
Specifies the API to an underlying int[] buffer of ARGB values that can be converted into an Image object and a short[] for z-buffer depth.
Platform3D(GenericPlatform) - Constructor for class org.jmol.g3d.Platform3D
 
platformspeed - Static variable in class org.jmol.script.T
 
platformSpeed - Variable in class org.jmol.viewer.GlobalSettings
 
play - Static variable in class org.jmol.script.T
 
PLAY - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
playrev - Static variable in class org.jmol.script.T
 
pLeft - Variable in class org.jmol.g3d.HermiteRenderer
 
plot(int, int, int, int, int, String, Font, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.TextRenderer
 
plot - Static variable in class org.jmol.script.T
 
plot(T[]) - Method in class org.jmol.scriptext.CmdExt
 
plot3d - Static variable in class org.jmol.script.T
 
Plot3D - Class in org.jmol.shapesurface
 
Plot3D() - Constructor for class org.jmol.shapesurface.Plot3D
 
Plot3DRenderer - Class in org.jmol.rendersurface
 
Plot3DRenderer() - Constructor for class org.jmol.rendersurface.Plot3DRenderer
 
plotByCharacter(int, int, int, int, int, String, Font, Graphics3D, JmolRendererInterface, boolean) - Static method in class org.jmol.g3d.TextRenderer
 
plotCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
 
plotCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
 
plotDashedLine(int, int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
 
plotFilledCircleCenteredClipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
 
plotFilledCircleCenteredUnclipped(int, int, int, int) - Method in class org.jmol.g3d.CircleRenderer
 
plotImage(int, int, int, Object, short, int, int) - Method in class org.jmol.export.___Exporter
 
plotImage(int, int, int, Object, short, int, int) - Method in class org.jmol.export.__CartesianExporter
 
plotImage(int, int, int, Object, short, int, int) - Method in class org.jmol.export.JSExporter
 
plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotImage(int, int, int, Object, Graphics3D, JmolRendererInterface, boolean, int, int, int) - Static method in class org.jmol.g3d.ImageRenderer
 
plotImage(int, int, int, Object, JmolRendererInterface, short, int, int) - Method in class org.jmol.util.GData
 
plotImagePixel(int, int, int, int, int, int, int, int, int[], Object, int) - Method in interface org.jmol.api.JmolRendererInterface
 
plotImagePixel(int, int, int, int, int, int, int, int, int[], Object, int) - Method in class org.jmol.export.Export3D
 
plotImagePixel(int, int, int, int, int, int, int, int, int[], Object, int) - Method in class org.jmol.g3d.Graphics3D
 
plotLine(int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
 
plotLineClipped(int, int, int, int, int, int, int, int, boolean, int, int) - Method in class org.jmol.g3d.LineRenderer
 
plotLineDelta(int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
 
plotLineDeltaA(int[], int[], int, int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
 
plotLineDeltaBits(int[], int[], int, int, int, int, int, int, int, boolean) - Method in class org.jmol.g3d.LineRenderer
 
plotPixelClipped(int, int, int) - Method in class org.jmol.export.Export3D
 
plotPixelClippedArgb(int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelClippedP3i(P3i) - Method in interface org.jmol.api.JmolRendererInterface
 
plotPixelClippedP3i(P3i) - Method in class org.jmol.export.Export3D
 
plotPixelClippedP3i(P3i) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsClipped(int, int, int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsClippedRaster(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsUnclippedCount(int, int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelsUnclippedRaster(int, int, int, int, int, Rgb16, Rgb16) - Method in class org.jmol.g3d.Graphics3D
 
plotPixelUnclipped(int, int, int, int, int, int[], Pixelator) - Method in class org.jmol.g3d.Graphics3D
 
plotPoints(int, int[], int, int) - Method in class org.jmol.g3d.Graphics3D
 
plotProp() - Method in class org.jmol.scriptext.CmdExt
 
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export.___Exporter
 
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export.__CartesianExporter
 
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export._VrmlExporter
 
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export._X3dExporter
 
plotText(int, int, int, short, String, Font) - Method in class org.jmol.export.JSExporter
 
plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
 
plotText(int, int, int, int, int, String, Font, JmolRendererInterface) - Method in class org.jmol.util.GData
 
PltFormattedReader - Class in org.jmol.jvxl.readers
 
PltFormattedReader() - Constructor for class org.jmol.jvxl.readers.PltFormattedReader
 
plus - Static variable in class org.jmol.script.T
 
plusMinus(String, float, String) - Static method in class org.jmol.symmetry.SymmetryOperation
 
plusPlus - Static variable in class org.jmol.script.T
 
pm - Variable in class org.jmol.scriptext.MathExt
 
pm - Variable in class org.jmol.viewer.Viewer
 
pmesh - Static variable in class org.jmol.script.T
 
Pmesh - Class in org.jmol.shapesurface
 
Pmesh() - Constructor for class org.jmol.shapesurface.Pmesh
 
Pmesh4Reader - Class in org.jmol.jvxl.readers
 
Pmesh4Reader() - Constructor for class org.jmol.jvxl.readers.Pmesh4Reader
 
PMESH_BINARY_MAGIC_NUMBER - Static variable in class org.jmol.io.JmolBinary
 
pmeshError - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
 
pmeshError - Variable in class org.jmol.jvxl.readers.PmeshReader
 
PmeshReader - Class in org.jmol.jvxl.readers
 
PmeshReader() - Constructor for class org.jmol.jvxl.readers.PmeshReader
 
PmeshRenderer - Class in org.jmol.rendersurface
 
PmeshRenderer() - Constructor for class org.jmol.rendersurface.PmeshRenderer
 
png_file_gamma - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
png_screen_gamma - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pngjCache - Variable in class org.jmol.io.JmolBinary
 
pocket - Variable in class org.jmol.jvxl.readers.Parameters
 
pocket - Static variable in class org.jmol.script.T
 
point - Variable in class org.jmol.jvxl.readers.Parameters
 
point - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
point - Static variable in class org.jmol.script.T
 
point3f - Static variable in class org.jmol.script.T
 
Point3fi - Class in org.jmol.util
the Point3fi class allows storage of critical information involving an atom, picked bond, or measurement point, including: xyz position screen position screen radius (-1 for a simple point) index (for atoms or for an associated bond that has be picked) associated modelIndex (for measurement points)
Point3fi() - Constructor for class org.jmol.util.Point3fi
 
point3fScreenTemp - Variable in class org.jmol.viewer.TransformManager
 
point3iScreenTemp - Variable in class org.jmol.viewer.TransformManager
 
point4f - Static variable in class org.jmol.script.T
 
pointA - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
pointA - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pointArrowHead - Variable in class org.jmol.renderspecial.VectorsRenderer
 
pointAt(Lst<Object>, int, P3) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
pointB - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
pointer - Variable in class org.jmol.modelset.Object2d
 
pointer - Variable in class org.jmol.render.LabelsRenderer
 
POINTER_BACKGROUND - Static variable in class org.jmol.viewer.JC
 
POINTER_NONE - Static variable in class org.jmol.viewer.JC
 
POINTER_ON - Static variable in class org.jmol.viewer.JC
 
pointerPt - Variable in class org.jmol.modelset.Text
 
pointGroup - Variable in class org.jmol.modelset.ModelSet
 
pointgroup - Static variable in class org.jmol.script.T
 
PointGroup - Class in org.jmol.symmetry
 
PointGroup() - Constructor for class org.jmol.symmetry.PointGroup
 
pointGroup - Variable in class org.jmol.symmetry.Symmetry
 
PointGroup.Operation - Class in org.jmol.symmetry
 
pointgroupdistancetolerance - Static variable in class org.jmol.script.T
 
pointGroupDistanceTolerance - Variable in class org.jmol.viewer.GlobalSettings
 
pointgrouplineartolerance - Static variable in class org.jmol.script.T
 
pointGroupLinearTolerance - Variable in class org.jmol.viewer.GlobalSettings
 
pointGuides - Variable in class org.jmol.navigate.Navigator
 
pointPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d, boolean) - Static method in class org.jmol.minimize.Util
calculates angle of a to plane bcd, returning a value > pi/2 in highly distorted trigonal pyramidal situations
points - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
points - Variable in class org.jmol.jvxl.readers.Parameters
 
points - Variable in class org.jmol.modelset.MeasurementData
 
points - Variable in class org.jmol.navigate.Navigator
 
points - Variable in class org.jmol.quantum.QuantumCalculation
 
points - Variable in class org.jmol.renderspecial.DipolesRenderer
 
points - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
points - Variable in class org.jmol.smiles.SmilesMeasure
 
points - Variable in class org.jmol.symmetry.PointGroup
 
POINTS_ALL - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
POINTS_HETS - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
POINTS_MCMC - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
POINTS_MCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
POINTS_SCSC - Static variable in class org.jmol.jvxl.readers.KinemageReader
 
pointSize - Variable in class org.jmol.jvxl.data.JvxlData
 
pointSize - Variable in class org.jmol.jvxl.readers.Parameters
 
pointsPerAngstrom - Variable in class org.jmol.jvxl.data.JvxlData
 
pointsperangstrom - Static variable in class org.jmol.script.T
 
pointT - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
pointT - Variable in class org.jmol.render.FontLineShapeRenderer
 
pointT - Variable in class org.jmol.renderbio.BioShapeRenderer
 
pointT2 - Variable in class org.jmol.render.FontLineShapeRenderer
 
pointT2 - Variable in class org.jmol.viewer.TransformManager
 
pointT3 - Variable in class org.jmol.render.FontLineShapeRenderer
 
pointType - Variable in class org.jmol.jvxl.readers.KinemageReader
 
pointVectorEnd - Variable in class org.jmol.renderspecial.VectorsRenderer
 
pointVectorStart - Variable in class org.jmol.renderspecial.VectorsRenderer
 
polar_neighbor_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
polygon - Static variable in class org.jmol.script.T
 
polygon - Variable in class org.jmol.shapespecial.Draw
 
polygonColorData - Variable in class org.jmol.jvxl.data.MeshData
 
polygonCount0 - Variable in class org.jmol.util.MeshSurface
 
PolygonFileReader - Class in org.jmol.jvxl.readers
 
PolygonFileReader() - Constructor for class org.jmol.jvxl.readers.PolygonFileReader
 
polyhedra - Static variable in class org.jmol.script.T
 
polyhedra() - Method in class org.jmol.scriptext.CmdExt
 
Polyhedra - Class in org.jmol.shapespecial
 
Polyhedra() - Constructor for class org.jmol.shapespecial.Polyhedra
 
PolyhedraRenderer - Class in org.jmol.renderspecial
 
PolyhedraRenderer() - Constructor for class org.jmol.renderspecial.PolyhedraRenderer
 
Polyhedron - Class in org.jmol.shapespecial
 
Polyhedron(Atom, int, int, int, P3[], short[], byte[], boolean, float, float) - Constructor for class org.jmol.shapespecial.Polyhedron
 
polyhedronCount - Variable in class org.jmol.shapespecial.Polyhedra
 
polyhedrons - Variable in class org.jmol.shapespecial.Polyhedra
 
polymer - Static variable in class org.jmol.script.T
 
polymerlength - Static variable in class org.jmol.script.T
 
pop() - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
pop - Static variable in class org.jmol.script.T
 
popContext(boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
popHoldRepaint(boolean, String) - Method in interface org.jmol.api.JmolRepaintManager
 
popHoldRepaint(String) - Method in class org.jmol.api.JmolViewer
 
popHoldRepaint(boolean, String) - Method in class org.jmol.render.RepaintManager
 
popHoldRepaint(String) - Method in class org.jmol.viewer.Viewer
 
popInHeight - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
PopInJmol - Class in org.openscience.jmol.app.webexport
 
PopInJmol(Viewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.PopInJmol
 
popInWidth - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
popup - Variable in class org.jmol.popup.AwtSwingPopupHelper
 
popup - Variable in class org.jmol.popup.JSSwingPopupHelper
used here and by SwingController to refer to the Java class being handled by this helper.
PopupHelper - Interface in org.jmol.popup
 
popupMenu - Variable in class org.jmol.popup.GenericSwingPopup
 
popupMenu(int, int, char) - Method in class org.jmol.viewer.Viewer
 
PopupResource - Class in org.jmol.popup
 
PopupResource(String, Properties) - Constructor for class org.jmol.popup.PopupResource
 
port - Variable in class org.openscience.jmol.app.JmolApp
The data model.
port - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
posCorner - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
position - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
position - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
position - Variable in class org.openscience.jvxl.MonitorInputStream
 
positionAfterPrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
positionBeforePrompt - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
positionMin - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
positionSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
positionThicknessPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
postByteArray(String, byte[]) - Method in class org.jmol.viewer.FileManager
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
postProcessVertices() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
potentials - Variable in class org.jmol.quantum.MepCalculation
 
povrayAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PovrayAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PovrayAction
 
povrayActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PovrayDialog - Class in org.openscience.jmol.app.jmolpanel
A dialog for controling the creation of a povray input file from a Chemframe and a display.
PovrayDialog(JFrame, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog
Creates a dialog for getting info related to output frames in povray format.
PovrayDialog.PovrayWindowListener - Class in org.openscience.jmol.app.jmolpanel
Listener for responding to dialog window events.
povrayPathButton - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
povrayPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
PovrayWindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.PovrayDialog.PovrayWindowListener
 
power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
power4 - Static variable in class org.jmol.geodesic.EnvelopeCalculation
 
pqr_workarounds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pqrLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
PqrReader - Class in org.jmol.adapter.readers.pdb
PQR file reader.
PqrReader() - Constructor for class org.jmol.adapter.readers.pdb.PqrReader
 
precalculateVoxelData - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
precision - Variable in class org.jmol.modelset.LabelToken
 
predefinedGroup1Names - Static variable in class org.jmol.modelsetbio.Resolver
 
predefinedGroup3Names - Static variable in class org.jmol.modelsetbio.Resolver
 
predefinedset - Static variable in class org.jmol.script.T
 
predefinedStatic - Static variable in class org.jmol.viewer.JC
 
predefinedVariable - Static variable in class org.jmol.viewer.JC
 
preDefining - Variable in class org.jmol.script.ScriptCompiler
 
predragBinding - Variable in class org.jmol.viewer.ActionManager
 
preferencesDialog - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PreferencesDialog - Class in org.openscience.jmol.app.jmolpanel
 
PreferencesDialog(JmolPanel, JFrame, GuiMap, Viewer) - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
PreferencesDialog.PrefsAction - Class in org.openscience.jmol.app.jmolpanel
 
prefsAction - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
PrefsAction() - Constructor for class org.openscience.jmol.app.jmolpanel.PreferencesDialog.PrefsAction
 
preloadClassIndex - Variable in class org.jmol.applet.AppletWrapper
 
preloadClassNames - Variable in class org.jmol.applet.AppletWrapper
 
preloadImage - Variable in class org.jmol.applet.AppletWrapper
 
preloadImageName - Variable in class org.jmol.applet.AppletWrapper
 
preloadImagePainted - Variable in class org.jmol.applet.AppletWrapper
 
preloadImageReadyForDisplay - Variable in class org.jmol.applet.AppletWrapper
 
preloadTextMessage - Variable in class org.jmol.applet.AppletWrapper
 
preloadThreadCount - Variable in class org.jmol.applet.AppletWrapper
 
preProcessPlanes - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
presentation - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
presentation_auto_quit - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
presentation_auto_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
presentation_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
preserve_chempy_ids - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
preserveState - Variable in class org.jmol.modelset.AtomCollection
 
preservestate - Static variable in class org.jmol.script.T
 
preserveState - Variable in class org.jmol.viewer.GlobalSettings
 
pressAction - Variable in class org.jmol.viewer.ActionManager
 
pressed(long, int, int, int, boolean) - Method in class org.jmol.awtjs2d.Mouse
 
pressed - Variable in class org.jmol.viewer.ActionManager
 
pressedCount - Variable in class org.jmol.viewer.ActionManager
 
prev - Static variable in class org.jmol.script.T
 
prev - Variable in class org.jmol.util.MeshCapper.CapVertex
edge double links
prevAtom - Variable in class org.jmol.smiles.SmilesGenerator
 
prevCovalentVersion - Static variable in class org.jmol.script.ScriptManager
 
prevFrame - Variable in class org.jmol.viewer.Viewer
 
PREVIOUS - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.Mesh
 
PREVIOUS_MESH_ID - Static variable in class org.jmol.shape.MeshCollection
 
previousClassName - Variable in class org.jmol.applet.AppletWrapper
 
previousMeshID - Variable in class org.jmol.shape.MeshCollection
 
previousMoveTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
previousScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
previousSpaceGroup - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
previousUnitCell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
previousX - Variable in class org.jmol.viewer.TransformManager
 
previousY - Variable in class org.jmol.viewer.TransformManager
 
prevline - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
prevMorphModel - Variable in class org.jmol.viewer.Viewer
 
prevSp2Atoms - Variable in class org.jmol.smiles.SmilesGenerator
 
prevZoomSetting - Variable in class org.jmol.viewer.TransformManager
 
pRight - Variable in class org.jmol.g3d.HermiteRenderer
 
primitiveCode - Variable in class org.jmol.symmetry.HallRotationTerm
 
primitiveData - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
primitiveDensity - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
primitiveHallSymbol - Variable in class org.jmol.symmetry.HallInfo
 
primitives - Variable in class org.jmol.smiles.SmilesAtom
 
primitives - Variable in class org.jmol.smiles.SmilesBond
 
primitiveToCryst - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
primitiveToIndex - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
primitiveVolume - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
principalAxis - Variable in class org.jmol.symmetry.PointGroup
 
principalPlane - Variable in class org.jmol.symmetry.PointGroup
 
principalQuantumNumber - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
print - Static variable in class org.jmol.script.T
 
print(Graphics, PageFormat, int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
print() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
added print command, so that it can be used by RasmolScriptHandler
printAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
PrintAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.PrintAction
 
printActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
privateKey - Variable in class org.jmol.export.___Exporter
 
privateKey - Variable in class org.jmol.export.Export3D
 
privateKey - Variable in class org.jmol.viewer.OutputManager
 
privateKey - Variable in class org.jmol.viewer.Viewer
 
probe - Static variable in class org.jmol.script.T
 
proc - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
process(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
The main processor.
process(int, int, float) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
Data mapping function to radically increase speed and reduce memory requirements of mapping data when the mapping comes from the same data set as the points, so isosurface creation and data mapping can be carried out both in the first (and only) pass.
process() - Method in class org.jmol.quantum.MepCalculation
 
process() - Method in class org.jmol.quantum.MOCalculation
 
process() - Method in class org.jmol.quantum.NciCalculation
 
process(int, int, float) - Method in class org.jmol.quantum.NciCalculation
Passing the grid points of the two ends of an edge and a fraction to this method returns the value at a triangle point.
process() - Method in class org.jmol.quantum.QuantumCalculation
 
process - Variable in class org.jmol.script.ScriptProcessRunnable
 
process - Static variable in class org.jmol.script.T
 
process(MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
Handle the point; mark as processed.
processAddedData() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processAssemblyGenBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processAtom(Atom, String, char, String, int, int, char, boolean, String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
processAtom() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
 
processAtom2(Atom, int, float, float, float, int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
processAtomicCharges() - Method in class org.jmol.adapter.readers.simple.MopacReader
Reads the section in MOPAC files with atomic charges.
processAtomObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processAtoms() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processAtoms(int, int, int, int) - Method in class org.jmol.quantum.NciCalculation
At each grid point we need to calculate the sum of the atom-based promolecular data.
processAtomSiteLoopBlock(boolean) - Method in class org.jmol.adapter.readers.cif.CifReader
reads atom data in any order
processAtomTypeLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.
processBasisObject(String) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processBinaryDocument() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
processBinaryDocument() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
processBinaryDocument() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
processBirth(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processBondObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processBonds() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processCellParameter() - Method in class org.jmol.adapter.readers.cif.CifReader
unit cell parameters -- two options, so we use MOD 6
processCGO(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create a CGO JmolObject, just passing on key information.
processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.SinglePointGesture
incorporates double-click gesture
processChange(List<TouchPoint>, TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processChangeSync(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processCharges() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processChemCompLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
a general name definition field.
processChemicalInfo(String) - Method in class org.jmol.adapter.readers.cif.CifReader
reads some of the more interesting info into specific atomSetAuxiliaryInfo elements
processCitationListBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
 
processClickCallback(SC, String) - Method in class org.jmol.popup.GenericSwingPopup
 
processCmdfAtoms() - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
processCommand(int) - Method in class org.jmol.script.ScriptEval
 
processComponentKeyEvent(KeyEvent) - Method in class org.jmol.console.AppletConsole.ControlEnterTextArea
 
processConnectorObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processCoord() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processCoordinates() - Method in class org.jmol.adapter.readers.simple.MopacReader
Reads the section in MOPAC files with cartesian coordinates.
processCtab(boolean) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
processDataAssemblyGen() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processDataNonpoly() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processDataParameter() - Method in class org.jmol.adapter.readers.cif.CifReader
initialize a new atom set
processDeath(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processDefinitions() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create a JmolObject that will define atom sets based on PyMOL objects
processDeletedModelAtoms(BS) - Method in class org.jmol.viewer.SelectionManager
 
processDOM(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processDOM(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
processDSSR(GenericLineReader, Map<String, String>) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
processDSSR(Map<String, Object>, GenericLineReader, String, Map<String, String>) - Method in interface org.jmol.api.JmolAnnotationParser
 
processDSSR(Map<String, Object>, GenericLineReader, String, Map<String, String>) - Method in class org.jmol.dssx.AnnotationParser
 
processEnd2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
processEndElement(String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
processEntry() - Method in class org.jmol.adapter.readers.cif.MSCifRdr
 
processes - Variable in class org.jmol.script.ScriptParallelProcessor
 
processEvent(int, int, int, int, long) - Method in class org.jmol.awt.Mouse
 
processEvent(int, int, int, int, long) - Method in class org.jmol.awtjs2d.Mouse
 
processEvent(int, Event) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
Translate the specialized Sparsh UI information into a format that Jmol's ActionManager can understand without any special classes.
processFile(String, File, File, boolean, boolean) - Method in class org.openscience.chimetojmol.ChimePanel
 
processGadget(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Only process _e_pot objects -- which we need for color settings
processGeomBondLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
reads bond data -- N_ijk symmetry business is ignored, so we only indicate bonds within the unit cell to just the original set of atoms.
processHeader() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processInfo() - Method in class org.jmol.adapter.readers.simple.GhemicalMMReader
 
processing - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processJSON(JsonNioService.JSONObject, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
processKey(int, int, boolean) - Method in class org.jmol.console.GenericConsole
 
processKeyEvent(KeyEvent) - Method in class org.jmol.console.ScriptEditor.EditorTextPane
 
processKeyEvent(KeyEvent) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
Custom key event processing for command 0 implementation.
processLigandBondLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processLocalTransform() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processLock - Variable in class org.jmol.script.ScriptProcessRunnable
 
processLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
processes loop_ blocks of interest or skips the data
processLoopBlock() - Method in class org.jmol.adapter.readers.cif.MSCifRdr
creates entries in htModulation with a key of the form: type_id_axis;atomLabel@model where type = W|F|D|O (wave vector, Fourier index, displacement, occupancy); id = 1|2|3|0|S (Fourier index, Crenel(0), sawtooth); axis (optional) = 0|x|y|z (0 indicates irrelevant -- occupancy); and ;atomLabel is only for D and O.
processMap(Lst<Object>, boolean, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create mapObjects and volumeData; create an ISOSURFACE JmolObject.
processMeasure(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create a MEASURE JmolObject.
processMeshes() - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create mesh or mep JmolObjects.
processMessage(byte[], NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
processModelData(String, String, String, String, String, float, float, boolean) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
processModelData(String, String, String, String, String, float, float, boolean) - Method in interface org.jmol.api.JmolJDXMOLReader
 
processMol() - Method in class org.jmol.adapter.readers.simple.HyperChemReader
 
processMolCryst(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Pick up the crystal data.
processMolecularOrbitalObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processMolecule() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
processMolecule(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create everything necessary to generate a molecule in Jmol.
processMolSdHeader() - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
processMonotonic(MeshCapper.CapVertex, boolean) - Method in class org.jmol.util.MeshCapper
Process a standard monotonic region, cleaving off as many triangles as possible.
processMouseEvent(int, int, int, int, long) - Method in class org.jmol.appletjs.Jmol
 
processMouseEvent(int, int, int, int, long) - Method in class org.jmol.viewer.Viewer
 
processMove(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
processMovie(Lst<Object>, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create a JmolObject that will represent the movie.
processMultiFrameOutput(String, BS, int, Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
 
processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.multitouch.ActionManagerMT
 
processMultitouchEvent(int, int, int, int, P3, long) - Method in interface org.jmol.multitouch.JmolMultiTouchClient
 
processMultitouchEvent(int, int, int, int, P3, long) - Method in class org.jmol.viewer.ActionManager
Specific to ActionManagerMT -- for processing SparshUI gestures
processName - Variable in class org.jmol.script.ScriptProcess
 
processNextMeasure(Measurement) - Method in interface org.jmol.api.JmolMeasurementClient
 
processNextMeasure(Measurement) - Method in class org.jmol.modelset.MeasurementData
if this is the client, then this method is called by MeasurementData when a measurement is ready
processNextMeasure(Measurement) - Method in class org.jmol.shape.Measures
 
processNonpolyLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
a HETERO name definition field.
processObject(Lst<Object>, boolean, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
The main object processor.
processOneCubical(int, int, int, int, int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
processPeakData() - Method in class org.jmol.adapter.readers.more.JcampdxReader
integrate the records into the associated models, and delete unreferenced n.m models
processPeakSelectAtom(int, String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
processPeakSelectModel(int, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
processPoints() - Method in class org.jmol.quantum.MOCalculation
 
processPoints() - Method in class org.jmol.quantum.QuantumCalculation
 
processPosition(String, Atom, boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
We process the Pos#n record here.
processPt(T3) - Method in interface org.jmol.api.MOCalculationInterface
 
processPt(T3) - Method in class org.jmol.quantum.QuantumCalculation
 
processResult() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
processScript(Object[]) - Method in class org.jmol.viewer.StatusManager
 
processSelectionsAndScenes(Map<String, Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
A PyMOL scene consists of one or more of: view frame visibilities, by object colors, by color reps, by type currently just extracts viewpoint
processSequence() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processShapeCommand(int) - Method in class org.jmol.script.ScriptEval
 
processShell(int) - Method in class org.jmol.quantum.MOCalculation
 
processSlater(int) - Method in class org.jmol.quantum.MOCalculation
 
processSplit(MeshCapper.CapVertex, MeshCapper.CapVertex) - Method in class org.jmol.util.MeshCapper
Process what M3O refer to as a "split" vertex, which we handle differently here, cloning the "helper" point and the "split" point, creating a new region if necessary, and then swapping pointers.
processStart2(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlArgusReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlMolproReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
processStartElement(String) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
processState() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
processStructConfLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
identifies ranges for HELIX and TURN
processStructOperListBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processStructSheetRangeLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
identifies sheet ranges
processStructSiteBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
identifies structure sites
processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.CifReader
 
processSubclassAtom(Atom, String, String) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.CifReader
 
processSubclassEntry() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
 
processSubclassLoopBlock() - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
processSubsystemLoopBlock() - Method in class org.jmol.adapter.readers.cif.MSCifRdr
 
processSupportedRecord(int) - Method in class org.jmol.adapter.readers.xtal.ShelxReader
 
processSymmetryOperationsLoopBlock() - Method in class org.jmol.adapter.readers.cif.CifReader
retrieves symmetry operations
processSymmetrySpaceGroupName() - Method in class org.jmol.adapter.readers.cif.CifReader
done by AtomSetCollectionReader
processSync(String, int) - Method in interface org.jmol.api.JmolJSpecView
 
processSync(String, int) - Method in class org.jmol.jsv.JSpecView
 
processTokenList(short, boolean) - Method in class org.jmol.script.ScriptCompiler
 
processTotalEnergy() - Method in class org.jmol.adapter.readers.simple.MopacReader
 
processTriangles(int) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
processTriangles(int) - Method in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
processTry(Map<String, SV>) - Method in class org.jmol.script.ScriptEval
 
processTwoPointGesture(float[][][]) - Method in class org.jmol.appletjs.Jmol
 
processTwoPointGesture(float[][][]) - Method in class org.jmol.awt.Mouse
 
processTwoPointGesture(float[][][]) - Method in class org.jmol.awtjs2d.Mouse
called by JSmol as processTwoPointGesture(canvas.touches);
processTwoPointGesture(float[][][]) - Method in class org.jmol.viewer.Viewer
 
processType() - Method in class org.jmol.util.Tensor
Sets typeFactor, altType, isIsotropic, forThermalEllipsoid; type "iso" changed to "" here.
processUnitCellTransform() - Method in class org.jmol.adapter.readers.cif.CifReader
 
processUnitCellTransformMatrix() - Method in class org.jmol.adapter.readers.cif.CifReader
the PDB transformation matrix cartesian --> fractional
processVibrationObject() - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
processWriteOrCapture(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
 
processWriteOrCapture(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
from eval write command only includes option to write set of files
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlChem3dReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlMagResReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlQEReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlVaspReader
 
processXml(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlXsdReader
 
procSpinner - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
programInfo - Variable in class org.jmol.atomdata.AtomData
 
prompt(String, String, String[], boolean) - Static method in class org.jmol.awt.Display
 
prompt(String, String, String[], boolean) - Method in class org.jmol.awt.Platform
 
prompt(String, String, String[], boolean) - Static method in class org.jmol.awtjs2d.Display
 
prompt(String, String, String[], boolean) - Method in class org.jmol.awtjs2d.Platform
 
prompt - Static variable in class org.jmol.script.T
 
prompt(String, String, String[], boolean) - Method in class org.jmol.viewer.Viewer
 
prompt - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
prop - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
PROP_ANIMATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_APPLET_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ATOM_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ATOM_LIST - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_AUXILIARY_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_BOND_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_BOUNDBOX_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_CENTER_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_CHAIN_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_CONSOLE_TEXT - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_COUNT - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_DATA_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_DOM_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ERROR_MESSAGE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_EVALUATE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_EXTRACT_MODEL - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILECONTENTS - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILECONTENTS_PATH - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILEHEADER - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_FILENAME - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_IMAGE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ISOSURFACE_DATA - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ISOSURFACE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_JMOL_STATUS - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_JMOL_VIEWER - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_JSPECVIEW - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_LIGAND_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MEASUREMENT_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MENU - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MESSAGE_QUEUE - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MINIMIZATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MODEL_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MOLECULE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_MOUSE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_NMR_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_ORIENTATION_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_POINTGROUP_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_POLYMER_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_SCRIPT_QUEUE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_SHAPE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_STATE_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_TRANSFORM_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_VAL_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
PROP_VAR_INFO - Static variable in class org.jmol.viewer.PropertyManager
 
properties - Variable in class org.jmol.modelset.Model
 
properties - Variable in class org.openscience.jmol.app.HistoryFile
The data stored in the history file.
propertiesFileName - Static variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
propertiesTextArea - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
property - Static variable in class org.jmol.script.T
 
PROPERTY_MODES - Static variable in class org.jmol.shapespecial.Ellipsoids
 
propertyatomnumbercolumncount - Static variable in class org.jmol.script.T
 
propertyatomnumberfield - Static variable in class org.jmol.script.T
 
propertyChange(PropertyChangeEvent) - Method in class org.jmol.dialog.FilePreview
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
propertyChange(PropertyChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.ActionChangedListener
 
propertycolorscheme - Static variable in class org.jmol.script.T
 
propertyColorScheme - Variable in class org.jmol.viewer.GlobalSettings
 
propertyCount - Variable in class org.jmol.adapter.readers.cif.CifReader
 
propertydatacolumncount - Static variable in class org.jmol.script.T
 
propertydatafield - Static variable in class org.jmol.script.T
 
propertyDistanceMax - Variable in class org.jmol.jvxl.readers.Parameters
 
PROPERTYFLAGS - Static variable in class org.jmol.script.T
 
propertyItemCounts - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
PropertyManager - Class in org.jmol.viewer
The PropertyManager handles all operations relating to delivery of properties with the getProperty() method, or its specifically cast forms getPropertyString() or getPropertyJSON().
PropertyManager() - Constructor for class org.jmol.viewer.PropertyManager
 
propertyOf - Variable in class org.jmol.adapter.readers.cif.CifReader
 
propertySmoothing - Variable in class org.jmol.jvxl.readers.Parameters
 
propertySmoothingPower - Variable in class org.jmol.jvxl.readers.Parameters
 
propertyTypes - Static variable in class org.jmol.viewer.PropertyManager
 
props - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
propselector - Static variable in class org.jmol.script.T
 
protein - Static variable in class org.jmol.script.T
 
proteinStructure - Variable in class org.jmol.modelsetbio.AlphaMonomer
 
ProteinStructure - Class in org.jmol.modelsetbio
 
ProteinStructure() - Constructor for class org.jmol.modelsetbio.ProteinStructure
 
proteinstructurePending - Variable in class org.jmol.renderbio.RocketRenderer
 
proteinStructureTainted - Variable in class org.jmol.modelset.ModelSet
 
pS - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
psi - Variable in class org.jmol.modelsetbio.Monomer
 
psi - Static variable in class org.jmol.script.T
 
psi_l - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_l - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_m - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_m - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_monteCarloCount - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_n - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_n - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_normalization - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
psi_Znuc - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
psi_Znuc - Variable in class org.jmol.jvxl.readers.Parameters
 
psiContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
PsiReader - Class in org.jmol.adapter.readers.quantum
Reader for Psi3 output files.
PsiReader() - Constructor for class org.jmol.adapter.readers.quantum.PsiReader
 
pt - Variable in enum org.jmol.c.VDW
 
pt - Variable in class org.jmol.jvxl.readers.DelPhiBinaryReader
 
pt - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
pt - Variable in class org.jmol.jvxl.readers.NffReader
 
pt - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
pt - Variable in class org.jmol.jvxl.readers.UhbdReader
 
pt - Variable in class org.jmol.jvxl.readers.VaspChgcarReader
 
pt - Variable in class org.jmol.modelset.LabelToken
 
pt - Variable in class org.jmol.render.CageRenderer
 
pt - Variable in class org.jmol.renderbio.BioShapeRenderer
 
pt - Variable in class org.jmol.script.ScriptQueueThread
 
pt - Variable in class org.jmol.util.ContactPair
 
pt - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
 
pt0 - Variable in class org.jmol.adapter.readers.simple.InputReader
 
pt0 - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
pt0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
pt0 - Variable in class org.jmol.renderspecial.DrawRenderer
 
pt0 - Variable in class org.jmol.script.ScriptFlowContext
 
pt0 - Variable in class org.jmol.script.ScriptFunction
 
pt0 - Static variable in class org.jmol.script.SV
 
pt0 - Static variable in class org.jmol.shape.Axes
 
pt0f - Variable in class org.jmol.renderspecial.DrawRenderer
 
pt0i - Variable in class org.jmol.render.FontLineShapeRenderer
 
pt0i - Variable in class org.jmol.renderspecial.DrawRenderer
 
pt1 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
pt1 - Variable in class org.jmol.renderbio.BioShapeRenderer
 
pt1 - Variable in class org.jmol.renderspecial.DrawRenderer
 
pt1 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
pt1 - Variable in class org.jmol.shapesurface.Contact
 
pt1f - Variable in class org.jmol.render.MeshRenderer
 
pt1i - Variable in class org.jmol.render.FontLineShapeRenderer
 
pt1i - Variable in class org.jmol.render.MeshRenderer
 
pt2 - Variable in class org.jmol.renderspecial.DrawRenderer
 
pt2 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
pt2 - Variable in class org.jmol.shapesurface.Contact
 
pt2f - Variable in class org.jmol.render.MeshRenderer
 
pt2i - Variable in class org.jmol.render.FontLineShapeRenderer
 
pt2i - Variable in class org.jmol.render.MeshRenderer
 
pt3 - Variable in class org.jmol.rendercgo.CGORenderer
 
pt3i - Variable in class org.jmol.render.MeshRenderer
 
pt4Value(SV) - Static method in class org.jmol.script.SV
 
PT_BITSET - Static variable in class org.jmol.shapespecial.Draw
 
PT_CHARGE - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
PT_CONNECT - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
PT_COORD - Static variable in class org.jmol.shapespecial.Draw
 
PT_ELEMENT - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
PT_IDENTIFIER - Static variable in class org.jmol.shapespecial.Draw
 
PT_MODEL_BASED_POINTS - Static variable in class org.jmol.shapespecial.Draw
 
PT_MODEL_INDEX - Static variable in class org.jmol.shapespecial.Draw
 
ptA - Variable in class org.jmol.export.Export3D
 
ptAi - Variable in class org.jmol.export.Export3D
 
ptB - Variable in class org.jmol.export.Export3D
 
ptBi - Variable in class org.jmol.export.Export3D
 
ptC - Variable in class org.jmol.export.Export3D
 
ptC - Variable in class org.jmol.renderbio.RocketRenderer
 
ptCenter - Variable in class org.jmol.shape.Mesh
 
ptCenter - Variable in class org.jmol.shapespecial.Polyhedron
 
ptCenters - Variable in class org.jmol.shapespecial.DrawMesh
 
ptColor - Variable in class org.jmol.rendercgo.CGORenderer
 
ptCommand - Variable in class org.jmol.script.ScriptFlowContext
 
ptD - Variable in class org.jmol.export.Export3D
 
ptDefault - Variable in class org.jmol.script.ScriptFlowContext
 
ptDefaultLattice - Variable in class org.jmol.viewer.GlobalSettings
 
pTemp - Variable in class org.jmol.render.LabelsRenderer
 
ptFloat - Variable in class org.jmol.adapter.readers.more.MdCrdReader
 
ptid - Variable in class org.jmol.script.ScriptMathProcessor
 
ptLine - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ptLine - Variable in class org.jmol.script.ScriptFlowContext
 
ptList - Variable in class org.jmol.shapespecial.Draw
 
ptMax - Variable in class org.jmol.export._IdtfExporter
 
ptMin - Variable in class org.jmol.export._IdtfExporter
 
ptMoveToCenter - Variable in class org.jmol.thread.MoveToThread
 
ptNewSetModifier - Variable in class org.jmol.script.ScriptTokenParser
 
ptNext - Variable in class org.jmol.renderbio.BioShapeRenderer
 
ptNext - Variable in class org.jmol.viewer.Gesture
 
ptNormal - Variable in class org.jmol.rendercgo.CGORenderer
 
pto - Variable in class org.jmol.script.ScriptMathProcessor
 
ptOffset - Variable in class org.jmol.adapter.readers.cif.CifReader
 
ptOffset - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
ptOffset - Variable in class org.jmol.viewer.TransformManager
 
pTopLeft - Variable in class org.jmol.g3d.HermiteRenderer
 
pTopRight - Variable in class org.jmol.g3d.HermiteRenderer
 
ptOriginShift - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
ptPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
 
ptPsi - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
ptRef - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
pts - Variable in class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
pts - Variable in class org.jmol.modelset.Measurement
 
pts - Variable in class org.jmol.util.MeshSlicer
 
ptS1 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
ptS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
ptScaled - Variable in class org.jmol.export.__CartesianExporter
 
ptSemi - Variable in class org.jmol.script.ScriptCompiler
 
ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
ptSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
ptSupercell - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
ptTemp - Static variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
ptTemp - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
ptTemp - Variable in class org.jmol.export._ObjExporter
 
ptTemp - Variable in class org.jmol.g3d.SphereRenderer
 
ptTemp - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
ptTemp - Variable in class org.jmol.jvxl.data.VolumeData
 
ptTemp - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
ptTemp - Variable in class org.jmol.modelset.ModelSet
 
ptTemp - Variable in class org.jmol.modelsetbio.AminoMonomer
 
ptTemp - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
ptTemp - Variable in class org.jmol.render.HoverRenderer
 
ptTemp - Variable in class org.jmol.renderspecial.VectorsRenderer
 
ptTemp - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
ptTemp - Variable in class org.jmol.script.ScriptExpr
 
ptTemp - Variable in class org.jmol.shape.Axes
 
ptTemp - Variable in class org.jmol.shape.Labels
 
ptTemp - Variable in class org.jmol.util.ModulationSet
 
ptTemp - Variable in class org.jmol.viewer.Viewer
 
ptTemp1 - Variable in class org.jmol.modelset.ModelSet
 
ptTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
ptTemp2 - Variable in class org.jmol.modelset.ModelSet
 
ptTempi - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
ptTest1 - Variable in class org.jmol.viewer.TransformManager
 
ptTest2 - Variable in class org.jmol.viewer.TransformManager
 
ptTest3 - Variable in class org.jmol.viewer.TransformManager
 
ptTip - Variable in class org.jmol.renderbio.RocketRenderer
 
ptTrans - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
ptV - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
ptValue(SV, boolean) - Method in class org.jmol.script.ScriptMathProcessor
 
ptValue(SV) - Static method in class org.jmol.script.SV
 
ptVibTemp - Variable in class org.jmol.viewer.TransformManager
 
ptx - Variable in class org.jmol.script.ScriptMathProcessor
 
ptXY - Variable in class org.jmol.shape.Sticks
 
ptXY - Variable in class org.jmol.shapespecial.Draw
 
ptXY - Variable in class org.jmol.shapesurface.Isosurface
 
ptXyzTemp - Variable in class org.jmol.jvxl.data.VolumeData
 
ptY0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
ptZ0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
pubChemFormat - Variable in class org.jmol.viewer.GlobalSettings
 
purging - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
 
purine - Static variable in class org.jmol.script.T
 
PURPLE - Static variable in class org.jmol.util.C
 
push(Object) - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
push - Static variable in class org.jmol.script.T
 
pushContext(ContextToken, String) - Method in class org.jmol.script.ScriptEval
 
pushContext2(ContextToken, String) - Method in class org.jmol.script.ScriptEval
 
pushContextDown(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
pushContextDown(String) - Method in class org.jmol.script.ScriptEval
 
pushCount - Variable in class org.jmol.script.ScriptCompiler
 
pushHoldRepaint(String) - Method in interface org.jmol.api.JmolRepaintManager
 
pushHoldRepaint() - Method in class org.jmol.api.JmolViewer
 
pushHoldRepaint(String) - Method in class org.jmol.render.RepaintManager
 
pushHoldRepaint() - Method in class org.jmol.viewer.Viewer
 
pushHoldRepaintWhy(String) - Method in class org.jmol.viewer.Viewer
 
pushPop(SV, SV) - Method in class org.jmol.script.SV
Script variables are pushed after cloning, because the name comes with them when we do otherwise they are not mutable anyway.
put(int, int) - Method in class org.jmol.util.Int2IntHash
 
putBox(int, float[]) - Method in class org.jmol.shape.Labels
 
putCoord(V3d, double[]) - Static method in class org.jmol.minimize.Util
 
putFileContents(File, String) - Method in class org.openscience.chimetojmol.ChimePanel
 
putIf(char) - Method in class org.jmol.script.ScriptMathProcessor
 
putLabel(int, Text) - Method in class org.jmol.shape.Labels
 
putMark(int) - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
putMemo(int, boolean) - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
putOp(T) - Method in class org.jmol.script.ScriptMathProcessor
 
PUTTY_AbsoluteLinear - Static variable in class org.jmol.shapebio.Trace
 
PUTTY_AbsoluteNonlinear - Static variable in class org.jmol.shapebio.Trace
 
PUTTY_ImpliedRMS - Static variable in class org.jmol.shapebio.Trace
 
PUTTY_NormalizedLinear - Static variable in class org.jmol.shapebio.Trace
 
PUTTY_NormalizedNonlinear - Static variable in class org.jmol.shapebio.Trace
 
PUTTY_RelativeLinear - Static variable in class org.jmol.shapebio.Trace
 
PUTTY_RelativeNonlinear - Static variable in class org.jmol.shapebio.Trace
 
PUTTY_ScaledLinear - Static variable in class org.jmol.shapebio.Trace
 
PUTTY_ScaledNonlinear - Static variable in class org.jmol.shapebio.Trace
 
putX(SV) - Method in class org.jmol.script.ScriptMathProcessor
 
Pwr2 - Static variable in class org.jmol.util.TriangleData
 
PX(XmlReader, Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
PyMOL - Class in org.jmol.adapter.readers.pymol
PyMOL settings and constants.
PyMOL() - Constructor for class org.jmol.adapter.readers.pymol.PyMOL
 
pymol - Static variable in class org.jmol.script.T
 
pymol_space_max_blue - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pymol_space_max_green - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pymol_space_max_red - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
pymol_space_min_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
PymolAtomReader - Interface in org.jmol.api
 
pymolFrame - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
PyMOLGroup - Class in org.jmol.adapter.readers.pymol
 
PyMOLGroup(String) - Constructor for class org.jmol.adapter.readers.pymol.PyMOLGroup
 
PyMOLMeshReader - Class in org.jmol.jvxl.readers
PyMOL surface/mesh reader.
PyMOLMeshReader() - Constructor for class org.jmol.jvxl.readers.PyMOLMeshReader
 
pymolOffset - Variable in class org.jmol.modelset.Object2d
 
PyMOLReader - Class in org.jmol.adapter.readers.pymol
PyMOL PSE (binary Python session) file reader.
PyMOLReader() - Constructor for class org.jmol.adapter.readers.pymol.PyMOLReader
 
pymolScene - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
PyMOLScene - Class in org.jmol.adapter.readers.pymol
A class to allow manipulation of scenes dissociated from file loading.
PyMOLScene(PymolAtomReader, Viewer, Lst<Object>, Map<Integer, Lst<Object>>, int, boolean, int, int, boolean, String) - Constructor for class org.jmol.adapter.readers.pymol.PyMOLScene
 
pymolStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
pymolType - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
pymolVersion - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
pymolVersion - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
pymolView - Variable in class org.jmol.modelset.Orientation
 
pyrimidine - Static variable in class org.jmol.script.T
 

Q

q - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
Q_FACTOR - Static variable in class org.jmol.quantum.NMRCalculation
 
qchemContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
QchemReader - Class in org.jmol.adapter.readers.quantum
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
QchemReader() - Constructor for class org.jmol.adapter.readers.quantum.QchemReader
 
QchemReader.MOInfo - Class in org.jmol.adapter.readers.quantum
 
qCoefs - Variable in class org.jmol.util.Modulation
 
qColor - Static variable in class org.jmol.modelsetbio.BioPolymer
 
QConst - Static variable in class org.jmol.modelset.HBond
 
QI - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
qi() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
qicount - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
qlist100 - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
qm_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_marginAngstroms - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_moLinearCombination - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_moNumber - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_nAtoms - Variable in class org.jmol.jvxl.readers.Parameters
 
qm_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_GAUSSIAN - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_NCI_PRO - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_NCI_SCF - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_SLATER - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_UNKNOWN - Static variable in class org.jmol.jvxl.readers.Parameters
 
QM_TYPE_VOLUME_DATA - Static variable in class org.jmol.jvxl.readers.Parameters
 
QMAtom - Class in org.jmol.quantum
 
QMAtom(int, Atom, float[], float[], float[], float[], float[], float[], float) - Constructor for class org.jmol.quantum.QMAtom
 
qmAtoms - Variable in class org.jmol.quantum.QuantumCalculation
 
qMods - Static variable in class org.jmol.script.ScriptMathProcessor
 
qmOrbitalCount - Variable in class org.jmol.jvxl.readers.Parameters
 
qmOrbitalType - Variable in class org.jmol.jvxl.readers.Parameters
 
qnext - Variable in class org.jmol.util.MeshCapper.CapVertex
Y-X scan queue forward link
qPanelJPEG - Variable in class org.jmol.dialog.Dialog
 
qPanelPNG - Variable in class org.jmol.dialog.Dialog
 
qpc - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
qpt2 - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
qs - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
QS - Class in org.jmol.quantum
Constants and static methods for quantum shells.
QS() - Constructor for class org.jmol.quantum.QS
 
qSetupDone - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
qSliderJPEG - Variable in class org.jmol.dialog.Dialog
 
qSliderPNG - Variable in class org.jmol.dialog.Dialog
 
qtOffset - Variable in class org.jmol.util.ModulationSet
 
QUADRIC - Static variable in class org.jmol.shapecgo.CGOMesh
 
quadruple(int, short[]) - Static method in class org.jmol.util.Geodesic
 
QUADRUPOLE_MOMENT - Static variable in class org.jmol.quantum.NMRCalculation
 
qualityJ - Variable in class org.jmol.dialog.Dialog
 
qualityJPG - Static variable in class org.jmol.dialog.Dialog
 
qualityJPG - Variable in class org.jmol.viewer.StatusManager
 
qualityJPG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
QualityListener(boolean, JSlider) - Constructor for class org.jmol.dialog.Dialog.QualityListener
 
qualityP - Variable in class org.jmol.dialog.Dialog
 
qualityPNG - Static variable in class org.jmol.dialog.Dialog
 
qualityPNG - Variable in class org.jmol.viewer.StatusManager
 
qualityPNG - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
quantize(float, boolean) - Method in class org.jmol.util.ColorEncoder
gets the value at the color boundary for this color range fraction
quantize4(float, float, float, int) - Static method in class org.jmol.util.ColorEncoder
 
QuantumCalculation - Class in org.jmol.quantum
 
QuantumCalculation() - Constructor for class org.jmol.quantum.QuantumCalculation
 
QuantumPlaneCalculationInterface - Interface in org.jmol.api
Allows modification of the planes prior to isosurface creation Used by Noncovalent Interaction Calculation for progressive readers
quaternion - Static variable in class org.jmol.script.T
 
quaternionframe - Static variable in class org.jmol.script.T
 
quaternionFrame - Variable in class org.jmol.viewer.GlobalSettings
 
queueAtom(int, Point3fi) - Method in class org.jmol.viewer.ActionManager
 
queueOnHold - Variable in class org.jmol.viewer.Viewer
 
queueThreadFinished(int) - Method in interface org.jmol.api.JmolScriptManager
 
queueThreadFinished(int) - Method in class org.jmol.script.ScriptManager
 
queueThreads - Variable in class org.jmol.script.ScriptManager
 
quit - Static variable in class org.jmol.script.T
 

R

r - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
r - Variable in class org.jmol.quantum.SlaterData
 
r - Variable in class org.jmol.util.Rgb16
 
r0 - Variable in class org.jmol.minimize.forcefield.MMFFDistanceCalc
 
r0 - Variable in class org.jmol.minimize.forcefield.UFFDistanceCalc
 
r0 - Variable in class org.jmol.util.ModulationSet
 
R3 - Static variable in class org.jmol.minimize.forcefield.ForceField
 
R4 - Static variable in class org.jmol.minimize.forcefield.ForceField
 
R5 - Static variable in class org.jmol.minimize.forcefield.ForceField
 
R56 - Static variable in class org.jmol.minimize.forcefield.ForceField
 
rab - Variable in class org.jmol.minimize.forcefield.Calculation
 
rad - Static variable in class org.jmol.script.T
 
RAD_COV_BODR_2014_02_22 - Static variable in class org.jmol.util.Elements
 
RAD_COV_IONIC_OB1_100_1 - Static variable in class org.jmol.util.Elements
 
RAD_PER_DEG - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
 
RAD_TO_DEG - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
 
RAD_TO_DEG - Static variable in class org.jmol.minimize.forcefield.Calculations
 
RAD_TO_DEG - Static variable in class org.jmol.minimize.Util
 
radialPart(double) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
RADIANS - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
radiansPerDegree - Static variable in class org.jmol.smiles.SmilesMeasure
 
radiansPerDegree - Static variable in class org.jmol.viewer.JC
 
radiansXStep - Variable in class org.jmol.thread.MoveToThread
 
radiansYStep - Variable in class org.jmol.thread.MoveToThread
 
radiansZStep - Variable in class org.jmol.thread.MoveToThread
 
radical - Static variable in class org.jmol.script.T
 
radii - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
radii - Variable in class org.jmol.util.ContactPair
 
radiiIP2 - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
radius - Variable in class org.jmol.adapter.smarter.Atom
 
radius - Variable in class org.jmol.adapter.smarter.Bond
 
radius - Variable in class org.jmol.bspt.CubeIterator
 
radius - Variable in class org.jmol.g3d.CylinderRenderer
 
radius - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
radius - Static variable in class org.jmol.script.T
 
radius - Variable in class org.jmol.shapespecial.Polyhedra
 
radius - Variable in class org.jmol.symmetry.PointGroup
 
radius2 - Variable in class org.jmol.g3d.CylinderRenderer
 
RADIUS_GLOBAL - Static variable in class org.jmol.modelset.Atom
 
RADIUS_MAX - Static variable in class org.jmol.modelset.Atom
 
RADIUS_MAX - Static variable in class org.jmol.shape.Shape
 
RADIUS_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for vector radius.
RADIUS_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Initial value of vector radius.
radiusData - Variable in class org.jmol.atomdata.AtomData
 
RadiusData - Class in org.jmol.atomdata
 
RadiusData(float[], float, RadiusData.EnumType, VDW) - Constructor for class org.jmol.atomdata.RadiusData
 
radiusData - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
radiusData - Variable in class org.jmol.modelset.MeasurementData
 
radiusData - Variable in class org.jmol.shape.Measures
 
RadiusData.EnumType - Enum in org.jmol.atomdata
 
radiusHermites - Variable in class org.jmol.renderbio.BioShapeRenderer
 
radiusI - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
radiusP - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
radiusSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
radiusValue - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
raise_exceptions - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ramachandran - Static variable in class org.jmol.script.T
 
ramp_blend_nearby_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
random - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
random - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
random - Static variable in class org.jmol.script.T
 
randomizeUnitVector(V3d) - Static method in class org.jmol.minimize.Util
 
randomPoint() - Static method in class org.jmol.shapespecial.Draw
 
randomPoint - Static variable in class org.jmol.shapespecial.Polyhedra
 
randomSeed - Variable in class org.jmol.jvxl.readers.Parameters
 
range - Static variable in class org.jmol.script.T
 
range - Variable in class org.jmol.shapebio.BioShape
 
range(double) - Method in class org.jmol.util.Modulation
Check that left < x4 < right, but allow for folding
rangeAll - Variable in class org.jmol.jvxl.readers.Parameters
 
rangeBohrOrAngstroms - Variable in class org.jmol.quantum.QuantumCalculation
 
rangeDefined - Variable in class org.jmol.jvxl.readers.Parameters
 
rangeSelected - Variable in class org.jmol.jvxl.readers.Parameters
 
rangeselected - Static variable in class org.jmol.script.T
 
rangeSelected - Variable in class org.jmol.viewer.GlobalSettings
 
rank_assisted_sorts - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
rAS - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
rAS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
rasmol - Static variable in class org.jmol.script.T
 
