org.jmol.viewer

Class Viewer

public class Viewer extends JmolViewer implements AtomDataServer

Field Summary
booleanantialiasDisplay
StringappletCodeBase
StringappletDocumentBase
booleanautoExit
booleanaxesAreTainted
booleanchecking
booleancheckScriptOnly
ColorManagercolorManager
CommandHistorycommandHistory
Compilercompiler
booleancreatingImage
intcurrentCursor
static intCURSOR_CROSSHAIR
static intCURSOR_DEFAULT
static intCURSOR_HAND
static intCURSOR_MOVE
static intCURSOR_WAIT
DataManagerdataManager
DimensiondimScreen
Componentdisplay
Evaleval
HashtableevalVariables
FileManagerfileManager
booleanfileOpenCheck
booleanfrankOn
StringfullName
Graphics3Dg3d
StateManager.GlobalSettingsglobal
booleanhaveDisplay
inthoverAtomIndex
StringhoverText
StringhtmlName
floatimageFontScaling
StringinterruptScript
booleanisApplet
booleanisPreviewOnly
booleanisScriptQueued
booleanisSignedApplet
booleanisSilent
booleanisTainted
booleanjvm11orGreater
booleanjvm12orGreater
booleanjvm14orGreater
booleanlistCommands
intmaximumSize
MinimizerInterfaceminimizer
JmolAdaptermodelAdapter
ModelManagermodelManager
ModelSetmodelSet
intmotionEventNumber
MouseManagermouseManager
booleanmustRender
booleannoneSelected
PickingManagerpickingManager
intprevFrame
booleanrefreshing
RepaintManagerrepaintManager
intscriptIndex
ScriptManagerscriptManager
SelectionManagerselectionManager
StateManagerstateManager
StatusManagerstatusManager
StringstrJavaVendor
StringstrJavaVersion
StringstrOSName
StringsyncId
static StringSTATE_VERSION_STAMP
TempArraytempManager
static ObjecttestData
static ObjecttestData2
TransformManagertransformManager
booleanuseCommandThread
booleanwasInMotion
StringwriteInfo
Constructor Summary
Viewer(Component display, JmolAdapter modelAdapter)
Method Summary
voidaddCommand(String command)
Adds one or more commands to the command history
voidaddLoadScript(String script)
voidaddSelectionListener(JmolSelectionListener listener)
voidaddStateScript(String script, boolean addFrameNumber, boolean postDefinitions)
voidaddStateScript(String script1, BitSet bsBonds, BitSet bsAtoms1, BitSet bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)
static JmolViewerallocateViewer(Component display, JmolAdapter modelAdapter)
NOTE: for APPLICATION AND APPLET call setModeMouse(JmolConstants.MOUSE_NONE); before setting viewer=null in order to remove references to display window in listeners and hoverWatcher This is the main access point for creating an application or applet viewer.
byte[]allocTempBytes(int size)
Point3f[]allocTempPoints(int size)
Point3i[]allocTempScreens(int size)
booleanallowRotateSelected()
booleanareAxesTainted()
voidassignAromaticBonds()
voidatomPicked(int atomIndex, Point3f ptClicked, int modifiers)
intautoHbond(BitSet bsBonds)
intautoHbond(BitSet bsFrom, BitSet bsTo, BitSet bsBonds)
voidcalcBoundBoxDimensions(BitSet bs)
floatcalcRotationRadius(Point3f center)
floatcalcRotationRadius(BitSet bs)
voidcalcSelectedGroupsCount()
voidcalcSelectedMoleculesCount()
voidcalcSelectedMonomersCount()
Vector3fcalculateMolecularDipole()
StringcalculatePointGroup()
voidcalculateStraightness()
voidcalculateStructures(BitSet bsAtoms)
Point3f[]calculateSurface(BitSet bsSelected, float envelopeRadius)
booleancheckHalt(String strScript)
Point3fcheckObjectClicked(int x, int y, int modifiers)
voidcheckObjectDragged(int prevX, int prevY, int deltaX, int deltaY, int modifiers)
booleancheckObjectHovered(int x, int y)
booleancheckResume(String strScript)
voidclear()
voidclearAllMeasurements()
voidclearBfactorRange()
voidclearClickCount()
voidclearConsole()
voidclearMeasurements()
voidclearMinimization()
voidclearScriptQueue()
voidclearSelection()
voidcreateImage(String type_name)
StringcreateImage(String file, String type, Object text_or_bytes, int quality, int width, int height)
voiddefineMeasurement(Vector monitorExpressions, float[] rangeMinMax, boolean isDelete, boolean isAll, boolean isAllConnected, boolean isOn, boolean isOff, String strFormat)
intdeleteAtoms(BitSet bs, boolean fullModels)
voiddeleteMeasurement(int i)
voiddeleteMeasurement(int[] atomCountPlusIndices)
voiddepthByPixels(int pixels)
voiddepthToPercent(int percentDepth)
StringdialogAsk(String type, String fileName)
voiddisplay(BitSet bs, boolean isQuiet)
voidechoMessage(String msg)
Stringeval(String strEval)
StringevalFile(String strFilename)
StringevalString(String strScript)
StringevalStringQuiet(String strScript)
StringevalStringQuiet(String strScript, boolean isQuiet, boolean allowSyncScript)
ObjectevalStringWaitStatus(String returnType, String strScript, String statusList)
ObjectevalStringWaitStatus(String returnType, String strScript, String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)
ObjectevaluateExpression(Object stringOrTokens)
voidfillAtomData(AtomData atomData, int mode)
protected voidfinalize()
voidfinalizeTransformParameters()
intfindNearestAtomIndex(int x, int y)
StringformatText(String text0)
booleanfrankClicked(int x, int y)
voidfreeTempBytes(byte[] tempBytes)
voidfreeTempPoints(Point3f[] tempPoints)
voidfreeTempScreens(Point3i[] tempScreens)
float[][]functionXY(String functionName, int nX, int nY)
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.
