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
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
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 - 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
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
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
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 - 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