RASMOL - Static variable in class org.jmol.util.ColorEncoder
 
rasmolBinding - Variable in class org.jmol.viewer.ActionManager
 
RasmolBinding - Class in org.jmol.viewer.binding
 
RasmolBinding() - Constructor for class org.jmol.viewer.binding.RasmolBinding
 
rasmolDefaultsButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
rasmolHeteroSetting - Variable in class org.jmol.viewer.GlobalSettings
 
rasmolHydrogenSetting - Variable in class org.jmol.viewer.GlobalSettings
 
rasmolOverrides - Static variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
rasmolScale - Static variable in class org.jmol.util.ColorEncoder
 
rasterCount - Variable in class org.jmol.g3d.CylinderRenderer
 
RAW_RGB - Static variable in class org.jmol.util.C
 
RAW_RGB_INT - Static variable in class org.jmol.util.C
 
rawAtomTypes - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
rawBondCount - Variable in class org.jmol.minimize.Minimizer
 
rawBondTypes - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
rawIndex - Variable in class org.jmol.minimize.MinBond
 
rawMMFF94Charges - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
ray_blend_blue - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_blend_colors - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_blend_green - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_blend_red - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_clip_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_color_ramps - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_default_renderer - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_direct_shade - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_hint_camera - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_hint_shadow - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_improve_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_interior_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_interior_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_interior_reflect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_interior_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_interior_texture - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_label_specular - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_legacy_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_max_passes - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_opaque_background - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_orthoscopic - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_oversample_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_pixel_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_scatter - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_shadow_decay_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_shadow_decay_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_shadow_fudge - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_spec_local - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_texture - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_texture_settings - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_depth_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_disco_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_fog - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_fog_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_frames - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_gain - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_persist_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_slope_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_trace_trans_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_transparency_contrast - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_transparency_oblique - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_transparency_oblique_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_transparency_shadows - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_transparency_spec_cut - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_transparency_specular - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_triangle_fudge - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ray_volume - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
rBS - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
rBS2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
rd() - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
rd - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
rd() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
rd() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
rd() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
rd() - Method in interface org.jmol.api.JmolJDXMOLReader
 
rd() - Method in class org.jmol.dssx.AnnotationParser
 
rd() - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
rd - Variable in class org.jmol.shape.AtomShape
 
rd - Variable in class org.jmol.viewer.Viewer
 
rdLast - Variable in class org.jmol.shapespecial.Dots
 
rdLine() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
rdVDW - Static variable in class org.jmol.shapesurface.Contact
 
read() - Method in class org.openscience.jvxl.MonitorInputStream
 
read(byte[]) - Method in class org.openscience.jvxl.MonitorInputStream
 
read(byte[], int, int) - Method in class org.openscience.jvxl.MonitorInputStream
 
read3Vectors(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block
readableTypes - Static variable in class org.jmol.viewer.PropertyManager
 
readACDAssignments(int, boolean) - Method in interface org.jmol.api.JmolJDXMOLParser
 
readACDAssignments(int, boolean) - Method in class org.jmol.jsv.JDXMOLParser
 
readACDMolFile() - Method in interface org.jmol.api.JmolJDXMOLParser
 
readACDMolFile() - Method in class org.jmol.jsv.JDXMOLParser
MOL file embedded in JDX file
readAllData() - Method in class org.jmol.adapter.readers.cif.CifReader
 
readAllData() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readAllData - Variable in class org.jmol.jvxl.readers.Parameters
 
readAndSetVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readAparam() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
readArchive(String, boolean, int, boolean) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readArchive() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readArchiveHeader() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readAtom(String[], boolean) - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
readAtom() - Method in class org.jmol.adapter.readers.xtal.MagresReader
Allowing for BOHR units here; probably unnecessary.
readAtomCountAndOrigin() - Method in class org.jmol.adapter.readers.simple.CubeReader
 
readAtomCountAndSetNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readAtomData(float) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readAtomicOrbitalOrder() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readAtomicPos(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readAtomNames() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readAtomRecord(Atom, P3, P3, boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
Read the atom or pos# record, including occupancy, various flags, and, especially, modulations.
readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
readAtoms(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
readAtoms() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
readAtoms(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Reads the output coordinates section into a new AtomSet.
readAtoms(boolean) - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readAtoms(int, boolean) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.SpartanReader
 
readAtoms() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readAtoms() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
 
readAtoms() - Method in class org.jmol.adapter.readers.simple.CubeReader
 
readAtoms(int, boolean) - Method in class org.jmol.adapter.readers.simple.FoldingXyzReader
Lots of possibilities here: atom count is real; atom count is one less than true atom count sixth column is atom type; sixth column is first bond
readAtoms(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
 
readAtoms(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
 
readAtoms() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
readAtoms() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readAtoms() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
readAtoms() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
readAtomsAndBonds(int, int) - Method in class org.jmol.adapter.readers.molxyz.MolReader
 
readAtomsAndBonds(String[]) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
readAtomsCartGeomThenCell() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
readAtomSet(String, boolean, boolean) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readAtomsInAngstromCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
readAtomsInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readAtomSpecies() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
readAtSign() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readBasis() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readBasisInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readBasisNormalized() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readBilbaoDataFile() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
readBilbaoFormat(String, float) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
readBinaryHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readBlock(String) - Method in class org.jmol.adapter.readers.simple.InputReader
 
readBonds(int) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
readBonds(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readBonds() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readBonds(int) - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readBonds() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readBonds() - Method in class org.jmol.adapter.readers.simple.AlchemyReader
 
readBonds(int) - Method in class org.jmol.adapter.readers.simple.JmeReader
 
readBonds(String[]) - Method in class org.jmol.adapter.readers.simple.JSONReader
 
readBornChargeTensors() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readBrickLayer() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
readBulges(int) - Method in class org.jmol.dssx.AnnotationParser
 
readCalculationInfo(String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readCalculationType() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readCellParam() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
readCellParam(boolean) - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
readCellParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readCellParams() - Method in class org.jmol.adapter.readers.xtal.MagresReader
 
readCellThenAtomsCartesian() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
readCFI() - Method in class org.jmol.adapter.readers.simple.InputReader
 
readCharges() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readCifData() - Method in class org.jmol.adapter.readers.cif.CifReader
 
readColor() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
 
readColorData() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readColorData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readConFile() - Method in class org.jmol.adapter.readers.simple.InputReader
 
readConstraints() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readControlInfo() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readCoord() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.quantum.AdfReader
Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.quantum.DgridReader
Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.simple.AmpacReader
Reads a set of coordinates
readCoordinates() - Method in class org.jmol.adapter.readers.simple.MopacArchiveReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
readCoordinates() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
readCoordLines() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
Read coordinates, either input or crystallographic, just saving their lines in a vector for now.
readCrystalInfo() - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readData(String, int) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
For spin and magnetic moment data, read the data block and save it as property_spin or propert_magneticMoment.
readData() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readData31(String) - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readData46() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readData47() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readDataObject(Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readDimensionality() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readDipole() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readDipoleMoment() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readDisplacements(float) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
readDots() - Method in class org.jmol.jvxl.readers.KinemageReader
 
readEFPInBohrCoordinates() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readElementNames() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readEmbeddedScript() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
readEnergy() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readEnergy() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readEnergy(int, String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readEnergy() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
reader - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
 
reader - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
reader - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
reader - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
reader - Variable in class org.jmol.dssx.AnnotationParser
 
reader - Variable in class org.jmol.io.FileReader
 
READER_NOT_FOUND - Static variable in class org.jmol.viewer.JC
 
readerClosed - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
readerData - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
readerList - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
readerName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readerSets - Static variable in class org.jmol.adapter.smarter.Resolver
 
readESym(boolean) - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readEventCount - Variable in class org.openscience.jvxl.MonitorInputStream
 
readExtents(int) - Method in class org.jmol.jvxl.readers.JaguarReader
read the extentx=, extenty=, extentz= lines and cache them then read the npts= line and construct the necessary data
readFileData() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readFinalCell() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readFloatArray() - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
readFloatArray() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
 
readFreq() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
readFreqFragments() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
Select only specific atoms for frequency generation.
readFreqsAndModes() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.AdfReader
Reads a set of vibrations.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readFrequencies(String, boolean) - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Reads the AtomSet and projected frequencies in the frequency section.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.QchemReader
Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.quantum.SpartanReader
 
readFrequencies() - Method in class org.jmol.adapter.readers.simple.AmpacReader
Reads a set of vibrations.
readFrequencies() - Method in class org.jmol.adapter.readers.simple.MopacReader
Interprets the Harmonic frequencies section.
readFrequencies() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readFrequency() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readGaussianBasis(String, String) - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readGaussianBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readGeometryOptimization() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readGradient() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
Read minimization measures
readGradients() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Reads the energy gradients section into a new AtomSet.
readHBonds(int) - Method in class org.jmol.dssx.AnnotationParser
 
readHeader(boolean) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
readHeader() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readHeader() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readIdeal - Variable in class org.jmol.adapter.readers.cif.CifReader
 
readInfo(String, int) - Method in class org.jmol.dssx.AnnotationParser
Default for no real processing -- just the lines
readInitialCoordinates() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readInputAtoms() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readInputDeck() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readInputHeader() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readInputRecords() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readIntiallattice() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
readJaguarMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readJobTitle() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
readJunctions(int) - Method in class org.jmol.dssx.AnnotationParser
 
readKeywords() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
readLatticeAbc() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readLatticeCart() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readLatticeParams(boolean) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
Read the lattice parameters.
readLatticeVector(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
readLengthUnit(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readLine() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readLine() - Method in class org.jmol.jsv.JDXMOLParser
 
readLines(int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readLoops(int) - Method in class org.jmol.dssx.AnnotationParser
 
readM40Data(boolean) - Method in class org.jmol.adapter.readers.xtal.JanaReader
read the M40 file, possibly as the extension of M50+M40
readM40FloatLines(int, int) - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
readM40Floats() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
readM40WaveVectors() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
readMdyn() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readModels() - Method in interface org.jmol.api.JmolJDXMOLParser
 
readModels() - Method in class org.jmol.jsv.JDXMOLParser
 
readMolecularFormula() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
readMolecularObitals() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readMolecularOrbital() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readMolecularOrbital() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readMolecularOrbitals(String) - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
 
readMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readMolecularOrbitals(boolean) - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
readMolecularOrbitals(int) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
readMore(Map<String, Object>, boolean, boolean) - Method in class org.jmol.dssx.AnnotationParser
 
readMOs() - Method in class org.jmol.adapter.readers.quantum.GenNBOReader
 
readMOs() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
readMOs(boolean, QchemReader.MOInfo[]) - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readMotifs(int) - Method in class org.jmol.dssx.AnnotationParser
 
readMultipole(String[]) - Method in class org.jmol.adapter.readers.xtal.AimsReader
 
readMyTransform() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readNextLine() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
readNoatom() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
readNostep() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
readNotypes() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
readNTList(String, String, int) - Method in class org.jmol.dssx.AnnotationParser
 
readOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
readOutput() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readOutputAtomIndex() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readOutputAtoms() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readOutputBornChargeTensors() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readOutputCharges() - Method in class org.jmol.adapter.readers.xtal.CastepReader
read Mulliken or Hirshfield charges
readOutputUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPairs(int) - Method in class org.jmol.dssx.AnnotationParser
 
readParameters() - Method in class org.jmol.jvxl.readers.ApbsReader
 
readParameters() - Method in class org.jmol.jvxl.readers.CastepDensityReader
 
readParameters() - Method in class org.jmol.jvxl.readers.CubeReader
 
readParameters() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
this reader has the critical scaling information at the end, so we just load the data straight into an array.
readParameters() - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
readParameters() - Method in class org.jmol.jvxl.readers.JaguarReader
nothing much here
readParameters() - Method in class org.jmol.jvxl.readers.JvxlReader
 
readParameters() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readParameters() - Method in class org.jmol.jvxl.readers.MrcBinaryReader
 
readParameters() - Method in class org.jmol.jvxl.readers.PltFormattedReader
 
readParameters() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
 
readParameters() - Method in class org.jmol.jvxl.readers.UhbdReader
 
readParameters() - Method in class org.jmol.jvxl.readers.VaspChgcarReader
 
readParameters() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readParameters() - Method in class org.jmol.jvxl.readers.XplorReader
 
readParameters() - Method in class org.jmol.jvxl.readers.XsfReader
 
readParams(BufferedReader, int, Map<Object, Object>) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GamessUSReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianFchkReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Reads partial charges and assigns them only to the last atom set.
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Reads partial charges and assigns them only to the last atom set.
readPartialCharges() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.simple.AmpacReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readPartialCharges() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readPeaks(boolean, int) - Method in interface org.jmol.api.JmolJDXMOLParser
 
readPeaks(boolean, int) - Method in class org.jmol.jsv.JDXMOLParser
 
readPhononFractionalCoord() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPhononFrequencies() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPhononTrajectories() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPhononUnitCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPolygons() - Method in class org.jmol.jvxl.readers.KinemageReader
 
readPolygons() - Method in class org.jmol.jvxl.readers.MsmsReader
 
readPolygons() - Method in class org.jmol.jvxl.readers.ObjReader
 
readPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readPolygonsPM() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readPOSITION() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readPositionsAbs() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPositionsFrac() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
readPrimitiveMapping() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readProperties() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readProperties() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
readProperty() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readPsiMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readQchemMolecularOrbitals() - Method in class org.jmol.adapter.readers.quantum.QchemReader
 
readResInfo(int) - Method in class org.jmol.adapter.readers.more.Mol2Reader
 
readSCFDone() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Interprets the SCF Done: section.
readSCFDone() - Method in class org.jmol.adapter.readers.quantum.PsiReader
Interprets the SCF Done: section.
readSecondOrderData() - Method in class org.jmol.adapter.readers.quantum.MOReader
 
readSets(String, int, int, int) - Method in class org.jmol.dssx.AnnotationParser
 
readShift() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
Read the origin shift
readSingleAtom() - Method in class org.jmol.adapter.readers.cif.CifReader
No need for anything other than the atom name and symbol; coordinates will be (0 0 0), and no other information is needed.
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.DgridReader
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.MopacGraphfReader
 
readSlaterBasis() - Method in class org.jmol.adapter.readers.quantum.WebMOReader
 
readSpaceGroup() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
readSpaceGroup() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
readStacks(int) - Method in class org.jmol.dssx.AnnotationParser
List of 40 coaxial stacks 1 Helix#1 contains 4 stems: [#1,#2,#3,#4] 2 Helix#4 contains 4 stems: [#6,#7,#9,#13] 3 Helix#10 contains 3 stems: [#16,#17,#18] 4 Helix#13 contains 2 stems: [#21,#22]
readString() - Method in class org.jmol.adapter.readers.pymol.PickleReader
 
readString() - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
 
readStructure() - Method in class org.jmol.dssx.AnnotationParser
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PeriodicVolumeFileReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readSurfaceData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readSurfaceDataJXR() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readSurfaceDataVDR(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readSurfaceDataVFR(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readSurfaceDataXML() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readSymmetries() - Method in class org.jmol.adapter.readers.quantum.AdfReader
 
readSymmetry() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Read the symmetry information and set the property.
readSymmetry() - Method in class org.jmol.adapter.readers.xtal.MagresReader
not doing anything with this -- P1 assumed
readSymmetry() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
readTensor() - Method in class org.jmol.adapter.readers.xtal.MagresReader
Read a tensor line.
readTitleLines() - Method in class org.jmol.adapter.readers.simple.CubeReader
 
readTlsData() - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
readTotal() - Method in class org.jmol.adapter.readers.quantum.NWChemReader
Interpret a line starting with a line with "Total" in it.
readTotalAtomicCharges() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
readTransform() - Method in class org.jmol.adapter.readers.quantum.SpartanInputReader
 
readTransformationMatrix() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
Read transform matrix primitive to conventional.
readTurns(int) - Method in class org.jmol.dssx.AnnotationParser
 
readTypesequence() - Method in class org.jmol.adapter.readers.xtal.AbinitReader
 
readUniqueAtoms() - Method in class org.jmol.adapter.readers.quantum.PsiReader
 
readUnitCell() - Method in class org.jmol.adapter.readers.more.GromacsReader
 
readUnitCell() - Method in class org.jmol.adapter.readers.xtal.Wien2kReader
 
readUnitCell() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
readUnitCellVectors() - Method in class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
readUnnormalizedBasis() - Method in class org.jmol.adapter.readers.quantum.JaguarReader
 
readUserData(int) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
readVector(int) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVectors() - Method in class org.jmol.jvxl.readers.KinemageReader
 
readVertices() - Method in class org.jmol.jvxl.readers.KinemageReader
 
readVertices() - Method in class org.jmol.jvxl.readers.MsmsReader
 
readVertices() - Method in class org.jmol.jvxl.readers.ObjReader
 
readVertices() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
 
readVertices() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.NffReader
 
readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.Pmesh4Reader
 
readVerticesAndPolygons() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readVerticesPM() - Method in class org.jmol.jvxl.readers.PmeshReader
 
readVFI() - Method in class org.jmol.adapter.readers.simple.InputReader
 
readVibFreqs() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
readVirtual() - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVolumeData(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVolumeDataVFR(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.KinemageReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.PolygonFileReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVolumeParameters(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVolumetricHeader() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
readVoxelDataIndividually(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
readVoxelVector(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
reallocRgb16s(Rgb16[], int) - Method in class org.jmol.g3d.TriangleRenderer
 
rebond() - Method in class org.jmol.api.JmolViewer
 
rebond() - Method in class org.jmol.viewer.Viewer
 
rebond() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
rebondState(boolean) - Method in class org.jmol.viewer.Viewer
 
recachePngjBytes(String, byte[]) - Method in class org.jmol.io.JmolBinary
 
recalc() - Method in class org.jmol.modelset.Object2d
 
recalc() - Method in class org.jmol.modelset.Text
 
recalcAltVertices - Variable in class org.jmol.shape.Mesh
 
reCalculate(BS, M3) - Method in class org.jmol.geodesic.EnvelopeCalculation
problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
recalculateLeadMidpointsAndWingVectors(int) - Method in class org.jmol.modelset.ModelSet
 
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioModel
 
recalculateLeadMidpointsAndWingVectors() - Method in class org.jmol.modelsetbio.BioPolymer
 
recalculatePoints(ModelSet, int) - Method in class org.jmol.modelset.Model
 
recalculatePoints(ModelSet, int) - Method in class org.jmol.modelsetbio.BioModel
 
recalculatePositionDependentQuantities(BS, M4) - Method in class org.jmol.modelset.ModelSet
 
recalculateWordsInUse() - Method in class org.jmol.java.BS
Sets the field wordsInUse to the logical size in words of the bit set.
recallCommand(boolean) - Method in class org.jmol.console.GenericConsole
 
recallCommand(boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
Recall command history.
recentFiles - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
recentFilesAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
RecentFilesAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.RecentFilesAction
 
RecentFilesDialog - Class in org.openscience.jmol.app.jmolpanel
Manages a list of recently opened files.
RecentFilesDialog(Frame) - Constructor for class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
Creates a hidden recent files dialog
reciprocalsOf(V3[]) - Method in class org.jmol.adapter.readers.cif.Subsystem
 
recordData(float) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
records - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
recordStatus(String) - Method in class org.jmol.viewer.StatusManager
 
recordTime(int) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
Rectangle - Class in org.jmol.util
 
Rectangle() - Constructor for class org.jmol.util.Rectangle
 
rectClip - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
rectRubber - Variable in class org.jmol.viewer.ActionManager
 
RED - Static variable in class org.jmol.util.C
 
redo() - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
redoButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
redomove - Static variable in class org.jmol.script.T
 
reducedAnisotropy() - Method in class org.jmol.util.Tensor
reduced anisotropy = largest difference from isotropy (may be negative)
reduceFilename(String) - Static method in class org.jmol.viewer.ModelManager
 
reference - Variable in class org.jmol.modelset.TickInfo
 
reference - Static variable in class org.jmol.script.T
 
referenceCenter - Variable in class org.jmol.export.___Exporter
 
referencePlaneOffset - Variable in class org.jmol.viewer.TransformManager
 
reflect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
reflect_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
reformatDistanceIfSelected() - Method in class org.jmol.modelset.Measurement
 
reformatDistances() - Method in class org.jmol.shape.Measures
 
refresh(int, String) - Method in class org.jmol.api.JmolViewer
 
refresh(Point3fi[]) - Method in class org.jmol.modelset.Measurement
 
refresh(boolean) - Method in class org.jmol.script.ScriptEval
Refresh the display NOW
refresh(boolean) - Method in class org.jmol.script.ScriptExpr
 
refresh - Static variable in class org.jmol.script.T
 
refresh(int, String) - Method in class org.jmol.viewer.Viewer
initiate a repaint/update sequence if it has not already been requested.
refreshButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
refreshing - Static variable in class org.jmol.script.T
 
refreshing - Variable in class org.jmol.viewer.Viewer
 
refreshMeasures(boolean) - Method in class org.jmol.viewer.Viewer
 
refreshShapeTrajectories(int, BS, M4) - Method in class org.jmol.viewer.ShapeManager
 
region - Variable in class org.jmol.util.MeshCapper.CapVertex
dynamic region pointers
register(String, JmolSyncInterface) - Method in interface org.jmol.api.JmolSyncInterface
 
register(String, JmolSyncInterface) - Method in class org.jmol.util.GenericApplet
 
register(String, JmolSyncInterface) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
reinitializeLightingAndColor(Viewer) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
rejectAtomName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
RELATIVE_DRAG_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
RELATIVE_DRAG_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
release() - Method in interface org.jmol.api.AtomIndexIterator
 
release() - Method in class org.jmol.bspt.CubeIterator
nulls internal references
release() - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
releaseBuffers() - Method in class org.jmol.g3d.Graphics3D
 
releaseBuffers() - Method in class org.jmol.g3d.Platform3D
 
released(long, int, int, int) - Method in class org.jmol.awtjs2d.Mouse
 
releaseModelSet() - Method in class org.jmol.modelset.AtomCollection
 
releaseModelSet() - Method in class org.jmol.modelset.BondCollection
 
releaseModelSet() - Method in class org.jmol.modelset.ModelSet
 
releaseModelSetAC() - Method in class org.jmol.modelset.AtomCollection
 
releaseModelSetBC() - Method in class org.jmol.modelset.BondCollection
 
releaseScreenImage() - Method in class org.jmol.api.JmolViewer
 
releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
 
releaseScreenImage() - Method in class org.jmol.util.GData
 
releaseScreenImage() - Method in class org.jmol.viewer.Viewer
 
releaseShape(int) - Method in class org.jmol.viewer.ShapeManager
 
remapColors(Viewer, ColorEncoder, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
remaps colors based on a new color scheme or translucency level
remark290() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
remark350() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
remarkTls() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
rememberCheckbox(String, SC) - Method in class org.jmol.popup.GenericSwingPopup
 
remoteAppletPath - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
remoteAppletPath - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
remove(int) - Method in class org.jmol.popup.AwtSwingComponent
 
remove - Static variable in class org.jmol.script.T
 
remove(int, int) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
removeAll() - Method in class org.jmol.popup.AwtSwingComponent
 
removeAtomSet(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
note that sets must be iterated from LAST to FIRST
removeBinding(Iterator<String>, String) - Method in class org.jmol.viewer.binding.Binding
 
removeCommand() - Method in class org.jmol.util.CommandHistory
 
removeCommand(int) - Method in class org.jmol.util.CommandHistory
 
removeCommand() - Method in class org.jmol.viewer.Viewer
Removes one command from the command history
removeCurrentAtomSet() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
removeFunction(String) - Method in class org.jmol.viewer.Viewer
 
removeMonomer(int) - Method in class org.jmol.modelsetbio.ProteinStructure
should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.
removeParam(String) - Method in class org.jmol.viewer.GlobalSettings
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.jmol.awt.FileDropper
 
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.api.JmolViewer
 
removeSelectionListener(JmolSelectionListener) - Method in class org.jmol.viewer.Viewer
 
removeUnnecessaryBonds(Atom, boolean) - Method in class org.jmol.modelset.BondCollection
 
removeUserVariable(String) - Method in class org.jmol.viewer.GlobalSettings
 
removeUserVariable(String) - Method in class org.jmol.viewer.Viewer
 
render(GData, ModelSet, boolean, int[]) - Method in interface org.jmol.api.JmolRepaintManager
 
render(short, short, int, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.CylinderRenderer
 
render(int[], int, int, int, int, M3, double[], M4, int, P3i[]) - Method in class org.jmol.g3d.SphereRenderer
 
render() - Method in class org.jmol.render.AxesRenderer
 
render() - Method in class org.jmol.render.BallsRenderer
 
render() - Method in class org.jmol.render.BbcageRenderer
 
render() - Method in class org.jmol.render.EchoRenderer
 
render() - Method in class org.jmol.render.FrankRenderer
 
render() - Method in class org.jmol.render.HalosRenderer
 
render() - Method in class org.jmol.render.HoverRenderer
 
render() - Method in class org.jmol.render.LabelsRenderer
 
render() - Method in class org.jmol.render.MeasuresRenderer
 
render() - Method in class org.jmol.render.MeshRenderer
 
render(GData, ModelSet, boolean, int[]) - Method in class org.jmol.render.RepaintManager
 
render() - Method in class org.jmol.render.ShapeRenderer
 
render() - Method in class org.jmol.render.StarsRenderer
 
render() - Method in class org.jmol.render.SticksRenderer
 
render(Text, JmolRendererInterface, float, float, boolean, float[], float[]) - Static method in class org.jmol.render.TextRenderer
 
render() - Method in class org.jmol.render.UccageRenderer
 
render() - Method in class org.jmol.renderbio.BioShapeRenderer
 
render() - Method in class org.jmol.rendercgo.CGORenderer
 
render() - Method in class org.jmol.renderspecial.DipolesRenderer
 
render() - Method in class org.jmol.renderspecial.DotsRenderer
 
render() - Method in class org.jmol.renderspecial.DrawRenderer
 
render() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
render() - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
 
render() - Method in class org.jmol.renderspecial.PolyhedraRenderer
 
render() - Method in class org.jmol.renderspecial.VectorsRenderer
 
render() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
render() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
 
render() - Method in class org.jmol.viewer.Viewer
 
render1(Atom) - Method in class org.jmol.render.HalosRenderer
 
render1(Atom, short) - Method in class org.jmol.render.StarsRenderer
 
render1(int) - Method in class org.jmol.render.UccageRenderer
 
render1(Dots) - Method in class org.jmol.renderspecial.DotsRenderer
 
render1(Polyhedron, short) - Method in class org.jmol.renderspecial.PolyhedraRenderer
 
render1(Object, Object, int, int) - Method in class org.jmol.viewer.Viewer
 
render2(boolean) - Method in class org.jmol.render.MeshRenderer
 
render2(boolean) - Method in class org.jmol.renderspecial.DrawRenderer
 
render2(boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
render2b(boolean) - Method in class org.jmol.render.MeshRenderer
 
render2Strand(boolean, float, float) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
render_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
renderAllStrings(Object) - Method in interface org.jmol.api.JmolGraphicsInterface
 
renderAllStrings(Object) - Method in class org.jmol.export.Export3D
 
renderAllStrings(Object) - Method in class org.jmol.g3d.Graphics3D
 
renderAllStrings(Object) - Method in class org.jmol.util.GData
 
renderAngle(String, Point3fi, Point3fi, Point3fi) - Method in class org.jmol.render.MeasuresRenderer
 
renderArc - Variable in class org.jmol.modelset.Measurement
 
renderArc(int, int) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
renderArcs() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
renderArrowHead(T3, T3, float, boolean, boolean, boolean) - Method in class org.jmol.renderspecial.DrawRenderer
 
renderArrowHeads - Variable in class org.jmol.renderbio.RocketRenderer
 
renderArrowHeads - Variable in class org.jmol.renderbio.RocketsRenderer
 
renderArrows() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
renderAxes() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
renderAxis - Variable in class org.jmol.modelset.Measurement
 
renderBackground(JmolRendererInterface) - Method in interface org.jmol.api.JmolRendererInterface
 
renderBackground(JmolRendererInterface) - Method in class org.jmol.export.Export3D
 
renderBackground(JmolRendererInterface) - Method in class org.jmol.g3d.Graphics3D
 
renderBackground(JmolRendererInterface) - Method in class org.jmol.util.GData
 
renderBall() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.BackboneRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.BioShapeRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.CartoonRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.RibbonsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.RocketsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.StrandsRenderer
 
renderBioShape(BioShape) - Method in class org.jmol.renderbio.TraceRenderer
 
renderBits(short, byte, int, float, float, float, float, float, float) - Method in class org.jmol.g3d.CylinderRenderer
 
renderBond() - Method in class org.jmol.render.SticksRenderer
 
renderCage(int, P3[], P3[], int, int, int, float) - Method in class org.jmol.render.CageRenderer
 
renderCone(short, byte, int, float, float, float, float, float, float, boolean, boolean) - Method in class org.jmol.g3d.CylinderRenderer
 
renderContourLines() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.DotsRenderer
generic renderer -- dots and geosurface
renderConvex(short, BS, int) - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
 
renderCrossHairs(int[], int, int, P3, float) - Method in interface org.jmol.api.JmolRendererInterface
 
renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.export.Export3D
 
renderCrossHairs(int[], int, int, P3, float) - Method in class org.jmol.g3d.Graphics3D
 
renderCyl(P3i, P3i, P3, P3) - Method in class org.jmol.renderbio.NucleicRenderer
 
renderDipoleVector(Dipole, BS) - Method in class org.jmol.renderspecial.DipolesRenderer
 
renderDistance(String, Point3fi, Point3fi) - Method in class org.jmol.render.MeasuresRenderer
 
renderDots(int) - Method in class org.jmol.renderspecial.DotsRenderer
also called by GeoSurface when in motion
renderDots() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
renderEdge(P3i[], P3[], int, int) - Method in class org.jmol.renderbio.NucleicRenderer
 
renderEdges - Variable in class org.jmol.renderbio.NucleicRenderer
 
renderEllipsoids(Map<?, Ellipsoid>, boolean) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
renderers - Variable in class org.jmol.render.RepaintManager
 
renderExport(GData, ModelSet, Map<String, Object>) - Method in interface org.jmol.api.JmolRepaintManager
 
renderExport(GData, ModelSet, Map<String, Object>) - Method in class org.jmol.render.RepaintManager
 
renderFlatEndcap(boolean, boolean, int[][]) - Method in class org.jmol.g3d.CylinderRenderer
 
renderFrameTitle(String) - Method in class org.jmol.render.EchoRenderer
 
renderHandles() - Method in class org.jmol.renderspecial.DrawRenderer
 
renderHermiteArrowHead(int) - Method in class org.jmol.renderbio.BioShapeRenderer
 
renderHermiteConic(int, boolean, int) - Method in class org.jmol.renderbio.BioShapeRenderer
 
renderHermiteCylinder(P3i[], int) - Method in class org.jmol.renderbio.BioShapeRenderer
 
renderHermiteRibbon(boolean, boolean, int, P3i, P3i, P3i, P3i, P3i, P3i, P3i, P3i, int, int) - Method in class org.jmol.g3d.HermiteRenderer
 
renderHermiteRibbon(boolean, int, boolean) - Method in class org.jmol.renderbio.BioShapeRenderer
 
renderHermiteRope(boolean, int, int, int, int, P3i, P3i, P3i, P3i) - Method in class org.jmol.g3d.HermiteRenderer
 
renderInfo() - Method in class org.jmol.render.UccageRenderer
 
renderInfo() - Method in class org.jmol.renderspecial.DrawRenderer
 
renderInfo() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderInfo() - Method in class org.jmol.rendersurface.MolecularOrbitalRenderer
 
rendering - Variable in class org.jmol.jvxl.data.JvxlData
 
renderIso() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderLabel(String, float, float, float, float, float) - Method in class org.jmol.render.AxesRenderer
 
renderLabelOrMeasure(Text, String) - Method in class org.jmol.render.LabelsRenderer
 
renderLeontisWesthofEdges(NucleicMonomer) - Method in class org.jmol.renderbio.NucleicRenderer
 
renderLine(P3, P3, int, P3i, P3i, boolean) - Method in class org.jmol.render.FontLineShapeRenderer
 
renderLonePair(boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderLow - Variable in class org.jmol.g3d.Graphics3D
 
renderLow - Variable in class org.jmol.render.MeshRenderer
 
renderMeasurement(boolean) - Method in class org.jmol.render.MeasuresRenderer
 
renderMesh(Mesh) - Method in class org.jmol.render.MeshRenderer
 
renderMesh(Mesh) - Method in class org.jmol.rendercgo.CGORenderer
 
renderMesh(Mesh) - Method in class org.jmol.renderspecial.DrawRenderer
 
renderMesh2(Mesh) - Method in class org.jmol.render.MeshRenderer
 
renderMeshes() - Method in class org.jmol.renderbio.BioShapeRenderer
 
renderMeshRibbon() - Method in class org.jmol.renderbio.MeshRibbonRenderer
 
renderMeshSlab() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderNormals() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderNucleic(BioShapeRenderer) - Method in class org.jmol.renderbio.NucleicRenderer
 
renderNucleicBaseStep(int) - Method in class org.jmol.renderbio.NucleicRenderer
 
renderOne(Ellipsoid) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
renderParallelPair(boolean, int, P3i, P3i, P3i, P3i, P3i, P3i, P3i, P3i) - Method in class org.jmol.g3d.HermiteRenderer
 
renderPass2(short) - Static method in class org.jmol.util.C
 
renderPending() - Method in class org.jmol.renderbio.RocketRenderer
 
renderPendingMeasurement() - Method in class org.jmol.render.MeasuresRenderer
 
renderPendingRocketSegment(int, P3, P3, P3, boolean) - Method in class org.jmol.renderbio.RocketRenderer
 
renderPendingSheetPlank(P3, P3, P3, boolean) - Method in class org.jmol.renderbio.RocketRenderer
 
renderPoints() - Method in class org.jmol.render.MeshRenderer
 
renderPoints() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderProtein() - Method in class org.jmol.renderbio.CartoonRenderer
 
renderQuadrant(int, int) - Method in class org.jmol.g3d.SphereRenderer
 
renderQuadrantClipped(int, int, int) - Method in class org.jmol.g3d.SphereRenderer
 
renderQuadrantUnclipped(int, int, int) - Method in class org.jmol.g3d.SphereRenderer
 
renderRibose - Variable in class org.jmol.renderbio.NucleicRenderer
 
renderRibose() - Method in class org.jmol.renderbio.NucleicRenderer
 
renderRing5() - Method in class org.jmol.renderbio.NucleicRenderer
 
renderRing6() - Method in class org.jmol.renderbio.NucleicRenderer
 
renderRockets() - Method in class org.jmol.renderbio.RocketRenderer
 
renderRockets() - Method in class org.jmol.renderbio.RocketsRenderer
 
renderScreenImage(Object, Object, Object) - Method in class org.jmol.api.JmolViewer
Deprecated.
renderScreenImage(Object, int, int) - Method in class org.jmol.api.JmolViewer
 
renderScreenImage(PlatformViewer, Object, Object) - Static method in class org.jmol.awt.Display
Deprecated.
renderScreenImage(Object, Object) - Method in class org.jmol.awt.Platform
legacy apps will use this
renderScreenImage(PlatformViewer, Object, Object) - Static method in class org.jmol.awtjs2d.Display
legacy apps will use this
renderScreenImage(Object, Object) - Method in class org.jmol.awtjs2d.Platform
legacy apps will use this
renderScreenImage(Object, int, int) - Method in class org.jmol.viewer.Viewer
JmolViewer interface uses this, but that is all
renderScreenImageStereo(Object, boolean, int, int) - Method in class org.jmol.viewer.Viewer
 
renderShape(JmolRendererInterface, ModelSet, Shape) - Method in class org.jmol.render.ShapeRenderer
 
renderShapes() - Method in class org.jmol.renderbio.BioShapeRenderer
 
renderSimpleLabel(JmolRendererInterface, Font, String, short, short, float[], int, int, int, int, float, int, boolean, short, boolean) - Static method in class org.jmol.render.TextRenderer
 
renderSpecialSegment(AlphaMonomer, short, short) - Method in class org.jmol.renderbio.RocketRenderer
 
renderSphereClipped(int[], int, int, int, int) - Method in class org.jmol.g3d.SphereRenderer
 
renderSphereUnclipped(int[], int, int) - Method in class org.jmol.g3d.SphereRenderer
 
renderSphericalEndcaps() - Method in class org.jmol.g3d.CylinderRenderer
 
renderStrand(P3i[]) - Method in class org.jmol.renderbio.StrandsRenderer
 
renderStrands() - Method in class org.jmol.renderbio.StrandsRenderer
 
renderStrandShape() - Method in class org.jmol.renderbio.StrandsRenderer
 
renderSurface(BS) - Method in class org.jmol.renderspecial.GeoSurfaceRenderer
 
renderTorsion(String, Point3fi, Point3fi, Point3fi, Point3fi) - Method in class org.jmol.render.MeasuresRenderer
 
renderTrace() - Method in class org.jmol.renderbio.TraceRenderer
 
renderTriangle(P3i[], P3[], int, int, int, boolean) - Method in class org.jmol.renderbio.NucleicRenderer
 
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.render.MeshRenderer
 
renderTriangles(boolean, boolean, boolean) - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
renderVector(V3, P3, P3, float, boolean) - Method in class org.jmol.renderspecial.DipolesRenderer
 
renderVector(Atom) - Method in class org.jmol.renderspecial.VectorsRenderer
 
renderXyArrow(int) - Method in class org.jmol.renderspecial.DrawRenderer
 
REP_ANGLES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_CALLBACK - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_CARTOON - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_CELL - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_CGO - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_DASHES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_DIHEDRALS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_DOTS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_ELLIPSOID - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_EXTENT - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_JMOL_MAX - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_JMOL_PUTTY - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_JMOL_TRACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_LABELS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_LINES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_LIST - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_MAX - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_MESH - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_NBSPHERES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_NONBONDED - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_RIBBON - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_SLICE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_SPHERES - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_STICKS - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_SURFACE - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
REP_VOLUME - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
repaint(Object) - Static method in class org.jmol.awt.Display
 
repaint(Object) - Method in class org.jmol.awt.Platform
 
repaint(Object) - Method in class org.jmol.awtjs2d.Platform
 
REPAINT_IGNORE - Static variable in class org.jmol.viewer.JC
 
repaintClock() - Method in class org.jmol.applet.AppletWrapper
 
repaintDone() - Method in interface org.jmol.api.JmolRepaintManager
 
repaintDone() - Method in class org.jmol.render.RepaintManager
 
repaintDone() - Method in class org.jmol.viewer.AnimationManager
 
repaintIfReady(String) - Method in interface org.jmol.api.JmolRepaintManager
 
repaintIfReady(String) - Method in class org.jmol.render.RepaintManager
 
RepaintManager - Class in org.jmol.render
 
RepaintManager() - Constructor for class org.jmol.render.RepaintManager
 
repaintNow(String) - Method in class org.jmol.render.RepaintManager
 
repaintPending - Variable in class org.jmol.render.RepaintManager
 
repaintwaitms - Static variable in class org.jmol.script.T
 
repaintWaitMs - Variable in class org.jmol.viewer.GlobalSettings
 
repeatCheckBox - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
replace - Static variable in class org.jmol.script.T
 
replace(int, int, String, AttributeSet) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
replaceCommand(T) - Method in class org.jmol.script.ScriptCompiler
 
replaceCommand(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
Replaces current command on script.
replaceQuotedStrings(String, ArrayList<String>, ArrayList<String>) - Static method in class org.openscience.jmol.app.webexport.WebPanel
 
replaceXn(String, int) - Static method in class org.jmol.symmetry.SymmetryOperation
 
report(String, boolean) - Method in class org.jmol.minimize.Minimizer
 
report(String) - Method in class org.jmol.script.ScriptEval
 
report(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
reportAll - Variable in class org.jmol.shape.Sticks
 
reportEnergy() - Method in class org.jmol.minimize.Minimizer
 
reportSelection(String) - Method in class org.jmol.viewer.Viewer
 
repositionWindow(String, Component, int, int, boolean) - Method in class org.openscience.jmol.app.HistoryFile
Uses the informations in the history to reposition the window.
repositionWindow(String, Component) - Method in class org.openscience.jmol.app.HistoryFile
Uses the informations in the history to reposition the window.
reps - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
requestFocusInWindow(Object) - Static method in class org.jmol.awt.Display
 
requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
 
requestFocusInWindow(Object) - Static method in class org.jmol.awtjs2d.Display
 
requestFocusInWindow(Object) - Method in class org.jmol.awtjs2d.Platform
 
requestRepaintAndWait(String) - Method in interface org.jmol.api.JmolRepaintManager
 
requestRepaintAndWait(String) - Method in class org.jmol.render.RepaintManager
 
requestRepaintAndWait(String) - Method in class org.jmol.viewer.Viewer
 
requireTranslucent - Variable in class org.jmol.renderspecial.GeoSurfaceRenderer
 
reset() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
reset() - Method in class org.jmol.bspt.Bspt
 
reset - Static variable in class org.jmol.script.T
 
reset() - Method in class org.jmol.smiles.SmilesParser
 
reset() - Method in class org.jmol.symmetry.UnitCell
 
reset() - Method in class org.jmol.thread.JmolThread
 
reset() - Method in class org.jmol.util.BoxInfo
 
reset(int) - Method in class org.jmol.util.CommandHistory
Resets instance.
reset() - Method in class org.jmol.viewer.ActionManager
 
reset(boolean) - Method in class org.jmol.viewer.Viewer
 
reset() - Method in class org.openscience.jvxl.MonitorInputStream
 
RESET_NORMAL - Static variable in class org.jmol.shapecgo.CGOMesh
 
resetAromatic() - Method in class org.jmol.modelset.BondCollection
 
resetAxes() - Method in class org.jmol.modelsetbio.ProteinStructure
 
resetAxisCoordinates() - Method in class org.jmol.render.SticksRenderer
 
resetBioshapes(BS) - Method in class org.jmol.viewer.ShapeManager
 
resetBoundCount() - Method in class org.jmol.modelset.Model
 
resetDefaults(String[]) - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
resetError() - Method in class org.jmol.script.ScriptEval
 
resetFitToScreen(boolean) - Method in class org.jmol.viewer.TransformManager
 
resetFlag - Static variable in class org.openscience.jmol.app.webexport.LogPanel
 
resetForMapping(boolean) - Method in class org.jmol.jvxl.readers.Parameters
reset some parameters at the "MAP" keyword or initially
resetHydrogenPoint() - Method in class org.jmol.modelsetbio.AminoMonomer
 
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.AminoPolymer
 
resetHydrogenPoints() - Method in class org.jmol.modelsetbio.BioPolymer
 
resetIndexPlane(int[][]) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
resetIsosurface() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
resetKey - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
resetLighting() - Method in class org.jmol.viewer.StateManager
Reset lighting to Jmol defaults
resetMeasurement() - Method in class org.jmol.viewer.ActionManager
 
resetMessage - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
resetMolecules() - Method in class org.jmol.modelset.BondCollection
 
resetNavigationPoint(boolean) - Method in class org.jmol.viewer.TransformManager
something has arisen that requires resetting of the navigation point.
resetNeeded - Variable in class org.jmol.multitouch.ActionManagerMT
 
resetObjects() - Method in class org.jmol.shapespecial.Draw
 
resetPlane(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
resetRasmolBonds(Model, BS) - Method in class org.jmol.modelset.Model
 
resetRasmolBonds(Model, BS) - Method in class org.jmol.modelsetbio.BioModel
 
resetRotation() - Method in class org.jmol.viewer.TransformManager
 
resetRotation() - Method in class org.jmol.viewer.TransformManager4D
 
resetShapes() - Method in class org.jmol.viewer.ShapeManager
 
resetShapes(boolean) - Method in class org.jmol.viewer.Viewer
 
resetSlab() - Method in class org.jmol.util.MeshSurface
 
resetTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
resetValue(String, GlobalSettings) - Method in class org.jmol.viewer.GlobalSettings
 
resetVoxelData(float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
resetXYCenter(int, int) - Method in class org.jmol.viewer.TransformManager
 
residue - Static variable in class org.jmol.script.T
 
residueChar - Variable in class org.jmol.smiles.SmilesAtom
 
residueName - Variable in class org.jmol.smiles.SmilesAtom
 
residueSpecCodeGenerated - Variable in class org.jmol.script.ScriptTokenParser
 
resizeAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ResizeAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ResizeAction
 
resizeDisplay(int, int) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
resizeImage(int, int, boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
resizeInnerPanel(String) - Method in interface org.jmol.api.JmolStatusListener
 
resizeInnerPanel(int, int) - Method in class org.jmol.api.JmolViewer
 
resizeInnerPanel(String) - Method in class org.jmol.applet.Jmol
 
resizeInnerPanel(String) - Method in class org.jmol.util.GenericApplet
 
resizeInnerPanel(int, int) - Method in class org.jmol.viewer.StatusManager
 
resizeInnerPanel(int, int) - Method in class org.jmol.viewer.Viewer
 
resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
resizeInnerPanel(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
resMap - Variable in class org.jmol.adapter.readers.cif.MMCifValidationParser
 
resMap - Variable in class org.jmol.modelsetbio.ProteinStructure
 
resno - Static variable in class org.jmol.script.T
 
resolution - Variable in class org.jmol.jvxl.readers.Parameters
 
resolution - Static variable in class org.jmol.script.T
 
resolveDataBase(String, String) - Method in class org.jmol.viewer.GlobalSettings
 
resolveDatabaseFormat(String) - Method in class org.jmol.viewer.Viewer
 
resolveEntity(String, String, String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
resolveEntity(String, String) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
Resolver - Class in org.jmol.adapter.smarter
 
Resolver() - Constructor for class org.jmol.adapter.smarter.Resolver
 
Resolver - Class in org.jmol.modelsetbio
a class used by ModelLoader to handle all loading of operations specific to PDB/mmCIF files.
Resolver() - Constructor for class org.jmol.modelsetbio.Resolver
 
Resolver.BondSorter - Class in org.jmol.modelsetbio
 
Resource - Class in org.jmol.i18n
 
Resource(Object, String) - Constructor for class org.jmol.i18n.Resource
 
resource - Variable in class org.jmol.i18n.Resource
 
resource - Static variable in class org.jmol.quantum.NMRCalculation
NOTE! Do not change this txt file! Instead, edit trunk/Jmol/_documents/nmr_data.xls and then clip its contents to org/jmol/quantum/nmr_data.txt.
resourceCount - Variable in class org.jmol.i18n.GT
 
resourceMap - Variable in class org.jmol.i18n.Resource
 
resourceName - Variable in class org.jmol.quantum.MepCalculation
 
resources - Variable in class org.jmol.export._IdtfExporter
 
resources - Variable in class org.jmol.i18n.GT
 
restorativeForceAndAngleRadians(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndDistance(V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndOutOfPlaneAngleRadians(V3d, V3d, V3d, V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
restorativeForceAndTorsionAngleRadians(V3d, V3d, V3d, V3d) - Static method in class org.jmol.minimize.Util
 
restore(float, boolean) - Method in class org.jmol.modelset.Orientation
 
restore - Static variable in class org.jmol.script.T
 
restore() - Method in class org.jmol.viewer.Connections
 
restore(Viewer, float) - Method in class org.jmol.viewer.Scene
 
restoreBonds(String) - Method in class org.jmol.viewer.StateManager
 
restoreCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
 
restoreCoordinates() - Method in class org.jmol.minimize.Minimizer
 
restoreFunction(JmolScriptFunction, Lst<SV>, SV) - Method in class org.jmol.script.ScriptEval
note that functions requiring motion cannot be run in JavaScript
restoreModelOrientation(int) - Method in class org.jmol.viewer.Viewer
 
restoreModelRotation(int) - Method in class org.jmol.viewer.Viewer
 
restoreOrientation(String, float, boolean) - Method in class org.jmol.viewer.StateManager
 
restoreScene(String, float) - Method in class org.jmol.viewer.StateManager
 
restoreScriptContext(ScriptContext, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
restoreSelection(String) - Method in class org.jmol.viewer.StateManager
 
restrict - Static variable in class org.jmol.script.T
 
restrictSelected(boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
restrictSelected(boolean, boolean) - Method in class org.jmol.script.ScriptParam
 
restrictSelected(boolean, boolean) - Method in class org.jmol.viewer.ShapeManager
 
RESU - Static variable in class org.jmol.util.ColorEncoder
 
resume - Static variable in class org.jmol.script.T
 
resumeAnimation() - Method in class org.jmol.viewer.AnimationManager
 
resumeButton - Variable in class org.jmol.console.ScriptEditor
 
resumeEval(ScriptContext) - Method in interface org.jmol.api.JmolScriptEvaluator
 
resumeEval(ScriptContext) - Method in class org.jmol.script.ScriptEval
From dispatchCommands and JmolThread resumeEval.
resumeEval() - Method in class org.jmol.thread.JmolThread
 
resumePausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
 
resumePausedExecution() - Method in class org.jmol.script.ScriptEval
 
resumeViewer(String) - Method in class org.jmol.script.ScriptEval
 
ret - Variable in class org.jmol.export.JSExporter
 
retain_order - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
retrieveCount - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
returncmd - Static variable in class org.jmol.script.T
 
returnToken() - Method in class org.jmol.script.ScriptTokenParser
 
returnValue - Variable in class org.jmol.script.ScriptFunction
 
reverse - Static variable in class org.jmol.script.T
 
reverseAnimation() - Method in class org.jmol.viewer.AnimationManager
 
reverseArray(int[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
reverseAtomSets() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
reverseChirality(String) - Method in interface org.jmol.api.SmilesMatcherInterface
 
reverseChirality(String) - Method in class org.jmol.smiles.SmilesMatcher
 
reversecolor - Static variable in class org.jmol.script.T
 
reversed - Variable in class org.jmol.modelsetbio.BioPolymer
 
reversed - Variable in class org.jmol.renderbio.BioShapeRenderer
 
reverseList(Lst<?>) - Static method in class org.jmol.adapter.smarter.AtomSetCollection
 
reverseModels - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
reverseObject(Object[]) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
reverseSets(AtomSetObject[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
rewind - Static variable in class org.jmol.script.T
 
REWIND - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
rewindAnimation() - Method in class org.jmol.viewer.AnimationManager
 
rfactor - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
Rgb16 - Class in org.jmol.util
 
Rgb16() - Constructor for class org.jmol.util.Rgb16
 
rgb16sE - Variable in class org.jmol.g3d.TriangleRenderer
 
rgb16sGouraud - Variable in class org.jmol.g3d.TriangleRenderer
 
rgb16sW - Variable in class org.jmol.g3d.TriangleRenderer
 
rgb16t1 - Variable in class org.jmol.g3d.TriangleRenderer
 
rgb16t2 - Variable in class org.jmol.g3d.TriangleRenderer
 
rgbColorModel - Static variable in class org.jmol.awt.Image
 
rgbFractionalFromArgb(int) - Method in class org.jmol.export.___Exporter
 
rgbFractionalFromColix(short) - Method in class org.jmol.export.___Exporter
 
rho - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
rhoMin - Variable in class org.jmol.quantum.NciCalculation
 
rhoMolecules - Variable in class org.jmol.quantum.NciCalculation
 
rhoParam - Variable in class org.jmol.quantum.NciCalculation
 
rhoPlot - Variable in class org.jmol.quantum.NciCalculation
 
rI - Variable in class org.jmol.util.ModulationSet
 
ribbon - Static variable in class org.jmol.script.T
 
ribbon_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_nucleic_acid_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_power_b - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_sampling - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_side_chain_helper - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_throw - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_trace_atoms - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbon_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ribbonaspectratio - Static variable in class org.jmol.script.T
 
ribbonAspectRatio - Variable in class org.jmol.viewer.GlobalSettings
 
ribbonBorder - Variable in class org.jmol.renderbio.BioShapeRenderer
 
ribbonborder - Static variable in class org.jmol.script.T
 
ribbonBorder - Variable in class org.jmol.viewer.GlobalSettings
 
ribbonBottomScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
 
ribbonColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
Ribbons - Class in org.jmol.shapebio
 
Ribbons() - Constructor for class org.jmol.shapebio.Ribbons
 
RibbonsRenderer - Class in org.jmol.renderbio
 
RibbonsRenderer() - Constructor for class org.jmol.renderbio.RibbonsRenderer
 
ribbonTopScreens - Variable in class org.jmol.renderbio.BioShapeRenderer
 
ribbonTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
riboseOffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
right - Static variable in class org.jmol.script.T
 
right - Variable in class org.jmol.util.Modulation
 
RIGHT - Static variable in class org.jmol.viewer.binding.Binding
 
rightAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
rightbrace - Static variable in class org.jmol.script.T
 
rightOn - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
rightparen - Static variable in class org.jmol.script.T
 
rightPlane - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
rightsquare - Static variable in class org.jmol.script.T
 
ring5OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
ring6OffsetIndexes - Static variable in class org.jmol.modelsetbio.NucleicMonomer
 
ringBonds - Variable in class org.jmol.smiles.SmilesParser
 
ringConnections - Variable in class org.jmol.smiles.SmilesSearch
 
ringConnectivity - Variable in class org.jmol.smiles.SmilesAtom
 
ringCounts - Variable in class org.jmol.smiles.SmilesSearch
 
ringData - Variable in class org.jmol.smiles.SmilesSearch
 
ringDataMax - Variable in class org.jmol.smiles.SmilesSearch
 
ringMembership - Variable in class org.jmol.smiles.SmilesAtom
 
ringSets - Variable in class org.jmol.smiles.SmilesGenerator
 
ringSets - Variable in class org.jmol.smiles.SmilesSearch
 
ringSize - Variable in class org.jmol.smiles.SmilesAtom
 
RL() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
rm - Variable in class org.jmol.viewer.Viewer
 
rmaxx - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
rmaxy - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
rmaxz - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
rminx - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
rminy - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
rminz - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
rmsd - Static variable in class org.jmol.script.T
 
rna - Static variable in class org.jmol.script.T
 
rna3d - Static variable in class org.jmol.script.T
 
rnl - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
robust_logs - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
rock - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
rock - Static variable in class org.jmol.script.T
 
rock_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
rocket - Static variable in class org.jmol.script.T
 
rocketbarrels - Static variable in class org.jmol.script.T
 
rocketBarrels - Variable in class org.jmol.viewer.GlobalSettings
 
RocketRenderer - Class in org.jmol.renderbio
 
RocketRenderer(RocketsRenderer, boolean) - Constructor for class org.jmol.renderbio.RocketRenderer
 
Rockets - Class in org.jmol.shapebio
 
Rockets() - Constructor for class org.jmol.shapebio.Rockets
 
RocketsRenderer - Class in org.jmol.renderbio
 
RocketsRenderer() - Constructor for class org.jmol.renderbio.RocketsRenderer
 
ROOT2 - Static variable in class org.jmol.jvxl.readers.IsoShapeReader
 
ROOT3 - Static variable in class org.jmol.adapter.readers.quantum.JaguarReader
 
ROOT3 - Static variable in class org.jmol.quantum.MOCalculation
 
rootDir - Variable in class org.openscience.chimetojmol.ChimePanel
 
rootPickingStyle - Variable in class org.jmol.viewer.ActionManager
 
rotate - Static variable in class org.jmol.script.T
 
rotate3DBall(float, float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotate45 - Static variable in class org.jmol.script.T
 
rotate4DBall(float, float, float) - Method in class org.jmol.viewer.TransformManager4D
 
ROTATE_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
ROTATE_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
rotateAboutPointsInternal(JmolScriptEvaluator, T3, T3, float, float, boolean, boolean, BS, boolean, V3, Lst<P3>, float[], M4) - Method in class org.jmol.viewer.TransformManager
 
rotateAboutPointsInternal(JmolScriptEvaluator, P3, P3, float, float, boolean, BS, V3, Lst<P3>, float[], M4) - Method in class org.jmol.viewer.Viewer
 
rotateAxes(int, V3[], P3, M3) - Method in interface org.jmol.api.SymmetryInterface
 
rotateAxes(int, V3[], P3, M3) - Method in class org.jmol.symmetry.Symmetry
 
rotateAxes(V3[], UnitCell, P3, M3) - Method in class org.jmol.symmetry.SymmetryOperation
 
rotateAxisAngle(V3, float) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngle2(A4, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleAtCenter(JmolScriptEvaluator, P3, V3, float, float, boolean, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleAtCenter(JmolScriptEvaluator, P3, V3, float, float, boolean, BS) - Method in class org.jmol.viewer.Viewer
 
rotateAxisAngleRadiansFixed(float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateAxisAngleRadiansInternal(float, BS, M4) - Method in class org.jmol.viewer.TransformManager
 
rotateBondIndex - Variable in class org.jmol.viewer.Viewer
 
rotateFront() - Method in class org.jmol.api.JmolViewer
 
rotateFront() - Method in class org.jmol.viewer.Viewer
 
rotatePoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
 
rotatePrev1 - Variable in class org.jmol.viewer.Viewer
 
rotatePrev2 - Variable in class org.jmol.viewer.Viewer
 
rotateSelected - Static variable in class org.jmol.script.T
 
rotateSelected(float, float, BS) - Method in class org.jmol.viewer.Viewer
 
rotateToSuperCell(V3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
rotateTranslate(Quat, T3, boolean) - Method in class org.jmol.shape.Mesh
 
rotateXRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateXYBy(float, float, BS) - Method in class org.jmol.viewer.TransformManager4D
 
rotateXYBy(float, float) - Method in class org.jmol.viewer.Viewer
 
rotateYRadians(float, BS) - Method in class org.jmol.viewer.TransformManager
 
rotateZBy(int, int, int) - Method in class org.jmol.viewer.TransformManager
 
rotateZBy(int, int, int) - Method in class org.jmol.viewer.Viewer
 
rotateZRadians(float) - Method in class org.jmol.viewer.TransformManager
 
rotation - Static variable in class org.jmol.script.T
 
rotation - Variable in class org.jmol.symmetry.HallRotationTerm
 
rotationAxis - Variable in class org.jmol.shapesurface.LcaoCartoon
 
rotationAxis - Variable in class org.jmol.viewer.TransformManager
 
rotationCenterDefault - Variable in class org.jmol.viewer.TransformManager
 
rotationMatrix - Variable in class org.jmol.modelset.Orientation
 
rotationOrder - Variable in class org.jmol.symmetry.HallTranslation
 
rotationRadius - Variable in class org.jmol.modelset.Orientation
 
rotationradius - Static variable in class org.jmol.script.T
 
rotationRadius - Variable in class org.jmol.thread.MoveToThread
 
rotationRadiusDefault - Variable in class org.jmol.viewer.TransformManager
 
rotationRate - Variable in class org.jmol.viewer.TransformManager
 
rotationShift12ths - Variable in class org.jmol.symmetry.HallTranslation
 
rotationTerms - Variable in class org.jmol.symmetry.HallInfo
 
rotCode - Variable in class org.jmol.symmetry.HallRotation
 
rotTransCart(SymmetryOperation, SymmetryInterface, P3, V3) - Static method in class org.jmol.symmetry.SymmetryDesc
 
round(double) - Static method in class org.jmol.export.___Exporter
 
round(T3) - Static method in class org.jmol.export.___Exporter
 
roundInt(int) - Static method in class org.jmol.util.GData
JavaScript won't really have an integer here after integer division.
route - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
roving_byres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_cartoon - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_detail - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_isomesh - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_isosurface - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_labels - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_lines - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_map1_level - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_map1_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_map2_level - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_map2_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_map3_level - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_map3_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_nb_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_nonbonded - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_origin - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_origin_z - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_origin_z_cushion - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_polar_contacts - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_polar_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_ribbon - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_spheres - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
roving_sticks - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
row - Static variable in class org.jmol.script.T
 