StringgenerateOutput(String type, String fileName, int width, int height)
VectorgetAllAtomInfo(Object atomExpression)
VectorgetAllBondInfo(Object atomExpression)
HashtablegetAllChainInfo(Object atomExpression)
booleangetAllowEmbeddedScripts()
HashtablegetAllPolymerInfo(Object atomExpression)
StringgetAllSettings(String prefix)
StringgetAltLocListInModel(int modelIndex)
static intgetAmbientPercent()
intgetAnimationDirection()
intgetAnimationFps()
HashtablegetAnimationInfo()
intgetAnimationReplayMode()
booleangetAppendNew()
HashtablegetAppletInfo()
booleangetApplySymmetryToBonds()
intgetAtomArgb(int i)
BitSetgetAtomBits(int tokType, Object specInfo)
BitSetgetAtomBitSet(Object atomExpression)
VectorgetAtomBitSetVector(Object atomExpression)
StringgetAtomChain(int i)
intgetAtomCount()
intgetAtomCountInModel(int modelIndex)
voidgetAtomIdentityInfo(int atomIndex, Hashtable info)
intgetAtomIndexFromAtomNumber(int atomNumber)
int[]getAtomIndices(BitSet bs)
StringgetAtomInfo(int atomIndex)
StringgetAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
intgetAtomModelIndex(int i)
StringgetAtomName(int i)
intgetAtomNumber(int i)
booleangetAtomPicking()
Point3fgetAtomPoint3f(int i)
floatgetAtomRadius(int i)
BitSetgetAtomsConnected(float min, float max, int intType, BitSet bs)
BitSetgetAtomsWithin(float distance, Point3f coord)
BitSetgetAtomsWithin(float distance, Point4f plane)
BitSetgetAtomsWithin(float distance, BitSet bs, boolean isWithinModelSet)
StringgetAtomSequenceCode(int i)
Point3fgetAtomSetCenter(BitSet bs)
floatgetAtomVdwRadius(int i)
floatgetAtomX(int i)
floatgetAtomY(int i)
floatgetAtomZ(int i)
booleangetAutoBond()
booleangetAutoFps()
HashtablegetAuxiliaryInfo(Object atomExpression)
Point3fgetAverageAtomPoint()
ComponentgetAwtComponent()
intgetAxesMode()
booleangetAxesOrientationRasmol()
floatgetAxesScale()
voidgetAxisAngle(AxisAngle4f axisAngle)
Point3f[]getAxisPoints()
intgetBackgroundArgb()
intgetBackgroundModelIndex()
BitSetgetBitSetSelection()
BitSetgetBitSetTrajectories()
intgetBondArgb1(int i)
intgetBondArgb2(int i)
intgetBondCount()
For use in setting a for() construct max value
intgetBondCountInModel(int modelIndex)
from JmolPopup.udateModelSetComputedMenu
intgetBondModelIndex(int i)
shortgetBondOrder(int i)
booleangetBondPicking()
Point3fgetBondPoint3f1(int i)
Point3fgetBondPoint3f2(int i)
floatgetBondRadius(int i)
BitSetgetBondsForSelectedAtoms(BitSet bsAtoms)
booleangetBondSelectionModeOr()
floatgetBondTolerance()
booleangetBooleanProperty(String key)
booleangetBooleanProperty(String key, boolean doICare)
Point3fgetBoundBoxCenter()