ROYGB - Static variable in class org.jmol.util.ColorEncoder
 
rpower - Static variable in class org.jmol.quantum.NciCalculation
 
rPt - Variable in class org.jmol.renderbio.NucleicRenderer
 
rPt5 - Variable in class org.jmol.renderbio.NucleicRenderer
 
rr - Variable in class org.jmol.renderbio.RocketRenderer
 
rr - Variable in class org.jmol.renderbio.RocketsRenderer
 
rs - Variable in class org.jmol.jvxl.readers.AtomDataReader
atom radius + solvent radius
rs2 - Variable in class org.jmol.jvxl.readers.AtomDataReader
square of (atom radius + solvent radius)
rScr - Variable in class org.jmol.renderbio.NucleicRenderer
 
rScr5 - Variable in class org.jmol.renderbio.NucleicRenderer
 
rsvs - Variable in class org.jmol.symmetry.SymmetryOperation
 
rsvs - Variable in class org.jmol.util.ModulationSet
 
rubberband - Static variable in class org.jmol.script.T
 
rubberbandSelectionMode - Variable in class org.jmol.viewer.ActionManager
 
run() - Method in class org.jmol.applet.ClassPreloader
 
run() - Method in class org.jmol.applet.TickerThread
 
run() - Method in class org.jmol.applet.WrappedAppletLoader
 
run() - Method in class org.jmol.io.DOMReader
 
run() - Method in class org.jmol.io.FileReader
 
run() - Method in class org.jmol.io.FilesReader
 
run() - Method in class org.jmol.script.CommandWatcherThread
 
run() - Method in class org.jmol.script.ScriptProcessRunnable
 
run() - Method in class org.jmol.thread.JmolThread
 
run() - Method in class org.openscience.jmol.app.InputScannerThread
 
run() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
run() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ExecuteCommandThread
 
run() - Method in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
 
run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioServerThread
 
run() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JsonNioThread
 
run1(int) - Method in class org.jmol.minimize.MinimizationThread
 
run1(int) - Method in class org.jmol.navigate.Navigator
 
run1(int) - Method in class org.jmol.script.CommandWatcherThread
 
run1(int) - Method in class org.jmol.script.FileLoadThread
 
run1(int) - Method in class org.jmol.script.ScriptDelayThread
 
run1(int) - Method in class org.jmol.script.ScriptQueueThread
 
run1(int) - Method in class org.jmol.thread.AnimationThread
 
run1(int) - Method in class org.jmol.thread.HoverWatcherThread
 
run1(int) - Method in class org.jmol.thread.JmolThread
 
run1(int) - Method in class org.jmol.thread.MoveToThread
 
run1(int) - Method in class org.jmol.thread.SpinThread
Java: run1(INIT) while(!interrupted()) { run1(MAIN) } run1(FINISH) JavaScript: run1(INIT) run1(MAIN) --> setTimeout to run1(CHECK) or run1(FINISH) and return run1(CHECK) --> setTimeout to run1(CHECK) or run1(MAIN) or run1(FINISH) and return
run1(int) - Method in class org.jmol.thread.TimeoutThread
 
run1(int) - Method in class org.jmol.thread.VibrationThread
 
run1Move(int) - Method in class org.jmol.thread.MoveToThread
 
run1MoveTo(int) - Method in class org.jmol.thread.MoveToThread
 
runAllProcesses(Viewer) - Method in interface org.jmol.api.JmolParallelProcessor
 
runAllProcesses(Viewer) - Method in class org.jmol.script.ScriptParallelProcessor
 
runButton - Variable in class org.jmol.console.GenericConsole
 
runButton - Variable in class org.jmol.console.ScriptEditor
 
runFunctionAndRet(JmolScriptFunction, String, Lst<SV>, SV, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptEval
 
runNextScript() - Method in class org.jmol.script.ScriptQueueThread
 
runPanel - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
runPovCheck - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
runProcess(ScriptProcess, ShapeManager) - Method in class org.jmol.script.ScriptParallelProcessor
 
runScript(String) - Method in interface org.jmol.api.JmolScriptEvaluator
 
runScript(String) - Method in class org.jmol.api.JmolViewer
run a script immediately and return output buffer string Jmol 13.1.15
runScript(String) - Method in interface org.jmol.api.JSVInterface
 
runScript(String) - Method in class org.jmol.script.ScriptEval
 
runScript(String) - Method in class org.jmol.viewer.ActionManager
 
runScript(String) - Method in class org.jmol.viewer.Viewer
 
runScript(String, boolean, JmolViewer) - Method in class org.openscience.jmol.app.JmolApp
 
runScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
no queuing here -- called by MainFrame
runScriptBuffer(String, SB) - Method in interface org.jmol.api.JmolScriptEvaluator
 
runScriptBuffer(String, SB) - Method in class org.jmol.script.ScriptEval
runs a script immediately and sends selected output to a provided SB
runScriptNow() - Method in class org.jmol.script.ScriptManager
 
runSleep(int, int) - Method in class org.jmol.thread.JmolThread
 
runStatus - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
RWB - Static variable in class org.jmol.util.ColorEncoder
 

S

S - Static variable in class org.jmol.quantum.QS
 
s0 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
s1 - Variable in class org.jmol.render.FontLineShapeRenderer
 
s1 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
s10 - Static variable in class org.jmol.symmetry.PointGroup
 
s12 - Static variable in class org.jmol.symmetry.PointGroup
 
s2 - Variable in class org.jmol.render.FontLineShapeRenderer
 
s2 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
s3 - Static variable in class org.jmol.symmetry.PointGroup
 
s4 - Static variable in class org.jmol.symmetry.PointGroup
 
s5 - Static variable in class org.jmol.symmetry.PointGroup
 
s6 - Static variable in class org.jmol.symmetry.PointGroup
 
s8 - Static variable in class org.jmol.symmetry.PointGroup
 
sameAs(int, int) - Method in class org.jmol.modelset.Measurement
 
sameAsIJ(int[], Point3fi[], int, int) - Method in class org.jmol.modelset.Measurement
 
sameAsPoints(int[], Point3fi[]) - Method in class org.jmol.modelset.Measurement
 
sampleModelBitMasks - Static variable in class org.jmol.awt.Image
 
sasurface - Static variable in class org.jmol.script.T
 
SAUSAGE - Static variable in class org.jmol.shapecgo.CGOMesh
 
save - Static variable in class org.jmol.script.T
 
save() - Method in class org.openscience.jmol.app.HistoryFile
Saves properties to the history file.
SAVE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
save() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
save() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
save_pdb_ss - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
saveAmbient - Variable in class org.jmol.g3d.Graphics3D
 
saveBonds(String) - Method in class org.jmol.viewer.StateManager
 
saveButton - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
saveButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
saveChooser - Static variable in class org.jmol.dialog.Dialog
 
saveChooser - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
saveContext(String) - Method in class org.jmol.script.ScriptEval
 
saveContext(String, Object) - Method in class org.jmol.viewer.StateManager
 
saveCoordinates() - Method in class org.jmol.minimize.forcefield.ForceField
 
saveCoordinates() - Method in class org.jmol.minimize.Minimizer
 
saveCoordinates(String, BS) - Method in class org.jmol.viewer.StateManager
 
saved - Static variable in class org.jmol.script.T
 
saved - Variable in class org.jmol.viewer.StateManager
 
saveDiffuse - Variable in class org.jmol.g3d.Graphics3D
 
saveField - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
saveField - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
saveHistory() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
Just saves the path settings from this session.
saveHistory() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Just saves the path settings from this session.
saveHistory() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
saveHistory() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
saveList - Static variable in class org.jmol.script.ScriptEval
 
saveList() - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
Saves the list to the history file.
saveModelOrientation(int, Orientation) - Method in class org.jmol.modelset.ModelSet
 
saveModelOrientation() - Method in class org.jmol.viewer.Viewer
 
saveName - Variable in class org.jmol.modelset.Orientation
 
saveName - Variable in class org.jmol.viewer.Connections
 
saveName - Variable in class org.jmol.viewer.Scene
 
saveOrientation(String, float[]) - Method in class org.jmol.viewer.StateManager
 
savePathLabel - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
saveProperties(Properties) - Method in interface org.jmol.api.JSVInterface
 
saveProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
saveproteinstructurestate - Static variable in class org.jmol.script.T
 
saveProteinStructureState - Variable in class org.jmol.viewer.GlobalSettings
 
saveScene(String, Map<String, Object>) - Method in class org.jmol.viewer.StateManager
 
saveSelection(String, BS) - Method in class org.jmol.viewer.StateManager
 
saveState(String) - Method in class org.jmol.viewer.StateManager
 
saveStructure(String) - Method in class org.jmol.viewer.StateManager
 
saveVertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
saveWindowSizes() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
saveXYZCollection() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Saves the currently active collection as a multistep XYZ file.
say(String) - Method in class org.openscience.jmol.app.InputScannerThread
 
say(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
sb - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
sbCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
sbConect - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
sbIgnored - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
sbKey - Variable in class org.jmol.minimize.MinAngle
 
sbMap - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
sbmb - Variable in class org.jmol.minimize.forcefield.AtomType
 
sbSelected - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
sbTemp - Variable in class org.jmol.export._IdtfExporter
 
sbTlsErrors - Variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
sbTlsErrors - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
sbType - Variable in class org.jmol.minimize.MinAngle
 
sc - Variable in class org.jmol.thread.JmolThread
 
scalarDictRef - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
scalarDictValue - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
scalarTitle - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
scale(int) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
scale - Variable in class org.jmol.adapter.readers.simple.JSONReader
 
scale(float) - Method in class org.jmol.export.__CartesianExporter
used only for VRML and X3D; could be expanded
scale - Variable in class org.jmol.jvxl.readers.Parameters
 
scale - Variable in class org.jmol.modelset.TickInfo
 
scale - Static variable in class org.jmol.script.T
 
scale - Variable in class org.jmol.shape.Axes
 
scale(Mesh, float) - Method in class org.jmol.shapecgo.CGO
 
scale(Mesh, float) - Method in class org.jmol.shapespecial.Draw
 
scale - Variable in class org.jmol.shapespecial.DrawMesh
 
scale - Variable in class org.jmol.shapespecial.Ellipsoid
 
scale - Variable in class org.jmol.symmetry.PointGroup
 
scale - Variable in class org.jmol.util.ModulationSet
 
scale3d - Variable in class org.jmol.jvxl.data.JvxlData
 
scale3d - Variable in class org.jmol.jvxl.readers.Parameters
 
scale3d - Static variable in class org.jmol.script.T
 
scale3d - Variable in class org.jmol.shape.Mesh
 
scale3d - Variable in class org.jmol.shapesurface.Isosurface
 
scale3D - Variable in class org.jmol.viewer.TransformManager
 
scale3DAngstromsPerInch - Variable in class org.jmol.viewer.TransformManager
 
SCALE_MAX - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Maximum value for vector scale.
SCALE_PRECISION - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Precision of the vector scale slider
SCALE_VALUE - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Initial value of vector scale.
scaleangstromsperinch - Static variable in class org.jmol.script.T
 
scaleBox(P3[], float) - Static method in class org.jmol.util.BoxInfo
 
scaleDefaultPixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
 
scaleFitToScreen(boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
 
scaleFractionalVibs() - Method in class org.jmol.adapter.smarter.XtalSymmetry
magCIF files have moments expressed as Bohr magnetons along the cryrstallographic axes.
scaleIsosurface(float) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
scalePixelsPerAngstrom - Variable in class org.jmol.export.___Exporter
 
scalePixelsPerAngstrom - Variable in class org.jmol.viewer.TransformManager
 
scalePixelsPerMicron - Variable in class org.jmol.modelset.Object2d
 
scalePixelsPerMicron - Variable in class org.jmol.render.LabelsRenderer
 
scalePixelsPerMicron - Variable in class org.jmol.render.MeshRenderer
 
scalePixelsPerMicron - Variable in class org.jmol.shape.Labels
 
scalePrimitiveData(int, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
scalePt(T3) - Method in class org.jmol.export.__CartesianExporter
used only for VRML and X3D; could be expanded
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.MopacSlaterReader
overrides method in SlaterReader to allow for MOPAC's treatment of the radial exponent differently depending upon position in the periodic table -- noble gases and transition metals and for the fact that these are spherical functions (5D, not 6D) ignores any F orbitals.
scaleSlater(int, int, int, int, double) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
Perform implementation-specific scaling.
scaleSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
scaleToPerspective(int, float) - Method in class org.jmol.viewer.TransformManager
 
scaleToScreen(int, int) - Method in class org.jmol.modelset.Group
 
scaleToScreen(int, int) - Method in class org.jmol.viewer.TransformManager
 
scaleVectorsToMax(float) - Method in class org.jmol.modelset.AtomCollection
Scales vibrations and associated vectors such that the maximum length is the given value
scaleVibration(float) - Method in interface org.jmol.api.JmolModulationSet
 
scaleVibration(float) - Method in class org.jmol.util.ModulationSet
 
scanForOffsets(int, int[], byte[]) - Static method in class org.jmol.modelsetbio.Monomer
 
scanInput - Variable in class org.openscience.jmol.app.JmolApp
 
scanner - Variable in class org.openscience.jmol.app.InputScannerThread
 
scanPoint - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
The scan point, where -1 denotes no scan information.
scene - Static variable in class org.jmol.script.T
 
Scene - Class in org.jmol.viewer
 
Scene(Map<String, Object>) - Constructor for class org.jmol.viewer.Scene
 
scene - Variable in class org.jmol.viewer.Scene
 
scene_animation - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
scene_animation_duration - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
scene_buttons - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
scene_buttons_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
scene_current_name - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
scene_frame_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
scene_loop - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
scene_restart_movie_delay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SCENE_TAG - Static variable in class org.jmol.viewer.OutputManager
 
sceneOrder - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
scenes_changed - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
schemes - Variable in class org.jmol.util.ColorEncoder
 
scm - Variable in class org.jmol.viewer.Viewer
 
score - Variable in class org.jmol.util.ContactPair
 
screen - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
screen - Variable in class org.jmol.render.LabelsRenderer
 
screenA - Variable in class org.jmol.renderbio.RocketRenderer
 
screenArrowBot - Variable in class org.jmol.renderbio.BioShapeRenderer
 
screenArrowBotPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
 
screenArrowHead - Variable in class org.jmol.renderspecial.VectorsRenderer
 
screenArrowTop - Variable in class org.jmol.renderbio.BioShapeRenderer
 
screenArrowTopPrev - Variable in class org.jmol.renderbio.BioShapeRenderer
 
screenB - Variable in class org.jmol.renderbio.RocketRenderer
 
screenC - Variable in class org.jmol.renderbio.RocketRenderer
 
screenCoordinates - Variable in class org.jmol.renderspecial.DotsRenderer
 
screenCorners - Variable in class org.jmol.renderbio.RocketRenderer
 
screenDotCount - Variable in class org.jmol.renderspecial.DotsRenderer
 
screenHeight - Variable in class org.jmol.export.___Exporter
 
screenHeight - Variable in class org.jmol.viewer.TransformManager
 
screenLevel - Variable in class org.jmol.renderspecial.DotsRenderer
 
screenPixelCount - Variable in class org.jmol.viewer.TransformManager
 
screens - Variable in class org.jmol.render.AxesRenderer
 
screens - Variable in class org.jmol.render.CageRenderer
 
screens - Variable in class org.jmol.render.MeshRenderer
 
screens - Variable in class org.jmol.renderspecial.DipolesRenderer
 
screens - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
screens - Variable in class org.jmol.renderspecial.PolyhedraRenderer
 
screenSize - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
screenVectorEnd - Variable in class org.jmol.renderspecial.VectorsRenderer
 
screenVectorStart - Variable in class org.jmol.renderspecial.VectorsRenderer
 
screenWidth - Variable in class org.jmol.export.___Exporter
 
screenWidth - Variable in class org.jmol.viewer.TransformManager
 
screenx - Static variable in class org.jmol.script.T
 
screenxyz - Static variable in class org.jmol.script.T
 
screeny - Static variable in class org.jmol.script.T
 
screenz - Static variable in class org.jmol.script.T
 
script(String) - Method in interface org.jmol.api.JmolAppletInterface
 
script(String) - Method in class org.jmol.api.JmolViewer
 
script - Variable in class org.jmol.jvxl.readers.Parameters
 
script - Variable in class org.jmol.modelset.Object2d
 
script - Variable in class org.jmol.script.ScriptContext
 
script - Variable in class org.jmol.script.ScriptEval
 
script - Variable in class org.jmol.script.ScriptFunction
 
script - Variable in class org.jmol.script.ScriptTokenParser
 
script - Static variable in class org.jmol.script.T
 
script - Variable in class org.jmol.shapesurface.Isosurface
 
script - Variable in class org.jmol.thread.TimeoutThread
 
script(String) - Method in class org.jmol.util.GenericApplet
 
script(String) - Method in class org.jmol.viewer.Viewer
 
script(String) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.AnimButton
 
script - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.NewAction
 
script - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
script1 - Variable in class org.jmol.modelset.StateScript
 
script1 - Variable in class org.openscience.jmol.app.JmolApp
 
script2 - Variable in class org.jmol.modelset.StateScript
 
script2 - Variable in class org.openscience.jmol.app.JmolApp
 
SCRIPT_CHECK - Static variable in class org.jmol.util.GenericApplet
 
SCRIPT_COMPLETED - Static variable in class org.jmol.viewer.JC
 
SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JC
 
SCRIPT_NOWAIT - Static variable in class org.jmol.util.GenericApplet
 
SCRIPT_WAIT - Static variable in class org.jmol.util.GenericApplet
 
SCRIPT_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
scriptAppendix - Variable in class org.jmol.shapesurface.Isosurface
 
scriptButtonPercent - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
ScriptButtons - Class in org.openscience.jmol.app.webexport
 
ScriptButtons(Viewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.ScriptButtons
 
scriptCallback(String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
from StatusManager
scriptCallback(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
scriptCheck(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptCheck(String) - Method in class org.jmol.api.JmolViewer
 
scriptCheck(String) - Method in class org.jmol.util.GenericApplet
 
scriptCheck(String) - Method in class org.jmol.viewer.Viewer
 
scriptCheckRet(String, boolean) - Method in interface org.jmol.api.JmolScriptManager
 
scriptCheckRet(String, boolean) - Method in class org.jmol.script.ScriptManager
 
scriptCheckRet(String, boolean) - Method in class org.jmol.viewer.Viewer
 
scriptCommand - Static variable in class org.jmol.script.T
 
scriptCommand - Variable in class org.jmol.shape.Mesh
 
ScriptCompiler - Class in org.jmol.script
 
ScriptCompiler(Viewer) - Constructor for class org.jmol.script.ScriptCompiler
 
ScriptContext - Class in org.jmol.script
 
ScriptContext() - Constructor for class org.jmol.script.ScriptContext
 
scriptDelay - Variable in class org.jmol.viewer.GlobalSettings
 
ScriptDelayThread - Class in org.jmol.script
 
ScriptDelayThread(JmolScriptEvaluator, Viewer, int) - Constructor for class org.jmol.script.ScriptDelayThread
 
scriptDelayThread - Variable in class org.jmol.script.ScriptEval
 
scriptEcho(String) - Method in class org.jmol.viewer.Viewer
 
scriptEditor - Variable in class org.jmol.console.JmolConsole
 
ScriptEditor - Class in org.jmol.console
 
ScriptEditor() - Constructor for class org.jmol.console.ScriptEditor
 
ScriptEditor(Viewer, JFrame, JmolConsole) - Constructor for class org.jmol.console.ScriptEditor
 
scriptEditor - Variable in class org.jmol.viewer.Viewer
 
ScriptEditor.EditorDocument - Class in org.jmol.console
 
ScriptEditor.EditorDocument.MyUndoableEditListener - Class in org.jmol.console
 
ScriptEditor.EditorTextPane - Class in org.jmol.console
 
ScriptEditorAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptEditorAction
 
scriptEditorVisible - Variable in class org.jmol.viewer.Viewer
 
ScriptError - Class in org.jmol.script
Error handling for ScriptEvaluator, ScriptProcess, and ScriptParams
ScriptError() - Constructor for class org.jmol.script.ScriptError
 
ScriptEval - Class in org.jmol.script
 
ScriptEval() - Constructor for class org.jmol.script.ScriptEval
 
ScriptException - Exception in org.jmol.script
 
ScriptException(ScriptError, String, String, boolean) - Constructor for exception org.jmol.script.ScriptException
 
ScriptExpr - Class in org.jmol.script
The ScriptExpr class holds the main functions for processing mathematical and atom selection expressions.
ScriptExpr() - Constructor for class org.jmol.script.ScriptExpr
 
scriptExtensions - Variable in class org.jmol.script.ScriptCompiler
 
scriptExtensions - Variable in class org.jmol.script.ScriptContext
 
scriptExtensions - Variable in class org.jmol.script.ScriptEval
 
scriptFileName - Variable in class org.jmol.script.ScriptContext
 
scriptFileName - Variable in class org.jmol.script.ScriptEval
 
scriptFilename - Variable in class org.openscience.jmol.app.JmolApp
 
scriptFilePrefixes - Static variable in class org.jmol.viewer.FileManager
 
ScriptFlowContext - Class in org.jmol.script
 
ScriptFlowContext(ScriptCompiler, ContextToken, int, ScriptFlowContext) - Constructor for class org.jmol.script.ScriptFlowContext
 
ScriptFunction - Class in org.jmol.script
 
ScriptFunction() - Constructor for class org.jmol.script.ScriptFunction
 
ScriptFunction(String, int) - Constructor for class org.jmol.script.ScriptFunction
 
scriptIndex - Variable in class org.jmol.script.ScriptManager
 
ScriptInterruption - Exception in org.jmol.script
 
ScriptInterruption(ScriptEval, String, int) - Constructor for exception org.jmol.script.ScriptInterruption
 
scriptLevel - Variable in class org.jmol.script.ScriptContext
 
scriptLevel - Variable in class org.jmol.script.ScriptEval
 
scriptLevelMax - Static variable in class org.jmol.script.ScriptEval
 
scriptManager - Variable in class org.jmol.script.CommandWatcherThread
 
ScriptManager - Class in org.jmol.script
 
ScriptManager() - Constructor for class org.jmol.script.ScriptManager
 
scriptManager - Variable in class org.jmol.script.ScriptQueueThread
 
ScriptMathProcessor - Class in org.jmol.script
 
ScriptMathProcessor(ScriptExpr, boolean, boolean, boolean, boolean, boolean, String) - Constructor for class org.jmol.script.ScriptMathProcessor
 
scriptNoWait(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptNoWait(String) - Method in class org.jmol.util.GenericApplet
 
ScriptParallelProcessor - Class in org.jmol.script
 
ScriptParallelProcessor() - Constructor for class org.jmol.script.ScriptParallelProcessor
parallel operations
ScriptParam - Class in org.jmol.script
The ScriptParam class holds methods used to parse parameters in Jmol scripts.
ScriptParam() - Constructor for class org.jmol.script.ScriptParam
 
ScriptProcess - Class in org.jmol.script
the idea here is that the process { ...
ScriptProcess(String, ScriptContext) - Constructor for class org.jmol.script.ScriptProcess
 
scriptProcessor(String, String, int) - Method in class org.jmol.util.GenericApplet
 
ScriptProcessRunnable - Class in org.jmol.script
 
ScriptProcessRunnable(ScriptParallelProcessor, ScriptProcess, Object, ShapeManager) - Constructor for class org.jmol.script.ScriptProcessRunnable
 
scriptQueue - Variable in class org.jmol.script.ScriptManager
 
scriptqueue - Static variable in class org.jmol.script.T
 
scriptQueueRunning - Variable in class org.jmol.script.ScriptManager
 
ScriptQueueThread - Class in org.jmol.script
 
ScriptQueueThread(JmolScriptManager, Viewer, boolean, int) - Constructor for class org.jmol.script.ScriptQueueThread
 
scriptReportingLevel - Variable in class org.jmol.script.ScriptEval
 
scriptreportinglevel - Static variable in class org.jmol.script.T
 
scriptStatus(String) - Method in class org.jmol.viewer.Viewer
 
scriptStatusMsg(String, String) - Method in class org.jmol.viewer.Viewer
 
ScriptTokenParser - Class in org.jmol.script
 
ScriptTokenParser() - Constructor for class org.jmol.script.ScriptTokenParser
 
scriptWait(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptWait(String, String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptWait(String) - Method in class org.jmol.api.JmolViewer
 
scriptWait(String) - Method in class org.jmol.util.GenericApplet
 
scriptWait(String, String) - Method in class org.jmol.util.GenericApplet
 
scriptWait(String) - Method in class org.jmol.viewer.Viewer
 
scriptWaitOutput(String) - Method in interface org.jmol.api.JmolAppletInterface
 
scriptWaitOutput(String) - Method in class org.jmol.util.GenericApplet
 
scriptWaitStatus(String, String) - Method in class org.jmol.api.JmolViewer
 
scriptWaitStatus(String, String) - Method in class org.jmol.viewer.Viewer
 
ScriptWindowAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ScriptWindowAction
 
scroller - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
sculpt_angl_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_auto_center - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_avd_excl - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_avd_gap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_avd_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_avd_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_bond_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_field_mask - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_hb_overlap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_hb_overlap_base - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_line_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_max_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_max_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_max_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_max_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_memory - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_min_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_min_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_min_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_min_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_nb_interval - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_plan_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_pyra_inv_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_pyra_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_tors_tolerance - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_tors_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_tri_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_tri_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_tri_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_tri_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_tri_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_vdw_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_vdw_scale14 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_vdw_vis_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_vdw_vis_mid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_vdw_vis_min - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_vdw_vis_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_vdw_weight - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpt_vdw_weight14 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sculpting_cycles - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sD - Variable in class org.jmol.util.Point3fi
screen diameter
SDIM - Static variable in class org.jmol.util.Shader
 
sdof_drag_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
search - Static variable in class org.jmol.script.T
 
search - Variable in class org.jmol.smiles.SmilesMeasure
 
search(boolean) - Method in class org.jmol.smiles.SmilesSearch
the start of the search.
searchForTurns(AlphaPolymer.Code[], float[], STR[]) - Method in class org.jmol.modelsetbio.AlphaPolymer
 
secondary_structure - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
secondCharOnly - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
seconds - Variable in class org.jmol.script.ScriptDelayThread
 
security - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seed - Variable in class org.jmol.util.Shader
 
SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
 
segments - Variable in class org.jmol.modelsetbio.ProteinStructure
 
seitzMatrix - Variable in class org.jmol.symmetry.HallRotation
 
seitzMatrix12ths - Variable in class org.jmol.symmetry.HallRotationTerm
 
seitzMatrixInv - Variable in class org.jmol.symmetry.HallRotation
 
sel_counter - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
select - Static variable in class org.jmol.script.T
 
select(BS, int, boolean) - Method in class org.jmol.viewer.SelectionManager
 
select(BS, boolean, int, boolean) - Method in class org.jmol.viewer.Viewer
 
select - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
selectAll() - Method in class org.jmol.api.JmolViewer
 
selectAll(boolean) - Method in class org.jmol.viewer.SelectionManager
 
selectAll() - Method in class org.jmol.viewer.Viewer
 
selectAllAtoms(Lst<Object>, int, BS) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Collect all the atoms specified by an object state into a bit set.
selectallmodels - Static variable in class org.jmol.script.T
 
selectAllModels - Variable in class org.jmol.viewer.GlobalSettings
 
selectAtoms(BS) - Method in class org.jmol.modelset.Group
 
selectAtoms(String) - Method in class org.jmol.viewer.ActionManager
 
selectBonds(BS) - Method in class org.jmol.viewer.Viewer
 
selectDisplayedTrajectories(BS) - Method in class org.jmol.modelset.ModelSet
 
selected - Static variable in class org.jmol.script.T
 
selected - Variable in class org.jmol.smiles.SmilesAtom
 
selectedAtomCount - Variable in class org.jmol.smiles.SmilesSearch
 
selectedAtoms - Variable in class org.jmol.shapespecial.Ellipsoids
 
selectedBonds - Variable in class org.jmol.shape.Sticks
 
selectedFileName - Variable in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
selectedfloat - Static variable in class org.jmol.script.T
 
selectedGroupCount - Variable in class org.jmol.modelset.Chain
 
selectedIndex - Variable in class org.jmol.modelset.Group
 
selectedMeasurementRow - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
selectedModel - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
selectedMolecules - Variable in class org.jmol.modelset.ModelSet
 
selectedMonomerCount - Variable in class org.jmol.modelsetbio.BioPolymer
 
selectedOctant - Variable in class org.jmol.g3d.SphereRenderer
 
selectedOctant - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
selectedPoints - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
selectedPolyOnly - Variable in class org.jmol.render.MeshRenderer
 
selectedTrajectory - Variable in class org.jmol.modelset.Model
 
selectField - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
selecthetero - Static variable in class org.jmol.script.T
 
selecthydrogen - Static variable in class org.jmol.script.T
 
selection - Static variable in class org.jmol.script.T
 
selection_overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
selection_round_points - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
selection_visible_only - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
selection_width - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
selection_width_max - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
selection_width_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
selectionChanged(BS) - Method in interface org.jmol.api.JmolSelectionListener
Called when the selected atoms change
selectionChanged(boolean) - Method in class org.jmol.viewer.SelectionManager
 
selectionHaloEnabled - Variable in class org.jmol.modelset.ModelSet
 
selectionhalos - Static variable in class org.jmol.script.T
 
SelectionManager - Class in org.jmol.viewer
 
SelectionManager(Viewer) - Constructor for class org.jmol.viewer.SelectionManager
 
selectionWorking - Variable in class org.jmol.viewer.ActionManager
 
selectItemTok(T, int) - Static method in class org.jmol.script.SV
 
selectItemVar(SV) - Static method in class org.jmol.script.SV
 
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
selectPocket(boolean) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
selectRb(int) - Method in class org.jmol.viewer.ActionManager
 
selectReaderAndGo(Object) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
selectSeqcodeRange(int, int, int, BS) - Method in class org.jmol.modelset.Chain
 
selectSlider - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
semicolon - Static variable in class org.jmol.script.T
 
send(int, String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
from JmolPanel and SYNC command
send(int, String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
sendConsoleEcho(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
sendConsoleEcho(String) - Method in class org.jmol.console.GenericConsole
 
sendConsoleEcho(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
sendConsoleMessage(String) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
sendConsoleMessage(String) - Method in class org.jmol.console.GenericConsole
 
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
sendConsoleMessage(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
sendJSpecView(String) - Method in class org.jmol.jsv.JSpecView
 
sendKeyBuffer() - Method in class org.jmol.awt.Mouse
 
sendKeyBuffer() - Method in class org.jmol.awtjs2d.Mouse
 
sendMessage(JsonNioService.JSONObject, String, NIOSocket) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
sendNioMessage(int, String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
sendScript(String, String, boolean, boolean) - Method in class org.jmol.util.GenericApplet
 
sendScript(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
sep - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
seq_view - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_alignment - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_discrete_by_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_fill_char - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_fill_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_format - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_label_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_label_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_label_spacing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_label_start - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_location - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_overlay - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_unaligned_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seq_view_unaligned_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
seqAdv() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
seqcode - Variable in class org.jmol.modelset.Group
 
seqcode - Static variable in class org.jmol.script.T
 
seqcodes - Variable in class org.jmol.modelset.ModelLoader
 
seqid - Static variable in class org.jmol.script.T
 
seqMode - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
sequence - Static variable in class org.jmol.script.T
 
SEQUENCE_NUMBER_FLAG - Static variable in class org.jmol.modelset.Group
 
SEQUENCE_NUMBER_SHIFT - Static variable in class org.jmol.modelset.Group
 
sequenceNumber - Variable in class org.jmol.adapter.smarter.Atom
 
sequenceNumbers - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
serial - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
SERIAL_NO - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
serialArrayListFlavor - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
serialID - Variable in class org.jmol.adapter.smarter.Structure
 
serialID - Variable in class org.jmol.modelsetbio.ProteinStructure
 
serialVersionUID - Static variable in class org.openscience.jmol.app.webexport.Test
 
serMode - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
serverConnection - Variable in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
serverPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
serverService - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
serverSocket - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
serverThread - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
service - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SERVICE_LOST - Static variable in class org.jmol.multitouch.ActionManagerMT
 
session_cache_optimize - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
session_changed - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
session_compression - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
session_file - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
session_migration - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
session_version_check - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
 
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
set() - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
set(int, int, char, int, int, char, int, int) - Method in class org.jmol.adapter.smarter.Structure
 
set(AtomSetCollectionReader) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
set(Viewer) - Method in interface org.jmol.api.JmolDataManager
 
set(FileManager, Viewer, Object, Map<String, Object>) - Method in interface org.jmol.api.JmolDomReaderInterface
 
set(AtomDataServer, int, short[]) - Method in interface org.jmol.api.JmolEnvCalc
 
set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in interface org.jmol.api.JmolFilesReaderInterface
 
set(JmolJDXMOLReader, String, Map<String, Object>) - Method in interface org.jmol.api.JmolJDXMOLParser
 
set(TransformManager, Viewer) - Method in interface org.jmol.api.JmolNavigatorInterface
 
set(String, int) - Method in interface org.jmol.api.JmolParallelProcessor
 
set(Viewer, ShapeManager) - Method in interface org.jmol.api.JmolRepaintManager
 
set(Viewer) - Method in interface org.jmol.api.MepCalculationInterface
 
set(Bspt) - Method in class org.jmol.bspt.CubeIterator
 
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.CircleRenderer
 
set(JmolRendererInterface, GData) - Method in interface org.jmol.g3d.G3DRenderer
 
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.HermiteRenderer
 
set(int, int, int) - Method in class org.jmol.g3d.PixelatorShaded
 
set(JmolRendererInterface, GData) - Method in class org.jmol.g3d.TriangleRenderer
 
set(AtomDataServer, int, short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
set(FileManager, Viewer, Object, Map<String, Object>) - Method in class org.jmol.io.DOMReader
 
set(FileManager, Viewer, String[], String[], String[], DataReader[], Map<String, Object>, boolean) - Method in class org.jmol.io.FilesReader
 
set(int) - Method in class org.jmol.java.BS
Sets the bit at the specified index to true.
set(JmolJDXMOLReader, String, Map<String, Object>) - Method in class org.jmol.jsv.JDXMOLParser
 
set(Calculations) - Method in class org.jmol.minimize.forcefield.Calculation
 
set() - Method in class org.jmol.minimize.MinAtom
 
set(int) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
 
set(String, int) - Method in class org.jmol.modelset.LabelToken
 
set(int, Map<String, Integer>, RadiusData, String, String, TickInfo, boolean, boolean, Boolean, boolean, int, short, Text) - Method in class org.jmol.modelset.MeasurementData
 
set(ModelSet) - Method in class org.jmol.modelset.MeasurementPending
 
set(ModelSet, int, int, String, Properties, Map<String, Object>) - Method in class org.jmol.modelset.Model
 
set(Font, short, int, boolean, float, float[]) - Method in class org.jmol.modelset.Text
 
set(Monomer[]) - Method in class org.jmol.modelsetbio.BioPolymer
 
set(TransformManager, Viewer) - Method in class org.jmol.navigate.Navigator
 
set(Viewer) - Method in class org.jmol.quantum.MepCalculation
 
set(Viewer, ShapeManager) - Method in class org.jmol.render.RepaintManager
 
set(String, int) - Method in class org.jmol.script.ScriptFunction
 
set - Static variable in class org.jmol.script.T
 
set(Lst<Object>) - Method in class org.jmol.shapecgo.CGOMesh
 
set(Dipole) - Method in class org.jmol.shapespecial.Dipole
 
set(SmilesBond) - Method in class org.jmol.smiles.SmilesBond
 
set(PointGroup, Atom[], BS, boolean, float, float) - Method in class org.jmol.symmetry.PointGroup
 
set(boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
set(int, String) - Method in class org.jmol.thread.TimeoutThread
 
set(MeshSlicer) - Method in class org.jmol.util.MeshCapper
 
set(MeshSurface) - Method in class org.jmol.util.MeshSlicer
 
set(float, float, float) - Method in interface org.jmol.util.Node
 
set(String) - Method in class org.jmol.viewer.binding.JmolBinding
 
set(Viewer) - Method in class org.jmol.viewer.DataManager
 
set(int, int, int, long) - Method in class org.jmol.viewer.MotionPoint
 
set(long, int, int, int) - Method in class org.jmol.viewer.MouseState
 
set2(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.Monomer
 
set2(P3, P3) - Method in class org.jmol.shapespecial.Dipole
 
set2(int, boolean) - Method in class org.jmol.smiles.SmilesBond
 
set2(P3, P3i) - Static method in class org.jmol.util.Point3fi
 
set2a(SmilesAtom, SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
 
set2AtomValue(Atom, Atom, float) - Method in class org.jmol.shapespecial.Dipole
 
set2D() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
set2dZ(int, int) - Method in class org.jmol.modelset.ModelLoader
 
set2Value(P3, P3, float) - Method in class org.jmol.shapespecial.Dipole
 
set3(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.PhosphorusMonomer
 
set3dContourVector(Lst<Object>, int[][], T3[]) - Static method in class org.jmol.jvxl.data.JvxlCoder
Interpret fractional data in terms of actual vertex positions and create the elements of a Vector in Vector[] vContours starting at the CONTOUR_POINTS position.
set4(Chain, String, int, int, int, byte[]) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
setAaTokenCompiled() - Method in class org.jmol.script.ScriptCompiler
 
setABC(int) - Method in class org.jmol.util.MeshSurface
 
setABC(V3, V3, V3) - Method in class org.jmol.util.SimpleUnitCell
 
setAbstractButtonLabels(Map<String, Object>, Map<String, String>) - Static method in class org.jmol.console.GenericConsole
 
setACDAssignments(String, String, int, Lst<String[]>, String) - Method in interface org.jmol.api.JmolJDXMOLParser
 
setACDAssignments(String, String, int, Lst<String[]>, String) - Method in class org.jmol.jsv.JDXMOLParser
 
setAction(int, long) - Method in class org.jmol.viewer.Gesture
 
setActionCommand(String) - Method in class org.jmol.popup.AwtSwingComponent
 
setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
Changes the activation state for a logging level.
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.P2nReader
 
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pdb.PdbReader
adaptable via subclassing
setAdditionalAtomParameters(Atom) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
setAlignment(int) - Method in class org.jmol.modelset.Object2d
 
setAlignment(int, int) - Method in class org.jmol.shape.Labels
 
setAlignmentLCR(String) - Method in class org.jmol.modelset.Object2d
 
setAll(int, int, int, int, int) - Method in class org.jmol.smiles.SmilesAtom
 
setAll(int) - Static method in class org.jmol.util.BSUtil
 
setAll(P3, M3, P3, float, float, float, float, float, float, float, float, float, float, float) - Method in class org.jmol.viewer.TransformManager
 
setAllDSSRParametersForModel(Viewer, int) - Method in interface org.jmol.api.JmolAnnotationParser
 
setAllDSSRParametersForModel(Viewer, int) - Method in class org.jmol.dssx.AnnotationParser
 
setAmbientOcclusion(int) - Method in class org.jmol.util.GData
 
setAmbientPercent(int) - Method in class org.jmol.util.GData
fractional distance from black for ambient color
setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.util.Rgb16
 
setAngleType(MinAngle) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
setAngleUnits(int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setAngleVariables(Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
 
setAnimation(int) - Method in class org.jmol.viewer.Viewer
 
setAnimationDirection(int) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationFps(int) - Method in class org.jmol.api.JmolViewer
 
setAnimationFps(int) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationFps(int) - Method in class org.jmol.viewer.Viewer
 
setAnimationLast() - Method in class org.jmol.viewer.AnimationManager
 
setAnimationMode(String) - Method in class org.jmol.viewer.Viewer
 
setAnimationNext() - Method in class org.jmol.viewer.AnimationManager
 
setAnimationOn(boolean) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setAnimationPrevious() - Method in class org.jmol.viewer.AnimationManager
 
setAnimationRange(int, int) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationRange(int, int) - Method in class org.jmol.viewer.Viewer
 
setAnimationRelative(int) - Method in class org.jmol.viewer.AnimationManager
 
setAnimationReplayMode(int, float, float) - Method in class org.jmol.viewer.AnimationManager
 
setAnimDisplay(BS) - Method in class org.jmol.viewer.Viewer
 
setAnisoBorU(Atom, float[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAnisotropy(P3) - Method in class org.jmol.jvxl.readers.Parameters
 
setAnnotationAtoms(Viewer, Map<String, SV>, int) - Method in class org.jmol.dssx.AnnotationParser
 
setAntialias(boolean) - Method in class org.jmol.viewer.TransformManager
 
setAntialias(int, boolean) - Method in class org.jmol.viewer.Viewer
 
setAPa(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.AtomCollection
 
setAPm(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
 
setApplet(Applet, boolean) - Method in class org.jmol.applet.Jmol
 
setApplet(Applet, boolean) - Method in interface org.jmol.applet.WrappedApplet
 
setAppletContext(String) - Method in class org.jmol.viewer.FileManager
 
setAppletPath(String, boolean) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setAppletProxy(String) - Method in class org.jmol.viewer.FileManager
 
setApplySymmetryToBonds(boolean) - Method in class org.jmol.viewer.Viewer
 
setAromatic56(Lst<Object>, BS, int, Lst<BS>) - Method in class org.jmol.smiles.SmilesSearch
 
setArrays(Atom[], BS, Bond[], int, boolean, boolean) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
setAsBallRotation(M4, float, float, float, float) - Method in class org.jmol.viewer.TransformManager4D
4D ball rotation from nominal dx, dy, dz motion.
setAtom(Atom, int, int, int, float, float, float) - Method in class org.jmol.adapter.readers.simple.InputReader
 
setAtom(int, int, P3, float, BS, int, short, int, boolean) - Method in class org.jmol.modelset.Atom
 
setAtom2(SmilesAtom) - Method in class org.jmol.smiles.SmilesBond
 
setAtom2dZ(Atom, Atom, V3, V3, V3) - Static method in class org.jmol.modelset.ModelLoader
 
setAtomArray() - Method in class org.jmol.smiles.SmilesSearch
 
setAtomBitSet(BS) - Method in class org.jmol.modelset.Chain
 
setAtomClickability() - Method in class org.jmol.shape.AtomShape
 
setAtomClickability() - Method in class org.jmol.shape.Balls
 
setAtomClickability() - Method in class org.jmol.shape.Labels
 
setAtomClickability() - Method in class org.jmol.shape.Shape
 
setAtomClickability() - Method in class org.jmol.shape.Sticks
 
setAtomClickability() - Method in class org.jmol.shapebio.Backbone
 
setAtomClickability() - Method in class org.jmol.shapebio.BioShape
 
setAtomClickability() - Method in class org.jmol.shapebio.BioShapeCollection
 
setAtomClickability() - Method in class org.jmol.shapespecial.Dots
 
setAtomClickability() - Method in class org.jmol.shapespecial.Ellipsoids
 
setAtomColor(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setAtomCoord(Atom) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoord(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoord2(BS, int, Object) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoordRelative(int, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomCoords(BS, int, Object) - Method in class org.jmol.modelset.ModelSet
 
setAtomCoords(BS, int, Object) - Method in class org.jmol.viewer.Viewer
 
setAtomCoordScaled(Atom, String[], int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoordsRelative(T3, BS) - Method in class org.jmol.modelset.ModelSet
 
setAtomCoordsRelative(T3, BS) - Method in class org.jmol.viewer.Viewer
 
setAtomCoordTokens(Atom, String[], int) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomCoordXYZ(Atom, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setAtomData(int, String, String, boolean) - Method in class org.jmol.modelset.AtomCollection
 
setAtomData(int, String, String, boolean) - Method in class org.jmol.viewer.Viewer
 
setAtomDefs() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setAtomI(int) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setAtomicAndIsotopeNumber(int) - Method in class org.jmol.modelset.Atom
 
setAtomicMass(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the atomic mass of the atom.
setAtomicOrbital(float[]) - Method in class org.jmol.jvxl.readers.Parameters
 
setAtomIndexes(int, int) - Method in class org.jmol.util.Tensor
 
setAtomInfo(int[], int[], int[], boolean[], float[]) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setAtomLabel(String, int) - Method in class org.jmol.viewer.ShapeManager
 
setAtomMap(int[], int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setAtomName(Atom, String, String) - Method in class org.jmol.adapter.readers.more.GromacsReader
 
setAtomName(int, String) - Method in class org.jmol.modelset.AtomCollection
 
setAtomName(String) - Method in class org.jmol.smiles.SmilesAtom
 
setAtomNames() - Method in class org.jmol.adapter.readers.xml.XmlCmlReader
 
setAtomNamesAndNumbers(int, int, AtomCollection) - Method in class org.jmol.modelset.ModelSet
 
setAtomNumber(int, int) - Method in class org.jmol.modelset.AtomCollection
 
setAtomPickingOption(String) - Method in class org.jmol.viewer.ActionManager
 
setAtomPickingOption(String) - Method in class org.jmol.viewer.Viewer
 
setAtomPositions() - Method in class org.jmol.minimize.Minimizer
 
setAtomPositions(int, int, P3[], P3[], float, V3[], boolean) - Method in class org.jmol.modelset.ModelSet
A generic way to set atom positions, possibly from trajectories but also possibly from an array.
setAtomProp(String, Object, BS) - Method in class org.jmol.script.ScriptEval
 
setAtomProp(String, Object, BS) - Method in class org.jmol.script.ScriptExpr
 
setAtomProperties(String, Object, int, boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomProperties() - Method in class org.jmol.modelset.ModelLoader
 
setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.modelset.ModelSet
 
setAtomProperty(BS, int, int, float, String, float[], String[]) - Method in class org.jmol.viewer.Viewer
 
setAtomsCoordRelative(BS, float, float, float) - Method in class org.jmol.modelset.AtomCollection
 
setAtomSeqID(int, int) - Method in class org.jmol.modelset.AtomCollection
 
setAtomSetCollectionPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the partial atomic charges based on asc auxiliary info
setAtomSetEnergy(String, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetFrequency(String, String, String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetInfo() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
setAtomSetInfoMd() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
setAtomSetModelProperty(String, String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets a property for the current AtomSet used specifically for creating directories and plots of frequencies and molecular energies
setAtomSetModelPropertyForSet(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the a property for the an AtomSet
setAtomSetName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the name for the current AtomSet
setAtomSetNames(String, int, BS) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the atom set names of the last n atomSets
setAtomSetNumber(int, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setAtomSetPartialCharges(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the partial atomic charges based on atomSet auxiliary info
setAtomSetPropertyForSets(String, String, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the same properties for the last n atomSets.
setAtomSetSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setAtomTensors(int, Lst<Object>) - Method in class org.jmol.modelset.AtomCollection
 
setAtomType(int, String) - Method in class org.jmol.modelset.AtomCollection
 
setAtomType(String) - Method in class org.jmol.smiles.SmilesAtom
 
setAtomTypes(Atom[], BS, SmilesMatcherInterface, Lst<BS>[], boolean) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
The file MMFF94-smarts.txt is derived from MMFF94-smarts.xlsx.
setAtomTypes(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
setAtomVibrationVector(int, T3) - Method in class org.jmol.modelset.AtomCollection
 
setAttr(String, float) - Method in class org.jmol.export._MayaExporter
 
setAttr(String, int) - Method in class org.jmol.export._MayaExporter
 
setAttr(String, T3) - Method in class org.jmol.export._MayaExporter
 
setAttributes() - Method in class org.jmol.console.ScriptEditor
 
setAutoBond(boolean) - Method in class org.jmol.api.JmolViewer
 
setAutoBond(boolean) - Method in class org.jmol.viewer.Viewer
 
setAutoscrolls(boolean) - Method in class org.jmol.popup.AwtSwingComponent
 
setAxes(int) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
setAxes(DrawMesh) - Static method in class org.jmol.shapespecial.Draw
 
setAxesMode(int) - Method in class org.jmol.viewer.Viewer
 
setAxesOrientationRasmol(boolean) - Method in class org.jmol.api.JmolViewer
 
setAxesOrientationRasmol(boolean) - Method in class org.jmol.viewer.Viewer
 
setAxesScale(float) - Method in class org.jmol.viewer.Viewer
 
setB(String, boolean) - Method in class org.jmol.viewer.GlobalSettings
 
setBackgroundArgb(int) - Method in class org.jmol.util.GData
sets background color to the specified argb value
setBackgroundColor(int) - Method in class org.jmol.g3d.Platform3D
 
setBackgroundImage(Object) - Method in class org.jmol.util.GData
 
setBackgroundImage(String, Object) - Method in class org.jmol.viewer.Viewer
 
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.AnimationManager
 
setBackgroundModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Platform3D
 
setBackgroundTransparent(boolean) - Method in class org.jmol.util.GData
 
setBanner(String, boolean) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
setBannerLabel(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setBannerLabel(String) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioClient
 
setBbcage(float) - Method in class org.jmol.util.BoxInfo
 
setBBox(T3, float) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setBBoxAll() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setBf(int) - Method in class org.jmol.modelset.AtomCollection
 
setBFactor(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setBgcolix(int, short) - Method in class org.jmol.shape.Labels
 
setBinding(Binding) - Method in class org.jmol.multitouch.ActionManagerMT
 
setBinding(Binding) - Method in class org.jmol.viewer.ActionManager
 
setBioAtom(char) - Method in class org.jmol.smiles.SmilesAtom
 
setBioColix(short) - Method in class org.jmol.renderbio.BioShapeRenderer
 
setBiomoleculeAtomCounts() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
setBiomolecules(Map<String, Object>) - Method in class org.jmol.adapter.readers.cif.MMCifReader
 
setBioPolymer(BioPolymer, int) - Method in class org.jmol.modelsetbio.Monomer
 
setBits(int, int) - Method in class org.jmol.java.BS
Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to true.
setBitSet(BS, BS, int) - Static method in class org.jmol.viewer.SelectionManager
 
setBitsetProperty(BS, int, int, float, T) - Method in class org.jmol.script.ScriptExpr
 
setBitTo(int, boolean) - Method in class org.jmol.java.BS
Sets the bit at the specified index to the specified value.
setBond(Bond, String[]) - Method in class org.jmol.adapter.readers.quantum.CsfReader
 
setBond(int, Bond) - Method in class org.jmol.modelset.BondCollection
 
setBondArray() - Method in class org.jmol.smiles.SmilesAtom
 
setBondDirections() - Method in class org.jmol.smiles.SmilesGenerator
Creates global BitSets bsBondsUp and bsBondsDown.
setBonding(AtomSetCollection, int) - Method in class org.jmol.adapter.readers.more.JcampdxReader
add bonding to a set of ModelData based on a MOL file only if the this set has no bonding already
setBondingAndMolecules() - Method in class org.jmol.adapter.readers.cif.CifReader
(1) If GEOM_BOND records are present, we (a) use them to generate bonds (b) add H atoms to bonds if necessary (c) turn off autoBonding ("hasBonds") (2) If MOLECULAR, then we (a) use {1 1 1} if lattice is not defined (b) use asc.bonds[] to construct a preliminary molecule and connect as we go (c) check symmetry for connections to molecule in any one of the 27 3x3 adjacent cells (d) move those atoms and their connected branch set (e) iterate as necessary to get all atoms desired (f) delete unselected atoms (g) set all coordinates as Cartesians (h) remove all unit cell information
setBondingRadius(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setBondOrder(int, char) - Method in class org.jmol.modelset.BondCollection
 
setBondParameters(Bond, int, float, float, int, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
used in PyMOL reader to set unique bond settings and for valence
setBondPickingOption(String) - Method in class org.jmol.viewer.ActionManager
 
setBondPickingOption(String) - Method in class org.jmol.viewer.Viewer
 
setBonds(SmilesBond[]) - Method in class org.jmol.smiles.SmilesAtom
 
setBondTolerance(float) - Method in class org.jmol.api.JmolViewer
 
setBondTolerance(float) - Method in class org.jmol.viewer.Viewer
 
setBondTypes(Bond[], int, BS) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
setBooleanProperty(String, boolean) - Method in class org.jmol.api.JmolViewer
 
setBooleanProperty(String, boolean) - Method in class org.jmol.script.ScriptParam
 
setBooleanProperty(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setBooleanPropertyTok(String, int, boolean) - Method in class org.jmol.viewer.Viewer
 
setBorder() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setBoundBox(P3, P3, boolean, float) - Method in class org.jmol.modelset.ModelSet
 
setBoundBox(P3, P3, boolean, float) - Method in class org.jmol.util.BoxInfo
 
setBoundingBox(P3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setBoundingBox(P3[]) - Method in class org.jmol.util.MeshSurface
 
setBox(float, float, P3, V3, V3, P3, float) - Method in class org.jmol.modelsetbio.Sheet
 
setBox(float, float, P3) - Method in class org.jmol.renderbio.RocketRenderer
 
setBox(P3, P3) - Method in class org.jmol.util.MeshSurface
 
setBoxOffsetsInWindow(float, float, float) - Method in class org.jmol.modelset.Object2d
 
setBoxXY(float, float, float, float, float[], boolean) - Static method in class org.jmol.modelset.Text
 
setBraceCount - Variable in class org.jmol.script.ScriptCompiler
 
setBranch2dZ(Atom, BS, BS, V3, V3, V3) - Static method in class org.jmol.modelset.ModelLoader
 
setBs(Atom[], int, BS[], BS) - Method in class org.jmol.adapter.readers.cif.CifReader
iteratively run through connected atoms, adding them to the set
setBsHidden(BS) - Method in class org.jmol.modelset.AtomCollection
 
setBsVdw() - Method in class org.jmol.shapesurface.Isosurface
 
setBuf() - Method in class org.jmol.g3d.Pixelator
 
setButton(String) - Method in class org.jmol.console.GenericConsole
 
setButton(String) - Method in class org.jmol.console.JmolConsole
 
setButton(String) - Method in class org.jmol.console.ScriptEditor
 
setButton(String) - Method in class org.jmol.consolejs.AppletConsole
 
setButton(String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
setC(short) - Method in interface org.jmol.api.JmolRendererInterface
sets current color from colix color index
setC(short) - Method in class org.jmol.export.Export3D
sets current color from colix color index
setC(short) - Method in class org.jmol.g3d.Graphics3D
sets current color from colix color index
setC(short) - Method in class org.jmol.util.GData
 
setCalculationType() - Method in class org.jmol.adapter.readers.quantum.GamessReader
 
setCallbackFunction(String, String) - Method in interface org.jmol.api.JmolCallbackListener
 
setCallbackFunction(String, String) - Method in class org.jmol.console.GenericConsole
 
setCallbackFunction(String, String) - Method in class org.jmol.util.GenericApplet
 
setCallbackFunction(String, String) - Method in class org.jmol.viewer.StatusManager
 
setCallbackFunction(String, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setCamera(float, float) - Method in class org.jmol.viewer.TransformManager
 
setCameraDepthPercent(float, boolean) - Method in class org.jmol.viewer.TransformManager
either as a percent -300, or as a float 3.0 note this percent is of zoom=100 size of model
setCapOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setCartesianOffset(T3) - Method in class org.jmol.symmetry.UnitCell
 
setCarveSets(Map<String, Lst<Object>>) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setCE(double, double, double, double, double) - Method in class org.jmol.quantum.MOCalculation
 
setCel(boolean) - Method in class org.jmol.util.GData
 
setCel(boolean, int, int) - Method in class org.jmol.util.Shader
 
setCell() - Method in class org.jmol.adapter.readers.xtal.SiestaReader
 
setCellParams() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
setCellParams() - Method in class org.jmol.util.SimpleUnitCell
 
setCelPower(int) - Method in class org.jmol.util.GData
 
setCenter(T3, float) - Method in interface org.jmol.api.AtomIndexIterator
 
setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
setCenter(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModelSet
 
setCenter(int) - Method in class org.jmol.shapespecial.DrawMesh
 
setCenter(P3) - Method in class org.jmol.shapespecial.Ellipsoid
 
setCenter() - Method in class org.jmol.viewer.TransformManager
 
setCenter2(T3, float) - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
setCenterAt(int, P3) - Method in class org.jmol.viewer.TransformManager
 
setCenterBitSet(BS, boolean) - Method in class org.jmol.viewer.Viewer
 
setCentering(V3, boolean) - Method in class org.jmol.symmetry.SymmetryOperation
assumption here is that these are in order of sets, as in ITA
setCenters() - Method in class org.jmol.shapespecial.DrawMesh
 
setCenterSelected() - Method in class org.jmol.api.JmolViewer
 
setCenterSelected() - Method in class org.jmol.viewer.Viewer
 
setCentroid(BS, int[]) - Method in class org.jmol.modelset.ModelSet
deletes molecules based on: CENTROID -- molecular centroid is not in unit cell CENTROID PACKED -- all molecule atoms are not in unit cell
setCGO(Lst<Object>) - Method in class org.jmol.shapecgo.CGO
 
setCGO(Lst<Object>) - Method in class org.jmol.viewer.Viewer
 
setChainID(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setCharge(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the charge of the atom.
setCharges() - Method in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
setChemicalShiftReference(String, float) - Method in interface org.jmol.api.JmolNMRInterface
 
setChemicalShiftReference(String, float) - Method in class org.jmol.quantum.NMRCalculation
 
setChiralClass(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the chiral class of the atom.
setChiralOrder(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the chiral order of the atom.
setClickable(int) - Method in class org.jmol.modelset.Atom
 
setClipboard(Object) - Static method in class org.jmol.awt.AwtClipboard
Transfers text or image into the clipboard.
setCoeffs(int, boolean) - Method in class org.jmol.quantum.MOCalculation
 
setColix(short) - Method in class org.jmol.render.MeshRenderer
 
setColix(short) - Method in class org.jmol.util.MeshSurface
 
setColixAndPalette(short, byte, int) - Method in class org.jmol.shape.AtomShape
 
setColixBack(short, BS) - Method in class org.jmol.shapebio.BioShape
 
setColixBack(short) - Method in class org.jmol.util.MeshSurface
 
setColixBackgroundContrast(int) - Method in class org.jmol.viewer.ColorManager
 
setColixBS(short, byte, BS) - Method in class org.jmol.shapebio.BioShape
 
setColixDipole(short, int, BS) - Method in class org.jmol.shapespecial.Dipoles
 
setColixes(short[], BS) - Method in class org.jmol.shapebio.BioShape
 
setCollectionName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setColor(short) - Method in class org.jmol.shape.Measures
 
setColor(int) - Method in class org.jmol.util.GData
 
setColorBackground(String) - Method in class org.jmol.api.JmolViewer
 
setColorBackground(String) - Method in class org.jmol.viewer.Viewer
 
setColorByScore(float, int) - Method in class org.jmol.shapesurface.Contact
 
setColorCommand() - Method in class org.jmol.shapesurface.IsosurfaceMesh
just sets the color command for this isosurface.
setColorNoisy(int) - Method in class org.jmol.g3d.Graphics3D
 
setColorOptions(SB, int, int, int) - Method in class org.jmol.scriptext.IsoExt
 
setColorPhase(IsosurfaceMesh, short, short) - Method in class org.jmol.shapesurface.Isosurface
 
setColors(short[], float) - Method in class org.jmol.adapter.readers.pymol.JmolObject
 
setColorScheme(String, boolean) - Method in class org.jmol.util.ColorEncoder
 
setColorsFromJvxlData(int) - Method in class org.jmol.shapesurface.IsosurfaceMesh
from Isosurface.notifySurfaceGenerationCompleted() starting with Jmol 12.1.50, JVXL files contain color, translucency, color scheme information, and vertex color mappings (as from COLOR ISOSURFACE {hydrophobic} WHITE), returning these settings when the JVXL file is opened.
setCommand(T) - Method in class org.jmol.script.ScriptCompiler
 
setCommonDefaults() - Method in class org.jmol.viewer.StateManager
 
setCompiler() - Method in interface org.jmol.api.JmolScriptEvaluator
 
setCompiler() - Method in class org.jmol.script.ScriptEval
 
setConformation(BS) - Method in class org.jmol.modelset.Model
 
setConformation(BS) - Method in class org.jmol.modelset.ModelSet
 
setConformation(BS) - Method in class org.jmol.modelsetbio.BioModel
 
setConformation(BS) - Method in class org.jmol.modelsetbio.BioPolymer
 
setConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
 
setConsole(JmolAppConsoleInterface) - Method in class org.jmol.api.JmolViewer
sets a custom console -- should be called IMMEDIATELY following allocateViewer create your console with, perhaps: new org.openscience.jmol.app.jmolPanel.AppConsole(vwr, displayFrame, externalJPanel, buttonsEnabled); (see examples/basic/org/jmol/Integration.java
setConsoleTextPane(AppConsole.ConsoleTextPane) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
setConstraints(Lst<Object[]>) - Method in class org.jmol.minimize.forcefield.Calculations
 
setConstraints(Minimizer) - Method in class org.jmol.minimize.forcefield.ForceField
 
setContactBitSets(BS, BS, boolean, float, RadiusData, boolean) - Method in interface org.jmol.script.JmolMathExtension
 
setContactBitSets(BS, BS, boolean, float, RadiusData, boolean) - Method in class org.jmol.scriptext.MathExt
 
setContacts(Object[], boolean) - Method in class org.jmol.shapesurface.Contact
 
setContext(ScriptContext) - Method in class org.jmol.console.ScriptEditor
 
setContourData(int, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setContourVector(Lst<Object>, int, BS, float, short, int, SB) - Static method in class org.jmol.shapesurface.IsosurfaceMesh
 
setCoordinatesAreFractional(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setCoords(Calculation, int) - Method in class org.jmol.minimize.forcefield.Calculations
 
setCount(int) - Method in class org.jmol.modelset.Measurement
 
setCount(int) - Method in class org.jmol.modelset.MeasurementPending
 
setCountM(int) - Method in class org.jmol.modelset.Measurement
 
setCrystallographicDefaults() - Method in class org.jmol.modelset.ModelSet
 
setCrystallographicDefaults() - Method in class org.jmol.viewer.StateManager
 
setCurrent(long, int, int, int) - Method in class org.jmol.viewer.ActionManager
 
setCurrent(MouseState, int) - Method in class org.jmol.viewer.MouseState
 
setCurrentAtomSetNumber(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets the number for the current AtomSet
setCurrentCage(String) - Method in class org.jmol.viewer.Viewer
 
setCurrentCagePts(T3[], String) - Method in class org.jmol.script.ScriptEval
 
setCurrentColorRange(String) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelID(String) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelIndex(int) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelIndexClear(int, boolean) - Method in class org.jmol.viewer.Viewer
 
setCurrentModelInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets auxiliary information for the AtomSet
setCursor(int, Object) - Static method in class org.jmol.awt.Display
 
setCursor(int, Object) - Method in class org.jmol.awt.Platform
 
setCursor(int, Object) - Static method in class org.jmol.awtjs2d.Display
 
setCursor(int, Object) - Method in class org.jmol.awtjs2d.Platform
 
setCursor(int) - Method in class org.jmol.viewer.Viewer
 
setCursorWait(boolean) - Method in class org.jmol.script.ScriptError
 
setCutoffAutomatic() - Method in class org.jmol.jvxl.readers.MapFileReader
 
setCutoffAutomatic() - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
 
setData(String, Object[], int, int, int, int, int, int) - Method in interface org.jmol.api.JmolDataManager
 
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.Calculation
 
setData(Lst<Object[]>, MinAngle) - Method in class org.jmol.minimize.forcefield.MMFFAngleCalc
 
setData(Lst<Object[]>, MinBond) - Method in class org.jmol.minimize.forcefield.MMFFDistanceCalc
 
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.MMFFESCalc
 
setData(Lst<Object[]>, int) - Method in class org.jmol.minimize.forcefield.MMFFOOPCalc
 
setData(Lst<Object[]>, MinAngle) - Method in class org.jmol.minimize.forcefield.MMFFSBCalc
 
setData(Lst<Object[]>, MinTorsion) - Method in class org.jmol.minimize.forcefield.MMFFTorsionCalc
 
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.MMFFVDWCalc
 
setData(Lst<Object[]>, int[]) - Method in class org.jmol.minimize.forcefield.UFFAngleCalc
 
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.UFFDistanceCalc
 
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.UFFOOPCalc
 
setData(Lst<Object[]>, int[]) - Method in class org.jmol.minimize.forcefield.UFFTorsionCalc
 
setData(Lst<Object[]>, int, int, double) - Method in class org.jmol.minimize.forcefield.UFFVDWCalc
 
setData(String, String, Object, Object) - Method in class org.jmol.script.FileLoadThread
Called by Jmol._loadFileAsyncDone(this.vwr.html5Applet).
setData(String, Object[], int, int, int, int, int, int) - Method in class org.jmol.viewer.DataManager
This method needs to be redone using a class instead of Object[]
setData(String, Object[], int, int, int, int, int) - Method in class org.jmol.viewer.Viewer
 
setDataDistanceToPlane(P4) - Method in interface org.jmol.api.VolumeDataInterface
 
setDataDistanceToPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
 
setDebugging() - Method in interface org.jmol.api.JmolScriptEvaluator
 
setDebugging() - Method in class org.jmol.script.ScriptEval
 
setDebugScript(boolean) - Method in class org.jmol.api.JmolViewer
 
setDebugScript(boolean) - Method in class org.jmol.viewer.Viewer
 
setDefaultColors(boolean) - Method in class org.jmol.viewer.ColorManager
 
setDefaultColors(boolean) - Method in class org.jmol.viewer.Viewer
 
setDefaultLattice(P3) - Method in class org.jmol.viewer.Viewer
 
setDefaultPerspective() - Method in class org.jmol.viewer.TransformManager
 
setDefaultRendering(int) - Method in class org.jmol.modelset.ModelLoader
 
setDefaults - Variable in class org.jmol.shape.Labels
 
setDefaultStructure(BS) - Method in class org.jmol.modelset.ModelSet
 
setDefaultsType(String) - Method in class org.jmol.viewer.Viewer
 
setDegree(int) - Method in class org.jmol.smiles.SmilesAtom
 
setDepth(int) - Method in class org.jmol.util.GData
clipping from the front and the back
setDesiredQpt(String) - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
setDialogLocation(Point) - Method in class org.jmol.dialog.FileChooser
 
setDialogSize(Dimension) - Method in class org.jmol.dialog.FileChooser
 
setDiffusePercent(int) - Method in class org.jmol.util.GData
df in I = df * (N dot L) + sf * (R dot V)^p
setDihedrals(float[], BS[], float) - Method in class org.jmol.modelset.ModelSet
 
setDihedrals(float[], BS[], float) - Method in class org.jmol.viewer.Viewer
 
setDipole(String[]) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
setDipole() - Method in class org.jmol.shapespecial.Dipoles
 
setDipoleAtoms(Atom, Atom, float, float) - Method in class org.jmol.shapespecial.Dipoles
 
setDirect() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
setDiscreteColixes(float[], short[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setDisplay(Object) - Method in class org.jmol.appletjs.Jmol
 
setDisplay(BS) - Method in class org.jmol.viewer.AnimationManager
 
setDisplay(Object) - Method in class org.jmol.viewer.Viewer
 
setDoTranslate(boolean) - Static method in class org.jmol.i18n.GT
 
setDotsConvexMax() - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setDrawing(int[]) - Method in class org.jmol.shapespecial.Draw
 
setDSSRPhos(Viewer, int, Map<String, Object>, BS, Map<String, BS>) - Method in class org.jmol.dssx.AnnotationParser
 
setDSSRRes(Viewer, String, BS, Map<String, BS>) - Method in class org.jmol.dssx.AnnotationParser
 
setE(double[], double) - Method in class org.jmol.quantum.MOCalculation
 
setEccentricity(P4) - Method in class org.jmol.jvxl.readers.Parameters
 
setEchoStateActive(boolean) - Method in class org.jmol.modelset.ModelSet
 
setEditorTextPane(ScriptEditor.EditorTextPane) - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
setElement(Atom, int) - Method in class org.jmol.modelset.AtomCollection
 
setElementAndIsotope(Atom, String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
allow 13C, 15N, 2H, etc.
setElementArgb(int, int) - Method in class org.jmol.viewer.ColorManager
 
setElementArgb(int, int) - Method in class org.jmol.viewer.Viewer
 
setElementColor(String, int) - Method in class org.jmol.script.ScriptEval
 
setEllipsoidAF(float[]) - Method in class org.jmol.jvxl.readers.Parameters
 
setEllipsoidP4(P4) - Method in class org.jmol.jvxl.readers.Parameters
 
setEnabled(boolean) - Method in interface org.jmol.api.JmolAbstractButton
 
setEnabled(boolean) - Method in class org.jmol.popup.AwtSwingComponent
 
setEnabled(JmolAbstractButton, boolean) - Static method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
setEnabled(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
setEnabled() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
setEnergies(String, String, int) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
setEnergy() - Method in class org.jmol.adapter.readers.quantum.GaussianReader
Interpret the Energy= line for non SCF type energy output
setEnergy(String, String) - Method in class org.jmol.adapter.readers.quantum.NWChemReader
 
setEnergy() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
setEnergy() - Method in class org.jmol.adapter.readers.xtal.DmolReader
 
setEnergy() - Method in class org.jmol.adapter.readers.xtal.EspressoReader
 
setEnergy() - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
setEnergyUnits() - Method in class org.jmol.minimize.Minimizer
 
setEqualPt - Variable in class org.jmol.script.ScriptCompiler
 
setError(Throwable) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setError(boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
setErrorMessage(String) - Method in class org.jmol.script.ScriptError
 
setErrorMessage(String, String) - Method in class org.jmol.viewer.Viewer
 
setEval(JmolScriptEvaluator) - Method in class org.jmol.thread.JmolThread
JavaScript only -- -- scriptDelay, moveTo, spin -- save context for restoration later -- move program counter forward one command
setException(ScriptException, String, String) - Method in class org.jmol.script.ScriptEval
 
setExplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of explicit hydrogen atoms bonded with this atom.
setF(String, float) - Method in class org.jmol.viewer.GlobalSettings
 
setFile() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
setFileData(Viewer, Object) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setFileInfo(String[]) - Method in class org.jmol.viewer.FileManager
 
setFileLoadStatus(String, String, String, String, int, boolean, Boolean) - Method in class org.jmol.viewer.StatusManager
 
setFileLoadStatus(FIL, String, String, String, String, Boolean) - Method in class org.jmol.viewer.Viewer
 
setFilename(String) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
setFilename(String) - Method in class org.jmol.console.ScriptEditor
 
setFilter(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setFilterAtomTypeStr(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setFinalOperations(String, P3[], int, int, boolean, String) - Method in interface org.jmol.api.SymmetryInterface
 
setFinalOperations(P3[], int, int, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
setFinalOperations(String, P3[], int, int, boolean, String) - Method in class org.jmol.symmetry.Symmetry
 
setFixedRotationCenter(T3) - Method in class org.jmol.viewer.TransformManager
 
setFlags(AtomType) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
setFloatProperty(String, float) - Method in class org.jmol.api.JmolViewer
 
setFloatProperty(String, float) - Method in class org.jmol.script.ScriptParam
 
setFloatProperty(String, float) - Method in class org.jmol.viewer.Viewer
 
setFloatPropertyTok(String, int, float) - Method in class org.jmol.viewer.Viewer
 
setFocus() - Method in class org.jmol.viewer.Viewer
 
setFont(Object, Font) - Method in interface org.jmol.api.GenericGraphics
 
setFont(Object, Font) - Method in class org.jmol.awt.AwtG2D
 
setFont(Object, Font) - Method in class org.jmol.awtjs2d.JsG2D
 
setFont(Font) - Method in class org.jmol.g3d.Graphics3D
 
setFont(Font, boolean) - Method in class org.jmol.modelset.Text
 
setFont(int, byte) - Method in class org.jmol.shape.Labels
 
setFont(Font) - Method in class org.jmol.util.GData
 
setFontFid(byte) - Method in class org.jmol.g3d.Graphics3D
 
setFontFid(byte) - Method in class org.jmol.util.GData
 
setFontFromFid(byte) - Method in class org.jmol.modelset.Text
 
setFontScale(float) - Method in class org.jmol.modelset.Text
 
setForcesUsingNumericalDerivative(MinAtom, int) - Method in class org.jmol.minimize.forcefield.ForceField
 
setFormalCharge(int) - Method in class org.jmol.modelset.Atom
 
setFormalCharges(BS, int) - Method in class org.jmol.modelset.AtomCollection
 
setFormats(String) - Method in class org.jmol.shape.Measures
 
setForVdwClash(boolean) - Method in class org.jmol.util.ContactPair
 
setFractional(SymmetryInterface, T3, P3, P3) - Static method in class org.jmol.symmetry.SymmetryDesc
Set pt01 to pt00, possibly adding offset into unit cell
setFractionalCoord(int, float, boolean) - Method in class org.jmol.modelset.Atom
 
setFractionalCoordinates(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setFractionalCoordPt(P3, P3, boolean) - Method in class org.jmol.modelset.Atom
 
setFractionalCoordTo(P3, boolean) - Method in class org.jmol.modelset.Atom
 
setFrame(int) - Method in class org.jmol.viewer.AnimationManager
 
setFrameDelayMs(long, BS) - Method in class org.jmol.modelset.ModelSet
 
setFrameDelayMs(long) - Method in class org.jmol.viewer.Viewer
 
setFrameObject(int, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setFrameOffset(int) - Method in class org.jmol.viewer.TransformManager
 
setFrameOffsets(BS) - Method in class org.jmol.viewer.Viewer
 
setFrameRangeVisible() - Method in class org.jmol.viewer.AnimationManager
 
setFrameTitle(BS, Object) - Method in class org.jmol.modelset.ModelSet
 
setFrameTitle(int, String) - Method in class org.jmol.viewer.Viewer
 
setFrameTitleObj(Object) - Method in class org.jmol.viewer.Viewer
 
setFrameVariables() - Method in class org.jmol.viewer.Viewer
 
setFrankMenu(String) - Method in class org.jmol.popup.JmolGenericPopup
 
setFrankOn(boolean) - Method in class org.jmol.api.JmolViewer
 
setFrankOn(boolean) - Method in class org.jmol.viewer.Viewer
 
setFreqValue(float, String[]) - Method in class org.jmol.adapter.readers.xtal.CrystalReader
 
setFromAsymmetricTensor(double[][], String, String) - Method in class org.jmol.util.Tensor
Standard constructor for QM tensors
setFromAxes(V3[]) - Method in class org.jmol.util.Tensor
Standard constructor for ellipsoids based on axes
setFromBits(int, BS) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setFromEigenVectors(V3[], float[], String, String, Tensor) - Method in class org.jmol.util.Tensor
Standard constructor for charge and iso.
setFromMatrix(float[], boolean) - Method in class org.jmol.symmetry.SymmetryOperation
 
setFromThermalEquation(double[], String) - Method in class org.jmol.util.Tensor
standard constructor for thermal ellipsoids convention beta (see http://www.iucr.org/iucr-top/comm/cnom/adp/finrepone/finrepone.html)
setFront(int, boolean) - Method in class org.jmol.shape.Labels
 
setFullPath(Map<String, Object>, String) - Method in class org.jmol.viewer.OutputManager
 
setFunction(ScriptFunction) - Method in class org.jmol.script.ScriptFlowContext
 
setFunction(ScriptFunction, String, int, int, short[], int[][], Lst<T[]>) - Static method in class org.jmol.script.ScriptFunction
 
setFunctionXY(Lst<Object>) - Method in class org.jmol.jvxl.readers.Parameters
 
setFunctionXYZ(Lst<Object>) - Method in class org.jmol.jvxl.readers.Parameters
 
setGamma(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
rsvs is the superspace group rotation-translation matrix.
setGeneralBindings() - Method in class org.jmol.viewer.binding.JmolBinding
 
setGestureSwipeFactor(float) - Method in class org.jmol.viewer.ActionManager
 
setGhostOn(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setGlobalBoolean(int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setGlobals() - Method in class org.jmol.renderbio.BioShapeRenderer
 
setGlobals() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
setGlobals() - Method in class org.jmol.rendersurface.IsosurfaceRenderer
 
setGouraud(int, int, int) - Method in class org.jmol.g3d.TriangleRenderer
 
setGraphicsColor(Object, GenericColor) - Method in interface org.jmol.api.GenericGraphics
 
setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awt.AwtG2D
 
setGraphicsColor(Object, GenericColor) - Method in class org.jmol.awtjs2d.JsG2D
 
setGreyscaleMode(boolean) - Method in class org.jmol.util.GData
controls greyscale rendering
setGridLimitsForAtom(P3, float, P3i, P3i) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setGroup(Group) - Method in class org.jmol.modelset.Atom
 
setGroup(Chain, String, int, int, int) - Method in class org.jmol.modelset.Group
 
setGroup(int, boolean) - Method in class org.jmol.shape.Labels
 
setGroup1(char) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
setGroupID(String) - Method in class org.jmol.modelset.Group
 
setGroupID(String) - Method in class org.jmol.modelsetbio.Monomer
 
setGroupLists(int) - Method in interface org.jmol.api.JmolBioResolver
 
setGroupLists(int) - Method in class org.jmol.modelsetbio.Resolver
 
setGroupParameter(int, float) - Method in class org.jmol.modelsetbio.Monomer
 
setGroupVisibilities() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setGroupVisible(PyMOLGroup, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Iterate through groups, setting visibility flags.
setHaveHsAlready(boolean) - Method in interface org.jmol.api.JmolBioResolver
 
setHaveHsAlready(boolean) - Method in class org.jmol.modelsetbio.Resolver
 
setHeader(String, String) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setHeader(String) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
setHeader() - Method in class org.jmol.jvxl.readers.NffReader
 
setHeader() - Method in class org.jmol.jvxl.readers.PmeshReader
 
setHideNotSelected(boolean) - Method in class org.jmol.viewer.SelectionManager
 
setHistory(String) - Method in class org.jmol.viewer.Viewer
 
setHoverLabel(String) - Method in class org.jmol.viewer.Viewer
 
setHydrogen(int, int, String, P3) - Method in class org.jmol.modelsetbio.Resolver
 
setHydrogenCount(SmilesSearch) - Method in class org.jmol.smiles.SmilesAtom
Finalizes the hydrogen count hydrogens in a SmilesMolecule.
setHydrophobicity(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setI(String, int) - Method in class org.jmol.viewer.GlobalSettings
 
setIcon(Object) - Method in class org.jmol.popup.AwtSwingComponent
 
setImage(Object) - Method in class org.jmol.modelset.Text
 
setImageDimensions(int, int) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Sets the output image dimensions.
setImageInfo(int, int, String) - Method in interface org.jmol.api.JmolDialogInterface
 
setImageInfo(int, int, String) - Method in class org.jmol.dialog.Dialog
 
setImplicitHydrogenCount(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of implicit hydrogen atoms bonded with this atom.
setIndex(int) - Method in class org.jmol.smiles.SmilesAtom
Constructs a SmilesAtom.
setIndexes(DefaultMutableTreeNode) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Sets the indexes to the atomSetIndex values of each leaf of the node.
setIndices() - Method in class org.jmol.shape.Measures
 
setInfo(String) - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
setInfo(String, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setInfo(int, Object, Object) - Method in class org.jmol.modelset.ModelSet
 
setInMotion(boolean) - Method in class org.jmol.api.JmolViewer
 
setInMotion(boolean) - Method in class org.jmol.viewer.Viewer
 
setInsertedCommand(String) - Method in class org.jmol.viewer.Viewer
 
setInt(int) - Method in class org.jmol.util.Rgb16
 
setIntProperty(String, int) - Method in class org.jmol.api.JmolViewer
 
setIntProperty(String, int) - Method in class org.jmol.script.ScriptParam
 
setIntProperty(String, int) - Method in class org.jmol.viewer.Viewer
 
setIntPropertyTok(String, int, int) - Method in class org.jmol.viewer.Viewer
 
setInverseNormixes() - Static method in class org.jmol.util.Normix
 
setIsoMeshColor(IsosurfaceMesh, String) - Method in class org.jmol.shapesurface.Isosurface
 
setIsPDB() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
SETITEM - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
SETITEMS - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
setIteratorForAtom(AtomIndexIterator, int, float) - Method in interface org.jmol.atomdata.AtomDataServer
 
setIteratorForAtom(AtomIndexIterator, int, int, float, RadiusData) - Method in class org.jmol.modelset.ModelSet
 
setIteratorForAtom(AtomIndexIterator, int, float) - Method in class org.jmol.viewer.Viewer
 
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in interface org.jmol.atomdata.AtomDataServer
 
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.modelset.ModelSet
 
setIteratorForPoint(AtomIndexIterator, int, T3, float) - Method in class org.jmol.viewer.Viewer
 
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.api.JmolViewer
 
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.StatusManager
 
setJmolCallbackListener(JmolCallbackListener) - Method in class org.jmol.viewer.Viewer
 
setJmolDataFrame(String, int, int) - Method in class org.jmol.modelset.ModelSet
 
setJmolDefaults() - Method in class org.jmol.api.JmolViewer
 
setJmolDefaults() - Method in class org.jmol.viewer.StateManager
 
setJmolDefaults() - Method in class org.jmol.viewer.Viewer
 
setJmolSize(Dimension) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.api.JmolViewer
 
setJmolStatusListener(JmolStatusListener, JmolCallbackListener) - Method in class org.jmol.viewer.StatusManager
 
setJmolStatusListener(JmolStatusListener) - Method in class org.jmol.viewer.Viewer
 
setJSpecView(String, boolean, boolean) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setJvxlColorMap(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
set up the jvxlData fields needed for either just the header (isAll = false) or the full file (isAll = true)
setJvxlData(JvxlData) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setJvxlDataRendering() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setJvxlInfo() - Method in class org.jmol.shapesurface.Isosurface
 
setKeepChars(boolean) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
setLabel(LabelToken[][], String, int) - Method in class org.jmol.shape.Labels
 
setLabel(Object, BS) - Method in class org.jmol.viewer.ShapeManager
 
setLabel(String) - Method in class org.openscience.jmol.app.jsonkiosk.BannerFrame
 
setLabelColix(int, short, byte) - Method in class org.jmol.shape.Labels
 
setLabelPosition(P3, float[]) - Static method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setLabels() - Method in class org.jmol.console.GenericConsole
 
setLastColix(int, boolean) - Method in class org.jmol.util.Shader
 
setLastGrey(int) - Static method in class org.jmol.util.C
 
setLattice(int) - Method in interface org.jmol.api.SymmetryInterface
set symmetry lattice type using Hall rotations
setLattice(char, boolean) - Method in class org.jmol.symmetry.SpaceGroup
 
setLattice(int) - Method in class org.jmol.symmetry.Symmetry
 
setLatticeCells() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setLatticeParam(int) - Method in class org.jmol.symmetry.SpaceGroup
 
setLatticeParameter(int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setLatticeVectors() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
setLcao(String, int) - Method in class org.jmol.jvxl.readers.Parameters
 
setLcao() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setLcaoOn(boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setLcaoOn(int, boolean) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setLength(int) - Method in class org.jmol.java.BS
 
setLengths() - Method in class org.jmol.shapespecial.Ellipsoid
 
setLigandModel(String, String) - Method in class org.jmol.viewer.Viewer
 
setLighting(int) - Method in class org.jmol.shape.Mesh
 
setLighting(boolean, BS) - Method in class org.jmol.shapespecial.Polyhedra
 
setLightSource(float, float, float) - Method in class org.jmol.util.Shader
 
setLine(String) - Method in interface org.jmol.api.JmolJDXMOLParser
 
setLine(String) - Method in class org.jmol.jsv.JDXMOLParser
 
setLine() - Method in class org.jmol.script.ScriptFlowContext
 
setLinearOffsets() - Method in class org.jmol.jvxl.calc.MarchingCubes
 
setLineBits(float, float) - Method in class org.jmol.g3d.LineRenderer
 
setLoader(ModelLoader) - Method in interface org.jmol.api.JmolBioResolver
 
setLoader(ModelLoader) - Method in class org.jmol.modelsetbio.Resolver
 
setLoadFormat(String, char, boolean) - Method in class org.jmol.viewer.Viewer
Jmol will either specify a type or look for it in the first character, making sure it is found using isDatabaseCode() first.
setLoadNote() - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setLoadParameters(Map<String, Object>, boolean) - Method in class org.jmol.viewer.Viewer
 
setLoadState(Map<String, Object>) - Method in class org.jmol.viewer.FileManager
 
setLobe(P4) - Method in class org.jmol.jvxl.readers.Parameters
 
setLocalPath(Viewer, String, boolean) - Static method in class org.jmol.viewer.FileManager
called by getImageFileNameFromDialog called by getOpenFileNameFromDialog called by getSaveFileNameFromDialog called by classifyName for any full file load called from the CD command currentLocalPath is set in all cases and is used specifically for dialogs as a first try defaultDirectoryLocal is set only when not from a dialog and is used only in getLocalPathForWritingFile or from an open/save dialog.
setLogFile(String) - Method in class org.jmol.viewer.OutputManager
 
setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
Replaces the current logger implementation by a new one.
setLoggingEnabled(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setLogic() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
setLogLevel(int) - Static method in class org.jmol.util.Logger
Activates all logging levels up through a given level.
setLp(P4) - Method in class org.jmol.jvxl.readers.Parameters
 
setM(ModelSet, Measurement, float, short, String, int) - Method in class org.jmol.modelset.Measurement
 
setMad(short) - Method in class org.jmol.modelset.Bond
 
setMad(short, BS, float[]) - Method in class org.jmol.shapebio.BioShape
 
setMadAtom(Viewer, RadiusData) - Method in class org.jmol.modelset.Atom
 
setMads(short[]) - Method in class org.jmol.geodesic.EnvelopeCalculation
 
setMads(int, boolean) - Method in class org.jmol.renderbio.BioShapeRenderer
set diameters for a bioshape
setManager(Object, Viewer, Object) - Method in class org.jmol.minimize.MinimizationThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.script.CommandWatcherThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.AnimationThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.JmolThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.MoveToThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.SpinThread
 
setManager(Object, Viewer, Object) - Method in class org.jmol.thread.VibrationThread
 
setManagerMove(Object[]) - Method in class org.jmol.thread.MoveToThread
MOVE is a much simpler command.
setManagerMoveTo(Object[]) - Method in class org.jmol.thread.MoveToThread
MOVETO is a more complex command.
setMapBitSet(Map<String, BS>, int, int, String) - Static method in class org.jmol.util.BSUtil
 
setMappingPlane(P4) - Method in class org.jmol.jvxl.data.VolumeData
 
setMapRanges(SurfaceReader, boolean) - Method in class org.jmol.jvxl.readers.Parameters
 
setMarBond(short) - Method in class org.jmol.api.JmolViewer
 
setMarBond(short) - Method in class org.jmol.viewer.Viewer
 
setMargin(float) - Method in class org.jmol.util.BoxInfo
 
setMatchingAtom(int) - Method in class org.jmol.smiles.SmilesAtom
Sets the number of a matching atom in a molecule.
setMatrices() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
setMatrix() - Method in class org.jmol.jvxl.data.VolumeData
 
setMatrix(boolean) - Method in class org.jmol.symmetry.SymmetryOperation
 
setMatrixFromXYZ(String, int, boolean) - Method in class org.jmol.symmetry.SymmetryOperation
 
setMaximumSize(int) - Method in class org.jmol.viewer.Viewer
 
setMaxSize(int) - Method in class org.jmol.util.CommandHistory
Resets maximum size of command queue.
setMenu(String, boolean) - Method in class org.jmol.api.JmolViewer
 
setMenu(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setMenuState() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
setMep(float[], boolean) - Method in class org.jmol.jvxl.readers.Parameters
 
setMerged(boolean) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setMesh(String) - Method in class org.jmol.shape.MeshCollection
 
setMeshCreator(Object) - Method in class org.jmol.viewer.Viewer
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
setMeshDisplayProperty(int, int, int) - Method in class org.jmol.script.ScriptEval
 
setMeshI() - Method in class org.jmol.shapesurface.Isosurface
 
setMeshTokenProperty(Mesh, int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
 
setMinBondDistance(float) - Method in class org.jmol.api.JmolViewer
 
setMinBondDistance(float) - Method in class org.jmol.viewer.Viewer
 
setMinimizationOn(boolean) - Method in class org.jmol.minimize.Minimizer
 
setMinMax(float, float) - Method in class org.jmol.jvxl.calc.MarchingSquares
 
setMinMax(int) - Method in class org.jmol.quantum.QuantumCalculation
 
setMinMax0(P3, P3) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
setMinMax0(P3, P3) - Method in interface org.jmol.adapter.smarter.MSInterface
 
setMinMaxLatticeParameters(P3i, P3i) - Method in interface org.jmol.api.SymmetryInterface
 
setMinMaxLatticeParameters(P3i, P3i) - Method in class org.jmol.symmetry.Symmetry
 
setMinMaxLatticeParameters(P3i, P3i) - Method in class org.jmol.symmetry.UnitCell
 
setMnemonic(char) - Method in interface org.jmol.api.JmolAbstractButton
 
setMnemonic(char) - Method in class org.jmol.console.JmolLabel
 
setMO(Map<String, Object>) - Method in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
setMO(int, float[]) - Method in class org.jmol.jvxl.readers.Parameters
 
setMod(String, P3, P3, int, Lst<Modulation>, M3, Matrix[], int, SymmetryInterface, Vibration) - Method in class org.jmol.util.ModulationSet
A collection of modulations for a specific atom.
setMOData(boolean) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
setMoData(Lst<Object[]>, int, float[], int, boolean, int, String, String) - Method in class org.jmol.scriptext.IsoExt
 
setModDim(int) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
setModDim(int) - Method in class org.jmol.symmetry.SymmetryOperation
 
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in interface org.jmol.api.AtomIndexIterator
 
setModel(int) - Method in interface org.jmol.api.JmolJSpecView
 
setModel(int) - Method in class org.jmol.jsv.JSpecView
 
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceField
 
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
setModel(BS, int) - Method in class org.jmol.minimize.forcefield.ForceFieldUFF
 
setModel(BS) - Method in class org.jmol.minimize.Minimizer
 
setModel(ModelSet, int, int, int, T3, float, RadiusData) - Method in class org.jmol.modelset.AtomIteratorWithinModel
 
setModel(int, boolean) - Method in class org.jmol.viewer.AnimationManager
 
setModelCage(int, SymmetryInterface) - Method in class org.jmol.modelset.ModelSet
 
setModelFields() - Method in class org.jmol.minimize.forcefield.ForceField
 
setModelIndex(short) - Method in class org.jmol.modelset.Measurement
 
setModelIndex(int) - Method in class org.jmol.modelset.StateScript
 
setModelIndex() - Method in class org.jmol.shapespecial.Dipoles
 
setModelInfoForSet(String, Object, int) - Method in class org.jmol.adapter.smarter.AtomSetCollection
Sets auxiliary information for an AtomSet
setModelKitMode(boolean) - Method in class org.jmol.viewer.Viewer
 
setModelkitMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setModelNameNumberProperties(int, int, String, int, Properties, Map<String, Object>, String) - Method in class org.jmol.modelset.ModelLoader
 
setModelParameters(boolean) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
setModelPDB(boolean) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setModels(int, int) - Method in class org.jmol.adapter.smarter.Structure
 
setModelSet(ModelSet) - Method in class org.jmol.modelset.MeasurementData
 
setModelSet(ModelSet) - Method in class org.jmol.shape.Shape
 
setModelSet(ModelSet) - Method in class org.jmol.viewer.ShapeManager
 
setModelSet(ModelSet) - Method in class org.jmol.viewer.Viewer
 
setModelVisibility() - Method in class org.jmol.viewer.ShapeManager
Sets shape visibility flags, including ATOM_VIS_INFRAME and ATOM_VIS_NOTHIDDEN.
setModelVisibility() - Method in class org.jmol.viewer.Viewer
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Bbcage
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Halos
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.MeshCollection
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Object2dShape
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shape.Shape
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Dipoles
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Draw
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Ellipsoids
 
setModelVisibilityFlags(BS) - Method in class org.jmol.shapespecial.Polyhedra
 
setModeMouse(int) - Method in class org.jmol.viewer.ActionManager
only NONE (-1) is implemented; it just stops the hoverWatcher thread so that the vwr references are all removed
setModified(boolean) - Method in class org.jmol.script.SV
 
setModTQ(T3, boolean, T3, boolean, float) - Method in interface org.jmol.api.JmolModulationSet
 
setModTQ(T3, boolean, T3, boolean, float) - Method in class org.jmol.util.ModulationSet
Set modulation "t" value, which sets which unit cell in sequence we are looking at; d=1 only.
setModulation(boolean, SymmetryInterface) - Method in class org.jmol.adapter.readers.cif.MSRdr
Both the Jana reader and the CIF reader will call this to set the modulation for a given model.
setModulation(boolean, SymmetryInterface) - Method in interface org.jmol.adapter.smarter.MSInterface
 
setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.modelset.ModelSet
Sets the modulation for all atoms in bs.
setModulation(BS, boolean, P3, boolean) - Method in class org.jmol.viewer.Viewer
 
setModulationForStructure(int, boolean) - Method in class org.jmol.adapter.readers.cif.MSRdr
Called when structure creation is complete and all modulation data has been collected.
setMolecularModulation(String, float, float) - Method in class org.jmol.adapter.readers.xtal.JanaReader
Add the modulation after applying rigid-body phase correction
setMoment() - Method in interface org.jmol.api.JmolModulationSet
 
setMoment() - Method in class org.jmol.util.ModulationSet
 
setMorphCount(int) - Method in class org.jmol.viewer.AnimationManager
 
setMOs(String) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
 
setMotion(int, boolean) - Method in class org.jmol.viewer.ActionManager
 
setMotionFixedAtoms(BS) - Method in class org.jmol.viewer.SelectionManager
 
setMotionFixedAtoms(BS) - Method in class org.jmol.viewer.Viewer
 
setMOType(Map<String, Object>, int) - Method in class org.jmol.adapter.readers.quantum.MOReader
 
setMouseActions(int, int, boolean) - Method in class org.jmol.viewer.ActionManager
 
setMouseDragFactor(float) - Method in class org.jmol.viewer.ActionManager
 
setMouseMode() - Method in class org.jmol.viewer.ActionManager
 
setMouseWheelFactor(float) - Method in class org.jmol.viewer.ActionManager
 
setMovableBitSet(BS, boolean) - Method in class org.jmol.viewer.Viewer
 
setMovableX(int) - Method in class org.jmol.modelset.Object2d
 
setMovableXPercent(int) - Method in class org.jmol.modelset.Object2d
 
setMovableY(int) - Method in class org.jmol.modelset.Object2d
 
setMovableYPercent(int) - Method in class org.jmol.modelset.Object2d
 
setMovableZPercent(int) - Method in class org.jmol.modelset.Object2d
 
setMovie(Map<String, Object>) - Method in class org.jmol.viewer.AnimationManager
support for PyMOL movies and anim FRAMES [....] currently no support for scripted movies
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in interface org.jmol.multitouch.JmolMultiTouchAdapter
 
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
setMultiTouchClient(Viewer, JmolMultiTouchClient, boolean) - Method in class org.jmol.multitouch.sparshui.JmolSparshClientAdapter
 
setMustResume() - Method in class org.jmol.script.ScriptContext
 
setMyError(String) - Method in class org.jmol.adapter.readers.xml.XmlReader
 
setName(String) - Method in class org.jmol.popup.AwtSwingComponent
 
setName(String) - Method in class org.jmol.script.SV
 
setNavFps(int) - Method in class org.jmol.viewer.TransformManager
 
setNavigatePt(P3) - Method in class org.jmol.viewer.TransformManager
scripted entry point for navigation
setNavigationDepthPercent(float) - Method in interface org.jmol.api.JmolNavigatorInterface
 
setNavigationDepthPercent(float) - Method in class org.jmol.navigate.Navigator
 
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.TransformManager
sets the position of the navigation offset relative to the model (50% center; 0% rear, 100% front; can be <0 or >100)
setNavigationDepthPercent(float) - Method in class org.jmol.viewer.Viewer
 
setNavigationMode(boolean) - Method in class org.jmol.viewer.TransformManager
 
setNavigationMode(boolean) - Method in class org.jmol.viewer.Viewer
 
setNavigationOffsetRelative() - Method in interface org.jmol.api.JmolNavigatorInterface
 
setNavigationOffsetRelative() - Method in class org.jmol.navigate.Navigator
 
setNavigationOffsetRelative() - Method in class org.jmol.viewer.TransformManager
 
setNavigationSlabOffsetPercent(float) - Method in class org.jmol.viewer.TransformManager
 
setNavOn(boolean) - Method in class org.jmol.viewer.TransformManager
 
setNavPercent(P3) - Method in class org.jmol.navigate.Navigator
 
setNavXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
 
setNboLabels(String[], int, Lst<Map<String, Object>>, int, String) - Method in class org.jmol.quantum.QS
 
setNBOType(Map<String, Object>, String) - Method in class org.jmol.scriptext.IsoExt
 
setNci(boolean) - Method in class org.jmol.jvxl.readers.Parameters
 
setNeighbors(int) - Method in class org.jmol.renderbio.BioShapeRenderer
 
setNested(int, Object) - Method in class org.jmol.smiles.SmilesSearch
 
setNewRotationCenter(P3, boolean) - Method in class org.jmol.viewer.TransformManager
 
setNewRotationCenter(P3) - Method in class org.jmol.viewer.Viewer
 
setNewSetCommand(boolean, String) - Method in class org.jmol.script.ScriptCompiler
 
setNewWindowParametersForExport() - Method in class org.jmol.util.GData
 
setNext(String, String, int[], int) - Static method in class org.jmol.jvxl.readers.XmlReader
shift pointer to a new tag or field contents
setNoAutoBond() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setNonhydrogenDegree(int) - Method in class org.jmol.smiles.SmilesAtom
 
setNoPrompt() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
setNormixes(V3[]) - Method in class org.jmol.shape.Mesh
 
setNotionalUnitCell(float[], M3, P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setO(String, Object) - Method in class org.jmol.viewer.GlobalSettings
 
setObjectArgb(String, int) - Method in class org.jmol.script.ScriptEval
 
setObjectArgb(String, int) - Method in class org.jmol.viewer.Viewer
 
setObjectColor(String, String) - Method in class org.jmol.viewer.Viewer
 
setObjectMad(int, String, int) - Method in class org.jmol.script.ScriptEval
 
setObjectMad(int, String, int) - Method in class org.jmol.viewer.Viewer
 
setObjectProp(String, int, int) - Method in class org.jmol.script.ScriptEval
 
setObjectProp(String, int) - Method in class org.jmol.viewer.Viewer
 
setObjectProperty() - Method in class org.jmol.script.ScriptEval
 
setObjectPropSafe(String, int) - Method in interface org.jmol.api.JmolScriptEvaluator
 
setObjectPropSafe(String, int) - Method in class org.jmol.script.ScriptEval
called by Viewer in setting up a PyMOL scene.
setObjectVisibility(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setOccupancy(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setOffset(int) - Method in interface org.jmol.api.SymmetryInterface
 
setOffset(int) - Method in class org.jmol.modelset.Object2d
 
setOffset(int) - Method in class org.jmol.symmetry.Symmetry
 
setOffset(P3[], int, int) - Method in class org.jmol.symmetry.SymmetryOperation
 
setOffset(T3) - Method in class org.jmol.symmetry.UnitCell
 
setOffsetPositions() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
setOffsetPt(T3) - Method in interface org.jmol.api.SymmetryInterface
 
setOffsetPt(P3) - Method in class org.jmol.shapespecial.Dipole
 
setOffsetPt(T3) - Method in class org.jmol.symmetry.Symmetry
 
setOffsets(int, int, boolean) - Method in class org.jmol.shape.Labels
 
setOopVariables(Calculation, boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setOpacity255(int) - Method in class org.jmol.awt.AwtColor
 
setOptions(String) - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
setOptions(Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
setOrbital(int, float[]) - Method in class org.jmol.shapesurface.MolecularOrbital
 
setOrbitalSymmetryAndOccupancy() - Method in class org.jmol.adapter.readers.quantum.GamessUKReader
 
setOrder(int) - Method in class org.jmol.modelset.Bond
 
setOutputChannel(GenericBinaryDocument, OC) - Method in interface org.jmol.jvxl.api.MeshDataServer
 
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
setOutputChannel(GenericBinaryDocument, OC) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setOutputChannel(OC) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setOutputChannel(GenericBinaryDocument, OC) - Method in class org.jmol.shapesurface.Isosurface
 
setP(Monomer[]) - Method in class org.jmol.modelsetbio.PhosphorusPolymer
 
setPairVariables(Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
 
setPanel(JPanel) - Method in class org.openscience.jmol.app.jsonkiosk.KioskFrame
 
setParallel() - Method in class org.jmol.viewer.ShapeManager
 
setParallel(boolean) - Method in class org.jmol.viewer.Viewer
 
setparam - Static variable in class org.jmol.script.T
 
setParameter(String, float) - Method in class org.jmol.adapter.readers.xtal.GulpReader
 
setParameters(VolumeData, Parameters) - Method in class org.jmol.jvxl.calc.MarchingCubes
 
setParams(Object[], int[], BS) - Method in class org.jmol.shapebio.BioShape
 
setParamsFromMatrix() - Method in class org.jmol.util.SimpleUnitCell
 
setPartialCharge(int, float) - Method in class org.jmol.modelset.AtomCollection
 
setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setPass2(boolean) - Method in class org.jmol.util.GData
 
setPathForAllFiles(String) - Method in class org.jmol.viewer.FileManager
 
setPdbConectBonding(int, int, BS) - Method in class org.jmol.modelset.ModelSet
 
setPeakData(Lst<Object[]>, int) - Method in class org.jmol.jsv.JDXMOLParser
 
setPendingMeasurement(MeasurementPending) - Method in class org.jmol.viewer.Viewer
 
setPercentVdwAtom(int) - Method in class org.jmol.api.JmolViewer
 
setPercentVdwAtom(int) - Method in class org.jmol.viewer.Viewer
 
setPerspectiveDepth(boolean) - Method in class org.jmol.api.JmolViewer
 
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.TransformManager
 
setPerspectiveDepth(boolean) - Method in class org.jmol.viewer.Viewer
 
setPhongExponent(int) - Method in class org.jmol.util.GData
p in I = df * (N dot L) + sf * (R dot V)^p
setPhononVector(float[], Atom, V3, V3, V3) - Method in class org.jmol.adapter.readers.xtal.CastepReader
transform complex vibration vector to a real vector by applying the appropriate translation, storing the results in v
setPicked(int) - Method in class org.jmol.viewer.Viewer
 
setPickingMode(int) - Method in class org.jmol.viewer.ActionManager
 
setPickingMode(String, int) - Method in class org.jmol.viewer.Viewer
 
setPickingStyle(int) - Method in class org.jmol.viewer.ActionManager
 
setPickingStyle(String, int) - Method in class org.jmol.viewer.Viewer
 
setPlane(int, float[]) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
setPlane(P4) - Method in class org.jmol.jvxl.readers.Parameters
 
setPlaneParameters(P4) - Method in interface org.jmol.api.VolumeDataInterface
 
setPlaneParameters(P4) - Method in class org.jmol.jvxl.data.VolumeData
 
setPlanes(float[][]) - Method in interface org.jmol.api.QuantumPlaneCalculationInterface
Planes to use for holding raw file data.
setPlanes(float[][]) - Method in class org.jmol.quantum.NciCalculation
Raw file data planes are passed to us here from VolumeFileReader
setPoint(float[], int, int, int) - Static method in class org.jmol.util.MeshSlicer
 
setPointer(int, int) - Method in class org.jmol.shape.Labels
 
setPointGroup(SymmetryInterface, Atom[], BS, boolean, float, float) - Method in interface org.jmol.api.SymmetryInterface
 
setPointGroup(SymmetryInterface, Atom[], BS, boolean, float, float) - Method in class org.jmol.symmetry.Symmetry
 
setPoints(ModelSet, int[], Point3fi[], TickInfo) - Method in class org.jmol.modelset.Measurement
 
setPoints(int, int) - Method in class org.jmol.shapespecial.Draw
 
setPolygon(int) - Method in class org.jmol.shapespecial.Draw
 
setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
 
setPopInDim(int, int) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setPos(float) - Method in class org.jmol.modelset.Text
 
setPosition(float, float, boolean, float[]) - Method in class org.jmol.modelset.Text
 
setPositions() - Method in class org.jmol.adapter.readers.simple.AmpacReader
 
setPreliminary(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setPreserveState(boolean) - Method in class org.jmol.modelset.AtomCollection
 
setPreviewOptions(boolean) - Method in class org.jmol.dialog.FilePreview
 
setPrimitiveMapping() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
Create arrays that maps primitive atoms to conventional atoms in a 1:1 fashion.
setPrimitiveVolumeAndDensity() - Method in class org.jmol.adapter.readers.xtal.CrystalReader
Read the primitive cell volume and density.
setPrincipalAxis(int, int) - Method in class org.jmol.symmetry.PointGroup
 
setPrincipalPlane(int, int) - Method in class org.jmol.symmetry.PointGroup
 
setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleDocument
 
setPrompt() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ConsoleTextPane
 
setProp(String, Object, BS) - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setProp(Ellipsoid, int, Object) - Method in class org.jmol.shapespecial.Ellipsoids
 
setPropAS(String, Object, BS) - Method in class org.jmol.shape.AtomShape
 
setPropBSC(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
setProperties(Lst<Object>) - Method in class org.jmol.adapter.readers.cif.MMCifValidationParser
Set property_xxx for atoms from list of name, data, modelIndex series.
setProperties(Properties) - Method in interface org.jmol.api.JSVInterface
 
setProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setProperty(String, Object) - Method in interface org.jmol.api.MinimizerInterface
 
setProperty(String, Object) - Method in class org.jmol.minimize.Minimizer
 
setProperty(String, Object, Object2d) - Static method in class org.jmol.modelset.Object2d
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Axes
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Balls
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Bbcage
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Echo
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Frank
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Halos
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Hover
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Labels
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Measures
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Shape
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Stars
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Sticks
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.TextShape
 
setProperty(String, Object, BS) - Method in class org.jmol.shape.Uccage
 
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Backbone
 
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShape
 
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
setProperty(String, Object, BS) - Method in class org.jmol.shapebio.Trace
 
setProperty(String, Object, BS) - Method in class org.jmol.shapecgo.CGO
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dipoles
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Dots
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Draw
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Ellipsoids
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Polyhedra
 
setProperty(String, Object, BS) - Method in class org.jmol.shapespecial.Vectors
 
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Contact
 
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
 
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.LcaoCartoon
 
setProperty(String, Object, BS) - Method in class org.jmol.shapesurface.MolecularOrbital
 
setPropertyColorRange(float, float) - Method in class org.jmol.viewer.ColorManager
 
setPropertyColorRangeData(float[], BS) - Method in class org.jmol.viewer.ColorManager
 
setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.ColorManager
 
setPropertyColorScheme(String, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
setPropertyFor(int, Dipole, int, float) - Method in class org.jmol.shapespecial.Dipoles
 
setPropertySuper(String, Object, BS) - Method in class org.jmol.shapecgo.CGO
 
setPropertySuper(String, Object, BS) - Method in class org.jmol.shapespecial.Draw
 
setPropertySuper(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
 
setPropertyTok(int, boolean, int, float) - Method in class org.jmol.shapespecial.Dipoles
 
setPropFLS(String, Object) - Method in class org.jmol.shape.FontLineShape
 
setPropFS(String, Object) - Method in class org.jmol.shape.FontShape
 
setPropI(String, Object, BS) - Method in class org.jmol.shapesurface.Isosurface
 
setPropMC(String, Object, BS) - Method in class org.jmol.shape.MeshCollection
 
setPropOS(String, Object, BS) - Method in class org.jmol.shape.Object2dShape
 
setPropS(String, Object, BS) - Method in class org.jmol.shape.Shape
 
setPropTS(String, Object, BS) - Method in class org.jmol.shape.TextShape
 
setProteinStructureType(STR, int) - Method in class org.jmol.modelset.Group
 
setProteinStructureType(STR, int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setProteinType(BS, STR) - Method in class org.jmol.modelset.ModelSet
 
setProteinType(STR, BS) - Method in class org.jmol.viewer.Viewer
 
setPt0(int, boolean) - Method in class org.jmol.script.ScriptFlowContext
 
setPtVector(P3, V3) - Method in class org.jmol.shapespecial.Dipole
 
setPutty(float[], BS) - Method in class org.jmol.shapebio.Trace
PyMOL-based "putty"
setPyMOLDefaults() - Method in class org.jmol.viewer.StateManager
 
setPymolOffset(int, float[]) - Method in class org.jmol.shape.Labels
 
setRadical(P4) - Method in class org.jmol.jvxl.readers.Parameters
 
setRadii() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setRadius(float) - Method in class org.jmol.modelset.Atom
 
setRange(float, float, boolean) - Method in class org.jmol.util.ColorEncoder
 
setRanges(float, int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setRasmolDefaults() - Method in class org.jmol.api.JmolViewer
 
setRasMolDefaults() - Method in class org.jmol.viewer.StateManager
 
setRasmolDefaults() - Method in class org.jmol.viewer.Viewer
 
setReader() - Method in class org.jmol.jvxl.readers.SurfaceGenerator
 
setReaderObjectInfo(String, int, String, boolean, Lst<Object>, Lst<Object>, String) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setReaderObjects() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setRefreshing(boolean) - Method in class org.jmol.viewer.Viewer
 
setRenderer(JmolRendererInterface) - Method in class org.jmol.export.___Exporter
 
setRgb(Rgb16) - Method in class org.jmol.util.Rgb16
 
setRigidBodyPhase(String, double[]) - Method in class org.jmol.adapter.readers.xtal.JanaReader
Adjust phases to match the difference between the atom's position and the rigid molecular fragment's reference point.
setRigidBodyRotations(String, float[][]) - Method in class org.jmol.adapter.readers.xtal.JanaReader
Transform unphased Fourier x,y,z cos/sin coefficients in a rigid body system based on distance from center.
setRingConnectivity(int) - Method in class org.jmol.smiles.SmilesAtom
 
setRingData(BS) - Method in class org.jmol.smiles.SmilesSearch
 
setRingMembership(int) - Method in class org.jmol.smiles.SmilesAtom
 
setRingsClickable() - Method in class org.jmol.modelsetbio.NucleicMonomer
 
setRingSize(int) - Method in class org.jmol.smiles.SmilesAtom
 
setRingsVisible(boolean) - Method in class org.jmol.modelsetbio.NucleicMonomer
 
setRotateBondIndex(int) - Method in class org.jmol.viewer.Viewer
 
setRotateMode() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setRotation(M3) - Method in class org.jmol.viewer.TransformManager
 
setRotationCenterAndRadiusXYZ(T3, boolean) - Method in class org.jmol.viewer.TransformManager
 
setRotationMatrix(M3) - Method in class org.jmol.g3d.Graphics3D
 
setRotationPointXY(P3) - Method in class org.jmol.viewer.TransformManager
 
setRotationRadius(int, float) - Method in class org.jmol.modelset.ModelSet
 
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.TransformManager
 
setRotationRadius(float, boolean) - Method in class org.jmol.viewer.Viewer
 
setRubberbandArgb(int) - Method in class org.jmol.viewer.ColorManager
 
setScale(float) - Method in class org.jmol.modelset.Text
 
setScale(float) - Method in class org.jmol.shape.Axes
 
setScale(float, boolean) - Method in class org.jmol.shapespecial.Ellipsoid
 
setScaleAngstromsPerInch(float) - Method in class org.jmol.viewer.TransformManager
 
setScalePixelsPerMicron(float) - Method in class org.jmol.modelset.Object2d
 
setScaling() - Method in class org.jmol.shape.Labels
 
setSceneObject(String, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Set scene object/state-specific global fields and settings based on the name and state or stored values from when the file was loaded.
setScreenDimension(int, int) - Method in class org.jmol.api.JmolViewer
 
setScreenDimension(int, int) - Method in class org.jmol.appletjs.Jmol
 
setScreenDimension(int, int) - Method in class org.jmol.viewer.Viewer
 
setScreened(boolean) - Method in class org.jmol.g3d.Graphics3D
 
setScreenParameters(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
 
setScreenParameters0(int, int, boolean, boolean, boolean, boolean) - Method in class org.jmol.viewer.TransformManager
 
setScript(String) - Method in class org.jmol.modelset.Object2d
 
setScript(String) - Method in class org.jmol.script.ScriptFunction
 
setScriptButtonPercent(int) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setScriptEcho(String, boolean) - Method in class org.jmol.viewer.StatusManager
 
setScriptExtensions() - Method in class org.jmol.script.ScriptEval
 
setScriptFileReferences(String, String, String, String) - Static method in class org.jmol.viewer.FileManager
 
setScriptFileRefs(String, String, boolean) - Static method in class org.jmol.viewer.FileManager
Sets all local file references in a script file to point to files within dataPath.
setScriptInfo(String) - Method in class org.jmol.shapesurface.Isosurface
 
setScriptQueue(boolean) - Method in class org.jmol.viewer.Viewer
 
setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.StatusManager
 
setScriptStatus(String, String, int, String) - Method in class org.jmol.viewer.Viewer
 
setSelectBindings() - Method in class org.jmol.viewer.binding.DragBinding
 
setSelectBindings() - Method in class org.jmol.viewer.binding.JmolBinding
 
setSelectBindings() - Method in class org.jmol.viewer.binding.PfaatBinding
 
setSelectBindings() - Method in class org.jmol.viewer.binding.RasmolBinding
 
setSelected(boolean) - Method in class org.jmol.popup.AwtSwingComponent
 
setSelected(BS) - Method in class org.jmol.smiles.SmilesSearch
 
setSelected(String, boolean) - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
setSelectedAtom(int, boolean) - Method in class org.jmol.viewer.SelectionManager
 
setSelectedFloats(float, BS, float[]) - Static method in class org.jmol.viewer.DataManager
 
setSelectedOctant() - Method in class org.jmol.renderspecial.EllipsoidsRenderer
 
setSelectedTranslation(BS, char, int) - Method in class org.jmol.viewer.TransformManager
 
setSelectedValue(int, int, SV) - Method in class org.jmol.script.SV
 
setSelectionHaloEnabled(boolean) - Method in class org.jmol.modelset.ModelSet
 
setSelectionHalos(boolean) - Method in class org.jmol.viewer.Viewer
 
setSelectionSet(BS) - Method in class org.jmol.api.JmolViewer
 
setSelectionSet(BS, int) - Method in class org.jmol.viewer.SelectionManager
 
setSelectionSet(BS) - Method in class org.jmol.viewer.Viewer
 
setSelectionSubset(BS) - Method in class org.jmol.viewer.SelectionManager
 
setShapeErrorState(int, String) - Method in class org.jmol.viewer.Viewer
 
setShapeId(int, int, boolean) - Method in class org.jmol.scriptext.CmdExt
 
setShapeNameParameter(int) - Method in class org.jmol.script.ScriptEval
 
setShapeProperty(int, String, Object) - Method in class org.jmol.script.ScriptEval
 
setShapeProperty(int, String, Object) - Method in class org.jmol.scriptext.CmdExt
 
setShapeProperty(int, String, Object) - Method in class org.jmol.viewer.Viewer
 
setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.script.ScriptEval
 
setShapePropertyBs(int, String, Object, BS) - Method in class org.jmol.viewer.ShapeManager
 
setShapeSize(int, RadiusData) - Method in class org.jmol.script.ScriptEval
 
setShapeSize(int, int, BS) - Method in class org.jmol.viewer.Viewer
 
setShapeSizeBs(int, int, BS) - Method in class org.jmol.script.ScriptEval
 
setShapeSizeBs(int, int, RadiusData, BS) - Method in class org.jmol.viewer.ShapeManager
 