intgetBoundBoxCenterX()
intgetBoundBoxCenterY()
StringgetBoundBoxCommand(boolean withOptions)
Vector3fgetBoundBoxCornerVector()
HashtablegetBoundBoxInfo()
BitSetgetBoundBoxModels()
BoxInfogetBoxInfo(BitSet bs)
BitSetgetBranchBitSet(int atomIndex, int atomIndexNot)
ObjectgetBufferedReaderForString(String string)
ObjectgetBufferedReaderOrErrorMessageFromName(String name, String[] fullPathNameReturn, boolean isBinary)
booleangetCartoonRocketFlag()
booleangetChainCaseSensitive()
intgetChainCount()
intgetChainCountInModel(int modelIndex)
intgetChainCountInModel(int modelIndex, boolean countWater)
StringgetChimeInfo(int tok)
BitSetgetClickableSet()
StringgetClientAtomStringProperty(Object clientAtom, String propertyName)
ObjectgetClientFile()
shortgetColix(Object object)
intgetColixArgb(short colix)
shortgetColixAtomPalette(Atom atom, byte pid)
shortgetColixBackgroundContrast()
shortgetColixForPropertyValue(float val)
shortgetColixRubberband()
Point3fgetColorPointForPropertyValue(float val)
int[]getColorSchemeArray(String colorScheme)
StringgetColorSchemeList(String colorScheme, boolean ifDefault)
CompilergetCompiler()
StringgetCoordinateState(BitSet bsSelected)
float[]getCurrentColorRange()
ObjectgetCurrentFileAsBytes()
StringgetCurrentFileAsString()
intgetCurrentModelIndex()
floatgetCurrentSolventProbeRadius()
SymmetryInterfacegetCurrentUnitCell()
Point3fgetCurrentUnitCellOffset()
intgetCursorX()
intgetCursorY()
Object[]getData(String type)
StringgetData(String atomExpression, String type)
float[]getDataFloat(String label)
floatgetDataFloat(String label, int atomIndex)
float[][]getDataFloat2D(String label)
StringgetDataSeparator()
booleangetDebugScript()
StringgetDefaultDirectory()
floatgetDefaultDrawArrowScale()
Point3fgetDefaultLattice()
StringgetDefaultLoadScript()
shortgetDefaultMadAtom()
StringgetDefaultMeasurementLabel(int nPoints)
floatgetDefaultTranslucent()
StringgetDefaultVdw(int iMode)
intgetDelayMaximum()
BitSetgetDeletedAtoms()
static intgetDiffusePercent()
floatgetDipoleScale()
booleangetDisablePopupMenu()
booleangetDisplayCellParameters()
intgetDisplayModelIndex()
intgetDotDensity()
booleangetDotsSelectedOnlyFlag()
booleangetDotSurfaceFlag()
booleangetDrawHover()
booleangetDrawPicking()
booleangetDynamicMeasurements()
booleangetEchoStateActive()
intgetElementNumber(int i)
BitSetgetElementsPresentBitSet(int modelIndex)
StringgetElementSymbol(int i)
HashtablegetEvalVariables()
StringgetExportDriverList()
JmolAdaptergetExportJmolAdapter()
This is the method that should be used to extract the model data from Jmol.