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shape.Shape
 
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.Backbone
 
setShapeSizeRD(int, RadiusData, BS) - Method in class org.jmol.shapebio.BioShapeCollection
 
setShapeTranslucency(int, String, String, float, BS) - Method in class org.jmol.script.ScriptEval
 
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Atom
 
setShapeVisibility(boolean) - Method in class org.jmol.modelset.Bond
 
setShapeVisibility(int, boolean) - Method in class org.jmol.modelset.Group
 
setShapeVisibility(Atom, boolean) - Method in class org.jmol.shape.Shape
 
setShowAxes(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowBbcage(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowHydrogens(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowHydrogens(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowMeasurements(boolean) - Method in class org.jmol.api.JmolViewer
 
setShowMeasurements(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowUnitCell(boolean) - Method in class org.jmol.viewer.Viewer
 
setShowWithin(Lst<P3>, float, boolean) - Method in class org.jmol.shape.Mesh
 
setSigma(String, Matrix) - Method in class org.jmol.symmetry.SymmetryOperation
 
setSilent(boolean) - Method in class org.jmol.minimize.forcefield.Calculations
 
setSingleItem(Lst<Object>) - Method in class org.jmol.shape.Measures
 
setSize(float) - Method in class org.jmol.adapter.readers.pymol.JmolObject
 
setSize(int, float) - Method in class org.jmol.script.ScriptEval
 
setSize(int, BS) - Method in class org.jmol.shape.AtomShape
 
setSize(int, BS) - Method in class org.jmol.shape.Balls
 
setSize(int, BS) - Method in class org.jmol.shape.Measures
 
setSize(int, BS) - Method in class org.jmol.shape.Shape
 
setSize(int, BS) - Method in class org.jmol.shape.Sticks
sets the size of a bond, or sets the selectedBonds set
setSize(int, BS) - Method in class org.jmol.shapespecial.Ellipsoids
 
setSize2(int, BS) - Method in class org.jmol.shape.AtomShape
 
setSizeBio(int) - Method in class org.jmol.script.ScriptEval
 
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.AtomShape
 
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Balls
 
setSizeRD(RadiusData, BS) - Method in class org.jmol.shape.Shape
 
setSizeRD(RadiusData, BS) - Method in class org.jmol.shapespecial.Dots
 
setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shape.AtomShape
 
setSizeRD2(int, RadiusData, boolean) - Method in class org.jmol.shapespecial.Vectors
 
setSlab(int) - Method in interface org.jmol.api.JmolGraphicsInterface
 
setSlab(int) - Method in class org.jmol.export.Export3D
 
setSlab(int) - Method in class org.jmol.util.GData
clipping from the front and the back
setSlabAndZShade(int, int, int, int, int) - Method in interface org.jmol.api.JmolGraphicsInterface
 
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.export.Export3D
 
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
setSlabAndZShade(int, int, int, int, int) - Method in class org.jmol.util.GData
 
setSlabDepthInternal(boolean) - Method in class org.jmol.viewer.TransformManager
set internal slab or depth from screen-based slab or depth
setSlabEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
 
setSlabRange(float) - Method in class org.jmol.viewer.TransformManager
 
setSlaters(boolean, boolean) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
after the vectors intinfo and floatinfo are completed, we
setSlice(float, float, float, float, P3, V3, boolean) - Method in class org.openscience.jmol.app.surfacetool.Slice
Sets the right plane and left plane bounding a slice.
setSlice(float, float, float, float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
Defines a slice within which isosurfaces (and in future? atoms) are displayed.
setSliceAnglefromZ(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSliceAngleXY(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSlicePosition(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSliceThickness(float) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSmilesBondCoordinates(SmilesAtom, SmilesAtom, int) - Method in class org.jmol.smiles.SmilesSearch
 
setSmilesCoordinates(Node, SmilesAtom, SmilesAtom, Node[]) - Method in class org.jmol.smiles.SmilesSearch
 
setSmilesString(String) - Method in class org.jmol.viewer.Viewer
 
setSolvent(String, float) - Method in class org.jmol.jvxl.readers.Parameters
 
setSpaceGroup(boolean) - Method in interface org.jmol.api.SymmetryInterface
 
setSpaceGroup(boolean) - Method in class org.jmol.symmetry.Symmetry
 
setSpaceGroupFrom(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
 
setSpaceGroupFrom(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
 
setSpaceGroupName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setSpectraMenu(SC, Lst<String>) - Method in class org.jmol.popup.JmolGenericPopup
 
setSpectrumPeaks(int, String, String) - Method in class org.jmol.adapter.readers.more.JcampdxReader
 
setSpectrumPeaks(int, String, String) - Method in interface org.jmol.api.JmolJDXMOLReader
 
setSpecular(boolean) - Method in class org.jmol.util.GData
 
setSpecularExponent(int) - Method in class org.jmol.util.GData
log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of shades
setSpecularPercent(int) - Method in class org.jmol.util.GData
sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything, really
setSpecularPower(int) - Method in class org.jmol.util.GData
fractional distance to white for specular dot
setSphere(float, boolean) - Method in class org.jmol.jvxl.readers.Parameters
 
setSphereMatrix(T3, float, float, float, A4, M4) - Method in class org.jmol.export.__CartesianExporter
 
setSpin(JmolScriptEvaluator, boolean, float, Lst<P3>, float[], BS, boolean) - Method in class org.jmol.viewer.TransformManager
 
setSpin(String, int) - Method in class org.jmol.viewer.Viewer
 
setSpinFps(int) - Method in class org.jmol.viewer.TransformManager
 
setSpinOff() - Method in class org.jmol.viewer.TransformManager
 
setSpinOn() - Method in class org.jmol.viewer.TransformManager
 
setSpinVectors() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setSpinXYZ(float, float, float) - Method in class org.jmol.viewer.TransformManager
 
setsSuccessful - Variable in class org.jmol.jvxl.data.MeshData
 
setStartupBooleans() - Method in class org.jmol.viewer.Viewer
 
setStateCount(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setStatement(T[]) - Method in class org.jmol.script.ScriptExpr
provides support for @x and @{....} in statements.
setStateScriptVersion(Viewer, String) - Static method in class org.jmol.script.ScriptManager
 
setStatus(int, String) - Method in class org.openscience.jmol.app.jmolpanel.StatusBar
 
SetStatusAction(String, String) - Constructor for class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
 
setStatusAppletReady(String, boolean) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomHovered(int, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomMoved(BS) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomPicked(int, String, Map<String, Object>) - Method in class org.jmol.viewer.StatusManager
 
setStatusAtomPicked(int, String, Map<String, Object>) - Method in class org.jmol.viewer.Viewer
 
setStatusChanged(String, int, Object, boolean) - Method in class org.jmol.viewer.StatusManager
 
setStatusClicked(int, int, int, int, int) - Method in class org.jmol.viewer.StatusManager
 
setStatusDragDropped(int, int, int, String) - Method in class org.jmol.appletjs.Jmol
 
setStatusDragDropped(int, int, int, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusDragDropped(int, int, int, String) - Method in class org.jmol.viewer.Viewer
 
setStatusFrameChanged(int, int, int, int, int, float, String) - Method in class org.jmol.viewer.StatusManager
 
setStatusFrameChanged(boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.StatusManager
 
setStatusMeasuring(String, int, String, float) - Method in class org.jmol.viewer.Viewer
 
setStatusObjectHovered(String, String, T3) - Method in class org.jmol.viewer.StatusManager
 
setStatusPicked(int, T3, Map<String, Object>) - Method in class org.jmol.shape.MeshCollection
 
setStatusResized(int, int) - Method in class org.jmol.viewer.StatusManager
 
setStatusResized(int, int) - Method in class org.jmol.viewer.Viewer
 
setStereo(boolean, Object) - Method in class org.jmol.viewer.Viewer
 
setStereoDegrees(float) - Method in class org.jmol.viewer.TransformManager
 
setStereoGraphics(boolean) - Method in interface org.jmol.api.JmolAppletInterface
 
setStereoGraphics(boolean) - Method in class org.jmol.applet.Jmol
 
setStereoGraphics(boolean) - Method in class org.jmol.appletjs.Jmol
 
setStereoMode(STER) - Method in class org.jmol.viewer.TransformManager
 
setStereoMode(int[], STER, float) - Method in class org.jmol.viewer.Viewer
 
setStereoMode2(int[]) - Method in class org.jmol.viewer.TransformManager
 
setStrandCount() - Method in class org.jmol.renderbio.StrandsRenderer
 
setStrandCount(int, int) - Method in class org.jmol.viewer.Viewer
 
setStream(String, boolean) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
setStringProperty(String, String) - Method in class org.jmol.api.JmolViewer
 
setStringProperty(String, String) - Method in class org.jmol.script.ScriptParam
 
setStringProperty(String, String) - Method in class org.jmol.util.GenericApplet
 
setStringProperty(String, String) - Method in class org.jmol.viewer.Viewer
 
setStringPropertyTok(String, int, String) - Method in class org.jmol.viewer.Viewer
 
setStrokeBold(Object, boolean) - Method in interface org.jmol.api.GenericGraphics
 
setStrokeBold(Object, boolean) - Method in class org.jmol.awt.AwtG2D
 
setStrokeBold(Object, boolean) - Method in class org.jmol.awtjs2d.JsG2D
 
setStrucNo(int) - Method in class org.jmol.modelset.Group
 
setStrucNo(int) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setStrucNo(int) - Method in class org.jmol.modelsetbio.Monomer
 
setStructure - Variable in class org.jmol.dssx.DSSP
 
setStructure(AminoPolymer, BS, STR) - Method in class org.jmol.dssx.DSSP
 
setStructure(ProteinStructure) - Method in class org.jmol.modelsetbio.AlphaMonomer
 
setStructure(JmolAdapterStructureIterator) - Method in class org.jmol.modelsetbio.Resolver
note that istart and iend will be adjusted.
setStructure(String, Translator) - Method in class org.jmol.popup.PopupResource
 
setStructureIndexes() - Method in class org.jmol.modelset.ModelSet
 
setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelset.Model
 
setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelset.ModelSet
 
setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.AminoPolymer
 
setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.BioModel
 
setStructureList(Map<STR, float[]>) - Method in class org.jmol.modelsetbio.BioPolymer
 
setStructureList(float[], STR) - Method in class org.jmol.viewer.GlobalSettings
 
setStructureList(float[], STR) - Method in class org.jmol.viewer.Viewer
 
setStructureTypes() - Method in class org.jmol.renderbio.BioShapeRenderer
 
setStrut(int, int, int, Lst<Atom>, BS, BS, Lst<Atom[]>, BS, BS, BS, int) - Static method in class org.jmol.modelsetbio.AlphaPolymer
 
setSubsystem(String, Subsystem) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
setSubsystemOptions() - Method in class org.jmol.adapter.readers.cif.MSRdr
 
setSupercellFromPoint(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setSurfaceInfo(P4, P3, int, String) - Method in class org.jmol.jvxl.data.JvxlData
 
setSurfaceInfoFromBitSet(BS, P4) - Method in class org.jmol.jvxl.data.JvxlData
 
setSurfaceInfoFromBitSetPts(BS, P4, P3) - Method in class org.jmol.jvxl.data.JvxlData
 
setSurfaceToolParam() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSymbol(String) - Method in class org.jmol.smiles.SmilesAtom
Sets the symbol of the atm.
setSymmetry(boolean) - Method in class org.jmol.adapter.readers.cif.Subsystem
 
setSymmetry() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
setSymmetry() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
setSymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setSymmetry(SymmetryInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setSymmetryInfo(int, Map<String, Object>, float[]) - Method in interface org.jmol.api.SymmetryInterface
 
setSymmetryInfo(int, Map<String, Object>, float[]) - Method in class org.jmol.symmetry.Symmetry
Set the symmetry in the
setSymmetryInfo(Map<String, Object>, float[]) - Method in class org.jmol.symmetry.SymmetryInfo
 
setSymmetryMinMax(P3) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setSymmetryOperator(String) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setSymmetryOps() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setSymmetryRange(float) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setSync(String) - Method in class org.jmol.viewer.StatusManager
 
setSync() - Method in class org.jmol.viewer.Viewer
 
setSyncDriver(int) - Method in class org.jmol.viewer.StatusManager
 
setSyncDriver(int) - Method in class org.jmol.viewer.Viewer
 
setSyncStarting() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setSyncTarget(int, boolean) - Method in class org.jmol.viewer.Viewer
 
settable - Static variable in class org.jmol.script.T
 
setTag(char[], BS, char) - Method in class org.jmol.dssx.DSSP
 
setTainted(boolean) - Method in class org.jmol.viewer.Viewer
 
setTaintedAtoms(BS, byte) - Method in class org.jmol.modelset.AtomCollection
 
setTempPoint(T3, T3, float, float) - Method in class org.jmol.util.ModulationSet
 
setTempPoint(T3, T3, float, float) - Method in class org.jmol.util.Vibration
 
setTempPoints(P3, P3, boolean) - Method in class org.jmol.export.__CartesianExporter
 
setTempVertex(T3, T3, T3) - Static method in class org.jmol.export.___Exporter
 
setTensor(Tensor) - Method in class org.jmol.shapespecial.Ellipsoid
 
setTensors() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setTensors() - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setText(String) - Method in interface org.jmol.api.JmolAbstractButton
 
setText(String) - Method in interface org.jmol.console.GenericTextArea
 
setText(String, Font, int, int, int, int, int) - Method in class org.jmol.g3d.TextString
 
setText(String) - Method in class org.jmol.modelset.Text
 
setText(String) - Method in class org.jmol.popup.AwtSwingComponent
 
setText(String, String) - Method in class org.jmol.popup.GenericSwingPopup
 
setTextLabel(int, Text) - Method in class org.jmol.shape.Labels
 
setTextPosition(int) - Method in class org.jmol.util.GData
 
setThisScheme(String, int[]) - Method in class org.jmol.util.ColorEncoder
 
setTimeout(Viewer, Map<String, Object>, String, int, String) - Static method in class org.jmol.thread.TimeoutThread
 
setTimeout(String, int, String) - Method in class org.jmol.viewer.Viewer
 
setTimeReversal(int, int) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
setTimeReversal(int, int) - Method in interface org.jmol.api.SymmetryInterface
 
setTimeReversal(int, int) - Method in class org.jmol.symmetry.Symmetry
 
setTimeReversal(int) - Method in class org.jmol.symmetry.SymmetryOperation
 
settings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setTitle(String) - Method in class org.jmol.adapter.readers.xtal.BilbaoReader
 
setTitle() - Method in class org.jmol.console.GenericConsole
 
setTitle() - Method in class org.jmol.console.JmolConsole
 
setTitle() - Method in class org.jmol.consolejs.AppletConsole
 
setTlsGroups(int, int, SymmetryInterface) - Method in class org.jmol.adapter.readers.pdb.PdbReader
Sets the atom property property_tlsGroup based on TLS group ranges and adds "TLS" key to model's auxiliaryInfo.
setTlsTensor(Atom, Map<String, Object>, SymmetryInterface) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
setToken(Viewer, String, LabelToken, int, int, Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
sets a label token based on a label string
setTokenProperty(int, boolean) - Method in class org.jmol.shape.Mesh
 
setTokenProperty(int, boolean, boolean) - Method in class org.jmol.shape.MeshCollection
 
setToolTipText(String) - Method in interface org.jmol.api.JmolAbstractButton
 
setTop(SmilesSearch) - Method in class org.jmol.smiles.SmilesSearch
 
setTorsionData(P3, P3, P3, P3, VTemp, boolean) - Static method in class org.jmol.smiles.SmilesMeasure
 
setTorsionType(MinTorsion) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
setTorsionVariables(Calculation) - Method in class org.jmol.minimize.forcefield.Calculations
 
setTrajectory() - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setTrajectory(int) - Method in class org.jmol.modelset.ModelSet
 
setTrajectoryBs(BS) - Method in class org.jmol.modelset.ModelSet
 
setTrajectoryName(String) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setTransform(float, float, float, float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setTranslationFractions() - Method in class org.jmol.viewer.TransformManager
 
setTranslations() - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
allows for web page material to be internationalized, inserting language-specific code, as for WebExport, or by inserting boiler-plate information, as for About_xx.html
setTranslucency(String, Font, Graphics3D) - Method in class org.jmol.g3d.TextRenderer
retrieve grey-scale pixel map from the platform, then round it off
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Atom
 
setTranslucent(boolean, float) - Method in class org.jmol.modelset.Bond
 
setTranslucent(float, boolean) - Method in class org.jmol.modelset.Object2d
 
setTranslucent(boolean, float) - Method in class org.jmol.shape.Mesh
 
setTranslucent(boolean, BS, float) - Method in class org.jmol.shapebio.BioShape
 
setTranslucent(boolean, float) - Method in class org.jmol.shapespecial.Dipole
 
setTranslucent(boolean, float) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setTranslucentVertices(BS) - Method in class org.jmol.util.MeshSurface
Must create bsTransPolygons, polygonTranslucencies, and new triangle set for partially translucent polygons
setTransparentCursor(Object) - Static method in class org.jmol.awt.Display
 
setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
 
setTransparentCursor(Object) - Static method in class org.jmol.awtjs2d.Display
 
setTransparentCursor(Object) - Method in class org.jmol.awtjs2d.Platform
 
setTriangleTranslucency(short, short, short) - Method in class org.jmol.g3d.Graphics3D
 
setType(String) - Method in class org.jmol.util.Tensor
Note that type may be null here to skip type initialization and allow later setting of type; this should be used with care.
setType(int) - Method in class org.jmol.util.Vibration
 
setU(Atom, int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollection
 
setUniqueBond(int, int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setUniqueBonds(BS, boolean) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setUniqueObjects(int, BS, int, int, int, float, int, float, float) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
setUniqueSettings(Lst<Object>) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
Create uniqueSettings from the "unique_settings" map item.
setUnitCell() - Method in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
setUnitCell() - Method in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
setUnitCell(float, float, float, float, float, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setUnitCell(float[], boolean) - Method in interface org.jmol.api.SymmetryInterface
 
setUnitCell(float[], boolean) - Method in class org.jmol.symmetry.Symmetry
 
setUnitCellItem(int, float) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setUnitCellOffset(SymmetryInterface, T3, int) - Method in class org.jmol.modelset.ModelSet
 
setUnits(boolean) - Method in class org.jmol.adapter.readers.xtal.MagresReader
catalog units
setUnits(String, int) - Method in class org.jmol.script.ScriptEval
 
setUnits(String) - Method in class org.jmol.viewer.GlobalSettings
 
setUnits(String, boolean) - Method in class org.jmol.viewer.Viewer
 
setUnitVectors() - Method in class org.jmol.jvxl.data.VolumeData
 
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.more.BinaryDcdReader
 
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
setup(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoFxyzReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMepReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoMOReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoPlaneReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
setup(boolean) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setup(int, float[], P3[], BS) - Method in class org.jmol.quantum.MepCalculation
 
setup(Viewer, Container, String) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
setup2() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setupAC() - Method in class org.jmol.modelset.AtomCollection
 
setupASCR(String, Map<String, Object>, Object) - Method in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
setupBC() - Method in class org.jmol.modelset.BondCollection
 
setupCalculation(VolumeDataInterface, BS, BS, BS[], String, T3[], int, Lst<int[]>, float[][], int[][], Object, float[], float[], boolean, float[][], float[], boolean, T3[], float[], int) - Method in interface org.jmol.api.MOCalculationInterface
 
setupCalculation() - Method in class org.jmol.jvxl.readers.IsoMOReader
 
setupCalculation(VolumeDataInterface, BS, BS, BS[], String, T3[], int, Lst<int[]>, float[][], int[][], Object, float[], float[], boolean, float[][], float[], boolean, T3[], float[], int) - Method in class org.jmol.quantum.MOCalculation
 
setupCalculation(VolumeDataInterface, BS, BS, BS[], String, T3[], int, Lst<int[]>, float[][], int[][], Object, float[], float[], boolean, float[][], float[], boolean, T3[], float[], int) - Method in class org.jmol.quantum.NciCalculation
 
setupCalculations() - Method in class org.jmol.minimize.forcefield.Calculations
 
setupCalculations() - Method in class org.jmol.minimize.forcefield.CalculationsMMFF
 
setupCalculations() - Method in class org.jmol.minimize.forcefield.CalculationsUFF
 
setupCoordinates(float[], float[], BS, T3[], T3[], boolean) - Method in class org.jmol.quantum.QuantumCalculation
 
setupLabels() - Method in class org.jmol.console.GenericConsole
 
setupLabels() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
setupLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
setupMinimization() - Method in class org.jmol.minimize.Minimizer
 
setupNav(float, P3[][], P3[], int, int) - Method in class org.jmol.navigate.Navigator
 
setupNavTo() - Method in class org.jmol.navigate.Navigator
 
setupPS(AlphaPolymer, STR, int, int) - Method in class org.jmol.modelsetbio.ProteinStructure
 
setupRR(BioShape, boolean) - Method in class org.jmol.renderbio.RocketsRenderer
 
setupType(String) - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
setupUI(boolean) - Method in interface org.jmol.api.JmolDialogInterface
 
setupUI(boolean) - Method in class org.jmol.dialog.Dialog
 
setupUIManager() - Static method in class org.jmol.dialog.Dialog
Setup the UIManager (for i18n)
setUseMolecular(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
setUserAtomTypes() - Method in class org.jmol.adapter.readers.more.ForceFieldReader
 
setUserScale(int[]) - Method in class org.jmol.util.ColorEncoder
 
setUserVariable(String, SV) - Method in class org.jmol.viewer.GlobalSettings
 
setUserVdw(VDW) - Method in class org.jmol.viewer.Viewer
 
setv(SV) - Method in class org.jmol.script.SV
Creates a NEW version of the variable.
setValence(int) - Method in class org.jmol.modelset.Atom
 
setValence(int) - Method in class org.jmol.smiles.SmilesAtom
 
setValue(float) - Method in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
setValue(float) - Method in class org.jmol.shapespecial.Dipole
 
setValue(String, String) - Method in class org.jmol.util.GenericApplet
 
setValueMinMax() - Method in class org.jmol.jvxl.readers.JvxlXmlReader
 
setValues(LabelToken[], Map<String, Object>) - Static method in class org.jmol.modelset.LabelToken
 
setValues(M3, P3, P3) - Method in class org.jmol.thread.MoveToThread
 
setVariable(int, int, String, boolean) - Method in class org.jmol.script.ScriptExpr
 
setVariables() - Method in class org.jmol.render.MeshRenderer
 
setVariables(Map<String, SV>, Lst<SV>) - Method in class org.jmol.script.ScriptFunction
 
setVdwStr(String) - Method in class org.jmol.viewer.Viewer
 
setVectorAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVectorScale(float) - Method in class org.jmol.api.JmolViewer
 
setVectorScale(float) - Method in class org.jmol.viewer.Viewer
 
setVersionSettings() - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
Attempt to adjust for PyMOL versions.
setVertexAnisotropy(T3) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVertexColixesForAtoms(Viewer, short[], int[], BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setVertexColorMap() - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
setVertexSets(boolean) - Method in class org.jmol.jvxl.data.MeshData
 
setVertexSource() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setVib(boolean) - Method in class org.jmol.util.ModulationSet
 
setVibrationOn(boolean) - Method in class org.jmol.viewer.TransformManager
 
setVibrationPeriod(float) - Method in class org.jmol.api.JmolViewer
 
setVibrationPeriod(float) - Method in class org.jmol.viewer.TransformManager
sets the period of vibration -- period > 0: sets the period and turns vibration on -- period < 0: sets the period but does not turn vibration on -- period = 0: sets the period to zero and turns vibration off -- period Float.NaN: uses current setting (frame change)
setVibrationPeriod(float) - Method in class org.jmol.viewer.Viewer
 
setVibrationScale(float) - Method in class org.jmol.api.JmolViewer
 
setVibrationScale(float) - Method in class org.jmol.viewer.TransformManager
 
setVibrationScale(float) - Method in class org.jmol.viewer.Viewer
 
setVibrationsFromProperties() - Method in class org.jmol.adapter.readers.quantum.SpartanArchive
 
setVibrationT(float) - Method in class org.jmol.viewer.TransformManager
 
setVibrationVector() - Method in class org.jmol.modelset.Atom
 
setVibrationVector(int, T3) - Method in class org.jmol.modelset.AtomCollection
 
setVibrationVector2(int, int, float) - Method in class org.jmol.modelset.AtomCollection
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolBioResolver
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolJSpecView
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolNMRInterface
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolPropertyManager
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptEvaluator
 
setViewer(Viewer) - Method in interface org.jmol.api.JmolScriptManager
 
setViewer(PlatformViewer, Object) - Method in class org.jmol.awt.Platform
 
setViewer(PlatformViewer, Object) - Method in class org.jmol.awtjs2d.Platform
 
setViewer(Viewer) - Method in class org.jmol.console.GenericConsole
 
setViewer(Viewer) - Method in class org.jmol.jsv.JSpecView
 
setViewer(Viewer) - Method in class org.jmol.modelsetbio.Resolver
 
setViewer(Viewer, String) - Method in class org.jmol.multitouch.ActionManagerMT
 
setViewer(Viewer) - Method in class org.jmol.quantum.NMRCalculation
 
setViewer(Viewer) - Method in class org.jmol.script.ScriptEval
 
setViewer(Viewer) - Method in class org.jmol.script.ScriptManager
 
setViewer(Viewer, String) - Method in class org.jmol.thread.JmolThread
 
setViewer(Viewer, String) - Method in class org.jmol.viewer.ActionManager
 
setViewer(boolean) - Method in class org.jmol.viewer.AnimationManager
 
setViewer(Viewer) - Method in class org.jmol.viewer.JmolStateCreator
 
setViewer(Viewer, double) - Method in class org.jmol.viewer.OutputManager
 
setViewer(Viewer) - Method in class org.jmol.viewer.PropertyManager
 
setViewer(Viewer) - Method in class org.jmol.viewer.StateCreator
 
setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
setViewer(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
setViewerG3dShapeID(Viewer, int) - Method in class org.jmol.render.ShapeRenderer
 
setVis(Map<?, Ellipsoid>, BS, Atom[]) - Method in class org.jmol.shapespecial.Ellipsoids
 
setVisibilityFlags(int) - Method in class org.jmol.shape.Mesh
 
setVisibilityInfo() - Method in class org.jmol.shape.Measures
 
setVisible(boolean) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
setVisible(boolean) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
setVisible(boolean) - Method in class org.jmol.console.AppletConsole
 
setVisible(boolean) - Method in class org.jmol.console.GenericConsole
 
setVisible(boolean) - Method in class org.jmol.console.JmolConsole
 
setVisible(boolean) - Method in class org.jmol.console.ScriptEditor
 
setVisible(boolean) - Method in class org.jmol.consolejs.AppletConsole
 
setVisible(boolean) - Method in class org.jmol.shapespecial.Polyhedra
 
setVisible(boolean) - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
setVolumeData() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setVolumeData() - Method in class org.jmol.jvxl.readers.AtomPropertyMapper
 
setVolumeData() - Method in class org.jmol.jvxl.readers.IsoFxyReader
 
setVolumeData() - Method in class org.jmol.jvxl.readers.IsoShapeReader
 
setVolumeData() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setVolumeData(int, VolumeData, ContactPair, float, int) - Method in class org.jmol.shapesurface.Contact
 
setVolumeDataADR() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setVolumeDataParams() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setVolumeDataV(VolumeData) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVolumeForPlane() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setVolumetricAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVolumetricOrigin(float, float, float) - Method in interface org.jmol.api.VolumeDataInterface
 
setVolumetricOrigin(float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVolumetricOriginAnisotropy() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
setVolumetricVector(int, float, float, float) - Method in interface org.jmol.api.VolumeDataInterface
 
setVolumetricVector(int, float, float, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVolumetricXml() - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxel(int, int, int, int, float) - Method in class org.jmol.jvxl.readers.AtomDataReader
 
setVoxelCounts(int, int, int) - Method in interface org.jmol.api.VolumeDataInterface
 
setVoxelCounts(int, int, int) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelData(int, float) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelDataAsArray(float[][][]) - Method in interface org.jmol.api.VolumeDataInterface
 
setVoxelDataAsArray(float[][][]) - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelMap() - Method in class org.jmol.jvxl.data.VolumeData
 
setVoxelMapValue(int, int, int, float) - Method in class org.jmol.jvxl.data.VolumeData
for sparse data mapping, as for a plane
setVoxelRange(int, float, float, float, int, float) - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
setVoxels() - Method in class org.jmol.jvxl.readers.IsoIntersectReader
 
setWebPageAuthor(String) - Static method in class org.openscience.jmol.app.webexport.WebExport
 
setWidthHeight(boolean) - Method in class org.jmol.util.GData
 
setWindow(int, int, float) - Method in class org.jmol.modelset.Object2d
 
setWindowCentered(boolean) - Method in class org.jmol.viewer.TransformManager
 
setWindowParameters(int, int) - Method in interface org.jmol.api.GenericGraphics
 
setWindowParameters(int, int) - Method in class org.jmol.awt.AwtG2D
 
setWindowParameters(int, int) - Method in class org.jmol.awtjs2d.JsG2D
 
setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
 
setWindowParameters(int, int, boolean) - Method in class org.jmol.util.GData
 
setWinParams(int, int, boolean) - Method in class org.jmol.util.GData
 
setXYA(float[], int) - Method in class org.jmol.modelset.Text
 
setXYZ(P3, boolean) - Method in class org.jmol.modelset.Object2d
 
setXYZ(QuantumCalculation, boolean) - Method in class org.jmol.quantum.QMAtom
 
setXYZ(T3) - Method in class org.jmol.util.ModulationSet
 
setXYZ(T3) - Method in class org.jmol.util.Vibration
 
setXYZBohr(T3[]) - Method in class org.jmol.quantum.QuantumCalculation
 
setXYZBohrI(float[], int, int, T3[]) - Method in class org.jmol.quantum.QuantumCalculation
 
setXYZs(int, int, int, int) - Method in class org.jmol.modelset.Object2d
 
setZcutoff() - Method in class org.jmol.render.LabelsRenderer
 
setZMargin(int) - Method in class org.jmol.g3d.Graphics3D
 
setZoomEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
 
setZoomHeight(boolean, boolean) - Method in class org.jmol.viewer.TransformManager
 
setZs(int, int) - Method in class org.jmol.modelset.Object2d
 
setZShadeEnabled(boolean) - Method in class org.jmol.viewer.TransformManager
 
sfacElementSymbols - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
sg - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
sg - Variable in class org.jmol.shapesurface.Isosurface
 
SG - Static variable in class org.jmol.symmetry.SpaceGroup
 
SG_ALIASES - Static variable in class org.jmol.adapter.readers.xtal.CgdReader
 
sgIndex - Static variable in class org.jmol.symmetry.SpaceGroup
 
sgName - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
sgName - Variable in class org.jmol.symmetry.SymmetryInfo
 
SHADE_INDEX_LAST - Static variable in class org.jmol.util.Shader
 
SHADE_INDEX_MAX - Static variable in class org.jmol.util.Shader
 
SHADE_INDEX_NOISY_LIMIT - Static variable in class org.jmol.util.Shader
 
SHADE_INDEX_NORMAL - Static variable in class org.jmol.util.Shader
 
SHADE_SLAB_CLIPPED - Static variable in class org.jmol.g3d.SphereRenderer
 
shadeIndexes - Variable in class org.jmol.g3d.Graphics3D
 
shadeIndexes2Sided - Variable in class org.jmol.g3d.Graphics3D
 
shader - Variable in class org.jmol.g3d.CylinderRenderer
 
shader - Variable in class org.jmol.g3d.LineRenderer
 
shader - Variable in class org.jmol.g3d.SphereRenderer
 
shader - Variable in class org.jmol.util.GData
 
Shader - Class in org.jmol.util
All functions.
Shader() - Constructor for class org.jmol.util.Shader
 
shader_path - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
shades - Variable in class org.jmol.g3d.SphereRenderer
 
shadesA - Variable in class org.jmol.g3d.CylinderRenderer
 
shadesB - Variable in class org.jmol.g3d.CylinderRenderer
 
shadesCurrent - Variable in class org.jmol.g3d.Graphics3D
 
shadeTextPixel(int, int, int, int, int, int[]) - Method in class org.jmol.g3d.Graphics3D
 
shape - Variable in class org.jmol.render.ShapeRenderer
 
shape - Static variable in class org.jmol.script.T
 
Shape - Class in org.jmol.shape
Shape now encompasses: AtomShape (abstract) | Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors | GeoSurface BioShapeCollection (abstract) | Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace Dipoles FontLineShape (abstract) | Axes, Bbcage, Frank, Uccage Measures MeshCollection (abstract) | | Draw Isosurface | LcaoCartoon, MolecularOrbital, Pmesh Sticks | Hsticks, Sssticks TextShape (abstract) | Echo, Hover
Shape() - Constructor for class org.jmol.shape.Shape
 
shape - Variable in class org.jmol.shapebio.BioShape
 
SHAPE_AXES - Static variable in class org.jmol.viewer.JC
 
SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JC
 
SHAPE_BALLS - Static variable in class org.jmol.viewer.JC
 
SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JC
 
SHAPE_CARTOON - Static variable in class org.jmol.viewer.JC
 
SHAPE_CGO - Static variable in class org.jmol.viewer.JC
 
SHAPE_CONTACT - Static variable in class org.jmol.viewer.JC
 
SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JC
 
SHAPE_DOTS - Static variable in class org.jmol.viewer.JC
 
SHAPE_DRAW - Static variable in class org.jmol.viewer.JC
 
SHAPE_ECHO - Static variable in class org.jmol.viewer.JC
 
SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JC
 
SHAPE_FRANK - Static variable in class org.jmol.viewer.JC
 
SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_HALOS - Static variable in class org.jmol.viewer.JC
 
SHAPE_HOVER - Static variable in class org.jmol.viewer.JC
 
SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JC
 
SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_LABELS - Static variable in class org.jmol.viewer.JC
 
SHAPE_LAST_ATOM_VIS_FLAG - Static variable in class org.jmol.viewer.JC
 
SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JC
 
SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_MEASURES - Static variable in class org.jmol.viewer.JC
 
SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_HAS_SETVIS - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_MESH_COLLECTION - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JC
 
SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_MO - Static variable in class org.jmol.viewer.JC
 
SHAPE_NBO - Static variable in class org.jmol.viewer.JC
 
SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JC
 
SHAPE_PMESH - Static variable in class org.jmol.viewer.JC
 
SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JC
 
SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JC
 
SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JC
 
SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JC
 
SHAPE_STARS - Static variable in class org.jmol.viewer.JC
 
SHAPE_STICKS - Static variable in class org.jmol.viewer.JC
 
SHAPE_STRANDS - Static variable in class org.jmol.viewer.JC
 
SHAPE_STRUTS - Static variable in class org.jmol.viewer.JC
 
SHAPE_TRACE - Static variable in class org.jmol.viewer.JC
 
SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JC
 
SHAPE_VECTORS - Static variable in class org.jmol.viewer.JC
 
shapeClassBases - Static variable in class org.jmol.viewer.JC
 
shapeCommand - Static variable in class org.jmol.script.T
 
shapeID - Variable in class org.jmol.render.ShapeRenderer
 
shapeID - Variable in class org.jmol.shape.Shape
 
shapely - Static variable in class org.jmol.script.T
 
SHAPELY - Static variable in class org.jmol.util.ColorEncoder
 
shapeManager - Variable in class org.jmol.render.RepaintManager
 
shapeManager - Variable in class org.jmol.script.ScriptProcessRunnable
 
ShapeManager - Class in org.jmol.viewer
 
ShapeManager(Viewer) - Constructor for class org.jmol.viewer.ShapeManager
 
ShapeRenderer - Class in org.jmol.render
 
ShapeRenderer() - Constructor for class org.jmol.render.ShapeRenderer
 
shapes - Variable in class org.jmol.viewer.ShapeManager
 
shapeTokenIndex(int) - Static method in class org.jmol.viewer.JC
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Atom
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Bond
 
shapeVisibilityFlags - Variable in class org.jmol.modelset.Group
 
shapeVisibilityFlags - Variable in class org.jmol.viewer.Connection
 
Sheet - Class in org.jmol.modelsetbio
 
Sheet(AlphaPolymer, int, int, STR) - Constructor for class org.jmol.modelsetbio.Sheet
 
sheet - Static variable in class org.jmol.script.T
 
SHEET_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
sheetOffsets - Variable in class org.jmol.dssx.DSSP
 
sheetSmoothing - Variable in class org.jmol.modelsetbio.BioPolymer
 
sheetSmoothing - Variable in class org.jmol.renderbio.BioShapeRenderer
 
sheetsmoothing - Static variable in class org.jmol.script.T
 
sheetSmoothing - Variable in class org.jmol.viewer.GlobalSettings
 
SHELL - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
shellCount - Variable in class org.jmol.adapter.readers.quantum.MOReader
 
shellCount - Variable in class org.jmol.adapter.readers.quantum.SpartanArchive
 
shellOrder - Static variable in class org.jmol.quantum.MOCalculation
 
shells - Variable in class org.jmol.adapter.readers.quantum.BasisFunctionReader
 
shells - Variable in class org.jmol.quantum.MOCalculation
 
shellsByUniqueAtom - Variable in class org.jmol.adapter.readers.quantum.PsiReader
 
shelxLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
ShelxReader - Class in org.jmol.adapter.readers.xtal
A reader for SHELX output (RES) files.
ShelxReader() - Constructor for class org.jmol.adapter.readers.xtal.ShelxReader
 
SHIFT - Static variable in class org.jmol.viewer.binding.Binding
 
shiftBits(BS, BS, boolean, int) - Static method in class org.jmol.util.BSUtil
this one slides bits to higher positions based on a pattern.
shiftRefsPPM - Variable in class org.jmol.quantum.NMRCalculation
 
shininess - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
shm - Variable in class org.jmol.viewer.Viewer
 
SHORT_BINSTRING - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
shortSceneFilename(String) - Static method in class org.jmol.io.JmolUtil
 
show(String[]) - Method in interface org.jmol.api.JmolScriptEditorInterface
 
show(String[]) - Method in class org.jmol.console.ScriptEditor
 
show(int, int, boolean) - Method in class org.jmol.popup.GenericSwingPopup
 
show - Static variable in class org.jmol.script.T
 
show() - Method in class org.jmol.scriptext.CmdExt
 
show - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
show2D(String) - Method in class org.jmol.viewer.Viewer
 
show_alpha_checker - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
show_frame_rate - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
show_progress - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
showAtomSetIndex(int, boolean) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Show an atom set from the indexes array
showAuxiliaryInfo(Map<String, Object>) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Shows the auxiliary information in the propertiesPane of the AtomSetChooser window
showaxes - Static variable in class org.jmol.script.T
 
showAxes - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
showboundbox - Static variable in class org.jmol.script.T
 
showBoundingBox - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
showBox(JmolRendererInterface, short, int, int, int, int, int, int, float, boolean) - Static method in class org.jmol.render.TextRenderer
 
showConsole(boolean) - Method in class org.jmol.viewer.Viewer
 
showContourLines - Variable in class org.jmol.shape.Mesh
 
showEditor(String[]) - Method in class org.jmol.viewer.Viewer
 
showfrank - Static variable in class org.jmol.script.T
 
showGridInfo() - Method in class org.jmol.jvxl.readers.VolumeDataReader
 
showhiddenselectionhalos - Static variable in class org.jmol.script.T
 
showHiddenSelectionHalos - Variable in class org.jmol.viewer.GlobalSettings
 
showHide(boolean) - Method in class org.jmol.shape.Measures
 
showHideM(Measurement, boolean) - Method in class org.jmol.shape.Measures
 
showhydrogens - Static variable in class org.jmol.script.T
 
showHydrogens - Variable in class org.jmol.viewer.GlobalSettings
 
showHydrogens - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
showInstanceButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
showKey - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
showkeystrokes - Static variable in class org.jmol.script.T
 
showKeyStrokes - Variable in class org.jmol.viewer.GlobalSettings
 
showmeasurements - Static variable in class org.jmol.script.T
 
showMeasurements - Variable in class org.jmol.viewer.GlobalSettings
 
showMeasurements - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
showModVecs - Variable in class org.jmol.renderspecial.VectorsRenderer
 
showmodvecs - Static variable in class org.jmol.script.T
 
showModVecs - Variable in class org.jmol.viewer.GlobalSettings
 
showMoleculesAndOrbitals - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
showMultipleBonds - Variable in class org.jmol.render.SticksRenderer
 
showmultiplebonds - Static variable in class org.jmol.script.T
 
showMultipleBonds - Variable in class org.jmol.viewer.GlobalSettings
 
shownavigationpointalways - Static variable in class org.jmol.script.T
 
showNavigationPointAlways - Variable in class org.jmol.viewer.GlobalSettings
 
showNBOPathDialog() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
Show a file selector when the savePath button is pressed.
showNumbers - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
showPaintTime - Variable in class org.jmol.applet.Jmol
 
showPaintTime - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
showParameter(String, boolean, int) - Method in class org.jmol.viewer.Viewer
 
showPoints - Variable in class org.jmol.shape.Mesh
 
showPovrayPathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Show a file selector when the savePath button is pressed.
showProgress() - Method in class org.openscience.chimetojmol.ChimePanel
 
showProperties(Properties) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
Shows the properties in the propertiesPane of the AtomSetChooser window
showRebondTimes - Variable in class org.jmol.modelset.ModelSet
 
showSaveDialog(Component, JFileChooser, File) - Method in class org.jmol.dialog.Dialog
 
showSavePathDialog() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Show a file selector when the savePath button is pressed.
showscript - Static variable in class org.jmol.script.T
 
showSelected - Variable in class org.jmol.viewer.Viewer
 
showSliceBoundaryPlanes(boolean) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
showSplashScreen() - Method in class org.openscience.jmol.app.jmolpanel.Splash
 
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
showStatus(String) - Method in class org.openscience.jmol.app.jmolpanel.Splash
 
showStatus(String) - Method in interface org.openscience.jmol.app.SplashInterface
 
showString(String) - Method in class org.jmol.script.ScriptError
 
showString(String) - Method in class org.jmol.script.ScriptEval
 
showString(String) - Method in class org.jmol.scriptext.CmdExt
 
showString(String, boolean) - Method in class org.jmol.viewer.Viewer
 
showStringPrint(String, boolean) - Method in class org.jmol.script.ScriptEval
 
showTimeout(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
 
showTimeout(String) - Method in class org.jmol.viewer.Viewer
 
showTimes(int, int, Graphics) - Method in class org.jmol.applet.Jmol
 
showTimes() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
showTiming - Variable in class org.jmol.jvxl.readers.Parameters
 
showtiming - Static variable in class org.jmol.script.T
 
showTiming - Variable in class org.jmol.viewer.GlobalSettings
 
showTriangles - Variable in class org.jmol.shape.Mesh
 
showunitcell - Static variable in class org.jmol.script.T
 
showunitcelldetails - Static variable in class org.jmol.script.T
 
showUnitCellDetails - Variable in class org.jmol.viewer.GlobalSettings
 
showUrl(String) - Method in interface org.jmol.api.JmolStatusListener
 
showUrl(String) - Method in class org.jmol.api.JmolViewer
 
showUrl(String) - Method in class org.jmol.util.GenericApplet
 
showUrl(String) - Method in class org.jmol.viewer.StatusManager
 
showUrl(String) - Method in class org.jmol.viewer.Viewer
 
showUrl(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
showWorkingPathDialog() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
Show a file selector when the savePath button is pressed.
sidechain - Static variable in class org.jmol.script.T
 
siestaContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
SiestaReader - Class in org.jmol.adapter.readers.xtal
SIESTA http://www.icmab.es/siesta/
SiestaReader() - Constructor for class org.jmol.adapter.readers.xtal.SiestaReader
 
sigma - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
sigma - Variable in class org.jmol.jvxl.readers.Parameters
 
sigma - Static variable in class org.jmol.script.T
 
sigma - Variable in class org.jmol.symmetry.SymmetryOperation
 
sigma - Variable in class org.jmol.util.ModulationSet
 
sign - Static variable in class org.jmol.script.T
 
SignedOnly - Variable in class org.jmol.popup.GenericSwingPopup
 
signFactor - Variable in class org.jmol.modelset.TickInfo
 
silent - Variable in class org.jmol.minimize.forcefield.Calculations
 
silent - Static variable in class org.jmol.script.T
 
SILVER - Static variable in class org.jmol.util.C
 
SIMPLE_LINE - Static variable in class org.jmol.shapecgo.CGOMesh
 
simpleCage - Variable in class org.jmol.modelset.Model
 
simpleEllipsoids - Variable in class org.jmol.shapespecial.Ellipsoids
 
SimpleMarchingCubes - Class in org.openscience.jvxl.simplewriter
 
SimpleMarchingCubes(VoxelDataCreator, VolumeData, Parameters, JvxlData, Lst<P3>, float[]) - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
SimpleMarchingCubesOld - Class in org.openscience.jvxl.simplewriter
 
SimpleMarchingCubesOld() - Constructor for class org.openscience.jvxl.simplewriter.SimpleMarchingCubesOld
 
simpleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
simpleQuoteIfContainsSpace(String) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
SimpleUnitCell - Class in org.jmol.util
general-purpose simple unit cell for calculations and as a super-class of unitcell, which is only part of Symmetry allows one-dimensional (polymer) and two-dimensional (slab) periodicity
SimpleUnitCell() - Constructor for class org.jmol.util.SimpleUnitCell
 
simplify_display_lists - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SIMULATION_PROTOCOL - Static variable in class org.jmol.viewer.FileManager
 
simulationPhase - Variable in class org.jmol.multitouch.ActionManagerMT
 
simulator - Variable in class org.jmol.multitouch.ActionManagerMT
 
sin - Static variable in class org.jmol.script.T
 
sinAlpha - Variable in class org.jmol.util.SimpleUnitCell
 
sinBeta - Variable in class org.jmol.util.SimpleUnitCell
 
sinGamma - Variable in class org.jmol.util.SimpleUnitCell
 
SINGLE - Static variable in class org.jmol.viewer.binding.Binding
 
single_image - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SINGLE_POINT_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
singleAtomID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SingleModelOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
SinglePointGesture - Class in org.jmol.multitouch.sparshui
SINGLE_POINT_GESTURE only passes single-touch gestures.
SinglePointGesture() - Constructor for class org.jmol.multitouch.sparshui.SinglePointGesture
 
sinPhi - Variable in class org.jmol.g3d.CylinderRenderer
 
site() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
site - Static variable in class org.jmol.script.T
 
SITE_ASYM_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
SITE_COMP_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
SITE_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
SITE_INS_CODE - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
SITE_MULT - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SITE_SEQ_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
siteScript - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
sixdots - Static variable in class org.jmol.render.FontLineShapeRenderer
 
size - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
size - Variable in class org.jmol.g3d.TextRenderer
 
size() - Method in class org.jmol.java.BS
Returns the number of bits of space actually in use by this BitSet to represent bit values.
size - Static variable in class org.jmol.script.T
 
sizeIsSticky - Variable in class org.jmol.java.BS
Whether the size of "words" is user-specified.
sizeOf(T) - Static method in class org.jmol.script.SV
 
sizes - Static variable in class org.jmol.shapecgo.CGOMesh
 
skew() - Method in class org.jmol.util.Tensor
a measure of asymmetry.
skip(long) - Method in class org.openscience.jvxl.MonitorInputStream
 
skipAtomSet(int) - Method in class org.jmol.adapter.readers.molxyz.XyzReader
 
skipComments(boolean) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.DelPhiBinaryReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.MrcBinaryReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.PyMOLMeshReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
skipData(int) - Method in class org.jmol.jvxl.readers.XsfReader
 
skipDataVFR(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
skipFloats(int) - Method in class org.jmol.adapter.readers.more.MdCrdReader
 
skipHeader() - Method in class org.jmol.dssx.AnnotationParser
Numbers are right justified in columns 0-3 followed by a space and a character; base-pair data start in column 5, but notes start with "Note: " or " ", both of which have a space in column 5.
skipHeader() - Method in class org.jmol.jvxl.readers.MsmsReader
 
skipping - Variable in class org.jmol.adapter.readers.cif.CifReader
 
skipping - Variable in class org.jmol.script.ScriptMathProcessor
 
skipPoints(int) - Method in class org.jmol.jvxl.readers.CastepDensityReader
 
skipTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
 
skipTo(String) - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
skipTo(String, boolean) - Method in class org.jmol.dssx.AnnotationParser
 
skipTo(String, String) - Method in class org.jmol.jvxl.readers.SurfaceFileReader
 
skipTo(String) - Method in class org.jmol.jvxl.readers.XmlReader
 
skipTo(String, int, char) - Static method in class org.jmol.smiles.SmilesParser
 
skipToNextAtom() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
skipVoxels(int) - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
slab - Variable in class org.jmol.export.Export3D
 
slab - Variable in class org.jmol.g3d.SphereRenderer
 
slab - Static variable in class org.jmol.script.T
 
slab - Variable in class org.jmol.thread.MoveToThread
 
slab - Variable in class org.jmol.util.GData
 
slabbing - Variable in class org.jmol.render.SticksRenderer
 
slabbingObject - Variable in class org.jmol.shape.Mesh
 
slabbingObject - Variable in class org.jmol.shapesurface.LcaoCartoon
 
slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSlicer
"slabs" an isosurface into the first Brillouin zone moving points as necessary.
slabBrillouin(P3[]) - Method in class org.jmol.util.MeshSurface
 
slabByAtom - Variable in class org.jmol.render.SticksRenderer
 
slabbyatom - Static variable in class org.jmol.script.T
 
slabByAtom - Variable in class org.jmol.viewer.GlobalSettings
 
slabbymolecule - Static variable in class org.jmol.script.T
 
slabByMolecule - Variable in class org.jmol.viewer.GlobalSettings
 
slabByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
 
slabByPixels(int) - Method in class org.jmol.viewer.Viewer
 
slabColix - Variable in class org.jmol.util.MeshSurface
 
slabData - Variable in class org.jmol.shapespecial.Draw
 
slabDepthByPercentagePoints(int) - Method in class org.jmol.viewer.TransformManager
 
slabDepthByPixels(int) - Method in class org.jmol.viewer.Viewer
 
slabDepthChanged() - Method in class org.jmol.viewer.TransformManager
 
slabenabled - Static variable in class org.jmol.script.T
 
slabEnabled - Variable in class org.jmol.viewer.TransformManager
 
slabInfo - Variable in class org.jmol.jvxl.data.JvxlData
 
slabInfo - Variable in class org.jmol.jvxl.readers.Parameters
 
slabInternal(P4, boolean) - Method in class org.jmol.viewer.TransformManager
 
slabIsosurface(Lst<Object[]>) - Method in class org.jmol.jvxl.readers.SurfaceReader
 
slabMeshType - Variable in class org.jmol.util.MeshSurface
 
slabOptions - Variable in class org.jmol.util.MeshSurface
 
slabPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
slabPlane - Variable in class org.jmol.viewer.TransformManager
 
slabPlaneOffset - Variable in class org.jmol.jvxl.readers.Parameters
 
slabPolygons(Object[]) - Method in class org.jmol.shapesurface.Isosurface
 
slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSlicer
 
slabPolygonsList(Lst<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
 
slabrange - Static variable in class org.jmol.script.T
 
slabRange - Variable in class org.jmol.viewer.TransformManager
 
slabReset() - Method in class org.jmol.viewer.TransformManager
 
slabToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
slabValue - Variable in class org.jmol.jvxl.data.JvxlData
 
slabValue - Variable in class org.jmol.viewer.TransformManager
 
slabZ - Variable in class org.jmol.export.___Exporter
 
slaterArray - Variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
SlaterData - Class in org.jmol.quantum
 
SlaterData(int, int, int, int, int, double, double) - Constructor for class org.jmol.quantum.SlaterData
 
SlaterReader - Class in org.jmol.adapter.readers.quantum
 
SlaterReader() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader
 
SlaterReader.OrbitalSorter - Class in org.jmol.adapter.readers.quantum
 
SlaterReader.SlaterSorter - Class in org.jmol.adapter.readers.quantum
 
slaters - Variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
slaters - Variable in class org.jmol.quantum.MOCalculation
 