ObjectgetFileAsImage(String pathName, Hashtable htParams)
StringgetFileAsString(String name)
booleangetFileAsString(String[] data)
StringgetFileHeader()
String[]getFileInfo()
StringgetFileName()
Font3DgetFont3D(String fontFace, String fontStyle, float fontSize)
booleangetFontScaling()
booleangetForceAutoBond()
FrameRenderergetFrameRenderer()
StringgetFrameTitle(int modelIndex)
StringgetFrameTitle()
StringgetFullPathName()
StateManager.GlobalSettingsgetGlobalSettings()
Graphics3DgetGraphics3D()
booleangetGreyscaleRendering()
intgetGroupCount()
intgetGroupCountInModel(int modelIndex)
booleangetHbondsBackbone()
booleangetHbondsSolid()
voidgetHelp(String what)
intgetHermiteLevel()
HashtablegetHeteroList(int modelIndex)
StringgetHexColorFromIndex(short colix)
BitSetgetHiddenSet()
booleangetHideNameInPopup()
booleangetHighResolution()
intgetHoverDelay()
StringgetHtmlName()
StringgetHybridizationAndAxes(int atomIndex, Vector3f z, Vector3f x, String lcaoType, boolean hybridizationCompatible)
ImagegetImage(boolean isDouble)
floatgetImageFontScaling()
chargetInlineChar()
booleangetInMotion()
StringgetInterruptScript()
booleangetIsosurfacePropertySmoothing()
StringgetJavaVendor()
StringgetJavaVersion()
intgetJmolDataFrameIndex(int modelIndex, String type)
intgetJmolDataSourceFrame(int modelIndex)
StringgetJmolFrameType(int modelIndex)
static StringgetJmolVersion()
static intgetJmolVersionInt()
ObjectgetJpeg(int quality, boolean asString)
booleangetJustifyMeasurements()
ObjectgetListVariable(String name, Object value)
StringgetLoadFormat()
StringgetLoadState()
static intgetLogLevel()
shortgetMadBond()
shortgetMarBond()
Matrix3fgetMatrixRotate()
Matrix4fgetMatrixtransform()
floatgetMaxZoomPercent()
booleangetMeasureAllModelsFlag()
StringgetMeasureDistanceUnits()
intgetMeasurementCount()
int[]getMeasurementCountPlusIndices(int i)
VectorgetMeasurementInfo()
StringgetMeasurementInfoAsString()
StringgetMeasurementStringValue(int i)
StringgetMenu(String type)
HashtablegetMessageQueue()
booleangetMessageStyleChime()
floatgetMinBondDistance()
StringgetMinimizationInfo()
MinimizerInterfacegetMinimizer()
BitSetgetModelAtomBitSet(int modelIndex, boolean asCopy)
HashtablegetModelAuxiliaryInfo(int modelIndex)
ObjectgetModelAuxiliaryInfo(int modelIndex, String keyName)
BitSetgetModelBitSet(BitSet atomList)
intgetModelCount()
Vector3fgetModelDipole()
StringgetModelExtract(Object atomExpression)
StringgetModelFileInfo()
StringgetModelFileInfoAll()
StringgetModelFileName(int modelIndex)
intgetModelFileNumber(int modelIndex)
HashtablegetModelInfo(Object atomExpression)
StringgetModelInfoAsString()
StringgetModelName(int modelIndex)
intgetModelNumber(int modelIndex)
StringgetModelNumberDotted(int modelIndex)
intgetModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
PropertiesgetModelProperties(int modelIndex)
StringgetModelProperty(int modelIndex, String propertyName)
ModelSetgetModelSet()
ObjectgetModelSetAuxiliaryInfo(String strKey)
HashtablegetModelSetAuxiliaryInfo()
StringgetModelSetFileName()
StringgetModelSetName()
StringgetModelSetPathName()
PropertiesgetModelSetProperties()
StringgetModelSetProperty(String strProp)
StringgetModelSetTypeName()
StringgetModelTitle(int modelIndex)
bytegetModeMultipleBond()
VectorgetMoleculeInfo(Object atomExpression)
intgetMotionEventNumber()
StringgetMoveToText(float timespan)
booleangetNavigating()
Point3fgetNavigationCenter()
booleangetNavigationCentered()
floatgetNavigationDepthPercent()
booleangetNavigationMode()
Point3fgetNavigationOffset()
floatgetNavigationOffsetPercent(char XorY)
booleangetNavigationPeriodic()
floatgetNavigationSpeed()
BooleangetNoneSelected()
intgetObjectArgb(int objId)
shortgetObjectColix(int objId)
intgetObjectMad(int objId)
StringgetObjectState(String name)
StringgetOpenFileError()
misnamed -- really this opens the file, gets the data, and returns error or null
StringgetOpenFileError(boolean isAppend)
the opener for Jmol
StringgetOperatingSystemName()
HashtablegetOrientationInfo()
StringgetOrientationText(int type)
ObjectgetParameter(String key)
ObjectgetParameterEscaped(String key)
float[]getPartialCharges()
StringgetPdbData(BitSet bs)
StringgetPdbData(int modelIndex, String type)
booleangetPdbLoadInfo(int type)
StringgetPDBHeader()
MeasurementPendinggetPendingMeasurement()