SlaterSorter() - Constructor for class org.jmol.adapter.readers.quantum.SlaterReader.SlaterSorter
 
sleepTime - Variable in class org.jmol.thread.JmolThread
 
sLeft - Variable in class org.jmol.g3d.HermiteRenderer
 
slen - Variable in class org.jmol.script.ScriptParam
 
slen - Variable in class org.jmol.scriptext.CmdExt
 
Slice - Class in org.openscience.jmol.app.surfacetool
 
Slice() - Constructor for class org.openscience.jmol.app.surfacetool.Slice
 
slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
slice - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
slice_dynamic_grid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
slice_dynamic_grid_resolution - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
slice_grid - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
slice_height_map - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
slice_height_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
slice_track_camera - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sliceObject(String, int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
slicer - Variable in class org.jmol.util.MeshCapper
source of edges; consumer of triangles
slicer - Variable in class org.jmol.util.MeshSurface
 
slicer - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
slicerFrame - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
sliceSelected() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SLIDE_ZOOM_X_PERCENT - Static variable in class org.jmol.viewer.ActionManager
 
slider - Variable in class org.jmol.dialog.Dialog.QualityListener
 
Slider(float, float) - Constructor for class org.jmol.thread.MoveToThread.Slider
 
sliderPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SLIM - Static variable in class org.jmol.util.Shader
 
slm - Variable in class org.jmol.viewer.Viewer
 
slope - Variable in class org.jmol.g3d.LineRenderer
 
slopeKey - Variable in class org.jmol.g3d.LineRenderer
 
slow_idle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sm - Variable in class org.jmol.modelset.ModelSet
 
sm - Variable in class org.jmol.script.ScriptEval
 
sm - Variable in class org.jmol.scriptext.SmilesExt
 
sm - Variable in class org.jmol.viewer.Viewer
 
smallmoleculemaxatoms - Static variable in class org.jmol.script.T
 
smallMoleculeMaxAtoms - Variable in class org.jmol.viewer.GlobalSettings
 
smartaromatic - Static variable in class org.jmol.script.T
 
smartAromatic - Variable in class org.jmol.viewer.GlobalSettings
 
SmarterJmolAdapter - Class in org.jmol.adapter.smarter
 
SmarterJmolAdapter() - Constructor for class org.jmol.adapter.smarter.SmarterJmolAdapter
 
smartsAtoms - Variable in class org.jmol.smiles.SmilesSearch
 
smartsCode - Variable in class org.jmol.minimize.forcefield.AtomType
 
smiles - Static variable in class org.jmol.script.T
 
smiles2dimageformat - Static variable in class org.jmol.script.T
 
SmilesAromatic - Class in org.jmol.smiles
 
SmilesAromatic() - Constructor for class org.jmol.smiles.SmilesAromatic
 
SmilesAtom - Class in org.jmol.smiles
This class represents an atom in a SmilesMolecule.
SmilesAtom() - Constructor for class org.jmol.smiles.SmilesAtom
 
SmilesBond - Class in org.jmol.smiles
Bond in a SmilesMolecule
SmilesBond(SmilesAtom, SmilesAtom, int, boolean) - Constructor for class org.jmol.smiles.SmilesBond
SmilesBond constructor
smilesExt - Variable in class org.jmol.script.ScriptEval
 
SmilesExt - Class in org.jmol.scriptext
 
SmilesExt() - Constructor for class org.jmol.scriptext.SmilesExt
 
SmilesGenerator - Class in org.jmol.smiles
Double bond, allene, square planar and tetrahedral stereochemistry only not octahedral or trigonal bipyramidal.
SmilesGenerator() - Constructor for class org.jmol.smiles.SmilesGenerator
 
SmilesMatcher - Class in org.jmol.smiles
Originating author: Nicholas Vervelle A class to handle a variety of SMILES/SMARTS-related functions, including: -- determining if two SMILES strings are equivalent -- determining the molecular formula of a SMILES or SMARTS string -- searching for specific runs of atoms in a 3D model -- searching for specific runs of atoms in a SMILES description -- generating valid (though not canonical) SMILES and bioSMILES strings -- getting atom-atom correlation maps to be used with biomolecular alignment methods
SmilesMatcher() - Constructor for class org.jmol.smiles.SmilesMatcher
 
smilesMatcher - Variable in class org.jmol.viewer.Viewer
 
SmilesMatcherInterface - Interface in org.jmol.api
 
SmilesMeasure - Class in org.jmol.smiles
 
SmilesMeasure(SmilesSearch, int, int, float, float, boolean) - Constructor for class org.jmol.smiles.SmilesMeasure
 
SmilesParser - Class in org.jmol.smiles
Parses a SMILES String to create a SmilesMolecule.
SmilesParser(boolean) - Constructor for class org.jmol.smiles.SmilesParser
 
SmilesSearch - Class in org.jmol.smiles
-- was SmilesMolecule, but this now includes more data than that and the search itself so as to keep this thread safe
SmilesSearch() - Constructor for class org.jmol.smiles.SmilesSearch
 
smilesurlformat - Static variable in class org.jmol.script.T
 
smilesUrlFormat - Variable in class org.jmol.viewer.GlobalSettings
 
smooth_color_triangle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
smooth_half_bonds - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
smoothingPower - Variable in class org.jmol.jvxl.readers.AtomPropertyMapper
 
snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
 
snapshotAnaglyphChannelBytes() - Method in class org.jmol.util.GData
 
Snn - Static variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
solid - Static variable in class org.jmol.script.T
 
solvent - Static variable in class org.jmol.script.T
 
solvent_gridMax - Variable in class org.jmol.jvxl.readers.Parameters
 
solvent_ptsPerAngstrom - Variable in class org.jmol.jvxl.readers.Parameters
 
solvent_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
solventAccessible - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
solventDistance(float, float, float, float, float, float) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
solventExtendedAtomRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
solventOn - Variable in class org.jmol.viewer.GlobalSettings
 
solventprobe - Static variable in class org.jmol.script.T
 
solventproberadius - Static variable in class org.jmol.script.T
 
solventProbeRadius - Variable in class org.jmol.viewer.GlobalSettings
 
solventRadius - Variable in class org.jmol.jvxl.readers.Parameters
 
someModelsAreModulated - Variable in class org.jmol.modelset.ModelLoader
 
someModelsHaveAromaticBonds - Variable in class org.jmol.modelset.ModelSet
 
someModelsHaveFractionalCoordinates - Variable in class org.jmol.modelset.ModelSet
 
someModelsHaveSymmetry - Variable in class org.jmol.modelset.ModelSet
 
someModelsHaveUnitcells - Variable in class org.jmol.modelset.ModelLoader
 
sort(int) - Method in class org.jmol.bspt.Leaf
 
sort - Static variable in class org.jmol.g3d.Graphics3D
 
Sort(int) - Constructor for class org.jmol.script.SV.Sort
 
sort - Static variable in class org.jmol.script.T
 
sort(MeshCapper.CapVertex[]) - Method in class org.jmol.util.MeshCapper.CapVertex
Generate qnext links based on scanning Y large to Y small and if Y1==Y2, then X small to large
sortAndNormalize() - Method in class org.jmol.util.Tensor
The expression: |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso| simply sorts the values from largest to smallest or smallest to largest, depending upon the direction of the asymmetry, always setting the last value to be the farthest from the mean.
sortInorganic(Node, Lst<Edge>) - Method in class org.jmol.smiles.SmilesGenerator
We must sort the bond vector such that a diaxial pair is first and last.
sortIso - Variable in class org.jmol.util.Tensor
 
sortMOs() - Method in class org.jmol.adapter.readers.quantum.MoldenReader
 
sortOop(int[]) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
sortOrbitalCoefficients(int[]) - Method in class org.jmol.adapter.readers.quantum.SlaterReader
sorts coefficients by atomic number for speed later
sortOrbitals() - Method in class org.jmol.adapter.readers.quantum.SlaterReader
sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
sortOrReverse(int) - Method in class org.jmol.script.SV
 
SortSet() - Constructor for class org.jmol.jvxl.data.MeshData.SortSet
 
source - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
sourceIndices - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
sourcePNGJ - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
sources - Variable in class org.jmol.util.MeshSlicer
 
sp - Variable in class org.jmol.bspt.CubeIterator
 
SP - Static variable in class org.jmol.quantum.QS
 
SP_LIST - Static variable in class org.jmol.adapter.readers.quantum.GenNBOReader
 
spacebeforesquare - Static variable in class org.jmol.script.T
 
spacefill - Static variable in class org.jmol.script.T
 
spacegroup - Static variable in class org.jmol.script.T
 
SpaceGroup - Class in org.jmol.symmetry
 
SpaceGroup(String, boolean) - Constructor for class org.jmol.symmetry.SpaceGroup
 
spaceGroup - Variable in class org.jmol.symmetry.Symmetry
 
spaceGroupName - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
span() - Method in class org.jmol.util.Tensor
width of the signal; |e2 - e0|
spanningVectors - Variable in class org.jmol.jvxl.data.VolumeData
 
spanningVectors - Variable in class org.jmol.util.MeshSurface
 
spardirCache - Variable in class org.jmol.io.JmolBinary
 
spardirPut(String, byte[]) - Method in class org.jmol.io.JmolBinary
 
SpartanArchive - Class in org.jmol.adapter.readers.quantum
 
SpartanArchive(BasisFunctionReader, String, String) - Constructor for class org.jmol.adapter.readers.quantum.SpartanArchive
 
spartanArchive - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
spartanBinaryContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
spartanContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
spartanFileList(GenericZipTools, String, String) - Method in interface org.jmol.api.JmolZipUtilities
 
spartanFileList(String, String) - Method in class org.jmol.io.JmolBinary
 
spartanFileList(GenericZipTools, String, String) - Method in class org.jmol.io.JmolUtil
Special loading for file directories.
SpartanInputReader - Class in org.jmol.adapter.readers.quantum
 
SpartanInputReader() - Constructor for class org.jmol.adapter.readers.quantum.SpartanInputReader
 
SpartanReader - Class in org.jmol.adapter.readers.quantum
 
SpartanReader() - Constructor for class org.jmol.adapter.readers.quantum.SpartanReader
 
spartanSmolLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
SpartanSmolReader - Class in org.jmol.adapter.readers.quantum
 
SpartanSmolReader() - Constructor for class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
spec_alternate - Static variable in class org.jmol.script.T
 
spec_atom - Static variable in class org.jmol.script.T
 
spec_chain - Static variable in class org.jmol.script.T
 
spec_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
spec_direct - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
spec_direct_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
spec_model - Static variable in class org.jmol.script.T
 
spec_model2 - Static variable in class org.jmol.script.T
 
spec_name_pattern - Static variable in class org.jmol.script.T
 
spec_power - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
spec_reflect - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
spec_resid - Static variable in class org.jmol.script.T
 
spec_seqcode - Static variable in class org.jmol.script.T
 
spec_seqcode_range - Static variable in class org.jmol.script.T
 
Special - Variable in class org.jmol.popup.JmolGenericPopup
 
SPECIAL_COLIX_MAX - Static variable in class org.jmol.util.C
 
specialAtomIndexes - Variable in class org.jmol.modelset.ModelLoader
 
specialAtomNames - Static variable in class org.jmol.modelset.Group
 
specialAtomNames - Static variable in class org.jmol.modelsetbio.Resolver
 
specialLabel - Variable in class org.jmol.shape.Hover
 
specialposition - Static variable in class org.jmol.script.T
 
specialTypes - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
specular - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
specular - Static variable in class org.jmol.script.T
 
specular_intensity - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
specularexponent - Static variable in class org.jmol.script.T
 
specularExponent - Variable in class org.jmol.util.Shader
 
specularFactor - Variable in class org.jmol.util.Shader
 
specularOn - Variable in class org.jmol.util.Shader
 
specularpercent - Static variable in class org.jmol.script.T
 
specularPercent - Variable in class org.jmol.util.Shader
 
specularpower - Static variable in class org.jmol.script.T
 
specularPower - Variable in class org.jmol.util.Shader
 
SPG - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
sphere - Static variable in class org.jmol.script.T
 
SPHERE - Static variable in class org.jmol.shapecgo.CGOMesh
 
sphere3d - Variable in class org.jmol.g3d.Graphics3D
 
sphere_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sphere_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sphere_point_max_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sphere_point_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sphere_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sphere_radiusAngstroms - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
sphere_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sphere_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sphere_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sphere_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sphereColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
sphereMatrix - Variable in class org.jmol.export.__CartesianExporter
 
sphereNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
SphereRenderer - Class in org.jmol.g3d
Implements high performance rendering of shaded spheres.
SphereRenderer(Graphics3D) - Constructor for class org.jmol.g3d.SphereRenderer
 
sphereScale - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
sphereShadeIndexes - Variable in class org.jmol.util.Shader
 
sphereShapeCache - Variable in class org.jmol.util.Shader
 
sphereTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
sphericalDValues - Static variable in class org.jmol.adapter.readers.quantum.MopacSlaterReader
 
spheroid_fill - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
spheroid_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
spheroid_smooth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
spin - Static variable in class org.jmol.script.T
 
SPIN_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
SPIN_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
SPIN_SAW_AX - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
SPIN_SAW_AY - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
SPIN_SAW_AZ - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
SPIN_SAW_C - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
SPIN_SAW_W - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
SPIN_SPEC_LABEL - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
spine - Static variable in class org.jmol.script.T
 
spinfps - Static variable in class org.jmol.script.T
 
spinFps - Variable in class org.jmol.viewer.TransformManager
 
spinIsGesture - Variable in class org.jmol.viewer.TransformManager
 
spinOn - Variable in class org.jmol.viewer.TransformManager
 
spinOn - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
SpinOnWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.SpinOnWidget
 
spinOp - Variable in class org.jmol.util.ModulationSet
 
SpinThread - Class in org.jmol.thread
 
SpinThread() - Constructor for class org.jmol.thread.SpinThread
 
spinThread - Variable in class org.jmol.viewer.TransformManager
 
spinx - Static variable in class org.jmol.script.T
 
spinX - Variable in class org.jmol.viewer.TransformManager
 
spinXYBy(int, int, float) - Method in class org.jmol.viewer.TransformManager
 
spinXYBy(int, int, float) - Method in class org.jmol.viewer.Viewer
 
spiny - Static variable in class org.jmol.script.T
 
spinY - Variable in class org.jmol.viewer.TransformManager
 
spinz - Static variable in class org.jmol.script.T
 
spinZ - Variable in class org.jmol.viewer.TransformManager
 
splash - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
Splash - Class in org.openscience.jmol.app.jmolpanel
 
Splash(Frame, ImageIcon) - Constructor for class org.openscience.jmol.app.jmolpanel.Splash
 
Splash.WindowListener - Class in org.openscience.jmol.app.jmolpanel
 
splashEnabled - Variable in class org.openscience.jmol.app.JmolApp
 
splashImage - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
SplashInterface - Interface in org.openscience.jmol.app
 
split(String, int) - Static method in class org.jmol.adapter.smarter.Resolver
 
split - Static variable in class org.jmol.script.T
 
splitCommandLine(String) - Static method in class org.jmol.console.GenericConsole
separate a command line into three sections: prefix....;cmd ........
sppm - Variable in class org.jmol.render.LabelsRenderer
 
sprintf(String, SV) - Static method in class org.jmol.script.SV
 
sprintf(String, SV, Object[], int[], float[], double[], boolean, boolean, boolean) - Static method in class org.jmol.script.SV
 
sptRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
sqrt - Static variable in class org.jmol.script.T
 
sqrt3_2 - Static variable in class org.jmol.modelset.AtomCollection
 
squareCount - Variable in class org.jmol.script.ScriptMathProcessor
 
squared - Static variable in class org.jmol.script.T
 
sr - Variable in class org.jmol.jvxl.data.VolumeData
 
sr - Variable in class org.jmol.jvxl.readers.AtomDataReader
solvent radius
sRight - Variable in class org.jmol.g3d.HermiteRenderer
 
ss_helix_phi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_helix_phi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_helix_phi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_helix_psi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_helix_psi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_helix_psi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_strand_phi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_strand_phi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_strand_phi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_strand_psi_exclude - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_strand_psi_include - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ss_strand_psi_target - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
ssbond - Static variable in class org.jmol.script.T
 
ssbondsBackbone - Variable in class org.jmol.render.SticksRenderer
 
ssbondsbackbone - Static variable in class org.jmol.script.T
 
ssbondsBackbone - Variable in class org.jmol.viewer.GlobalSettings
 
SSet(BS) - Constructor for class org.jmol.jvxl.data.MeshData.SSet
 
ssMapAtom - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
ssMapSeq - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
st - Variable in class org.jmol.script.ScriptParam
 
st - Variable in class org.jmol.scriptext.CmdExt
 
stack - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
stack - Variable in class org.jmol.bspt.CubeIterator
 
STAND_ALONE - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
STANDARD_LABEL - Static variable in class org.jmol.modelset.LabelToken
 
standardGroupList - Static variable in class org.jmol.modelset.Group
 
standardLevel - Static variable in class org.jmol.util.Geodesic
3 levels, 0 through 3
standardVector - Variable in class org.jmol.renderspecial.VectorsRenderer
 
star - Static variable in class org.jmol.script.T
 
Stars - Class in org.jmol.shape
 
Stars() - Constructor for class org.jmol.shape.Stars
 
StarsRenderer - Class in org.jmol.render
 
StarsRenderer() - Constructor for class org.jmol.render.StarsRenderer
 
START - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
start(Viewer) - Method in interface org.jmol.api.JmolAppConsoleInterface
 
start(Viewer) - Method in class org.jmol.console.AppletConsole
 
start(Viewer) - Method in class org.jmol.consolejs.AppletConsole
 
start() - Method in class org.jmol.thread.JmolThread
 
start - Variable in class org.jmol.thread.MoveToThread.Slider
 
start() - Method in class org.openscience.jmol.app.InputScannerThread
 
start(Viewer) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
start() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
startByteArrayReaderThread() - Method in class org.openscience.jmol.app.jmolpanel.LoopedStreams
 
startChainID - Variable in class org.jmol.adapter.smarter.Structure
 
startChainStr - Variable in class org.jmol.adapter.smarter.Structure
 
startCommandWatcher(boolean) - Method in interface org.jmol.api.JmolScriptManager
 
startCommandWatcher(boolean) - Method in class org.jmol.script.ScriptManager
 
startConsoleReaderThread(InputStream) - Method in class org.openscience.jmol.app.jmolpanel.console.ConsoleTextArea
 
startCoord - Variable in class org.jmol.shapespecial.Dipoles
 
startDocument() - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
startedByCommandThread - Variable in class org.jmol.script.ScriptQueueThread
 
startElement(String, String, String, Attributes) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
startGestureServer() - Method in interface org.jmol.api.JmolGestureServerInterface
 
startHoverWatcher(boolean) - Method in class org.jmol.appletjs.Jmol
 
startHoverWatcher(boolean) - Method in class org.jmol.viewer.ActionManager
 
startHoverWatcher(boolean) - Method in class org.jmol.viewer.Viewer
 
startIndexPending - Variable in class org.jmol.renderbio.RocketRenderer
 
startInsertionCode - Variable in class org.jmol.adapter.smarter.Structure
 
startJmol(JmolApp) - Static method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
startMinimization() - Method in interface org.jmol.api.MinimizerInterface
 
startMinimization() - Method in class org.jmol.minimize.Minimizer
 
startPaintClock() - Method in class org.jmol.applet.Jmol
 
startPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
startRecording() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
startScriptQueue(boolean) - Method in class org.jmol.script.ScriptManager
 
startSequenceNumber - Variable in class org.jmol.adapter.smarter.Structure
 
startServerService() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
startService(int, JsonNioClient, Viewer, String, int) - Method in interface org.openscience.jmol.app.jsonkiosk.JsonNioServer
 
startService(int, JsonNioClient, Viewer, String, int) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
startSimulator(Object) - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
startSparshUIService(boolean) - Method in class org.jmol.multitouch.ActionManagerMT
 
startSpinningAxis(T3, T3, boolean) - Method in class org.jmol.viewer.Viewer
 
startTime - Variable in class org.jmol.applet.AppletWrapper
 
startTime - Variable in class org.jmol.thread.JmolThread
 
startTimer(String) - Static method in class org.jmol.util.Logger
 
startupDimension - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
startupHeight - Variable in class org.openscience.jmol.app.JmolApp
 
startupHeight - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
startupWidth - Variable in class org.openscience.jmol.app.JmolApp
 
startupWidth - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
startViewer(JmolViewer, SplashInterface, boolean) - Method in class org.openscience.jmol.app.JmolApp
 
starwidth - Static variable in class org.jmol.script.T
 
starWidth - Variable in class org.jmol.viewer.GlobalSettings
 
state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
state - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
the current state
state - Variable in class org.jmol.jvxl.readers.Parameters
 
state - Static variable in class org.jmol.script.T
 
state_counter_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
STATE_DATA_COLORED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_DATA_READ - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_INITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_UNINITIALIZED - Static variable in class org.jmol.jvxl.readers.Parameters
 
STATE_VERSION_STAMP - Static variable in class org.jmol.viewer.JC
 
stateButton - Variable in class org.jmol.console.GenericConsole
 
stateButton - Variable in class org.jmol.console.ScriptEditor
 
StateButton - Variable in class org.openscience.jmol.app.webexport.Test
 
stateChanged(ChangeEvent) - Method in class org.jmol.dialog.Dialog.QualityListener
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
stateChanged(ChangeEvent) - Method in class org.openscience.jmol.app.webexport.PopInJmol
 
stateCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
stateCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
StateCreator - Class in org.jmol.viewer
StateCreator handles all aspects of working with the "state" as generally defined, including -- creating the state script -- general output, including logging -- handling undo/redo -- processing SYNC directives Called by reflection only; all state generation script here, for modularization in JavaScript
StateCreator() - Constructor for class org.jmol.viewer.StateCreator
 
StateManager - Class in org.jmol.viewer
 
StateManager(Viewer) - Constructor for class org.jmol.viewer.StateManager
 
statement - Variable in class org.jmol.script.ScriptContext
 
statementAsString(Viewer, T[], int, boolean) - Static method in class org.jmol.script.ScriptEval
 
statementLength - Variable in class org.jmol.script.ScriptContext
 
StateScript - Class in org.jmol.modelset
 
StateScript(int, String, BS, BS, BS, String, boolean) - Constructor for class org.jmol.modelset.StateScript
 
stateScripts - Variable in class org.jmol.modelset.ModelSet
 
stateScriptVersionInt - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
stateScriptVersionInt - Variable in class org.jmol.viewer.Viewer
 
stateSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
static_singletons - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
staticFunctions - Static variable in class org.jmol.viewer.Viewer
 
staticGetAtomSetCollection(AtomSetCollectionReader) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
 
staticGetAtomSetCollectionReader(String, String, Object, Map<String, Object>) - Static method in class org.jmol.adapter.smarter.SmarterJmolAdapter
The primary file or string reader -- returns just the reader now
stats() - Method in class org.jmol.bspt.Bspf
 
stats() - Method in class org.jmol.bspt.Bspt
prints some simple stats to stdout
status - Variable in class org.jmol.thread.TimeoutThread
 
status - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
status - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
status - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
status - Variable in class org.openscience.jmol.app.jmolpanel.StatusBar
 
StatusBar - Class in org.openscience.jmol.app.jmolpanel
 
StatusBar() - Constructor for class org.openscience.jmol.app.jmolpanel.StatusBar
 
statusForm - Variable in class org.jmol.util.GenericApplet
 
statusList - Variable in class org.jmol.viewer.StatusManager
 
statusListener - Variable in class org.jmol.awt.FileDropper
 
StatusListener - Class in org.openscience.jmol.app.jmolpanel
 
StatusListener(JmolPanel, DisplayPanel) - Constructor for class org.openscience.jmol.app.jmolpanel.StatusListener
 
StatusManager - Class in org.jmol.viewer
The StatusManager class handles all details of status reporting, including: 1) saving the message in a queue that replaces the "callback" mechanism, 2) sending messages off to the console, and 3) delivering messages back to the main Jmol.java class in app or applet to handle differences in capabilities, including true callbacks.
StatusManager(Viewer) - Constructor for class org.jmol.viewer.StatusManager
 
statusPtr - Variable in class org.jmol.viewer.StatusManager
 
statusreporting - Static variable in class org.jmol.script.T
 
statusReporting - Variable in class org.jmol.viewer.GlobalSettings
 
STATUSSIZE - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
 
statusText - Variable in class org.jmol.util.GenericApplet
 
statusText - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel.SetStatusAction
 
statusTextarea - Variable in class org.jmol.util.GenericApplet
 
statusTop - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
STD_ORIENTATION_ATOMIC_NUMBER_OFFSET - Static variable in class org.jmol.adapter.readers.quantum.GaussianReader
Word index of atomic number in line with atom coordinates in an orientation block.
stddev - Static variable in class org.jmol.script.T
 
stdinchi - Static variable in class org.jmol.script.T
 
stdinchikey - Static variable in class org.jmol.script.T
 
steepestDescentInitialize(int, double) - Method in class org.jmol.minimize.forcefield.ForceField
 
steepestDescentTakeNSteps(int) - Method in class org.jmol.minimize.forcefield.ForceField
 
step - Static variable in class org.jmol.script.T
 
stepAxisCoordinates() - Method in class org.jmol.render.SticksRenderer
 
stepBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
stepButton - Variable in class org.jmol.console.ScriptEditor
 
stepButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
stepMax - Variable in class org.jmol.minimize.forcefield.ForceField
 
stepMinimization() - Method in interface org.jmol.api.MinimizerInterface
 
stepMinimization() - Method in class org.jmol.minimize.Minimizer
 
stepNumber - Variable in class org.jmol.adapter.readers.quantum.GaussianReader
 
stepPausedExecution() - Method in interface org.jmol.api.JmolScriptEvaluator
 
stepPausedExecution() - Method in class org.jmol.script.ScriptEval
 
steps - Variable in class org.jmol.jvxl.readers.Parameters
 
steps - Variable in class org.jmol.minimize.Minimizer
 
STER - Enum in org.jmol.c
 
STER(String, boolean) - Constructor for enum org.jmol.c.STER
 
stereo - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stereo - Static variable in class org.jmol.script.T
 
stereo() - Method in class org.jmol.scriptext.CmdExt
 
stereo_angle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stereo_double_pump_mono - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stereo_dynamic_strength - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stereo_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stereo_shift - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
STEREOCHEMISTRY_ALLENE - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_DEFAULT - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_OCTAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_SQUARE_PLANAR - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_TETRAHEDRAL - Static variable in class org.jmol.smiles.SmilesAtom
 
STEREOCHEMISTRY_TRIGONAL_BIPYRAMIDAL - Static variable in class org.jmol.smiles.SmilesAtom
 
stereoColors - Variable in class org.jmol.viewer.TransformManager
 
stereodegrees - Static variable in class org.jmol.script.T
 
stereoDegrees - Variable in class org.jmol.viewer.TransformManager
 
stereoFrame - Variable in class org.jmol.viewer.TransformManager
 
stereoMode - Variable in class org.jmol.viewer.TransformManager
 
stereoRadians - Variable in class org.jmol.viewer.TransformManager
 
stereoState - Variable in class org.jmol.viewer.GlobalSettings
 
stereoSync - Variable in class org.jmol.viewer.StatusManager
 
StereoViewWidget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.StereoViewWidget
 
stick_as_cylinders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_ball - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_ball_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_ball_ratio - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_fixed_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_good_geometry - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_h_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_nub - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_overlap - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_round_nub - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stick_valence_scale - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
Sticks - Class in org.jmol.shape
 
Sticks() - Constructor for class org.jmol.shape.Sticks
 
SticksRenderer - Class in org.jmol.render
 
SticksRenderer() - Constructor for class org.jmol.render.SticksRenderer
 
stickTranslucency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
stm - Variable in class org.jmol.viewer.Viewer
 
STO_EXP - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
STOP - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
stop - Static variable in class org.jmol.script.T
 
STOP - Static variable in class org.jmol.shapecgo.CGOMesh
 
stop_on_exceptions - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
stopMinimization(boolean) - Method in class org.jmol.minimize.Minimizer
 
stopMinimization() - Method in class org.jmol.viewer.Viewer
 
stopMotion() - Method in class org.jmol.viewer.TransformManager
 
stopPaintClock() - Method in class org.jmol.applet.Jmol
 
stopPaintClock() - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
stopped - Variable in class org.jmol.thread.JmolThread
 
stopScriptThreads() - Method in interface org.jmol.api.JmolScriptEvaluator
 
stopScriptThreads() - Method in class org.jmol.script.ScriptEval
 
stopThread(boolean) - Method in class org.jmol.viewer.AnimationManager
 
STR - Enum in org.jmol.c
 
STR(int, int) - Constructor for enum org.jmol.c.STR
 
STR_SG - Static variable in class org.jmol.symmetry.SpaceGroup
 
straightness - Variable in class org.jmol.modelsetbio.Monomer
 
straightness - Static variable in class org.jmol.script.T
 
STRAND_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
strandCount - Variable in class org.jmol.adapter.smarter.Structure
 
strandCount - Variable in class org.jmol.modelsetbio.ProteinStructure
 
strandCount - Variable in class org.jmol.renderbio.StrandsRenderer
 
strandcount - Static variable in class org.jmol.script.T
 
strandcountformeshribbon - Static variable in class org.jmol.script.T
 
strandCountForMeshRibbon - Variable in class org.jmol.viewer.GlobalSettings
 
strandcountforstrands - Static variable in class org.jmol.script.T
 
strandCountForStrands - Variable in class org.jmol.viewer.GlobalSettings
 
strands - Static variable in class org.jmol.script.T
 
Strands - Class in org.jmol.shapebio
 
Strands() - Constructor for class org.jmol.shapebio.Strands
 
strandSeparation - Variable in class org.jmol.renderbio.StrandsRenderer
 
StrandsRenderer - Class in org.jmol.renderbio
 
StrandsRenderer() - Constructor for class org.jmol.renderbio.StrandsRenderer
 
strAtomicNumbers - Variable in class org.jmol.adapter.readers.quantum.CsfReader
 
strCommand - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole.ExecuteCommandThread
 
strCoord(T3, boolean) - Static method in class org.jmol.symmetry.SymmetryDesc
 
strFormat - Variable in class org.jmol.modelset.Measurement
 
strFormat - Variable in class org.jmol.modelset.MeasurementData
 
strFormat - Variable in class org.jmol.shape.Measures
 
strFractionTemp - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
strID - Variable in class org.jmol.shapesurface.MolecularOrbital
 
string - Static variable in class org.jmol.script.T
 
stringAt(Lst<Object>, int) - Static method in class org.jmol.adapter.readers.pymol.PyMOLReader
 
stringClass - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
stringCount - Variable in class org.jmol.g3d.Graphics3D
 
stringParameter(int) - Method in class org.jmol.script.ScriptParam
 
stringParameter(int) - Method in class org.jmol.scriptext.CmdExt
 
stringParameterSet(int) - Method in class org.jmol.script.ScriptParam
 
strings - Variable in class org.jmol.g3d.Graphics3D
 
strings - Variable in class org.jmol.shape.Labels
 
stringSetting(int) - Method in class org.jmol.adapter.readers.pymol.PyMOLScene
 
stringsResourceBundle - Variable in class org.openscience.jmol.app.jmolpanel.JmolResourceHandler
 
StringtoScriptButton - Variable in class org.openscience.jmol.app.webexport.Test
 
stringWidth(Object, String) - Static method in class org.jmol.awt.AwtFont
 
stringWidth(Font, String) - Static method in class org.jmol.awtjs.JSFont
 
stringWidth(Font, Object, String) - Static method in class org.jmol.awtjs2d.JSFont
 
stringWidth(String) - Method in class org.jmol.modelset.Text
 
stripPath(String) - Static method in class org.jmol.viewer.FileManager
 
strJavaVendor - Static variable in class org.jmol.viewer.Viewer
 
strJavaVersion - Static variable in class org.jmol.viewer.Viewer
 
strListValue(T) - Static method in class org.jmol.script.SV
 
strMeasurement - Variable in class org.jmol.modelset.Measurement
 
strMenuStructure - Variable in class org.jmol.popup.GenericSwingPopup
 
strokeBasic - Variable in class org.jmol.awt.AwtG2D
 
strokeBold - Variable in class org.jmol.awt.AwtG2D
 
strop - Variable in class org.jmol.util.ModulationSet
 
strOSName - Static variable in class org.jmol.viewer.Viewer
 
strparam - Static variable in class org.jmol.script.T
 
strproperty - Static variable in class org.jmol.script.T
 
strSupercell - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
strucid - Static variable in class org.jmol.script.T
 
strucNo - Variable in class org.jmol.modelsetbio.ProteinStructure
 
strucno - Static variable in class org.jmol.script.T
 
STRUCT_ID - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
STRUCT_REF_G1 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
STRUCT_REF_G3 - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
structConfFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
structRefFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
structSheetRangeFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
structSiteFields - Static variable in class org.jmol.adapter.readers.cif.MMCifReader
 
structure() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
Structure - Class in org.jmol.adapter.smarter
 
Structure(int, STR, STR, String, int, int) - Constructor for class org.jmol.adapter.smarter.Structure
 
structure - Variable in class org.jmol.adapter.smarter.StructureIterator
 
structure - Variable in class org.jmol.popup.PopupResource
 
structure - Static variable in class org.jmol.script.T
 
structureContents - Static variable in class org.jmol.modelkit.ModelKitPopupResourceBundle
 
structureContents - Static variable in class org.jmol.popup.MainPopupResourceBundle
 
structureCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
structureCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
structureCount - Variable in class org.jmol.adapter.smarter.StructureIterator
 
structureID - Variable in class org.jmol.adapter.smarter.Structure
 
structureID - Variable in class org.jmol.modelsetbio.ProteinStructure
 
StructureIterator - Class in org.jmol.adapter.smarter
 
StructureIterator(AtomSetCollection) - Constructor for class org.jmol.adapter.smarter.StructureIterator
 
structureList - Variable in class org.jmol.modelsetbio.AminoPolymer
 
structureList - Variable in class org.jmol.viewer.GlobalSettings
 
structures - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
structures - Variable in class org.jmol.adapter.smarter.StructureIterator
 
structuresDefinedInFile - Variable in class org.jmol.modelset.ModelLoader
 
structureTainted - Variable in class org.jmol.modelset.Model
 
structureType - Variable in class org.jmol.adapter.smarter.Structure
 
structureTypes - Variable in class org.jmol.renderbio.BioShapeRenderer
 
strutdefaultradius - Static variable in class org.jmol.script.T
 
strutDefaultRadius - Variable in class org.jmol.viewer.GlobalSettings
 
strutlengthmaximum - Static variable in class org.jmol.script.T
 
strutLengthMaximum - Variable in class org.jmol.viewer.GlobalSettings
 
strutPoint(int, int, int) - Static method in class org.jmol.modelsetbio.AlphaPolymer
 
struts - Static variable in class org.jmol.script.T
 
struts() - Method in class org.jmol.scriptext.CmdExt
 
strutsmultiple - Static variable in class org.jmol.script.T
 
strutsMultiple - Variable in class org.jmol.viewer.GlobalSettings
 
strutspacing - Static variable in class org.jmol.script.T
 
strutSpacing - Variable in class org.jmol.viewer.GlobalSettings
 
stub - Variable in class org.jmol.console.JmolConsole.FileChecker
 
sType - Variable in class org.jmol.minimize.MinAtom
 
sub(double[], double[], V3d) - Static method in class org.jmol.minimize.Util
 
sub - Static variable in class org.jmol.script.T
 
subsearch(SmilesSearch, boolean, boolean) - Method in class org.jmol.smiles.SmilesSearch
 
subSearches - Variable in class org.jmol.smiles.SmilesSearch
 
subset - Static variable in class org.jmol.script.T
 
substructure - Static variable in class org.jmol.script.T
 
substructureType - Variable in class org.jmol.adapter.smarter.Structure
 
SUBSYS_ID - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
Subsystem - Class in org.jmol.adapter.readers.cif
 
Subsystem(MSRdr, String, Matrix) - Constructor for class org.jmol.adapter.readers.cif.Subsystem
 
subsystem - Static variable in class org.jmol.script.T
 
subsystemCode - Variable in class org.jmol.symmetry.SymmetryOperation
 
subtype - Variable in class org.jmol.modelsetbio.ProteinStructure
 
sum - Variable in class org.jmol.quantum.MOCalculation
 
sum - Static variable in class org.jmol.script.T
 
sum2 - Static variable in class org.jmol.script.T
 
sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shape.Mesh
 
sumVertexNormals(T3[], V3[]) - Method in class org.jmol.shapesurface.IsosurfaceMesh
 
sumVertexNormals2(Mesh, T3[], V3[]) - Static method in class org.jmol.shape.Mesh
 
supercell - Static variable in class org.jmol.script.T
 
supercellSymmetry - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
supportedRecordTypes - Static variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
suppress_hidden - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface - Static variable in class org.jmol.script.T
 
SURFACE_ATOMICORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
 
surface_best - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_carve_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_carve_normal_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_carve_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_carve_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_cavity_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_cavity_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_cavity_radius - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_circumscribe - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_clear_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_clear_selection - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_clear_state - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_color_smoothing - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_color_smoothing_threshold - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_debug - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SURFACE_DISTANCE_FOR_CALCULATION - Static variable in class org.jmol.shapespecial.Dots
 
SURFACE_ELLIPSOID2 - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_ELLIPSOID3 - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_FUNCTIONXY - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_FUNCTIONXYZ - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_GEODESIC - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_INTERSECT - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_LCAOCARTOON - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_LOBE - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_LONEPAIR - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_MEP - Static variable in class org.jmol.jvxl.readers.Parameters
 
surface_miserable - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SURFACE_MLP - Static variable in class org.jmol.jvxl.readers.Parameters
 
surface_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SURFACE_MOLECULAR - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_MOLECULARORBITAL - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_NCI - Static variable in class org.jmol.jvxl.readers.Parameters
 
surface_negative_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_negative_visible - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SURFACE_NOMAP - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_NONE - Static variable in class org.jmol.jvxl.readers.Parameters
 
surface_normal - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_optimize_subsets - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_poor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SURFACE_PROPERTY - Static variable in class org.jmol.jvxl.readers.Parameters
 
surface_proximity - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_quality - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SURFACE_RADICAL - Static variable in class org.jmol.jvxl.readers.Parameters
 
surface_ramp_above_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_residue_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SURFACE_SASURFACE - Static variable in class org.jmol.jvxl.readers.Parameters
 
surface_solvent - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SURFACE_SOLVENT - Static variable in class org.jmol.jvxl.readers.Parameters
 
SURFACE_SPHERE - Static variable in class org.jmol.jvxl.readers.Parameters
 
surface_trim_cutoff - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_trim_factor - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_type - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surface_use_shader - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
surfaceColor - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
surfaceDataCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
surfacedistance - Static variable in class org.jmol.script.T
 
surfaceDistance100s - Variable in class org.jmol.modelset.AtomCollection
 
surfaceDistanceMax - Variable in class org.jmol.modelset.AtomCollection
 
surfaceDone - Variable in class org.jmol.jvxl.readers.IsoShapeReader
 
SurfaceFileReader - Class in org.jmol.jvxl.readers
PolygonFileReader or VolumeFileReader
SurfaceFileReader() - Constructor for class org.jmol.jvxl.readers.SurfaceFileReader
 
SurfaceGenerator - Class in org.jmol.jvxl.readers
 
SurfaceGenerator(AtomDataServer, MeshDataServer, MeshData, JvxlData) - Constructor for class org.jmol.jvxl.readers.SurfaceGenerator
 
surfaceInfoName - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
surfaceList - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SurfaceListCellRenderer() - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI.SurfaceListCellRenderer
 
surfaceMode - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
surfaceName - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
surfaceNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
surfacePoints - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
surfaceReader - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
surfaceReader - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
SurfaceReader - Class in org.jmol.jvxl.readers
 
SurfaceReader() - Constructor for class org.jmol.jvxl.readers.SurfaceReader
 
surfaces - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
surfaceScrollPane - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
surfaceSet - Variable in class org.jmol.util.MeshSurface
 
surfacesOnly - Variable in class org.jmol.export._ObjExporter
Flag to cause only surfaces to be output.
SurfaceStatus - Class in org.openscience.jmol.app.surfacetool
Class that holds the surface status information that the surface tool needs.
SurfaceStatus(Mesh, int) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
surfaceTool - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SurfaceTool - Class in org.openscience.jmol.app.surfacetool
 
SurfaceTool(JmolViewer, HistoryFile, String, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceTool
 
SURFACETOOL_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
surfaceToolAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SurfaceToolAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.SurfaceToolAction
 
surfaceToolActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
SurfaceToolGUI - Class in org.openscience.jmol.app.surfacetool
GUI for the Jmol surfaceTool
SurfaceToolGUI(JmolViewer, HistoryFile, String, SurfaceTool) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
Builds and opens a GUI to control slicing.
SurfaceToolGUI(LayoutManager) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SurfaceToolGUI(boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SurfaceToolGUI(LayoutManager, boolean) - Constructor for class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
SurfaceToolGUI.SurfaceListCellRenderer - Class in org.openscience.jmol.app.surfacetool
 
surfaceType - Variable in class org.jmol.jvxl.readers.Parameters
 
suspend_undo - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
suspend_undo_atom_count - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
suspend_updates - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
SV - Class in org.jmol.script
ScriptVariable class
SV() - Constructor for class org.jmol.script.SV
 
SV.Sort - Class in org.jmol.script
 
sVal - Variable in class org.jmol.minimize.forcefield.FFParam
 
sValue(T) - Static method in class org.jmol.script.SV
 
sValueArray(SB, SV, String, String, boolean, boolean, boolean, int, boolean) - Static method in class org.jmol.script.SV
 
swap(int[], int, int) - Static method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
swap_dsn6_bytes - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
swapXZ() - Method in class org.jmol.jvxl.readers.VolumeFileReader
 
sweep_angle - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sweep_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sweep_phase - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
sweep_speed - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
swipeCount - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
swipeCutoff - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
swipeDelayMs - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
swipeFactor - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
swipeStartTime - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
switchAtoms() - Method in class org.jmol.smiles.SmilesBond
 
switchAtoms() - Method in class org.jmol.util.ContactPair
 
switchcmd - Static variable in class org.jmol.script.T
 
sX - Variable in class org.jmol.util.Point3fi
screen X
sY - Variable in class org.jmol.util.Point3fi
screen Y
sym - Variable in class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
SYM - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
SYM - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
SYM_EQ_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_MAGN_CENTERING - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_MAGN_REV - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_MAGN_REV_PRELIM - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_MAGN_SSG_ALG - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_MAGN_SSG_CENT_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_MAGN_SSG_CENTERING - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_MAGN_SSG_REV - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_MAGN_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_SSG_ALG - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_SSG_EQ_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
SYM_XYZ - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
symbol - Static variable in class org.jmol.script.T
 
symbolicMap - Variable in class org.jmol.adapter.readers.simple.InputReader
 
symLine - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
symMatrix - Variable in class org.jmol.util.Tensor
 
symmetries - Variable in class org.jmol.adapter.readers.quantum.GamessUKReader
 
symmetry - Variable in class org.jmol.adapter.readers.cif.MSRdr
 
symmetry - Variable in class org.jmol.adapter.readers.cif.Subsystem
 
SYMMETRY - Static variable in class org.jmol.adapter.readers.xml.XmlCmlReader
state constants
symmetry() - Method in class org.jmol.adapter.readers.xtal.JanaReader
 
symmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
symmetry - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
symmetry - Static variable in class org.jmol.script.T
 
Symmetry - Class in org.jmol.symmetry
 
Symmetry() - Constructor for class org.jmol.symmetry.Symmetry
 
symmetry - Variable in class org.jmol.util.ModulationSet
 
symmetryAddAtoms(int, int, int, int, int, int, P3[], MSInterface) - Method in class org.jmol.adapter.smarter.XtalSymmetry
 
SymmetryData(int, String) - Constructor for class org.jmol.adapter.readers.quantum.AdfReader.SymmetryData
 
SymmetryDesc - Class in org.jmol.symmetry
A class to handle requests for information; removed from coresym.js because it is not often used
SymmetryDesc() - Constructor for class org.jmol.symmetry.SymmetryDesc
 
symmetryInfo - Variable in class org.jmol.symmetry.Symmetry
 
SymmetryInfo - Class in org.jmol.symmetry
 
SymmetryInfo() - Constructor for class org.jmol.symmetry.SymmetryInfo
 
SymmetryInterface - Interface in org.jmol.api
 
SymmetryOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
SymmetryOperation - Class in org.jmol.symmetry
 
SymmetryOperation(SymmetryOperation, P3[], int, int, boolean) - Constructor for class org.jmol.symmetry.SymmetryOperation
 
symmetryOperations - Variable in class org.jmol.symmetry.SymmetryInfo
 
symmetryOperationsFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
symmetryRange - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
symmetryRange - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
symop - Static variable in class org.jmol.script.T
 
symopColixes - Variable in class org.jmol.shape.Mesh
 
symopNormixes - Variable in class org.jmol.shape.Mesh
 
symops - Variable in class org.jmol.adapter.readers.cif.CifReader
 
symops - Variable in class org.jmol.shape.Mesh
 
symTemp - Variable in class org.jmol.modelset.ModelSet
 
sync - Static variable in class org.jmol.script.T
 
SYNC_DISABLE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_DRIVER - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_ENABLE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
 
SYNC_NO_GRAPHICS_MESSAGE - Static variable in class org.jmol.viewer.Viewer
 
SYNC_OFF - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_SLAVE - Static variable in class org.jmol.viewer.StatusManager
 
SYNC_STEREO - Static variable in class org.jmol.viewer.StatusManager
 
syncDisabled - Variable in class org.jmol.viewer.StatusManager
 
syncDone() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
syncId - Variable in class org.jmol.util.GenericApplet
 
syncId - Variable in class org.jmol.viewer.Viewer
 
syncingMouse - Variable in class org.jmol.viewer.StatusManager
 
syncingScripts - Variable in class org.jmol.viewer.StatusManager
 
syncLists() - Method in class org.openscience.jmol.app.webexport.WebPanel
 
syncmouse - Static variable in class org.jmol.script.T
 
syncScript(String) - Method in interface org.jmol.api.JmolSyncInterface
 
syncScript(String, String, int) - Method in class org.jmol.api.JmolViewer
 
syncscript - Static variable in class org.jmol.script.T
 
syncScript(String) - Method in class org.jmol.util.GenericApplet
 
syncScript(String, String, int) - Method in class org.jmol.viewer.JmolStateCreator
 
syncScript(String, String, int) - Method in class org.jmol.viewer.StateCreator
 
syncScript(String, String, int) - Method in class org.jmol.viewer.Viewer
 
syncScript(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
syncScript(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
syncScript(String) - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
syncSend(String, String, int) - Method in class org.jmol.viewer.StatusManager
 
syncToJmol(String) - Method in interface org.jmol.api.JSVInterface
 
syncToJmol(String) - Method in class org.openscience.jmol.app.jmolpanel.StatusListener
 
sZ - Variable in class org.jmol.util.Point3fi
screen Z

T

T - Class in org.jmol.script
Script token class.
T() - Constructor for class org.jmol.script.T
 
t(int) - Static method in class org.jmol.script.T
 
T1 - Variable in class org.jmol.g3d.HermiteRenderer
 
T2 - Variable in class org.jmol.g3d.HermiteRenderer
 
tabPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
tabSwitched() - Method in class org.openscience.jmol.app.jmolpanel.NBODialog
 
tags - Static variable in class org.jmol.adapter.readers.xtal.GulpReader
 
tags - Static variable in class org.jmol.quantum.QS
 
tags2 - Static variable in class org.jmol.quantum.QS
 
TAINT_ATOMNAME - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_ATOMNO - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_ATOMTYPE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_BONDINGRADIUS - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_COORD - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_ELEMENT - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_FORMALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_HYDROPHOBICITY - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_MAX - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_OCCUPANCY - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_PARTIALCHARGE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_SEQID - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_TEMPERATURE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VALENCE - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VANDERWAALS - Static variable in class org.jmol.modelset.AtomCollection
 
TAINT_VIBRATION - Static variable in class org.jmol.modelset.AtomCollection
 
taintAtom(int, byte) - Method in class org.jmol.modelset.AtomCollection
 
taintAtoms(BS, byte) - Method in class org.jmol.modelset.AtomCollection
 
tainted - Variable in class org.jmol.modelset.AtomCollection
 
tainted - Variable in class org.jmol.modelset.Measurement
 
target - Variable in class org.jmol.modelset.Object2d
 
targetTime - Variable in class org.jmol.thread.JmolThread
 
taskNumber - Variable in class org.jmol.adapter.readers.quantum.NWChemReader
The number of the task begin interpreted.
tau - Variable in class org.jmol.util.ModulationSet
 
TBI_AB - Static variable in class org.jmol.minimize.forcefield.ForceField
 
TBI_BC - Static variable in class org.jmol.minimize.forcefield.ForceField
 
TBI_CD - Static variable in class org.jmol.minimize.forcefield.ForceField
 
tButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
TEAL - Static variable in class org.jmol.util.C
 
temp - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
temp - Variable in class org.jmol.viewer.StateCreator
 
temp2 - Variable in class org.jmol.viewer.StateCreator
 
temp3 - Variable in class org.jmol.viewer.StateCreator
 
TempArray - Class in org.jmol.util
 
TempArray() - Constructor for class org.jmol.util.TempArray
 
tempArray - Variable in class org.jmol.viewer.Viewer
 
tempC - Variable in class org.jmol.export.___Exporter
 
tempDataXml - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
tempDipole - Variable in class org.jmol.shapespecial.Dipoles
 
temperature - Static variable in class org.jmol.script.T
 
TemperatureOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
templateAtomCount - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
tempP1 - Variable in class org.jmol.export.___Exporter
 
tempP2 - Variable in class org.jmol.export.___Exporter
 
tempP3 - Variable in class org.jmol.export.___Exporter
 
tempQ1 - Variable in class org.jmol.export._VrmlExporter
 
tempQ2 - Variable in class org.jmol.export._VrmlExporter
 
tempStatement - Variable in class org.jmol.script.ScriptExpr
 
tempV1 - Variable in class org.jmol.export.___Exporter
 
tempV2 - Variable in class org.jmol.export.___Exporter
 
tempXY - Variable in class org.jmol.render.HoverRenderer
 
tEndcapOpen - Variable in class org.jmol.g3d.CylinderRenderer
 
tensor - Static variable in class org.jmol.script.T
 
tensor - Variable in class org.jmol.shapespecial.Ellipsoid
 
Tensor - Class in org.jmol.util
 
Tensor() - Constructor for class org.jmol.util.Tensor
Although this constructor is public, to be a valid tensor, one must invoke one of the "setFrom" methods.
tensors - Variable in class org.jmol.adapter.smarter.Atom
 
term - Variable in class org.jmol.export.UseTable
 
terminateAfterStep() - Method in class org.jmol.script.ScriptEval
 
terminatorMessage - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
test(MeshCapper.CapVertex[]) - Method in class org.jmol.util.MeshCapper
 
Test - Class in org.openscience.jmol.app.webexport
 
Test(Viewer) - Constructor for class org.openscience.jmol.app.webexport.Test
 
test1 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
test1 - Variable in class org.jmol.quantum.NciCalculation
 
test2 - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
testAsync - Variable in class org.jmol.viewer.Viewer
 
testflag1 - Static variable in class org.jmol.script.T
 
testFlag1 - Variable in class org.jmol.viewer.GlobalSettings
 
testflag2 - Static variable in class org.jmol.script.T
 
testFlag2 - Variable in class org.jmol.viewer.GlobalSettings
 
testflag3 - Static variable in class org.jmol.script.T
 
testFlag3 - Variable in class org.jmol.viewer.GlobalSettings
 
testflag4 - Static variable in class org.jmol.script.T
 
testFlag4 - Variable in class org.jmol.viewer.GlobalSettings
 
testFlags - Variable in class org.jmol.jvxl.readers.Parameters
 
testing - Variable in class org.jmol.quantum.MOCalculation
 
testing - Variable in class org.jmol.util.MeshCapper
for debugging
testLinear - Static variable in class org.jmol.jvxl.readers.IsoSolventReader
 
testRadiusAdjust - Variable in class org.jmol.renderspecial.DotsRenderer
 
tEvenDiameter - Variable in class org.jmol.g3d.CylinderRenderer
 
text - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
text - Variable in class org.jmol.awt.AwtClipboard
 
text - Variable in class org.jmol.g3d.TextString
 
text - Variable in class org.jmol.modelset.LabelToken
 
text - Variable in class org.jmol.modelset.Measurement
 
text - Variable in class org.jmol.modelset.MeasurementData
 
Text - Class in org.jmol.modelset
 
Text(Viewer) - Constructor for class org.jmol.modelset.Text
 
text - Variable in class org.jmol.modelset.Text
 
text - Variable in class org.jmol.shape.Hover
 
text - Variable in class org.jmol.shape.Labels
 
textAlign - Variable in class org.jmol.render.LabelsRenderer
 
textColor - Variable in class org.jmol.applet.AppletWrapper
 
TEXTCOLOR - Static variable in class org.openscience.jmol.app.jmolpanel.Splash
 
textHeight - Variable in class org.jmol.modelset.Text
 
textInfo - Variable in class org.jmol.symmetry.PointGroup
 
TextRenderer - Class in org.jmol.g3d
implementation for text rendering
TextRenderer(String, Font) - Constructor for class org.jmol.g3d.TextRenderer
 
TextRenderer - Class in org.jmol.render
 
TextRenderer() - Constructor for class org.jmol.render.TextRenderer
 
TextShape - Class in org.jmol.shape
 
TextShape() - Constructor for class org.jmol.shape.TextShape
 
TextString - Class in org.jmol.g3d
 
TextString() - Constructor for class org.jmol.g3d.TextString
 
textUnformatted - Variable in class org.jmol.modelset.Text
 
texture_fonts - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
textureCode - Variable in class org.jmol.export._TachyonExporter
 
textureFiles - Variable in class org.jmol.export._ObjExporter
List of texture files created.
textures - Variable in class org.jmol.export._ObjExporter
HashSet for textures.
textures - Variable in class org.jmol.export._TachyonExporter
 
textWidth - Variable in class org.jmol.modelset.Text
 
textY - Variable in class org.jmol.util.GData
 
textY - Variable in class org.openscience.jmol.app.jmolpanel.Splash
 
tFactorInv - Variable in class org.jmol.util.ModulationSet
 
tHemisphere - Variable in class org.jmol.bspt.CubeIterator
 
thePlane - Variable in class org.jmol.jvxl.data.VolumeData
 
thePlane - Variable in class org.jmol.jvxl.readers.Parameters
 
thePlane - Variable in class org.jmol.render.MeshRenderer
 
thePlaneNormalMag - Variable in class org.jmol.jvxl.data.VolumeData
 
theProperty - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
theProperty - Variable in class org.jmol.jvxl.readers.Parameters
 
THERMAL_TYPE - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
theta - Variable in class org.jmol.minimize.forcefield.Calculation
 
theta - Variable in class org.jmol.modelsetbio.Monomer
 
theta - Static variable in class org.jmol.script.T
 
theta0 - Variable in class org.jmol.minimize.MinAngle
 
theTok - Variable in class org.jmol.script.ScriptContext
 
theTok - Variable in class org.jmol.script.ScriptParam
 
theTok - Variable in class org.jmol.script.ScriptTokenParser
 
theToken - Variable in class org.jmol.script.ScriptContext
 
theToken - Variable in class org.jmol.script.ScriptParam
 
theToken - Variable in class org.jmol.script.ScriptTokenParser
 
theValue - Variable in class org.jmol.script.ScriptTokenParser
 
theWidgets - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
thickness - Variable in class org.openscience.jmol.app.surfacetool.Slice
 
thickness - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
thicknessMax - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
thicknessSlider - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
thisArgb - Variable in class org.jmol.shapespecial.Dots
 
thisAtom - Variable in class org.jmol.quantum.QuantumCalculation
 
thisAtom - Variable in class org.jmol.shapespecial.Dots
 
thisAtomSet - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
thisBiomolecule - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
thisBiomolecule - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
thisChain - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
thisCommand - Variable in class org.jmol.script.ScriptEval
 
thisContext - Variable in class org.jmol.script.ScriptParam
 
thisContour - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
thisContour - Variable in class org.jmol.jvxl.data.JvxlData
 
thisContour - Variable in class org.jmol.jvxl.readers.Parameters
 
thisDataSetName - Variable in class org.jmol.adapter.readers.cif.CifReader
 
thisFormula - Variable in class org.jmol.adapter.readers.cif.CifReader
 
thisFunction - Variable in class org.jmol.script.ScriptCompiler
 
thisID - Variable in class org.jmol.modelset.Measurement
 
thisID - Variable in class org.jmol.modelset.MeasurementData
 
thisID - Variable in class org.jmol.shape.Mesh
 
thisID - Variable in class org.jmol.shape.Object2dShape
 
thisID - Variable in class org.jmol.shapespecial.Dipole
 
thisInside - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
thisMesh - Variable in class org.jmol.shapespecial.Draw
 
thisMesh - Variable in class org.jmol.shapesurface.Isosurface
 
thismodel - Static variable in class org.jmol.script.T
 
thisModel - Variable in class org.jmol.shapesurface.MolecularOrbital
 
thisModelID - Variable in class org.jmol.jsv.JDXMOLParser
 
thisName - Variable in class org.jmol.util.ColorEncoder
 
thisPlane - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
thisPlaneB - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
thisPopup - Variable in class org.jmol.popup.GenericSwingPopup
 
thisRadius - Variable in class org.jmol.shapespecial.Dots
 
thisScale - Variable in class org.jmol.util.ColorEncoder
 
thisSection - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
thisSet - Variable in class org.jmol.jvxl.data.JvxlData
 
thisSet - Variable in class org.jmol.shapesurface.LcaoCartoon
 
thisState - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
thisStateModel - Variable in class org.jmol.modelset.ModelSet
 
thisStructuralFormula - Variable in class org.jmol.adapter.readers.cif.CifReader
 
thisSub - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
thisType - Variable in class org.jmol.dialog.Dialog.TypeFilter
 
thisType - Variable in class org.jmol.shapesurface.LcaoCartoon
 
thisX - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
thisx - Variable in class org.jmol.popup.GenericSwingPopup
 
thisy - Variable in class org.jmol.popup.GenericSwingPopup
 
thread - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
threadIndex - Static variable in class org.jmol.thread.JmolThread
 
threadSafe - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
throwcmd - Static variable in class org.jmol.script.T
 
tickEdges - Variable in class org.jmol.render.CageRenderer
 
TickerThread - Class in org.jmol.applet
 
TickerThread(Applet) - Constructor for class org.jmol.applet.TickerThread
 
tickInfo - Variable in class org.jmol.modelset.Measurement
 
tickInfo - Variable in class org.jmol.modelset.MeasurementData
 
TickInfo - Class in org.jmol.modelset
 
TickInfo(P3) - Constructor for class org.jmol.modelset.TickInfo
 
tickInfo - Variable in class org.jmol.render.FontLineShapeRenderer
 
tickInfo - Variable in class org.jmol.shape.Measures
 
tickInfos - Variable in class org.jmol.shape.FontLineShape
 
tickLabelFormats - Variable in class org.jmol.modelset.TickInfo
 
tickParamAsStr(int, boolean, boolean, boolean) - Method in class org.jmol.script.ScriptParam
 
ticks - Variable in class org.jmol.modelset.TickInfo
 
ticks - Static variable in class org.jmol.script.T
 
time - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
time - Variable in class org.jmol.viewer.MotionPoint
 
time - Variable in class org.jmol.viewer.MouseState
 
time0 - Variable in class org.jmol.viewer.Gesture
 
timeBegin - Variable in class org.jmol.applet.Jmol
 
timeBegin - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
timeBegin - Variable in class org.openscience.jvxl.MonitorInputStream
 
timeBeginExecution - Variable in class org.jmol.script.ScriptEval
 
timeCount - Variable in class org.jmol.applet.Jmol
 
timeCount - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
timeEndExecution - Variable in class org.jmol.script.ScriptEval
 
timeLast - Variable in class org.jmol.applet.Jmol
 
timeLast - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
timeout - Static variable in class org.jmol.script.T
 
timeouts - Variable in class org.jmol.viewer.Viewer
 
TimeoutThread - Class in org.jmol.thread
 
TimeoutThread(Viewer, String, int, String) - Constructor for class org.jmol.thread.TimeoutThread
 
timePerStep - Variable in class org.jmol.thread.MoveToThread
 
timeReversal - Variable in class org.jmol.symmetry.SymmetryOperation
 
times - Static variable in class org.jmol.script.T
 
TimeStamp_WebLink() - Static method in class org.openscience.jmol.app.webexport.WebExport
 
timestimes - Static variable in class org.jmol.script.T
 
timeTotal - Variable in class org.jmol.applet.Jmol
 
timeTotal - Static variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
TinkerReader - Class in org.jmol.adapter.readers.simple
simple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu
TinkerReader() - Constructor for class org.jmol.adapter.readers.simple.TinkerReader
 
title - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
title() - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
title - Variable in class org.jmol.adapter.readers.quantum.DgridReader
 
title - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
TITLE - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
title - Variable in class org.jmol.console.ScriptEditor
 
title - Variable in class org.jmol.jvxl.data.JvxlData
 
title - Variable in class org.jmol.jvxl.readers.Parameters
 
title - Static variable in class org.jmol.script.T
 
title - Variable in class org.jmol.shape.Mesh
 
title - Variable in class org.jmol.shape.MeshCollection
 
title - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel.OpenUrlAction
 
titleformat - Static variable in class org.jmol.script.T
 
titleRecords - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
titles - Variable in class org.jmol.adapter.readers.quantum.SpartanSmolReader
 
titleWidthMax - Variable in class org.jmol.popup.JmolGenericPopup
 
TLnn - Static variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
tlsAddError(String) - Method in class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
tlsAddError(String) - Method in class org.jmol.adapter.readers.pdb.PdbReader
 
tlsDataOnlyFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
TlsDataOnlyReader - Class in org.jmol.adapter.readers.more
 
TlsDataOnlyReader() - Constructor for class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
tlsGroupID - Variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
tlsGroupID - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
tlsU - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
tm - Variable in class org.jmol.export.___Exporter
 
tm - Variable in class org.jmol.navigate.Navigator
 
tm - Variable in class org.jmol.render.ShapeRenderer
 
tm - Variable in class org.jmol.renderbio.NucleicRenderer
 
tm - Variable in class org.jmol.renderbio.RocketRenderer
 
tm - Variable in class org.jmol.viewer.Viewer
 
tmap - Variable in class org.jmol.g3d.TextRenderer
 
tmp - Variable in class org.jmol.g3d.PixelatorShaded
 
to - Static variable in class org.jmol.script.T
 
toArray() - Method in class org.jmol.script.SV
 
toCanonical - Static variable in class org.jmol.util.BoxInfo
 
toCartesian(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
toCartesian(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
 
toCartesian(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
 
toCartesian(T3, boolean) - Method in class org.jmol.viewer.Viewer
absolute or relative to origin of UNITCELL {x y z}
toFloat(String) - Static method in class org.jmol.script.SV
 
toFractional(T3, boolean) - Method in interface org.jmol.api.SymmetryInterface
 
toFractional(T3, boolean) - Method in class org.jmol.symmetry.Symmetry
 
toFractional(T3, boolean) - Method in class org.jmol.util.SimpleUnitCell
 
toFractional(T3, boolean) - Method in class org.jmol.viewer.Viewer
absolute or relative to origin of UNITCELL {x y z}
toFractionalX(float) - Static method in class org.jmol.symmetry.UnitCell
 
toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
toFront() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
Brings the surfaceTool to the front and updates sliders, etc...
toFrontOrGotFocus() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
toggle(Measurement) - Method in class org.jmol.shape.Measures
 
toggleInPlace(BS, BS) - Static method in class org.jmol.util.BSUtil
a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.
togglelabel - Static variable in class org.jmol.script.T
 
toggleMeasurement() - Method in class org.jmol.viewer.ActionManager
 
toggleMode() - Method in interface org.jmol.api.JmolTouchSimulatorInterface
 
toggleOn(int[]) - Method in class org.jmol.shape.Measures
 
toIntARGB(int[]) - Static method in class org.jmol.awtjs2d.Image
 
toJSON() - Method in class org.jmol.java.BS
 
toJSON() - Method in class org.jmol.script.SV
 
tok - Variable in class org.jmol.modelset.LabelToken
 
tok - Variable in class org.jmol.script.ScriptFunction
 
tok - Variable in class org.jmol.script.T
 
tokAction - Variable in class org.jmol.modelset.MeasurementData
 
tokAction - Variable in class org.jmol.shape.Measures
 
tokAt(int) - Method in class org.jmol.script.ScriptCompiler
 
tokAt(int) - Method in class org.jmol.script.ScriptParam
 
tokAt(int) - Method in class org.jmol.script.ScriptTokenParser
 
tokAt(int) - Method in class org.jmol.scriptext.CmdExt
 
tokAtArray(int, T[]) - Static method in class org.jmol.scriptext.CmdExt
 
tokAttr(int, int) - Static method in class org.jmol.script.T
 
tokAttrOr(int, int, int) - Static method in class org.jmol.script.T
 
tokCommand - Variable in class org.jmol.script.ScriptTokenParser
 
token - Variable in class org.jmol.script.ScriptContext
 
token - Variable in class org.jmol.script.ScriptFlowContext
 
TOKEN_AROMATIC - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
TOKEN_ELEMENT_ALLYLIC - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
TOKEN_ELEMENT_CHARGED - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
TOKEN_ELEMENT_CONNECTED - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
TOKEN_ELEMENT_ONLY - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
TOKEN_ELEMENT_SP - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
tokenAll - Static variable in class org.jmol.script.T
 
tokenAnd - Static variable in class org.jmol.script.T
 
tokenAndEquals - Variable in class org.jmol.script.ScriptTokenParser
 
tokenAndFALSE - Static variable in class org.jmol.script.T
 
tokenAndSpec - Static variable in class org.jmol.script.T
 
tokenArraySelector - Static variable in class org.jmol.script.T
 
tokenArraySquare - Static variable in class org.jmol.script.T
 
tokenAt(int) - Method in class org.jmol.script.ScriptCompiler
 
tokenAt(int, T[]) - Method in class org.jmol.scriptext.CmdExt
 
tokenAttr(T, int) - Static method in class org.jmol.script.ScriptTokenParser
 
tokenColon - Static variable in class org.jmol.script.T
 
tokenComma - Static variable in class org.jmol.script.T
 
tokenCommand - Variable in class org.jmol.script.ScriptTokenParser
 
tokenConnected - Static variable in class org.jmol.script.T
 
tokenCoordinateBegin - Static variable in class org.jmol.script.T
 
tokenCoordinateEnd - Static variable in class org.jmol.script.T
 
tokenCount - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
tokenDefineString - Static variable in class org.jmol.script.T
 
tokenDivide - Static variable in class org.jmol.script.T
 
tokenEquals - Static variable in class org.jmol.script.T
 
tokenExpressionBegin - Static variable in class org.jmol.script.T
 
tokenExpressionEnd - Static variable in class org.jmol.script.T
 
tokenIf - Static variable in class org.jmol.script.T
 
tokenize(String) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
Take the given string and chop it up into a series of strings on whitespace boundries.
tokenizeCastepCell() - Method in class org.jmol.adapter.readers.xtal.CastepReader
 
tokenizePlusPlus(int, boolean) - Method in class org.jmol.script.ScriptCompiler
 
tokenLeftParen - Static variable in class org.jmol.script.T
 
tokenMap - Static variable in class org.jmol.script.T
 
tokenMinus - Static variable in class org.jmol.script.T
 
tokenMul3 - Static variable in class org.jmol.script.T
 
tokenNext() - Method in class org.jmol.script.ScriptTokenParser
increments the pointer; does NOT set theToken or theValue
tokenNextTok(int) - Method in class org.jmol.script.ScriptTokenParser
 
tokenOff - Static variable in class org.jmol.script.T
 
tokenOn - Static variable in class org.jmol.script.T
 
tokenOpIf - Static variable in class org.jmol.script.T
 
tokenOr - Static variable in class org.jmol.script.T
 
tokenOrTRUE - Static variable in class org.jmol.script.T
 
tokenPlus - Static variable in class org.jmol.script.T
 
tokenRightBrace - Static variable in class org.jmol.script.T
 
tokenRightParen - Static variable in class org.jmol.script.T
 
tokens - Variable in class org.jmol.adapter.readers.simple.InputReader
 
tokens - Variable in class org.jmol.adapter.readers.xml.XmlCmlReader
 
tokens - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
tokens - Variable in class org.jmol.adapter.readers.xtal.CgdReader
 
tokens - Variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
tokens - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
 
tokens - Variable in class org.jmol.jvxl.readers.PmeshReader
 
tokenScript - Static variable in class org.jmol.script.T
 
tokenSet - Static variable in class org.jmol.script.T
 
tokenSetArray - Static variable in class org.jmol.script.T
 
tokenSetCmd - Static variable in class org.jmol.script.T
 
tokenSetProperty - Static variable in class org.jmol.script.T
 
tokenSetVar - Static variable in class org.jmol.script.T
 
tokenSpaceBeforeSquare - Static variable in class org.jmol.script.T
 
tokenSwitch - Static variable in class org.jmol.script.T
 
tokenTimes - Static variable in class org.jmol.script.T
 
tokenTypes - Static variable in class org.jmol.minimize.forcefield.ForceFieldUFF
 
tokInitialPlusPlus - Variable in class org.jmol.script.ScriptCompiler
 
tokLastMath - Variable in class org.jmol.script.ScriptCompiler
 
tokPeek() - Method in class org.jmol.script.ScriptTokenParser
 
tokPeekIs(int) - Method in class org.jmol.script.ScriptTokenParser
 
toolbar - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
toolbarButtonGroup - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
top - Static variable in class org.jmol.script.T
 
top - Variable in class org.jmol.smiles.SmilesSearch
 
toP3(double[]) - Method in class org.jmol.adapter.readers.cif.MSRdr
 
topAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
topButton - Variable in class org.jmol.console.ScriptEditor
 
topButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
topPanel - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
toRadians - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
toRadians - Static variable in class org.jmol.util.SimpleUnitCell
 
toReadable(String, Object) - Static method in class org.jmol.util.Escape
Used only for getProperty("readable",...)
torsion - Static variable in class org.jmol.script.T
 
torsionCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
torsionCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
torsionCount - Variable in class org.jmol.minimize.forcefield.Calculations
 
toString() - Method in class org.jmol.adapter.readers.cif.Subsystem
 
toString() - Method in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
toString() - Method in class org.jmol.atomdata.RadiusData
 
toString() - Method in class org.jmol.bspt.Leaf
 
toString() - Method in class org.jmol.bspt.Node
 
toString() - Method in class org.jmol.dssx.Bridge
 
toString() - Method in class org.jmol.g3d.TextString
 
toString() - Method in class org.jmol.java.BS
Returns a string representation of this bit set.
toString() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
toString() - Method in class org.jmol.jvxl.readers.IsoSolventReader.Face
 
toString() - Method in class org.jmol.minimize.MinAtom
 
toString() - Method in class org.jmol.minimize.MinObject
 
toString() - Method in class org.jmol.modelset.Atom
 
toString() - Method in class org.jmol.modelset.Bond
 
toString() - Method in class org.jmol.modelset.Group
 
toString() - Method in class org.jmol.modelset.StateScript
 
toString() - Method in class org.jmol.modelsetbio.BasePair
 
toString() - Method in class org.jmol.script.ScriptEval
 
toString() - Method in exception org.jmol.script.ScriptException
 
toString() - Method in class org.jmol.script.ScriptFlowContext
 
toString() - Method in class org.jmol.script.ScriptFunction
 
toString() - Method in class org.jmol.script.SV
 
toString() - Method in class org.jmol.script.T
 
toString() - Method in class org.jmol.smiles.SmilesAtom
 
toString() - Method in class org.jmol.smiles.SmilesBond
 
toString() - Method in class org.jmol.smiles.SmilesMeasure
 
toString() - Method in class org.jmol.smiles.SmilesSearch
 
toString() - Method in class org.jmol.symmetry.SymmetryOperation
 
toString() - Method in class org.jmol.thread.TimeoutThread
 
toString() - Method in class org.jmol.util.ContactPair
 
toString() - Method in class org.jmol.util.MeshCapper.CapVertex
 
toString() - Method in class org.jmol.util.Rgb16
 
toString() - Method in class org.jmol.util.Tensor
 
toString() - Method in class org.jmol.viewer.Gesture
 
toString() - Method in class org.jmol.viewer.MotionPoint
 
toString() - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser.AtomSet
 
toString() - Method in class org.openscience.jmol.app.jsonkiosk.JsonNioService.JSONObject
 
toString2() - Method in class org.jmol.script.T
 
toSupercell(P3) - Method in interface org.jmol.api.SymmetryInterface
 
toSupercell(P3) - Method in class org.jmol.symmetry.Symmetry
 
toSupercell(P3) - Method in class org.jmol.util.SimpleUnitCell
convenience return only after changing fpt
toTag(String) - Method in class org.jmol.jvxl.readers.XmlReader
 
totalAtomCount - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
totalSteps - Variable in class org.jmol.navigate.Navigator
 
totalSteps - Variable in class org.jmol.thread.MoveToThread
 
totE - Variable in class org.jmol.adapter.readers.xtal.DmolReader
 
totEne - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
totEnergy - Variable in class org.jmol.adapter.readers.xtal.EspressoReader
 
totEnergy - Variable in class org.jmol.adapter.readers.xtal.GulpReader
 
TOUCH_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
TOUCH_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
toUnitCell(P3, P3) - Method in interface org.jmol.api.SymmetryInterface
 
toUnitCell(P3, P3) - Method in class org.jmol.symmetry.Symmetry
 
toUnitCell(P3, P3) - Method in class org.jmol.symmetry.UnitCell
when offset is null,
toUnitCell(P3, P3) - Method in class org.jmol.viewer.Viewer
relative to origin without regard to UNITCELL {x y z}
toUnits(double, String) - Method in class org.jmol.minimize.forcefield.ForceField
 
toUserUnits(double) - Method in class org.jmol.minimize.forcefield.ForceField
 
toVector(boolean) - Method in class org.jmol.modelset.Measurement
 
toWebAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ToWebAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ToWebAction
 
toWebActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
tPending - Variable in class org.jmol.renderbio.RocketRenderer
 
tQuiet - Variable in class org.jmol.script.ScriptEval
 
trace - Static variable in class org.jmol.script.T
 
Trace - Class in org.jmol.shapebio
 
Trace() - Constructor for class org.jmol.shapebio.Trace
 
trace_atoms_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
tracealpha - Static variable in class org.jmol.script.T
 
traceAlpha - Variable in class org.jmol.viewer.GlobalSettings
 
TraceRenderer - Class in org.jmol.renderbio
 
TraceRenderer() - Constructor for class org.jmol.renderbio.TraceRenderer
 
traceX - Variable in class org.jmol.modelset.Measurement
 
traceY - Variable in class org.jmol.modelset.Measurement
 
trajectory - Static variable in class org.jmol.script.T
 
trajectoryBaseIndex - Variable in class org.jmol.modelset.Model
 
trajectoryNames - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
trajectoryPtr - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
trajectoryStep - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
trajectoryStepCount - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
trajectorySteps - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
trajectorySteps - Variable in class org.jmol.modelset.ModelSet
 
trajectoryUnitCells - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
trans - Variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
transferResource(File, String, File, String) - Method in class org.openscience.chimetojmol.ChimePanel
 
transform(V3, V3) - Method in interface org.jmol.api.VolumeDataInterface
 
transform(V3, V3) - Method in class org.jmol.jvxl.data.VolumeData
 
transform(short, Atom, Vibration, JmolModulationSet) - Method in class org.jmol.renderspecial.VectorsRenderer
 
transform - Static variable in class org.jmol.script.T
 
transformedVectors - Variable in class org.jmol.render.MeshRenderer
 
transformedVectors - Variable in class org.jmol.util.GData
 
TransformFields - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
transformManager - Variable in class org.jmol.thread.MoveToThread
 
transformManager - Variable in class org.jmol.thread.SpinThread
 
transformManager - Variable in class org.jmol.thread.VibrationThread
 
TransformManager - Class in org.jmol.viewer
 
TransformManager() - Constructor for class org.jmol.viewer.TransformManager
 
TransformManager4D - Class in org.jmol.viewer
 
TransformManager4D() - Constructor for class org.jmol.viewer.TransformManager4D
 
TRANSFORMMAT - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
transformPoints(int, T3[], P3i[]) - Method in class org.jmol.viewer.TransformManager
 
transformPt(T3) - Method in class org.jmol.viewer.TransformManager
CAUTION! returns a POINTER TO A TEMPORARY VARIABLE
transformPt2D(T3) - Method in class org.jmol.viewer.TransformManager
 
transformPt3f(T3, P3) - Method in class org.jmol.viewer.TransformManager
 
transformPtNoClip(P3, P3) - Method in class org.jmol.viewer.TransformManager
 
transformPtScr(T3, P3i) - Method in class org.jmol.viewer.TransformManager
 
transformPtVib(P3, Vibration) - Method in class org.jmol.viewer.TransformManager
 
transformVector(V3, V3) - Method in class org.jmol.viewer.TransformManager
 
translate(String) - Method in interface org.jmol.api.Translator
 
translate(String) - Method in class org.jmol.i18n.GT
used in custom menu translation only
translate - Static variable in class org.jmol.script.T
 
translate(char, float, char, BS) - Method in class org.jmol.viewer.Viewer
 
translate(String) - Static method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
translateScale(Object, double, double, double) - Method in interface org.jmol.api.GenericGraphics
 
translateScale(Object, double, double, double) - Method in class org.jmol.awt.AwtG2D
 
translateScale(Object, double, double, double) - Method in class org.jmol.awtjs2d.JsG2D
 
translateSelected - Static variable in class org.jmol.script.T
 
translateToPercent(char, float) - Method in class org.jmol.viewer.TransformManager
 
translateXYBy(int, int) - Method in class org.jmol.viewer.TransformManager
 
translateXYBy(int, int) - Method in class org.jmol.viewer.Viewer
 
translateZBy(int) - Method in class org.jmol.viewer.TransformManager
 
translation - Static variable in class org.jmol.script.T
 
translation - Variable in class org.jmol.symmetry.HallRotationTerm
 
translationCode - Variable in class org.jmol.symmetry.HallTranslation
 
translations - Static variable in class org.openscience.jmol.app.jmolpanel.GuiMap
 
translationString - Variable in class org.jmol.symmetry.HallRotationTerm
 
Translator - Interface in org.jmol.api
 
translucency - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
translucency - Static variable in class org.jmol.g3d.TextRenderer
 
translucency - Variable in class org.jmol.jvxl.data.JvxlData
 
translucency - Variable in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
translucencyFractionalFromColix(short) - Static method in class org.jmol.export.___Exporter
 
translucencyLog - Variable in class org.jmol.g3d.Graphics3D
 
translucencyMask - Variable in class org.jmol.g3d.Graphics3D
 
translucent - Static variable in class org.jmol.script.T
 
translucent - Variable in class org.jmol.viewer.GlobalSettings
 
TRANSLUCENT_MASK - Static variable in class org.jmol.util.C
 
TRANSLUCENT_SCREENED - Static variable in class org.jmol.util.C
 
TRANSLUCENT_SHIFT - Static variable in class org.jmol.util.C
 
translucentAllowed - Variable in class org.jmol.shape.Shape
 
translucentCoverOnly - Variable in class org.jmol.util.GData
 
translucentLevel - Variable in class org.jmol.shape.Shape
 
transparency - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
transparency - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
transparency - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
 
transparency_global_sort - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
transparency_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
transparency_picking_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
TRANSPARENT - Static variable in class org.jmol.util.C
 
transX - Variable in class org.jmol.thread.MoveToThread
 
transY - Variable in class org.jmol.thread.MoveToThread
 
tree - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
treeDepth - Variable in class org.jmol.bspt.Bspt
 
treeModel - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
triad(float, float, float) - Method in class org.jmol.export._TachyonExporter
 
triad(T3) - Method in class org.jmol.export._TachyonExporter
 
Triangle(int, int, int, int, int) - Constructor for class org.jmol.jvxl.calc.MarchingSquares.Triangle
 
triangle3d - Variable in class org.jmol.g3d.Graphics3D
 
triangle_max_passes - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
triangleCount - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
TriangleData - Class in org.jmol.util
 
TriangleData() - Constructor for class org.jmol.util.TriangleData
 
triangleFace - Variable in class org.jmol.export._IdtfExporter
 
triangleNum - Variable in class org.jmol.export._ObjExporter
Number for the next mesh of this type.
TriangleRenderer - Class in org.jmol.g3d
renders triangles
TriangleRenderer() - Constructor for class org.jmol.g3d.TriangleRenderer
 
triangles - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
triangles - Static variable in class org.jmol.script.T
 
triangleTable2 - Static variable in class org.jmol.util.TriangleData
 
triangulator - Variable in class org.jmol.modelset.ModelSet
 
Triangulator - Interface in org.jmol.util
 
TRICOLOR_TRIANGLE - Static variable in class org.jmol.shapecgo.CGOMesh
 
trigger(Map<String, Object>, String) - Static method in class org.jmol.thread.TimeoutThread
 
triggered - Variable in class org.jmol.thread.TimeoutThread
 
triggerTimeout(String) - Method in class org.jmol.viewer.Viewer
 
trim - Static variable in class org.jmol.script.T
 
trim_dots - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
trimAtomSet() - Method in class org.jmol.adapter.readers.cif.MSRdr
 
trimLine() - Method in class org.jmol.adapter.readers.xtal.MagresReader
All characters after hash ignored; lines are trimmed.
TRUE - Static variable in class org.jmol.viewer.SelectionManager
 
truncate0(SB, float) - Static method in class org.jmol.viewer.TransformManager
 
truncate2(SB, float) - Static method in class org.jmol.viewer.TransformManager
 
trycmd - Static variable in class org.jmol.script.T
 
tryPt - Variable in class org.jmol.script.ScriptContext
 
tryPt - Variable in class org.jmol.viewer.Viewer
 
tSort - Static variable in class org.jmol.util.Tensor
 
tsType - Variable in class org.jmol.adapter.readers.xtal.CastepReader
 
TUPLE - Static variable in class org.jmol.adapter.readers.pymol.PickleReader
 
tuples - Variable in class org.jmol.bspt.Leaf
 
Turn - Class in org.jmol.modelsetbio
 
Turn(AlphaPolymer, int, int) - Constructor for class org.jmol.modelsetbio.Turn
 
tv(int, int, Object) - Static method in class org.jmol.script.T
 
twelfths - Static variable in class org.jmol.symmetry.SymmetryOperation
 
twelfthsOf(float) - Static method in class org.jmol.symmetry.SymmetryOperation
 
twistedSheets - Variable in class org.jmol.modelsetbio.BioPolymer
 
twistedsheets - Static variable in class org.jmol.script.T
 
twistedSheets - Variable in class org.jmol.viewer.GlobalSettings
 
TWO_PI - Static variable in class org.jmol.minimize.forcefield.Calculations
 
TWO_POINT_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
two_sided_lighting - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
twoChar - Static variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
twoCharLabelTokenIds - Static variable in class org.jmol.modelset.LabelToken
 
twoCharLabelTokenParams - Static variable in class org.jmol.modelset.LabelToken
 
twodots - Static variable in class org.jmol.render.FontLineShapeRenderer
 
twoP2 - Static variable in class org.jmol.symmetry.UnitCell
 
twoPass - Variable in class org.jmol.g3d.Graphics3D
 
TWOPI - Static variable in class org.jmol.adapter.readers.xtal.CastepReader
 
TWOPI - Static variable in class org.jmol.util.Modulation
 
twoPI - Static variable in class org.jmol.util.Vibration
 
TwoPointGesture - Class in org.jmol.multitouch.sparshui
TWO_POINT_GESTURE This gesture requires two points of contact, but its type is not initially defined.
TwoPointGesture() - Constructor for class org.jmol.multitouch.sparshui.TwoPointGesture
 
Txt - Class in org.jmol.util
 
Txt() - Constructor for class org.jmol.util.Txt
 
type - Variable in class org.jmol.adapter.readers.more.JcampdxReader
 
type - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
type - Variable in enum org.jmol.c.VDW
 
type - Variable in class org.jmol.jvxl.readers.IsoMepReader
 
type - Variable in class org.jmol.jvxl.readers.Pmesh4Reader
 
type - Variable in class org.jmol.jvxl.readers.PmeshReader
 
type - Variable in class org.jmol.minimize.MinObject
 
type - Variable in class org.jmol.modelset.Measurement
 
type - Variable in class org.jmol.modelset.TickInfo
 
type - Variable in class org.jmol.modelsetbio.BioPolymer
 
type - Variable in class org.jmol.modelsetbio.ProteinStructure
 
type - Variable in class org.jmol.quantum.NciCalculation
 
type - Static variable in class org.jmol.script.T
 
type - Variable in class org.jmol.shapespecial.Dipole
 
type - Variable in class org.jmol.smiles.SmilesMeasure
 
type - Variable in class org.jmol.symmetry.PointGroup.Operation
 
type - Variable in class org.jmol.util.Modulation
 
type - Variable in class org.jmol.util.Tensor
 
type2 - Variable in enum org.jmol.c.VDW
 
TYPE_ADP - Static variable in class org.jmol.util.Tensor
 
TYPE_ALL - Static variable in class org.jmol.quantum.NciCalculation
 
TYPE_AMINO - Static variable in class org.jmol.modelsetbio.BioPolymer
 
TYPE_ANGLE - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_ANY - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_AROMATIC - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_ATROPISOMER_1 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_ATROPISOMER_2 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_BIO_PAIR - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_BIO_SEQUENCE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_BNDK - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_BOND - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_CARBOHYDRATE - Static variable in class org.jmol.modelsetbio.BioPolymer
 
TYPE_CHARGE - Static variable in class org.jmol.util.Tensor
 
TYPE_CHRG - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_DIFF - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_DIFF_PAIR - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_DIRECTIONAL_1 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_DIRECTIONAL_2 - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_DISP_FOURIER - Static variable in class org.jmol.util.Modulation
 
TYPE_DISP_LEGENDRE - Static variable in class org.jmol.util.Modulation
 
TYPE_DISP_SAWTOOTH - Static variable in class org.jmol.util.Modulation
 
TYPE_DOUBLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_EFG - Static variable in class org.jmol.util.Tensor
 
TYPE_FUNCTION - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_INTER - Static variable in class org.jmol.quantum.NciCalculation
 
TYPE_INTRA - Static variable in class org.jmol.quantum.NciCalculation
 
TYPE_ISC - Static variable in class org.jmol.util.Tensor
 
TYPE_ISO - Static variable in class org.jmol.util.Tensor
 
TYPE_LIGAND - Static variable in class org.jmol.quantum.NciCalculation
 
TYPE_MAX - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_MS - Static variable in class org.jmol.util.Tensor
 
TYPE_MULTIPLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_NOBONDING - Static variable in class org.jmol.modelsetbio.BioPolymer
 
TYPE_NONE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_NUCLEIC - Static variable in class org.jmol.modelsetbio.BioPolymer
 
TYPE_OCC_CRENEL - Static variable in class org.jmol.util.Modulation
 
TYPE_OCC_FOURIER - Static variable in class org.jmol.util.Modulation
 
TYPE_OOP - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_OTHER - Static variable in class org.jmol.util.Tensor
 
TYPE_PBCI - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_QUADRUPOLE - Static variable in class org.jmol.util.Tensor
 
TYPE_RING - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_SB - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_SBDEF - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_SINGLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_SPIN - Static variable in class org.jmol.util.Vibration
 
TYPE_SPIN_FOURIER - Static variable in class org.jmol.util.Modulation
 
TYPE_SPIN_SAWTOOTH - Static variable in class org.jmol.util.Modulation
 
TYPE_SUM - Static variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
TYPE_SYMBOL - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
TYPE_TLS_R - Static variable in class org.jmol.util.Tensor
 
TYPE_TLS_U - Static variable in class org.jmol.util.Tensor
 
TYPE_TORSION - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_TRIPLE - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_U_FOURIER - Static variable in class org.jmol.util.Modulation
 
TYPE_U_LEGENDRE - Static variable in class org.jmol.util.Modulation
 
TYPE_UNKNOWN - Static variable in class org.jmol.smiles.SmilesBond
 
TYPE_VDW - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPE_VIBRATION - Static variable in class org.jmol.util.Vibration
 
typeArray - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
 
typeData - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
typeFactor - Variable in class org.jmol.util.Tensor
 
TypeFilter(String) - Constructor for class org.jmol.dialog.Dialog.TypeFilter
 
typeName - Variable in class org.jmol.script.ScriptFunction
 
typeNames - Static variable in class org.jmol.symmetry.PointGroup
 
typeOf(int) - Method in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
typeOf(SV) - Static method in class org.jmol.script.ScriptMathProcessor
 
types - Static variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
TYPES - Static variable in class org.jmol.smiles.SmilesMeasure
 
typeSelected - Variable in class org.jmol.shapespecial.Ellipsoids
 

U

U_ISO_OR_EQUIV - Static variable in class org.jmol.adapter.readers.cif.CifReader
 
U_LIST - Static variable in class org.jmol.adapter.readers.cif.MSRdr
 
U_LIST - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
uABsM(String) - Static method in class org.jmol.util.Escape
 
Uccage - Class in org.jmol.shape
 
Uccage() - Constructor for class org.jmol.shape.Uccage
 
UccageRenderer - Class in org.jmol.render
 
UccageRenderer() - Constructor for class org.jmol.render.UccageRenderer
 
uccageTickEdges - Static variable in class org.jmol.util.BoxInfo
 
UFFAngleCalc - Class in org.jmol.minimize.forcefield
 
UFFAngleCalc() - Constructor for class org.jmol.minimize.forcefield.UFFAngleCalc
 
UFFDistanceCalc - Class in org.jmol.minimize.forcefield
 
UFFDistanceCalc() - Constructor for class org.jmol.minimize.forcefield.UFFDistanceCalc
 
UFFOOPCalc - Class in org.jmol.minimize.forcefield
 
UFFOOPCalc() - Constructor for class org.jmol.minimize.forcefield.UFFOOPCalc
 
UFFTorsionCalc - Class in org.jmol.minimize.forcefield
 
UFFTorsionCalc() - Constructor for class org.jmol.minimize.forcefield.UFFTorsionCalc
 
UFFVDWCalc - Class in org.jmol.minimize.forcefield
 
UFFVDWCalc() - Constructor for class org.jmol.minimize.forcefield.UFFVDWCalc
 
uguideAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
UguideAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.UguideAction
 
UhbdReader - Class in org.jmol.jvxl.readers
UHBD reader
UhbdReader() - Constructor for class org.jmol.jvxl.readers.UhbdReader
 
uicrcifContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
unaryMinus - Static variable in class org.jmol.script.T
 
unbind - Static variable in class org.jmol.script.T
 
unbindAction(String, String) - Method in class org.jmol.viewer.ActionManager
 
unbindAction(int, int) - Method in class org.jmol.viewer.binding.Binding
 
unBindAction(String, String) - Method in class org.jmol.viewer.Viewer
 
unbindJmolAction(int) - Method in class org.jmol.viewer.binding.Binding
 
unbindMouseAction(int) - Method in class org.jmol.viewer.binding.Binding
 
unbindName(int, String) - Method in class org.jmol.viewer.binding.Binding
 
unbindUserAction(String) - Method in class org.jmol.viewer.binding.Binding
 
UNBRACKETED_SET - Static variable in class org.jmol.smiles.SmilesAtom
 
unCentered - Variable in class org.jmol.symmetry.SymmetryOperation
 
undeleteAtom(int) - Method in class org.jmol.modelset.ModelLoader
called from org.jmol.modelsetbio.resolver when adding hydrogens.
undo - Variable in class org.jmol.console.ScriptEditor.EditorDocument
 
undo() - Method in class org.jmol.console.ScriptEditor.EditorDocument
 
undo - Static variable in class org.jmol.script.T
 
undoableEditHappened(UndoableEditEvent) - Method in class org.jmol.console.ScriptEditor.EditorDocument.MyUndoableEditListener
 
undoButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
undoClear() - Method in class org.jmol.viewer.Viewer
 
undoClear() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
undomove - Static variable in class org.jmol.script.T
 
undoMoveAction(int, int) - Method in class org.jmol.viewer.JmolStateCreator
 
undoMoveAction(int, int) - Method in class org.jmol.viewer.StateCreator
 
undoMoveAction(int, int) - Method in class org.jmol.viewer.Viewer
 
undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.JmolStateCreator
 
undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.StateCreator
 
undoMoveActionClear(int, int, boolean) - Method in class org.jmol.viewer.Viewer
 
undoPointer - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
undoRedo(boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
undoSave(boolean) - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
undoSaved - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
undoSetEnabled() - Method in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
undoStack - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
undoWorking - Variable in class org.jmol.viewer.StateCreator
 
unescape(String) - Static method in class org.jmol.java.BS
({ 1 2 3:5 }) or ({null}) or [{ 1 2 3:5 }]
unEscapeBitSetArray(BS) - Method in class org.jmol.script.SV
 
unEscapeBitSetArray(ArrayList<SV>, boolean) - Static method in class org.jmol.script.SV
 
unescapeMatrix(String) - Static method in class org.jmol.util.Escape
 
unescapePointOrBitsetAsVariable(Object) - Static method in class org.jmol.script.SV
 
unescapeStringArray(String) - Static method in class org.jmol.util.Escape
 
unescapeUnicode(String) - Static method in class org.jmol.util.Escape
 
uniqueAtomMap - Variable in class org.jmol.adapter.readers.quantum.PsiReader
 
uniqueAxis - Variable in class org.jmol.symmetry.SpaceGroup
 
uniqueID - Variable in class org.jmol.adapter.smarter.Bond
 
uniqueIDs - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
uniqueList - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
uniqueSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
uniqueSettings - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
unitAxisVectors - Static variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
unitAxisVectors - Static variable in class org.jmol.viewer.JC
 
unitBboxPoints - Static variable in class org.jmol.util.BoxInfo
 
unitcell - Variable in class org.jmol.render.UccageRenderer
 
unitcell - Static variable in class org.jmol.script.T
 
unitCell - Variable in class org.jmol.shape.Mesh
 
unitCell - Variable in class org.jmol.symmetry.Symmetry
 
UnitCell - Class in org.jmol.symmetry
a class private to the org.jmol.symmetry package to be accessed only through the SymmetryInterface API adds vertices and offsets orientation, and a variety of additional calculations that in principle could be put in SimpleUnitCell if desired, but for now are in this optional package.
UnitCell() - Constructor for class org.jmol.symmetry.UnitCell
 
unitcellcolor - Static variable in class org.jmol.script.T
 
unitCellData - Variable in class org.jmol.adapter.readers.xtal.DmolReader
 
unitCellData - Variable in class org.jmol.adapter.readers.xtal.SiestaReader
 
unitCellData - Variable in class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
unitCellData - Variable in class org.jmol.adapter.readers.xtal.XcrysdenReader
 
unitCellEquals(SymmetryInterface) - Method in interface org.jmol.api.SymmetryInterface
 
unitCellEquals(SymmetryInterface) - Method in class org.jmol.symmetry.Symmetry
 
unitCellMultiplier - Variable in class org.jmol.symmetry.UnitCell
 
unitCellOffset - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
unitCellOffset - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
unitCellOffsetFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
UnitcellOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
unitCells - Variable in class org.jmol.modelset.ModelSet
 
unitCellTranslations - Variable in class org.jmol.adapter.smarter.XtalSymmetry
 
unitCubePoints - Static variable in class org.jmol.util.BoxInfo
 
unitFactor - Variable in class org.jmol.quantum.QuantumCalculation
 
unitize(P3) - Method in interface org.jmol.api.SymmetryInterface
 
unitize(P3) - Method in class org.jmol.symmetry.Symmetry
 
unitize(P3) - Method in class org.jmol.symmetry.UnitCell
 
units - Variable in class org.jmol.minimize.Minimizer
 
units - Variable in class org.jmol.modelset.MeasurementData
 
UNITS_PI - Static variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
unitVectors - Static variable in class org.jmol.symmetry.UnitCell
 
unitVectorX - Variable in class org.jmol.modelsetbio.BioPolymer
 
unitVolumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
 
unitx - Static variable in class org.jmol.script.T
 
unitxyz - Static variable in class org.jmol.script.T
 
unity - Static variable in class org.jmol.script.T
 
unitz - Static variable in class org.jmol.script.T
 
UNKNOWN - Static variable in class org.jmol.viewer.SelectionManager
 
UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.util.C
 
unreportedProperties - Static variable in class org.jmol.viewer.GlobalSettings
 
unscaleToScreen(float, float) - Method in class org.jmol.viewer.TransformManager
 
UNSET - Static variable in class org.jmol.adapter.readers.xml.XmlArgusReader
 
unsetProperty(String) - Method in class org.jmol.viewer.Viewer
 
unsetUserVariable(String) - Method in class org.jmol.viewer.GlobalSettings
 
unsetVariables(Map<String, SV>, Lst<SV>) - Method in class org.jmol.script.ScriptFunction
 
unsetVoxelData() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
unsetVoxelData() - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
unsetVoxelData2() - Method in class org.jmol.jvxl.readers.AtomDataReader
 
unsupportedRecordTypes - Static variable in class org.jmol.adapter.readers.xtal.ShelxReader
 
untaint(int, byte) - Method in class org.jmol.modelset.AtomCollection
 
unTaintAtoms(BS, byte) - Method in class org.jmol.modelset.AtomCollection
 
untransformedPoint - Variable in class org.jmol.viewer.TransformManager
 
unTransformPoint(T3, T3) - Method in class org.jmol.viewer.TransformManager
 
untranslated - Variable in exception org.jmol.script.ScriptException
 
unused_boolean_def_true - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
uP(String) - Static method in class org.jmol.util.Escape
 
UP - Static variable in class org.jmol.viewer.binding.Binding
 
update(Graphics) - Method in class org.jmol.applet.AppletWrapper
 
update(Graphics) - Method in class org.jmol.applet.Jmol
 
update(Graphics, String) - Method in class org.jmol.applet.Jmol
 
update(Graphics) - Method in interface org.jmol.applet.WrappedApplet
 
update() - Method in class org.jmol.appletjs.Jmol
 
UPDATE_ALL - Static variable in class org.jmol.popup.JmolGenericPopup
 
UPDATE_CONFIG - Static variable in class org.jmol.popup.JmolGenericPopup
 
UPDATE_NEVER - Static variable in class org.jmol.popup.JmolGenericPopup
 
UPDATE_SHOW - Static variable in class org.jmol.popup.JmolGenericPopup
 
updateAboutSubmenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateAngleSliders() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
updateAtomXYZ() - Method in class org.jmol.minimize.Minimizer
 
updateButton(SC, String, String) - Method in class org.jmol.popup.GenericSwingPopup
 
updateCheckBoxesForShow() - Method in class org.jmol.popup.GenericSwingPopup
 
updateCommandLine() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
updateComponents() - Method in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
updateConfigurationComputedMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateCoordinates(M4, BS) - Method in class org.jmol.shapesurface.IsosurfaceMesh
bs will be null if this is a set from the new isosurface MOVE [mat4] command
updateElementsComputedMenu(BS) - Method in class org.jmol.popup.JmolGenericPopup
 
updateExisting(Mesh) - Method in class org.openscience.jmol.app.surfacetool.SurfaceStatus
 
updateFileMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateFileTypeDependentMenus() - Method in class org.jmol.popup.JmolGenericPopup
 
updateFRAMESbyModelComputedMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateGroup3List(SC, String) - Method in class org.jmol.popup.JmolGenericPopup
 
updateHeteroComputedMenu(Map<String, String>) - Method in class org.jmol.popup.JmolGenericPopup
 
updateInvalidatedVertices(BS) - Method in class org.jmol.jvxl.data.MeshData
 
updateJS() - Method in class org.jmol.viewer.Viewer
for JavaScript only
updateJSView(int, int) - Method in class org.jmol.viewer.Viewer
File has been loaded or model has been changed or atom picked.
updateLabels() - Method in class org.jmol.console.GenericConsole
 
updateLabels() - Method in class org.jmol.console.JmolConsole
 
updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.GuiMap
 
updateLabels() - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
updateLanguageSubmenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateLocations(TouchPoint) - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
updateMeasurementTableData() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
updateMeshInfo(Shape[], int) - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
updateMode - Variable in class org.jmol.popup.JmolGenericPopup
 
updateModel(int) - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
updateModelIDs(String, int, boolean) - Method in class org.jmol.adapter.readers.more.JcampdxReader
The first model set is allowed to be a single model and given no extension.
updateModelSetComputedMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateOffsetsForAlternativeLocations(Atom[], BS) - Method in class org.jmol.modelsetbio.Monomer
 
updateParameters() - Method in class org.jmol.multitouch.sparshui.TwoPointGesture
 
updatePDBComputedMenus() - Method in class org.jmol.popup.JmolGenericPopup
 
updatePositionSlider() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
updatePreview(Viewer, File) - Method in class org.jmol.dialog.FilePreview
Update preview
updateSceneComputedMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateScreen() - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog
Update screen informations
updateSelectMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateSignedAppletItems() - Method in class org.jmol.popup.GenericSwingPopup
 
updateSize(boolean) - Method in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
updateSlices() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
updateSpecialMenuItem(SC) - Method in class org.jmol.popup.JmolGenericPopup
 
updateSpectraMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateSurfaceData(String, float[], int, int, char) - Static method in class org.jmol.jvxl.data.JvxlData
 
updateSurfaceData() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
updateSurfaceInfo() - Method in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
updateSurfaceList() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
updateSurfMoComputedMenu(Map<String, Object>) - Method in class org.jmol.popup.JmolGenericPopup
 
updateSYMMETRYComputedMenus() - Method in class org.jmol.popup.JmolGenericPopup
 
updateSYMMETRYSelectComputedMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateSYMMETRYShowComputedMenu() - Method in class org.jmol.popup.JmolGenericPopup
 
updateTables() - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
updateThicknessSlider() - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
updateTriangles() - Method in class org.jmol.jvxl.readers.SurfaceReader
 
updateUI() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
updateVars() - Method in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
updateWindow(int, int) - Method in class org.jmol.viewer.Viewer
 
url - Static variable in class org.jmol.script.T
 
url - Variable in class org.openscience.jmol.app.jmolpanel.HelpDialog.PageLoader
 
urlEncode(String) - Method in class org.jmol.viewer.FileManager
 
urlPrefixPairs - Static variable in class org.jmol.awt.AwtFile
 
use_display_lists - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
USE_PALETTE - Static variable in class org.jmol.util.C
 
use_shaders - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
useAbsolute - Variable in class org.jmol.quantum.NciCalculation
 
useAltNames - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
useAppletJS - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
useAuthorChainID - Variable in class org.jmol.adapter.readers.cif.CifReader
 
useColix - Variable in class org.jmol.shape.Mesh
 
useColix - Variable in class org.jmol.shapecgo.CGO
 
useCommandThread - Variable in class org.jmol.viewer.Viewer
 
useCommandWatcherThread - Variable in class org.jmol.script.ScriptManager
 
useEmpiricalRules - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
useGUI - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
useLight - Variable in class org.jmol.util.Shader
 
useminimizationthread - Static variable in class org.jmol.script.T
 
useMinimizationThread - Variable in class org.jmol.viewer.GlobalSettings
 
useMinimizationThread() - Method in class org.jmol.viewer.Viewer
 
useMolecular - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
usenumberlocalization - Static variable in class org.jmol.script.T
 
useNumberLocalization - Variable in class org.jmol.viewer.GlobalSettings
 
useOriginStepsPoints - Variable in class org.jmol.jvxl.readers.VolumeDataReader
 
usePercent - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
usePhongExponent - Variable in class org.jmol.util.Shader
 
usePropertyForColorRange - Variable in class org.jmol.jvxl.readers.Parameters
 
user - Static variable in class org.jmol.script.T
 
USER - Static variable in class org.jmol.util.ColorEncoder
 
userAtomTypes - Variable in class org.jmol.adapter.readers.more.ForceFieldReader
 
usercolorscheme - Static variable in class org.jmol.script.T
 
userData - Variable in class org.jmol.adapter.readers.molxyz.V3000Rdr
 
userDatabases - Variable in class org.jmol.viewer.GlobalSettings
 
userDefinedVanDerWaalRadius - Variable in class org.jmol.modelset.Atom
 
userPropsFile - Variable in class org.openscience.jmol.app.JmolApp
 
userScale - Variable in class org.jmol.util.ColorEncoder
 
userSettableValues - Static variable in class org.jmol.modelset.AtomCollection
 
userVdwMars - Variable in class org.jmol.viewer.Viewer
 
userVdws - Variable in class org.jmol.viewer.Viewer
 
useScriptQueue - Variable in class org.jmol.viewer.GlobalSettings
 
useTable - Variable in class org.jmol.export._VrmlExporter
 
useTable - Variable in class org.jmol.export.JSExporter
 
UseTable - Class in org.jmol.export
 
UseTable(String) - Constructor for class org.jmol.export.UseTable
 
useThreads() - Method in class org.jmol.script.ScriptEval
 
useTimeout - Variable in class org.jmol.thread.JmolThread
 
useZoomLarge - Variable in class org.jmol.viewer.TransformManager
 
utens - Variable in class org.jmol.util.Modulation
 
Util - Class in org.jmol.minimize
 
Util() - Constructor for class org.jmol.minimize.Util
 

V

v - Variable in class org.jmol.console.JmolConsole.FileChecker
 
v - Variable in class org.jmol.jvxl.readers.IsoSolventReader.Edge
 
v - Variable in class org.jmol.smiles.SmilesSearch
 
v0 - Variable in class org.jmol.util.ModulationSet
 
v0Cart - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
v1 - Variable in class org.jmol.adapter.readers.simple.InputReader
 
v1 - Variable in class org.jmol.minimize.forcefield.Calculations
 
v1 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
v1 - Variable in class org.jmol.viewer.TransformManager4D
 
v2 - Variable in class org.jmol.adapter.readers.simple.InputReader
 
v2 - Variable in class org.jmol.minimize.forcefield.Calculations
 
v2 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
v3 - Variable in class org.jmol.minimize.forcefield.Calculations
 
v3 - Variable in class org.jmol.renderspecial.EllipsoidsRenderer
 
V3000Rdr - Class in org.jmol.adapter.readers.molxyz
A reader for Accelrys V3000 files.
V3000Rdr() - Constructor for class org.jmol.adapter.readers.molxyz.V3000Rdr
 
vA - Variable in class org.jmol.smiles.VTemp
 
vAB - Static variable in class org.jmol.g3d.HermiteRenderer
 
vAB - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
vAB - Variable in class org.jmol.modelsetbio.Resolver
 
vAB - Variable in class org.jmol.shape.Mesh
 
vAB - Variable in class org.jmol.shapespecial.Draw
 
vAB - Variable in class org.jmol.shapespecial.Polyhedra
 
vAB - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
vAC - Static variable in class org.jmol.g3d.HermiteRenderer
 
vAC - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
val - Variable in class org.jmol.minimize.forcefield.AtomType
 
val - Static variable in class org.jmol.script.T
 
valence - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
valence - Variable in class org.jmol.modelset.Atom
 
valence - Static variable in class org.jmol.script.T
 
valence - Variable in class org.jmol.smiles.SmilesAtom
 
valence_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
valence_size - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
validate(boolean) - Method in class org.jmol.shapespecial.Ellipsoid
 
VALIDATE - Static variable in class org.jmol.util.Geodesic
 
validate_object_names - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
validateAndAllocate(Chain, String, int, int, int, int[], Atom[]) - Static method in class org.jmol.modelsetbio.AminoMonomer
 
validateAndAllocate(Chain, String, int, int, int) - Static method in class org.jmol.modelsetbio.CarbohydrateMonomer
 
validateAndAllocate(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.NucleicMonomer
 
validateAndAllocateA(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.AlphaMonomer
 
validateAndAllocateP(Chain, String, int, int, int, int[]) - Static method in class org.jmol.modelsetbio.PhosphorusMonomer
 
validateBspf(boolean) - Method in class org.jmol.modelset.AtomCollection
 
validateBspfForModel(int, boolean) - Method in class org.jmol.modelset.AtomCollection
 
validateFace(int, int, int, IsoSolventReader.Edge, P3) - Method in class org.jmol.jvxl.readers.IsoSolventReader
 
validateModel(int, boolean) - Method in class org.jmol.bspt.Bspf
 
validatePolyhedronNew(Atom, int, P3[]) - Method in class org.jmol.shapespecial.Polyhedra
 
validation - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
validation - Static variable in class org.jmol.script.T
 
validSpheres - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
valign - Variable in class org.jmol.modelset.Object2d
 
VALIGN_BOTTOM - Static variable in class org.jmol.viewer.JC
 
VALIGN_MIDDLE - Static variable in class org.jmol.viewer.JC
 
VALIGN_TOP - Static variable in class org.jmol.viewer.JC
 
VALIGN_XY - Static variable in class org.jmol.viewer.JC
 
VALIGN_XYZ - Static variable in class org.jmol.viewer.JC
 
vAlignNames - Static variable in class org.jmol.viewer.JC
 
value - Variable in class org.jmol.atomdata.RadiusData
 
value - Variable in class org.jmol.jvxl.calc.MarchingSquares.ContourVertex
 
value - Variable in class org.jmol.modelset.Measurement
 
value - Variable in class org.jmol.script.T
 
value - Variable in class org.jmol.thread.MoveToThread.Slider
 
value - Variable in class org.jmol.util.Int2IntHashEntry
 
valueChanged(TreeSelectionEvent) - Method in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
valueChanged(ListSelectionEvent) - Method in class org.openscience.jmol.app.webexport.WebPanel
 
valueCount - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
valueExtended - Variable in class org.jmol.atomdata.RadiusData
 
valueFor(float, float, int) - Method in interface org.jmol.api.MepCalculationInterface
 
valueFor(float, float, int) - Method in class org.jmol.quantum.MepCalculation
 
valueMappedToBlue - Variable in class org.jmol.jvxl.data.JvxlData
 
valueMappedToBlue - Variable in class org.jmol.jvxl.readers.Parameters
 
valueMappedToRed - Variable in class org.jmol.jvxl.data.JvxlData
 
valueMappedToRed - Variable in class org.jmol.jvxl.readers.Parameters
 
valueMax - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
valueMin - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
valueMin - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
valueOf(String) - Static method in enum org.jmol.atomdata.RadiusData.EnumType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.CBK
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.FIL
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.HB
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.PAL
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.STER
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.STR
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.c.VDW
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.util.Edge.EnumBondOrder
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.viewer.Viewer.ACCESS
Returns the enum constant of this type with the specified name.
valuePeek() - Method in class org.jmol.script.ScriptTokenParser
 
valueRange - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
values() - Static method in enum org.jmol.atomdata.RadiusData.EnumType
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.jmol.atomdata.RadiusData
 
values() - Static method in enum org.jmol.c.CBK
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.FIL
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.HB
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.PAL
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.STER
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.STR
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.c.VDW
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.jmol.jvxl.readers.IsoFxyReader
 
values - Variable in class org.jmol.jvxl.readers.IsoIntersectReader
 
values() - Static method in enum org.jmol.modelsetbio.AlphaPolymer.Code
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.shapespecial.Draw.EnumDrawType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.util.Edge.EnumBondOrder
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.jmol.util.MeshSlicer
 
values() - Static method in enum org.jmol.viewer.Viewer.ACCESS
Returns an array containing the constants of this enum type, in the order they are declared.
vanderwaals - Static variable in class org.jmol.script.T
 
vanderwaalsMars - Static variable in class org.jmol.util.Elements
Default table of van der Waals Radii.
var - Variable in class org.jmol.script.ScriptFlowContext
 
var - Static variable in class org.jmol.script.T
 
varButton - Variable in class org.openscience.jmol.app.jmolpanel.console.AppConsole
 
varClip(String, String, int) - Static method in class org.jmol.viewer.StateManager
 
variable - Static variable in class org.jmol.script.T
 
variables - Variable in class org.jmol.script.ScriptFunction
 
variables - Static variable in class org.jmol.script.T
 
varray - Static variable in class org.jmol.script.T
 
vars - Variable in class org.jmol.script.ScriptContext
 
VaspChgcarReader - Class in org.jmol.adapter.readers.xtal
http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.
VaspChgcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspChgcarReader
 
VaspChgcarReader - Class in org.jmol.jvxl.readers
 
VaspChgcarReader() - Constructor for class org.jmol.jvxl.readers.VaspChgcarReader
 
vaspOutcarLineStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
VaspOutcarReader - Class in org.jmol.adapter.readers.xtal
http://cms.mpi.univie.ac.at/vasp/
VaspOutcarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspOutcarReader
 
VaspPoscarReader - Class in org.jmol.adapter.readers.xtal
http://cms.mpi.univie.ac.at/vasp/
VaspPoscarReader() - Constructor for class org.jmol.adapter.readers.xtal.VaspPoscarReader
 
vAtoms - Variable in class org.jmol.adapter.readers.simple.InputReader
 
vB - Variable in class org.jmol.smiles.VTemp
 
vBiomolecules - Variable in class org.jmol.adapter.readers.cif.MMCifReader
 
vBiomolecules - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
vBraces - Variable in class org.jmol.script.ScriptCompiler
 
vButton - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
vc - Variable in class org.jmol.util.MeshSurface
vertex count
vCompnds - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
vConnect - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
vContours - Variable in class org.jmol.jvxl.data.JvxlData
 
vCoords - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
vcs - Variable in class org.jmol.util.MeshSurface
vertex color index "colix" array
vd - Variable in class org.jmol.quantum.QuantumCalculation
 
vData - Variable in class org.jmol.shapespecial.Draw
 
vdc - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
vDist - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
VDW - Enum in org.jmol.c
 
VDW(int, String, String) - Constructor for enum org.jmol.c.VDW
 
vdw1 - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
vdwCalc - Variable in class org.jmol.minimize.forcefield.CalculationsMMFF
 
vdwCalc - Variable in class org.jmol.minimize.forcefield.CalculationsUFF
 
vdwKey - Variable in class org.jmol.minimize.MinAtom
 
vdwPercentSlider - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
VdwPROBE - Static variable in class org.jmol.util.Elements
 
vdws - Variable in class org.jmol.util.ContactPair
 
vdwType - Variable in class org.jmol.atomdata.RadiusData
 
vdwVolume - Variable in class org.jmol.util.ContactPair
 
vecs - Static variable in class org.jmol.adapter.readers.xtal.CgdReader
 
vector - Static variable in class org.jmol.script.T
 
vector - Variable in class org.jmol.shapespecial.Dipole
 
VECTOR - Static variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
String for prefix/resource identifier for the vector area.
vector12ths - Variable in class org.jmol.symmetry.HallInfo
 
vectorAB - Variable in class org.jmol.g3d.Graphics3D
 
vectorAC - Variable in class org.jmol.g3d.Graphics3D
 
vectorAngleRadians(V3d, V3d) - Static method in class org.jmol.minimize.Util
 
vectorCode - Variable in class org.jmol.symmetry.HallInfo
 
vectorNormal - Variable in class org.jmol.g3d.Graphics3D
 
vectorProjection - Variable in class org.jmol.modelsetbio.ProteinStructure
 
vectors - Variable in class org.jmol.jvxl.readers.MapFileReader
 
Vectors - Class in org.jmol.shapespecial
 
Vectors() - Constructor for class org.jmol.shapespecial.Vectors
 
vectorScale - Variable in class org.jmol.renderspecial.VectorsRenderer
 
vectorscale - Static variable in class org.jmol.script.T
 
vectorScale - Variable in class org.jmol.viewer.GlobalSettings
 
vectorsCentered - Variable in class org.jmol.renderspecial.VectorsRenderer
 
vectorscentered - Static variable in class org.jmol.script.T
 
vectorsCentered - Variable in class org.jmol.viewer.GlobalSettings
 
vectorShift12ths - Variable in class org.jmol.symmetry.HallTranslation
 
VectorsRenderer - Class in org.jmol.renderspecial
 
VectorsRenderer() - Constructor for class org.jmol.renderspecial.VectorsRenderer
 
vectorSymmetry - Variable in class org.jmol.renderspecial.VectorsRenderer
 
vectorsymmetry - Static variable in class org.jmol.script.T
 
vectorSymmetry - Variable in class org.jmol.viewer.GlobalSettings
 
vectorT - Variable in class org.jmol.render.FontLineShapeRenderer
 
vectorT - Variable in class org.jmol.viewer.TransformManager
 
vectorT2 - Variable in class org.jmol.render.FontLineShapeRenderer
 
vectorT2 - Variable in class org.jmol.viewer.TransformManager
 
vectorT3 - Variable in class org.jmol.render.FontLineShapeRenderer
 
vectorTemp - Variable in class org.jmol.viewer.TransformManager
 
vEdges - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
version - Variable in class org.jmol.jvxl.data.JvxlData
 
version - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
version - Static variable in class org.jmol.viewer.JC
 
version - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
VERSION - Static variable in class org.openscience.jvxl.Jvxl
 
version_date - Static variable in class org.jmol.viewer.Viewer
 
versionInt - Static variable in class org.jmol.viewer.JC
 
VERTEX - Static variable in class org.jmol.shapecgo.CGOMesh
 
VERTEX_POINT - Static variable in class org.jmol.jvxl.calc.MarchingSquares
 
vertexBase - Variable in class org.jmol.jvxl.readers.PmeshReader
 
vertexColorMap - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexColorMap - Variable in class org.jmol.shape.Mesh
 
vertexColors - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexCount - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexCount - Variable in class org.jmol.render.MeshRenderer
 
vertexCount0 - Variable in class org.jmol.util.MeshSurface
 
vertexCounts - Static variable in class org.jmol.util.Geodesic
 
vertexDataOnly - Variable in class org.jmol.jvxl.data.JvxlData
 
vertexDataOnly - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
VertexDataServer - Interface in org.jmol.jvxl.api
 
vertexIncrement - Variable in class org.jmol.jvxl.data.MeshData
 
vertexIncrement - Variable in class org.jmol.shapesurface.IsosurfaceMesh
 
vertexMap - Variable in class org.jmol.jvxl.readers.EfvetReader
 
vertexMap - Variable in class org.jmol.jvxl.readers.NffReader
 
vertexMap - Variable in class org.jmol.jvxl.readers.PmeshReader
 
vertexNext - Static variable in class org.jmol.util.Geodesic
 
vertexSets - Variable in class org.jmol.util.MeshSurface
 
vertexSource - Variable in class org.jmol.jvxl.readers.Parameters
 
vertexSource - Variable in class org.jmol.util.MeshSurface
 
vertexTest - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
vertexValues - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
vertexValues - Variable in class org.jmol.rendersurface.IsosurfaceRenderer
 
vertexVectors - Static variable in class org.jmol.util.Geodesic
 
vertexVectors - Static variable in class org.jmol.util.Normix
 
vertices - Variable in class org.jmol.render.MeshRenderer
 
vertices - Static variable in class org.jmol.script.T
 
vertices - Variable in class org.jmol.shapespecial.Polyhedron
 
vertices - Variable in class org.jmol.symmetry.UnitCell
 
vertices - Variable in class org.jmol.util.MeshCapper
 
verticesT - Variable in class org.jmol.render.UccageRenderer
 
verticesTransformed - Variable in class org.jmol.renderspecial.DotsRenderer
 
vF - Static variable in class org.jmol.script.SV
 
vf - Variable in class org.jmol.shape.Shape
shape visibility flag
vFaces - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
vFunctionStack - Variable in class org.jmol.script.ScriptCompiler
 
vH - Variable in class org.jmol.renderbio.RocketRenderer
 
vHBonds - Variable in class org.jmol.dssx.DSSP
 
vib - Variable in class org.jmol.adapter.smarter.Atom
 
vib - Variable in class org.jmol.util.ModulationSet
vib is a spin vector when the model has modulation; otherwise an unmodulated vibration.
VIB_ENERGY - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
vibFieldMap - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
vibFields - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
vibOnly - Variable in class org.jmol.adapter.readers.quantum.MoldenReader
 
vibration - Static variable in class org.jmol.script.T
 
Vibration - Class in org.jmol.util
A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.
Vibration() - Constructor for class org.jmol.util.Vibration
 
VIBRATION_VECTOR_FLAG - Static variable in class org.jmol.modelset.Atom
 
vibrationNumber - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
vibrationOn - Variable in class org.jmol.renderspecial.VectorsRenderer
 
vibrationOn - Variable in class org.jmol.viewer.TransformManager
 
VibrationOnly - Variable in class org.jmol.popup.JmolGenericPopup
 
vibrationperiod - Static variable in class org.jmol.script.T
 
vibrationPeriod - Variable in class org.jmol.viewer.GlobalSettings
 
vibrationPeriod - Variable in class org.jmol.viewer.TransformManager
 
vibrationPeriodMs - Variable in class org.jmol.viewer.TransformManager
 
vibrations - Variable in class org.jmol.modelset.AtomCollection
 
vibrationscale - Static variable in class org.jmol.script.T
 
vibrationScale - Variable in class org.jmol.viewer.GlobalSettings
 
vibrationScale - Variable in class org.jmol.viewer.TransformManager
 
vibrationSteps - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
vibrationSteps - Variable in class org.jmol.modelset.ModelSet
 
vibrationT - Variable in class org.jmol.viewer.TransformManager
 
VibrationThread - Class in org.jmol.thread
 
VibrationThread() - Constructor for class org.jmol.thread.VibrationThread
 
vibrationThread - Variable in class org.jmol.viewer.TransformManager
 
vibs - Variable in class org.jmol.renderspecial.PolyhedraRenderer
 
vibScale - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
vibScale - Variable in class org.jmol.jsv.JDXMOLParser
 
vibsFractional - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
vibTemp - Variable in class org.jmol.renderspecial.VectorsRenderer
 
vibx - Static variable in class org.jmol.script.T
 
vibxyz - Static variable in class org.jmol.script.T
 
viby - Static variable in class org.jmol.script.T
 
vibz - Static variable in class org.jmol.script.T
 
viewButton - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
viewCenterButton - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
viewer - Variable in class org.jmol.util.GenericApplet
 
Viewer - Class in org.jmol.viewer
 
Viewer(Map<String, Object>) - Constructor for class org.jmol.viewer.Viewer
new way...
Viewer.ACCESS - Enum in org.jmol.viewer
 
viewMeasurementTableAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
ViewMeasurementTableAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.ViewMeasurementTableAction
 
viewpoint - Variable in class org.jmol.export.__CartesianExporter
 
virtual_trackball - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
VIS_BACKBONE_FLAG - Static variable in class org.jmol.viewer.JC
 
VIS_BALLS_FLAG - Static variable in class org.jmol.viewer.JC
 
VIS_BOND_FLAG - Static variable in class org.jmol.viewer.JC
 
VIS_CARTOON_FLAG - Static variable in class org.jmol.viewer.JC
 
VIS_LABEL_FLAG - Static variable in class org.jmol.viewer.JC
 
VISIBILITY_CLIPPED - Static variable in class org.jmol.g3d.LineRenderer
 
VISIBILITY_OFFSCREEN - Static variable in class org.jmol.g3d.LineRenderer
 
VISIBILITY_UNCLIPPED - Static variable in class org.jmol.g3d.LineRenderer
 
visibilityFlags - Variable in class org.jmol.shape.Mesh
 
visibilityFlags - Variable in class org.jmol.shapespecial.Dipole
 
visibilityFlags - Variable in class org.jmol.shapespecial.Polyhedron
 
visible - Variable in class org.jmol.adapter.readers.pymol.JmolObject
 
visible - Variable in class org.jmol.adapter.readers.pymol.PyMOLGroup
 
visible - Variable in class org.jmol.modelset.Object2d
 
visible - Static variable in class org.jmol.script.T
 
visible - Variable in class org.jmol.shape.Mesh
 
visible - Variable in class org.jmol.shapespecial.Dipole
 
visible - Variable in class org.jmol.shapespecial.Ellipsoid
 
visible - Variable in class org.jmol.shapespecial.Polyhedron
 
visualrange - Static variable in class org.jmol.script.T
 
visualRangeAngstroms - Variable in class org.jmol.viewer.TransformManager
 
vl0 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
vl1 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
vl2 - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
vMax - Variable in class org.jmol.jvxl.readers.KinemageReader
 
vMin - Variable in class org.jmol.jvxl.readers.KinemageReader
 
vNorm - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
vNorm - Variable in class org.jmol.modelsetbio.Resolver
 
vNorm1 - Variable in class org.jmol.smiles.VTemp
 
vNorm2 - Variable in class org.jmol.smiles.VTemp
 
vNorm3 - Variable in class org.jmol.smiles.VTemp
 
vOcc - Variable in class org.jmol.util.ModulationSet
 
vOcc0 - Variable in class org.jmol.util.ModulationSet
 
volume - Variable in class org.jmol.jvxl.readers.VaspChgcarReader
 
volume - Variable in class org.jmol.quantum.QuantumCalculation
 
volume - Static variable in class org.jmol.script.T
 
volume - Variable in class org.jmol.util.ContactPair
 
volume - Variable in class org.jmol.util.SimpleUnitCell
 
volume_bit_depth - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
volume_color - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
volume_data_range - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
volume_layers - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
volumeData - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
volumeData - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
volumeData - Variable in class org.jmol.jvxl.calc.MarchingSquares
 
VolumeData - Class in org.jmol.jvxl.data
 
VolumeData() - Constructor for class org.jmol.jvxl.data.VolumeData
 
volumeData - Variable in class org.jmol.jvxl.readers.Parameters
 
volumeData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
volumeData - Variable in class org.openscience.jvxl.simplewriter.VoxelDataCreator
 
VolumeDataInterface - Interface in org.jmol.api
 
VolumeDataReader - Class in org.jmol.jvxl.readers
 
VolumeDataReader() - Constructor for class org.jmol.jvxl.readers.VolumeDataReader
 
volumeDataTemp - Variable in class org.jmol.jvxl.readers.SurfaceGenerator
 
VolumeFileReader - Class in org.jmol.jvxl.readers
 
VolumeFileReader() - Constructor for class org.jmol.jvxl.readers.VolumeFileReader
 
volumeRender(boolean) - Method in interface org.jmol.api.JmolRendererInterface
 
volumeRender(boolean) - Method in class org.jmol.export.Export3D
 
volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
 
volumeRender - Variable in class org.jmol.render.MeshRenderer
 
volumeRender4(int, int, int, int) - Method in interface org.jmol.api.JmolRendererInterface
 
volumeRender4(int, int, int, int) - Method in class org.jmol.export.Export3D
 
volumeRender4(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
 
volumeRenderPointSize - Variable in class org.jmol.shape.Mesh
 
volumetricMatrix - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricOrigin - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricOrigin - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
volumetricVectorLengths - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricVectors - Variable in class org.jmol.jvxl.data.VolumeData
 
volumetricVectors - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
vOrientations - Variable in class org.jmol.modelset.ModelSet
 
voxelCount - Variable in class org.jmol.jvxl.readers.UhbdReader
 
voxelCounts - Variable in class org.jmol.jvxl.data.VolumeData
 
voxelCounts - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
voxelData - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
voxelData - Variable in class org.jmol.jvxl.data.VolumeData
 
voxelData - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
voxelData - Variable in class org.jmol.quantum.QuantumCalculation
 
VoxelDataCreator - Class in org.openscience.jvxl.simplewriter
 
VoxelDataCreator(VolumeData) - Constructor for class org.openscience.jvxl.simplewriter.VoxelDataCreator
 
voxelDataTemp - Variable in class org.jmol.quantum.QuantumCalculation
 
voxelList - Variable in class org.jmol.jvxl.readers.PyMOLMeshReader
 
voxelMap - Variable in class org.jmol.jvxl.data.VolumeData
 
voxelPtToXYZ(int, int, int, T3) - Method in interface org.jmol.api.VolumeDataInterface
 
voxelPtToXYZ(int, int, int, T3) - Method in class org.jmol.jvxl.data.VolumeData
 
voxelSource - Variable in class org.jmol.jvxl.readers.AtomDataReader
 
voxelVertexVectors - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
voxelVolume - Variable in class org.jmol.jvxl.data.JvxlData
 
voxelVolume - Variable in class org.jmol.jvxl.data.VolumeData
 
vPrimitiveMapping - Variable in class org.jmol.adapter.readers.xtal.CrystalReader
 
vPush - Variable in class org.jmol.script.ScriptCompiler
 
vr - Variable in class org.jmol.adapter.readers.molxyz.MolReader
 
vR - Variable in class org.jmol.adapter.readers.xtal.JanaReader
 
vRef - Static variable in class org.jmol.modelset.AtomCollection
 
vReturn - Variable in class org.jmol.smiles.SmilesSearch
 
vRings - Variable in class org.jmol.minimize.forcefield.ForceFieldMMFF
 
vs - Variable in class org.jmol.util.MeshSurface
vertices
vStereo - Variable in class org.jmol.modelset.ModelLoader
 
vSymmetries - Variable in class org.jmol.adapter.readers.quantum.AdfReader
 
vT - Static variable in class org.jmol.script.SV
 
vTemp - Variable in class org.jmol.jvxl.readers.IsoMOReader
 
vTemp - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
vTemp - Variable in class org.jmol.modelset.ModelSet
 
vtemp - Variable in class org.jmol.renderbio.RocketRenderer
 
vTemp - Variable in class org.jmol.renderspecial.DrawRenderer
 
vTemp - Variable in class org.jmol.shape.Mesh
 
vTemp - Variable in class org.jmol.smiles.SmilesGenerator
 
VTemp - Class in org.jmol.smiles
 
VTemp() - Constructor for class org.jmol.smiles.VTemp
 
vTemp - Variable in class org.jmol.smiles.VTemp
 
vTemp - Variable in class org.jmol.symmetry.PointGroup
 
vTemp - Variable in class org.openscience.jvxl.simplewriter.SimpleMarchingCubes
 
vTemp1 - Variable in class org.jmol.smiles.VTemp
 
vTemp2 - Variable in class org.jmol.jvxl.readers.IsoSolventReader
 
vTemp2 - Variable in class org.jmol.renderspecial.DrawRenderer
 
vTemp2 - Variable in class org.jmol.smiles.VTemp
 
vTlsModels - Variable in class org.jmol.adapter.readers.more.TlsDataOnlyReader
 
vTlsModels - Variable in class org.jmol.adapter.readers.pdb.PdbReader
 
vvs - Variable in class org.jmol.util.MeshSurface
vertex values
vW - Variable in class org.jmol.renderbio.RocketRenderer
 
vwr - Variable in class org.jmol.adapter.readers.pymol.PickleReader
 
vwr - Variable in class org.jmol.adapter.readers.pymol.PyMOLScene
 
vwr - Variable in class org.jmol.adapter.smarter.AtomSetCollectionReader
 
vwr - Variable in class org.jmol.awt.FileDropper
 
vwr - Variable in class org.jmol.awt.Mouse
 
vwr - Variable in class org.jmol.awt.Platform
 
vwr - Variable in class org.jmol.awtjs2d.Mouse
 
vwr - Variable in class org.jmol.awtjs2d.Platform
 
vwr - Variable in class org.jmol.console.GenericConsole
 
vwr - Variable in class org.jmol.console.ScriptEditor
 
vwr - Variable in class org.jmol.dialog.Dialog
 
vwr - Variable in class org.jmol.dialog.FilePreview.FPPanel
 
vwr - Variable in class org.jmol.dialog.FilePreview
 
vwr - Variable in class org.jmol.export.___Exporter
 
vwr - Variable in class org.jmol.geodesic.EnvelopeCalculation
 
vwr - Static variable in class org.jmol.i18n.GT
 
vwr - Variable in class org.jmol.io.DOMReader
 
vwr - Variable in class org.jmol.io.FileReader
 
vwr - Variable in class org.jmol.io.FilesReader
 
vwr - Variable in class org.jmol.jsv.JSpecView
 
vwr - Variable in class org.jmol.minimize.Minimizer
 
vwr - Variable in class org.jmol.modelset.AtomCollection
 
vwr - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
vwr - Variable in class org.jmol.modelset.Measurement
 
vwr - Variable in class org.jmol.modelset.MeasurementData
 
vwr - Variable in class org.jmol.modelset.ModelLoader
 
vwr - Variable in class org.jmol.modelset.Orientation
 
vwr - Variable in class org.jmol.modelset.Text
 
vwr - Variable in class org.jmol.modelsetbio.Resolver
 
vwr - Variable in class org.jmol.multitouch.JmolMultiTouchClientAdapter
 
vwr - Variable in class org.jmol.popup.JmolGenericPopup
 
vwr - Variable in class org.jmol.quantum.MepCalculation
 
vwr - Variable in class org.jmol.quantum.NMRCalculation
 
vwr - Variable in class org.jmol.render.RepaintManager
 
vwr - Variable in class org.jmol.render.ShapeRenderer
 
vwr - Variable in class org.jmol.renderbio.NucleicRenderer
 
vwr - Variable in class org.jmol.renderbio.RocketRenderer
 
vwr - Variable in class org.jmol.script.ScriptError
 
vwr - Variable in class org.jmol.script.ScriptManager
 
vwr - Variable in class org.jmol.script.ScriptMathProcessor
 
vwr - Variable in class org.jmol.script.ScriptParallelProcessor
 
vwr - Variable in class org.jmol.script.ScriptTokenParser
 
vwr - Variable in class org.jmol.scriptext.CmdExt
 
vwr - Variable in class org.jmol.scriptext.MathExt
 
vwr - Variable in class org.jmol.shape.Shape
 
vwr - Variable in class org.jmol.thread.JmolThread
 
vwr - Variable in class org.jmol.util.ColorEncoder
 
vwr - Variable in class org.jmol.util.GData
 
vwr - Variable in class org.jmol.util.MeshSurface
 
vwr - Variable in class org.jmol.viewer.ActionManager
 
vwr - Variable in class org.jmol.viewer.AnimationManager
 
vwr - Variable in class org.jmol.viewer.ColorManager
 
vwr - Variable in class org.jmol.viewer.Connections
 
vwr - Variable in class org.jmol.viewer.DataManager
 
vwr - Variable in class org.jmol.viewer.FileManager
 
vwr - Variable in class org.jmol.viewer.Gesture
 
vwr - Variable in class org.jmol.viewer.GlobalSettings
 
vwr - Variable in class org.jmol.viewer.ModelManager
 
vwr - Variable in class org.jmol.viewer.OutputManager
 
vwr - Variable in class org.jmol.viewer.PropertyManager
 
vwr - Variable in class org.jmol.viewer.SelectionManager
 
vwr - Variable in class org.jmol.viewer.ShapeManager
 
vwr - Variable in class org.jmol.viewer.StateCreator
 
vwr - Variable in class org.jmol.viewer.StateManager
 
vwr - Variable in class org.jmol.viewer.StatusManager
 
vwr - Variable in class org.jmol.viewer.TransformManager
 
vwr - Variable in class org.openscience.jmol.app.InputScannerThread
 
vwr - Variable in class org.openscience.jmol.app.JmolData
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.AboutDialog
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.AtomSetChooser
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.GaussianDialog
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.MeasurementTable
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.PovrayDialog
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.PreferencesDialog
 
vwr - Variable in class org.openscience.jmol.app.jmolpanel.StatusListener
 
vwr - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
vwr - Variable in class org.openscience.jmol.app.surfacetool.SurfaceTool
 
vwr - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
vwr - Variable in class org.openscience.jmol.app.webexport.Test
 
vwr - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
vwrFrame - Variable in class org.jmol.console.JmolConsole
 
vwrOptions - Variable in class org.jmol.util.GenericApplet
 
vwrOptions - Variable in class org.jmol.viewer.Viewer
 
vwrOptions - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
vX - Variable in class org.jmol.shapesurface.Contact
 
vY - Variable in class org.jmol.shapesurface.Contact
 
vZ - Variable in class org.jmol.shapesurface.Contact
 

W

w - Variable in class org.jmol.adapter.readers.cif.Subsystem
 
w - Static variable in class org.jmol.script.T
 
waitForDisplay(PlatformViewer, Object) - Static method in class org.jmol.awt.Image
 
waitForDisplay(Object, Object) - Method in class org.jmol.awt.Platform
 
waitForDisplay(Object, Object) - Method in class org.jmol.awtjs2d.Platform
 
waitformoveto - Static variable in class org.jmol.script.T
 
waitForMoveTo - Variable in class org.jmol.viewer.GlobalSettings
 
waitForQueue() - Method in interface org.jmol.api.JmolScriptManager
 
waitForQueue() - Method in class org.jmol.script.ScriptManager
 
walkDOMTree() - Method in class org.jmol.adapter.readers.xml.XmlReader
 
warn(String) - Method in class org.jmol.util.DefaultLogger
 
warn(String) - Static method in class org.jmol.util.Logger
Writes a log at WARN level.
warn(String) - Method in interface org.jmol.util.LoggerInterface
Writes a log at WARN level.
warn(String) - Method in class org.jmol.viewer.Viewer
 
warnEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
 
warnEx(String, Throwable) - Static method in class org.jmol.util.Logger
Writes a log at WARN level with detail on exception.
warnEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
Writes a log at WARN level with detail on exception.
warning(SAXParseException) - Method in class org.jmol.adapter.readers.xml.XmlHandler
 
warning(int, String, String) - Method in class org.jmol.script.ScriptError
 
wasClicked(int, int) - Method in class org.jmol.shape.Frank
 
wasClicked(int, int) - Method in class org.jmol.shape.Shape
 
wasCubic - Variable in class org.jmol.jvxl.data.JvxlData
 
wasImpliedScript() - Method in class org.jmol.script.ScriptCompiler
Check for improperly parsed implied script command: only two tokens: [implied script] xxx.SORT/REVERSE/PUSH/POP more than two tokens: not a script function xxxx.spt(3,4,5)
wasJvxl - Variable in class org.jmol.jvxl.data.JvxlData
 
wasPerspectiveDepth - Variable in class org.jmol.export._TachyonExporter
 
wasScreened - Variable in class org.jmol.g3d.Graphics3D
 
wasSpinOn - Variable in class org.openscience.jmol.app.jsonkiosk.JsonNioService
 
wasSyntaxCheck - Variable in class org.jmol.script.ScriptMathProcessor
 
wasX - Variable in class org.jmol.script.ScriptMathProcessor
Reverse Polish Notation Engine for IF, SET, and @{...} -- Bob Hanson 2/16/2007 Just a (not so simple?) RPN processor that can handle boolean, int, float, String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f hansonr@stolaf.edu
WB - Static variable in class org.jmol.util.ColorEncoder
 
WEB_MAKER_WINDOW_NAME - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
webExport - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
WebExport - Class in org.openscience.jmol.app.webexport
 
WebExport(Viewer, HistoryFile) - Constructor for class org.openscience.jmol.app.webexport.WebExport
 
webExport - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
webFrame - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
webmoFileStartRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
WebMOReader - Class in org.jmol.adapter.readers.quantum
A molecular orbital reader for WebMO files.
WebMOReader() - Constructor for class org.jmol.adapter.readers.quantum.WebMOReader
 
webPageTitle - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
webPanel - Variable in class org.openscience.jmol.app.webexport.ArrayListTransferHandler
 
WebPanel - Class in org.openscience.jmol.app.webexport
 
WebPanel(Viewer, JFileChooser, WebPanel[], int) - Constructor for class org.openscience.jmol.app.webexport.WebPanel
 
WebPanel.InstanceCellRenderer - Class in org.openscience.jmol.app.webexport
 
webPanels - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
webPanels - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
whatsnewAction - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
WhatsNewAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WhatsNewAction
 
WhatsNewDialog - Class in org.openscience.jmol.app.jmolpanel
 
WhatsNewDialog(JFrame) - Constructor for class org.openscience.jmol.app.jmolpanel.WhatsNewDialog
 
WHEEL - Static variable in class org.jmol.viewer.binding.Binding
 
wheeled(long, int, int) - Method in class org.jmol.awtjs2d.Mouse
 
wheeling - Variable in class org.jmol.awt.Mouse
 
wheeling - Variable in class org.jmol.awtjs2d.Mouse
 
whichOrigin - Variable in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
whichWidgets - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
whilecmd - Static variable in class org.jmol.script.T
 
WHITE - Static variable in class org.jmol.util.C
 
Widget() - Constructor for class org.openscience.jmol.app.webexport.Widgets.Widget
 
widgetCheckboxes - Variable in class org.openscience.jmol.app.webexport.WebPanel
 
widgetList - Variable in class org.openscience.jmol.app.webexport.Widgets
 
Widgets - Class in org.openscience.jmol.app.webexport
 
Widgets() - Constructor for class org.openscience.jmol.app.webexport.Widgets
 
Widgets.AnimationWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.BackgroundColorWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.ConsoleWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.DownLoadWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.SpinOnWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.StereoViewWidget - Class in org.openscience.jmol.app.webexport
 
Widgets.Widget - Class in org.openscience.jmol.app.webexport
 
width - Variable in class org.jmol.export.Export3D
 
width - Variable in class org.jmol.g3d.Pixelator
 
width - Variable in class org.jmol.g3d.SphereRenderer
 
width - Variable in class org.jmol.g3d.TextRenderer
 
width - Variable in class org.jmol.modelset.LabelToken
 
width - Variable in class org.jmol.render.FontLineShapeRenderer
 
width - Variable in class org.jmol.render.MeshRenderer
 
width - Variable in class org.jmol.render.StarsRenderer
 
width - Static variable in class org.jmol.script.T
 
width - Variable in class org.jmol.shape.Mesh
 
width - Variable in class org.jmol.shapespecial.Draw
 
width - Variable in class org.jmol.util.GData
 
width - Variable in class org.jmol.util.Rectangle
 
width - Variable in class org.jmol.viewer.TransformManager
 
width - Variable in class org.openscience.jmol.app.webexport.JmolInstance
 
widthOffscreen - Variable in class org.jmol.g3d.Platform3D
 
widths - Variable in class org.jmol.modelset.Text
 
WIDTHSCALE - Static variable in class org.jmol.shapecgo.CGOMesh
 
widthUnitVector - Variable in class org.jmol.modelsetbio.Sheet
 
Wien2kReader - Class in org.jmol.adapter.readers.xtal
A reader for Wein2k DFT files.
Wien2kReader() - Constructor for class org.jmol.adapter.readers.xtal.Wien2kReader
 
wildcard - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
wildID - Variable in class org.jmol.shapespecial.Dipoles
 
windowActivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.Splash.WindowListener
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowActivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowcentered - Static variable in class org.jmol.script.T
 
windowCentered - Variable in class org.jmol.viewer.TransformManager
 
windowCenteredFlag - Variable in class org.jmol.modelset.Orientation
 
windowClosed(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowClosed(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowClosing(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowClosing(WindowEvent) - Method in class org.openscience.chimetojmol.ChimeToJmol.ApplicationCloser
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.JmolPanel.AppCloser
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.MeasurementTable.MeasurementListWindowListener
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.PovrayDialog.PovrayWindowListener
Closes the dialog when window closing event occurs.
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowClosing(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowDeactivated(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowDeactivated(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowDeiconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowDeiconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowGainedFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowHeight - Variable in class org.jmol.awtjs2d.JsG2D
 
windowHeight - Variable in class org.jmol.g3d.Platform3D
 
windowHeight - Variable in class org.jmol.modelset.Object2d
 
windowHeight - Variable in class org.jmol.util.GData
 
windowIconified(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowIconified(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
WindowListener() - Constructor for class org.openscience.jmol.app.jmolpanel.Splash.WindowListener
 
windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowLostFocus(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowName - Static variable in class org.openscience.jmol.app.webexport.WebExport
 
windowOpened(WindowEvent) - Method in class org.jmol.console.JmolConsole
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.jmolpanel.RecentFilesDialog
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.surfacetool.SurfaceToolGUI
 
windowOpened(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowSize - Variable in class org.jmol.g3d.Platform3D
 
windowStateChanged(WindowEvent) - Method in class org.openscience.jmol.app.webexport.WebExport
 
windowWidth - Variable in class org.jmol.awtjs2d.JsG2D
 
windowWidth - Variable in class org.jmol.g3d.Platform3D
 
windowWidth - Variable in class org.jmol.modelset.Object2d
 
windowWidth - Variable in class org.jmol.util.GData
 
wing - Variable in class org.jmol.renderbio.BioShapeRenderer
 
wing1 - Variable in class org.jmol.renderbio.BioShapeRenderer
 
wingHermites - Variable in class org.jmol.renderbio.BioShapeRenderer
 
wingT - Variable in class org.jmol.renderbio.BioShapeRenderer
 
wingVectors - Variable in class org.jmol.modelsetbio.BioPolymer
 
wingVectors - Variable in class org.jmol.renderbio.BioShapeRenderer
 
wingVectors - Variable in class org.jmol.shapebio.BioShape
 
wireframe - Static variable in class org.jmol.script.T
 
wireframeOnly - Variable in class org.jmol.render.SticksRenderer
 
wireframeOnly - Variable in class org.jmol.renderbio.BioShapeRenderer
 
wireframerotation - Static variable in class org.jmol.script.T
 
wireframeRotation - Variable in class org.jmol.viewer.GlobalSettings
 
within - Static variable in class org.jmol.script.T
 
withinDistance2 - Variable in class org.jmol.shapesurface.Isosurface
 
withinPoints - Variable in class org.jmol.shapesurface.Isosurface
 
wizard_prompt_mode - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
WMATRIX - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
WORD_MASK - Static variable in class org.jmol.java.BS
 
wordIndex(int) - Static method in class org.jmol.java.BS
Given a bit index, return word index containing it.
words - Variable in class org.jmol.java.BS
The internal field corresponding to the serialField "bits".
words - Variable in class org.jmol.popup.PopupResource
 
wordsInUse - Variable in class org.jmol.java.BS
The number of words in the logical size of this BitSet.
working - Static variable in class org.jmol.g3d.TextRenderer
 
workingPathLabel - Variable in class org.openscience.jmol.app.jmolpanel.NBODialog
 
wPlane - Variable in class org.jmol.util.MeshSlicer
 
wrap_output - Static variable in class org.jmol.adapter.readers.pymol.PyMOL
 
wrapPathForAllFiles(String, String) - Method in class org.jmol.viewer.OutputManager
 
wrappedApplet - Variable in class org.jmol.applet.AppletWrapper
 
WrappedApplet - Interface in org.jmol.applet
 
WrappedAppletLoader - Class in org.jmol.applet
 
WrappedAppletLoader(Applet, boolean) - Constructor for class org.jmol.applet.WrappedAppletLoader
 
write - Static variable in class org.jmol.script.T
 
write(T[]) - Method in class org.jmol.scriptext.CmdExt
 
writeAction - Variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
WriteAction() - Constructor for class org.openscience.jmol.app.jmolpanel.JmolPanel.WriteAction
 
writeActionProperty - Static variable in class org.openscience.jmol.app.jmolpanel.JmolPanel
 
writeFile(String, String) - Static method in class org.openscience.jvxl.Jvxl
 
writeFile(String, String) - Static method in class org.openscience.jvxl.simplewriter.ASimpleJvxlWriter
 
writeFileData(String, String, int, Object[]) - Method in class org.jmol.viewer.OutputManager
Generates file data and passes it on either to a FileOuputStream (Java) or via POSTing to a url using a ByteOutputStream (JavaScript)
writeFileData(String, String, int, Object[]) - Method in class org.jmol.viewer.Viewer
 
writeFileZipped(String[], byte[], int) - Static method in class org.openscience.jmol.app.webexport.WebPanel
 
writeFrame(int, String[], Map<String, Object>, SB) - Method in class org.jmol.viewer.OutputManager
 
writeMacros() - Method in class org.jmol.export._PovrayExporter
 
writeMacros2() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosAtom() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosBond() - Method in class org.jmol.export._PovrayExporter
 
writeMacrosFinish() - Method in class org.jmol.export._PovrayExporter
 
writeTextFile(String, String) - Method in class org.jmol.api.JmolViewer
 
writeTextFile(String, String) - Method in class org.jmol.viewer.Viewer
 
writeToOutputChannel(Map<String, Object>) - Method in class org.jmol.viewer.OutputManager
From handleOutputToFile, write text, byte[], or image data to a file;
writeZipFile(OC, Lst<Object>, String, String) - Method in class org.jmol.viewer.OutputManager
generic method to create a zip file based on http://www.exampledepot.com/egs/java.util.zip/CreateZip.html
WV_ID - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
WV_X - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
WV_Y - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 
WV_Z - Static variable in class org.jmol.adapter.readers.cif.MSCifRdr
 

X

x - Variable in class org.jmol.g3d.SphereRenderer
 
X - Variable in class org.jmol.quantum.QuantumCalculation
 
x - Variable in class org.jmol.quantum.SlaterData
 
x - Variable in class org.jmol.render.SticksRenderer
 
x - Static variable in class org.jmol.script.T
 
x - Variable in class org.jmol.shape.Frank
 
x - Variable in class org.jmol.util.Rectangle
 
x - Variable in class org.jmol.viewer.MotionPoint
 
x - Variable in class org.jmol.viewer.MouseState
 
x1t - Variable in class org.jmol.g3d.LineRenderer
 
X2 - Variable in class org.jmol.quantum.QuantumCalculation
 
x2t - Variable in class org.jmol.g3d.LineRenderer
 
xA - Variable in class org.jmol.g3d.CylinderRenderer
 
xA - Variable in class org.jmol.render.SticksRenderer
 
xAdj - Variable in class org.jmol.modelset.Text
 
xAf - Variable in class org.jmol.g3d.CylinderRenderer
 
xAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
xAxis1 - Variable in class org.jmol.render.SticksRenderer
 
xAxis2 - Variable in class org.jmol.render.SticksRenderer
 
xB - Variable in class org.jmol.render.SticksRenderer
 
xBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
xcrysDenContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
XcrysdenReader - Class in org.jmol.adapter.readers.xtal
 
XcrysdenReader() - Constructor for class org.jmol.adapter.readers.xtal.XcrysdenReader
 
xEndcap - Variable in class org.jmol.g3d.CylinderRenderer
 
xGT - Static variable in class org.jmol.util.GData
 
xLast - Variable in class org.jmol.util.GData
 
xlateAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
xLight - Variable in class org.jmol.util.Shader
 
xLT - Static variable in class org.jmol.util.GData
 
xMax - Variable in class org.jmol.quantum.QuantumCalculation
 
xMin - Variable in class org.jmol.quantum.QuantumCalculation
 
XmlArgusReader - Class in org.jmol.adapter.readers.xml
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
XmlArgusReader() - Constructor for class org.jmol.adapter.readers.xml.XmlArgusReader
 
XmlChem3dReader - Class in org.jmol.adapter.readers.xml
An chem3d c3xml reader
XmlChem3dReader() - Constructor for class org.jmol.adapter.readers.xml.XmlChem3dReader
 
XmlCmlReader - Class in org.jmol.adapter.readers.xml
A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.
XmlCmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlCmlReader
 
xmlContainsRecords - Static variable in class org.jmol.adapter.smarter.Resolver
 
xmlData - Variable in class org.jmol.jvxl.data.VolumeData
 
XmlHandler - Class in org.jmol.adapter.readers.xml
a SAX handler
XmlHandler() - Constructor for class org.jmol.adapter.readers.xml.XmlHandler
 
XmlMagResReader - Class in org.jmol.adapter.readers.xml
 
XmlMagResReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMagResReader
 
XmlMolproReader - Class in org.jmol.adapter.readers.xml
A Molpro 2005 reader
XmlMolproReader() - Constructor for class org.jmol.adapter.readers.xml.XmlMolproReader
 
XmlOdysseyReader - Class in org.jmol.adapter.readers.xml
An Odyssey xodydata reader
XmlOdysseyReader() - Constructor for class org.jmol.adapter.readers.xml.XmlOdysseyReader
 
XmlQEReader - Class in org.jmol.adapter.readers.xml
QuantumEspresso XML reader
XmlQEReader() - Constructor for class org.jmol.adapter.readers.xml.XmlQEReader
 
xmlReader - Variable in class org.jmol.adapter.readers.xml.XmlHandler
 
XmlReader - Class in org.jmol.adapter.readers.xml
A generic XML reader template -- by itself, does nothing.
XmlReader() - Constructor for class org.jmol.adapter.readers.xml.XmlReader
 
XmlReader - Class in org.jmol.jvxl.readers
 
XmlReader(BufferedReader) - Constructor for class org.jmol.jvxl.readers.XmlReader
 
XmlVaspReader - Class in org.jmol.adapter.readers.xml
Vasp vasprun.xml reader
XmlVaspReader() - Constructor for class org.jmol.adapter.readers.xml.XmlVaspReader
 
XmlXsdReader - Class in org.jmol.adapter.readers.xml
An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09
XmlXsdReader() - Constructor for class org.jmol.adapter.readers.xml.XmlXsdReader
 
xNav - Variable in class org.jmol.modelset.Orientation
 
xNav - Variable in class org.jmol.thread.MoveToThread
 
xor(BS) - Method in class org.jmol.java.BS
Performs a logical XOR of this bit set with the bit set argument.
XplorReader - Class in org.jmol.jvxl.readers
 
XplorReader() - Constructor for class org.jmol.jvxl.readers.XplorReader
 
xpos - Variable in class org.jmol.render.UccageRenderer
 
xPt - Variable in class org.jmol.script.ScriptMathProcessor
 
xr - Variable in class org.jmol.jvxl.readers.JvxlXmlReader
 
XsfReader - Class in org.jmol.jvxl.readers
 
XsfReader() - Constructor for class org.jmol.jvxl.readers.XsfReader
 
xStack - Variable in class org.jmol.script.ScriptMathProcessor
 
xtalSymmetry - Variable in class org.jmol.adapter.smarter.AtomSetCollection
 
XtalSymmetry - Class in org.jmol.adapter.smarter
A class used by AtomSetCollection for building the symmetry of a model and generating new atoms based on that symmetry.
XtalSymmetry() - Constructor for class org.jmol.adapter.smarter.XtalSymmetry
 
xTip - Variable in class org.jmol.g3d.CylinderRenderer
 
xTrans - Variable in class org.jmol.modelset.Orientation
 
xTrans - Variable in class org.jmol.navigate.Navigator
 
xTrans - Variable in class org.jmol.thread.MoveToThread
 
xTransDelta - Variable in class org.jmol.navigate.Navigator
 
xTranslationFraction - Variable in class org.jmol.viewer.TransformManager
 
xTransStart - Variable in class org.jmol.navigate.Navigator
 
xVdwClash - Variable in class org.jmol.util.ContactPair
 
xWhenPressed - Variable in class org.jmol.awt.Mouse
 
xWhenPressed - Variable in class org.jmol.awtjs2d.Mouse
 
xy - Variable in class org.jmol.render.LabelsRenderer
 
xy - Variable in class org.jmol.shape.Hover
 
XY_ZTOP - Static variable in class org.jmol.viewer.JC
 
xyCount - Variable in class org.jmol.jvxl.readers.Dsn6BinaryReader
 
xypParameter(int) - Method in class org.jmol.script.ScriptParam
 
xyRange - Variable in class org.jmol.viewer.ActionManager
 
XYZ - Static variable in class org.jmol.adapter.readers.quantum.CsfReader
 
XYZ - Static variable in class org.jmol.adapter.readers.xtal.JanaReader
 
xyz - Variable in class org.jmol.modelset.Object2d
 
xyz - Static variable in class org.jmol.script.T
 
xyz - Variable in class org.jmol.symmetry.SymmetryOperation
 
xyzFraction(float, boolean, boolean) - Static method in class org.jmol.symmetry.SymmetryOperation
 
xyzfRaster - Variable in class org.jmol.g3d.CylinderRenderer
 
xyzList - Variable in class org.jmol.symmetry.SpaceGroup
 
xyzMax - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
xyzMax - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
xyzMin - Variable in class org.jmol.adapter.readers.pymol.PyMOLReader
 
xyzMin - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
xyzOriginal - Variable in class org.jmol.symmetry.SymmetryOperation
 
XyzReader - Class in org.jmol.adapter.readers.molxyz
Minnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c
XyzReader() - Constructor for class org.jmol.adapter.readers.molxyz.XyzReader
 
xyzToVoxelPt(float, float, float, T3i) - Method in interface org.jmol.api.VolumeDataInterface
 
xyzToVoxelPt(float, float, float, T3i) - Method in class org.jmol.jvxl.data.VolumeData
 
xyztRaster - Variable in class org.jmol.g3d.CylinderRenderer
 

Y

y - Variable in class org.jmol.g3d.SphereRenderer
 
Y - Variable in class org.jmol.quantum.QuantumCalculation
 
y - Variable in class org.jmol.quantum.SlaterData
 
y - Variable in class org.jmol.render.SticksRenderer
 
y - Static variable in class org.jmol.script.T
 
y - Variable in class org.jmol.shape.Frank
 
y - Variable in class org.jmol.util.Rectangle
 
y - Variable in class org.jmol.viewer.MotionPoint
 
y - Variable in class org.jmol.viewer.MouseState
 
y0 - Variable in class org.jmol.modelset.Text
 
y1t - Variable in class org.jmol.g3d.LineRenderer
 
Y2 - Variable in class org.jmol.quantum.QuantumCalculation
 
y2t - Variable in class org.jmol.g3d.LineRenderer
 
yA - Variable in class org.jmol.g3d.CylinderRenderer
 
yA - Variable in class org.jmol.render.SticksRenderer
 
yAdj - Variable in class org.jmol.modelset.Text
 
yAf - Variable in class org.jmol.g3d.CylinderRenderer
 
yAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
yAxis1 - Variable in class org.jmol.render.SticksRenderer
 
yAxis2 - Variable in class org.jmol.render.SticksRenderer
 
yB - Variable in class org.jmol.render.SticksRenderer
 
yBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
YELLOW - Static variable in class org.jmol.util.C
 
yEndcap - Variable in class org.jmol.g3d.CylinderRenderer
 
yGT - Static variable in class org.jmol.util.GData
 
yLast - Variable in class org.jmol.util.GData
 
yLight - Variable in class org.jmol.util.Shader
 
yLT - Static variable in class org.jmol.util.GData
 
yMax - Variable in class org.jmol.quantum.QuantumCalculation
 
yMin - Variable in class org.jmol.quantum.QuantumCalculation
 
yNav - Variable in class org.jmol.modelset.Orientation
 
yNav - Variable in class org.jmol.thread.MoveToThread
 
ypos - Variable in class org.jmol.render.UccageRenderer
 
yTip - Variable in class org.jmol.g3d.CylinderRenderer
 
yTrans - Variable in class org.jmol.modelset.Orientation
 
yTrans - Variable in class org.jmol.navigate.Navigator
 
yTrans - Variable in class org.jmol.thread.MoveToThread
 
yTransDelta - Variable in class org.jmol.navigate.Navigator
 
yTranslationFraction - Variable in class org.jmol.viewer.TransformManager
 
yTransStart - Variable in class org.jmol.navigate.Navigator
 
yWhenPressed - Variable in class org.jmol.awt.Mouse
 
yWhenPressed - Variable in class org.jmol.awtjs2d.Mouse
 
yzCount - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
yzCount - Variable in class org.jmol.jvxl.data.VolumeData
 
yzCount - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
yzCount - Variable in class org.jmol.quantum.NciCalculation
 
yzPlanePts - Static variable in class org.jmol.jvxl.calc.MarchingCubes
 
yzPlanes - Variable in class org.jmol.jvxl.calc.MarchingCubes
 
yzPlanes - Variable in class org.jmol.jvxl.readers.SurfaceReader
 
yzPlanesRaw - Variable in class org.jmol.jvxl.readers.VolumeFileReader
 
yzPlanesRaw - Variable in class org.jmol.quantum.NciCalculation
 
yzPlanesRho - Variable in class org.jmol.quantum.NciCalculation
 

Z

z - Variable in class org.jmol.g3d.SphereRenderer
 
z - Variable in class org.jmol.modelset.Object2d
 
Z - Variable in class org.jmol.quantum.QuantumCalculation
 
z - Variable in class org.jmol.quantum.SlaterData
 
z - Variable in class org.jmol.render.SticksRenderer
 
z - Static variable in class org.jmol.script.T
 
z1t - Variable in class org.jmol.g3d.LineRenderer
 
Z2 - Variable in class org.jmol.quantum.QuantumCalculation
 
z2t - Variable in class org.jmol.g3d.LineRenderer
 
zA - Variable in class org.jmol.g3d.CylinderRenderer
 
zA - Variable in class org.jmol.render.SticksRenderer
 
zAf - Variable in class org.jmol.g3d.CylinderRenderer
 
zAll - Variable in class org.jmol.adapter.readers.more.BinaryDcdReader
 
zap() - Method in interface org.jmol.api.JmolAppConsoleInterface
 
zap() - Method in class org.jmol.console.GenericConsole
 
zap - Static variable in class org.jmol.script.T
 
zap() - Method in class org.jmol.viewer.ModelManager
 
zap(boolean, boolean, boolean) - Method in class org.jmol.viewer.Viewer
 
ZAP_TITLE - Static variable in class org.jmol.viewer.JC
 
zapMsg(String) - Method in class org.jmol.viewer.Viewer
 
zb - Variable in class org.jmol.g3d.Pixelator
 
zB - Variable in class org.jmol.render.SticksRenderer
 
zBohr - Variable in class org.jmol.quantum.QuantumCalculation
 
zBox - Variable in class org.jmol.render.LabelsRenderer
 
zbuf - Variable in class org.jmol.g3d.Graphics3D
 
zbuf - Variable in class org.jmol.g3d.SphereRenderer
 
zBuffer - Variable in class org.jmol.g3d.Platform3D
 
zBufferT - Variable in class org.jmol.g3d.Platform3D
 
zbufT - Variable in class org.jmol.g3d.Graphics3D
 
zCutoff - Variable in class org.jmol.render.LabelsRenderer
 
zDepth - Variable in class org.jmol.g3d.PixelatorShaded
 
zdepth - Static variable in class org.jmol.script.T
 
zDepth - Variable in class org.jmol.viewer.GlobalSettings
 
zDepthPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
zDepthToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
zDepthValue - Variable in class org.jmol.viewer.TransformManager
 
zEndcap - Variable in class org.jmol.g3d.CylinderRenderer
 
zero - Variable in class org.jmol.viewer.TransformManager4D
 
zeroBase - Variable in class org.jmol.modelset.AtomIteratorWithinModel
 
zerobasedxyzrasmol - Static variable in class org.jmol.script.T
 
zeroBasedXyzRasmol - Variable in class org.jmol.viewer.GlobalSettings
 
zeroFontId - Variable in class org.jmol.shape.Labels
 
zeroOffset - Static variable in class org.jmol.shape.Labels
 
zeroPad - Variable in class org.jmol.modelset.LabelToken
 
zeta - Variable in class org.jmol.quantum.SlaterData
 
zeta1 - Static variable in class org.jmol.quantum.NciCalculation
 
zeta2 - Static variable in class org.jmol.quantum.NciCalculation
 
zeta3 - Static variable in class org.jmol.quantum.NciCalculation
 
zGT - Static variable in class org.jmol.util.GData
 
zLight - Variable in class org.jmol.util.Shader
 
zLT - Static variable in class org.jmol.util.GData
 
zMargin - Variable in class org.jmol.g3d.Graphics3D
 
zMax - Variable in class org.jmol.quantum.QuantumCalculation
 
zMin - Variable in class org.jmol.quantum.QuantumCalculation
 
zmPct - Variable in class org.jmol.viewer.TransformManager
zoom percent zmPct is the current displayed zoom value, AFTER rendering; may not be the same as zmPctSet, particularly if zoom is not enabled
zmPctSet - Variable in class org.jmol.viewer.TransformManager
zoom percent setting the current setting of zoom; may not be the same as zmPct, particularly if zoom is not enabled
znuc - Variable in class org.jmol.quantum.QMAtom
 
znucl - Variable in class org.jmol.adapter.readers.xtal.AbinitReader
 
zOffset - Variable in class org.jmol.viewer.TransformManager4D
 
zoom - Variable in class org.jmol.modelset.Orientation
 
zoom - Static variable in class org.jmol.script.T
 
zoom - Variable in class org.jmol.thread.MoveToThread
 
ZOOM_EVENT - Static variable in class org.jmol.multitouch.ActionManagerMT
 
ZOOM_GESTURE - Static variable in class org.jmol.multitouch.ActionManagerMT
 
zoomAction - Variable in class org.openscience.jmol.app.jmolpanel.DisplayPanel
 
zoomBy(int) - Method in class org.jmol.viewer.TransformManager
standard response to user mouse vertical shift-drag
zoomBy(int) - Method in class org.jmol.viewer.Viewer
 
zoomByFactor(float, int, int) - Method in interface org.jmol.api.JmolNavigatorInterface
 
zoomByFactor(float, int, int) - Method in class org.jmol.navigate.Navigator
 
zoomByFactor(int, int, int) - Method in class org.jmol.viewer.ActionManager
 
zoomByFactor(float, int, int) - Method in class org.jmol.viewer.TransformManager
 
zoomByFactor(float, int, int) - Method in class org.jmol.viewer.Viewer
 
zoomByPercent(float) - Method in class org.jmol.viewer.TransformManager
 
zoomenabled - Static variable in class org.jmol.script.T
 
zoomEnabled - Variable in class org.jmol.viewer.TransformManager
 
zoomFactor - Variable in class org.jmol.viewer.TransformManager
 
zoomheight - Static variable in class org.jmol.script.T
 
zoomHeight - Variable in class org.jmol.viewer.GlobalSettings
 
zoomHeight - Variable in class org.jmol.viewer.TransformManager
 
zoomlarge - Static variable in class org.jmol.script.T
 
zoomLarge - Variable in class org.jmol.viewer.GlobalSettings
 
zoomPercent0 - Variable in class org.jmol.thread.MoveToThread
 
zoomRatio - Variable in class org.jmol.viewer.TransformManager
 
zoomTo - Static variable in class org.jmol.script.T
 
zoomTo(int) - Method in class org.jmol.viewer.ActionManager
 
zoomToPercent(float) - Method in class org.jmol.viewer.TransformManager
 
zroot - Variable in class org.jmol.g3d.SphereRenderer
 
zshade - Static variable in class org.jmol.script.T
 
zShadeEnabled - Variable in class org.jmol.viewer.TransformManager
 
zShadePower - Variable in class org.jmol.g3d.PixelatorShaded
 
zshadepower - Static variable in class org.jmol.script.T
 
zShadePower - Variable in class org.jmol.viewer.GlobalSettings
 
zSlab - Variable in class org.jmol.g3d.PixelatorShaded
 
zSlab - Variable in class org.jmol.modelset.Object2d
 
zSlab - Variable in class org.jmol.render.LabelsRenderer
 
zslab - Static variable in class org.jmol.script.T
 
zSlab - Variable in class org.jmol.viewer.GlobalSettings
 
zSlabPercentSetting - Variable in class org.jmol.viewer.TransformManager
 
zSlabPoint - Variable in class org.jmol.viewer.TransformManager
 
zSlabToPercent(int) - Method in class org.jmol.viewer.TransformManager
 
zSlabValue - Variable in class org.jmol.viewer.TransformManager
 
zTip - Variable in class org.jmol.g3d.CylinderRenderer
 
zValueFromPercent(int) - Method in class org.jmol.viewer.TransformManager
 

_

_(String) - Static method in class org.jmol.i18n.GT
 
_1_4pi - Static variable in class org.jmol.adapter.readers.quantum.SlaterReader
 
_8PI2_ - Static variable in class org.jmol.adapter.readers.pdb.PdbReader
 
___Exporter - Class in org.jmol.export
 
___Exporter() - Constructor for class org.jmol.export.___Exporter
 
__CartesianExporter - Class in org.jmol.export
 
__CartesianExporter() - Constructor for class org.jmol.export.__CartesianExporter
 
__RayTracerExporter - Class in org.jmol.export
 
__RayTracerExporter() - Constructor for class org.jmol.export.__RayTracerExporter
 
_activeLevels - Static variable in class org.jmol.util.Logger
 
_birth - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
_id1 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_id2 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_IdtfExporter - Class in org.jmol.export
 
_IdtfExporter() - Constructor for class org.jmol.export._IdtfExporter
 
_logger - Static variable in class org.jmol.util.Logger
 
_logLevel - Static variable in class org.jmol.util.Logger
 
_MayaExporter - Class in org.jmol.export
 
_MayaExporter() - Constructor for class org.jmol.export._MayaExporter
 
_myId - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
_myType - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_nCurrent - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
_nMoves - Variable in class org.jmol.multitouch.sparshui.SinglePointGesture
 
_nTraces - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_ObjExporter - Class in org.jmol.export
Class to export Wavefront OBJ files.
_ObjExporter() - Constructor for class org.jmol.export._ObjExporter
 
_offset - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_offsetCentroid - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_PovrayExporter - Class in org.jmol.export
 
_PovrayExporter() - Constructor for class org.jmol.export._PovrayExporter
 
_rotation - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_scale - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_TachyonExporter - Class in org.jmol.export
 
_TachyonExporter() - Constructor for class org.jmol.export._TachyonExporter
 
_traces1 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_traces2 - Variable in class org.jmol.multitouch.sparshui.TwoPointGesture
 
_VrmlExporter - Class in org.jmol.export
 
_VrmlExporter() - Constructor for class org.jmol.export._VrmlExporter
 
_X3dExporter - Class in org.jmol.export
 
_X3dExporter() - Constructor for class org.jmol.export._X3dExporter
 
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