intgetPercentVdwAtom()
booleangetPerspectiveDepth()
intgetPickingMode()
intgetPickingSpinRate()
intgetPickingStyle()
StringgetPointGroupAsString(boolean asDraw, String type, int index, float scale)
HashtablegetPointGroupInfo(Object atomExpression)
floatgetPointGroupTolerance(int type)
intgetPolymerCount()
intgetPolymerCountInModel(int modelIndex)
Point3f[]getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
voidgetPolymerPointsAndVectors(BitSet bs, Vector vList)
ObjectgetProperty(String returnType, String infoType, String paramInfo)
ObjectgetProperty(String returnType, String infoType, Object paramInfo)
StringgetPropertyColorScheme()
StringgetProteinStructureState()
chargetQuaternionFrame()
booleangetRasmolHeteroSetting()
booleangetRasmolHydrogenSetting()
booleangetRefreshing()
intgetRibbonAspectRatio()
booleangetRibbonBorder()
booleangetRocketBarrelFlag()
voidgetRotation(Matrix3f matrixRotation)
Point3fgetRotationCenter()
floatgetRotationRadius()
RectanglegetRubberBandSelection()
StringgetSavedCoordinates(String saveName)
StringgetSavedState(String saveName)
StringgetSavedStructure(String saveName)
floatgetScalePixelsPerAngstrom()
intgetScreenDim()
intgetScreenHeight()
ImagegetScreenImage()
intgetScreenWidth()
intgetScriptDelay()
booleangetSelectAllModels()
intgetSelectionCount()
booleangetSelectionHaloEnabled()
BitSetgetSelectionSet()
BitSetgetSelectionSubset()
BitSetgetSequenceBits(String specInfo, BitSet bs)
StringgetSetHistory(int howFarBack)
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;
intgetShapeIdFromObjectName(String objectName)
HashtablegetShapeInfo()
ObjectgetShapeProperty(int shapeType, String propertyName)
ObjectgetShapeProperty(int shapeType, String propertyName, int index)
intgetShapePropertyAsInt(int shapeID, String propertyName)
floatgetSheetSmoothing()
booleangetShowAxes()
booleangetShowBbcage()
booleangetShowFrank()
booleangetShowHiddenSelectionHalos()
booleangetShowHydrogens()
booleangetShowMeasurementLabels()
booleangetShowMeasurements()
booleangetShowMultipleBonds()
booleangetShowNavigationPoint()
booleangetShowUnitCell()
booleangetSlabEnabled()
booleangetSmartAromatic()
booleangetSolventOn()
floatgetSolventProbeRadius()
StringgetSpaceGroupInfoText(String spaceGroup)
booleangetSpecular()
static intgetSpecularPercent()
StringgetSpecularState()
floatgetSpinFps()
booleangetSpinOn()
StringgetSpinState()
floatgetSpinX()
floatgetSpinY()
floatgetSpinZ()
booleangetSsbondsBackbone()
StringgetStandardLabelFormat()
StringgetStateInfo()
StringgetStateInfo(String type)
ObjectgetStatusChanged(String statusNameList)
floatgetStereoDegrees()
ImagegetStereoImage(int stereoMode)
intgetStereoMode()
intgetStrandCount(int type)
StringgetStructureState()
intgetSurfaceDistanceMax()
StringgetSymmetryInfoAsString()
BitSetgetTaintedAtoms(byte type)
booleangetTestFlag1()
booleangetTestFlag2()
booleangetTestFlag3()
booleangetTestFlag4()
booleangetTraceAlpha()
StringgetTrajectoryInfo()
StringgetTransformText()
StringgetTranslationScript()
floatgetTranslationXPercent()
floatgetTranslationYPercent()
floatgetTranslationZPercent()
StringgetUnitCellInfoText()
Matrix4fgetUnscaledTransformMatrix()
booleangetUseNumberLocalization()
intgetVanderwaalsMar(int i)
intgetVanderwaalsMar(int i, int iMode)
floatgetVectorScale()
floatgetVibrationCoord(int atomIndex, char c)
floatgetVibrationPeriod()
floatgetVibrationScale()
Vector3fgetVibrationVector(int atomIndex)
BitSetgetVisibleFramesBitSet()
BitSetgetVisibleSet()
booleangetWireframeRotation()
AtomIndexIteratorgetWithinAtomSetIterator(int atomIndex, float distance, BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)
AtomIndexIteratorgetWithinModelIterator(Atom atom, float distance)
booleangetZeroBasedXyzRasmol()
booleangetZoomEnabled()
booleangetZoomLarge()
intgetZoomPercent()
floatgetZoomPercentFloat()
floatgetZoomSetting()
booleangetZShade()
voidhaltScriptExecution()
booleanhandleOldJvm10Event(Event e)
booleanhasCalculatedHBonds(BitSet bsAtoms)
booleanhaveFileSet()
booleanhaveFrame()
booleanhaveModelSet()
booleanhavePartialCharges()
voidhide(BitSet bs, boolean isQuiet)
voidhideMeasurements(boolean isOFF)
voidhomePosition()
voidhoverOff()
voidhoverOn(int atomIndex)
voidhoverOn(int x, int y, String text)
voidinitialize()
voidinitializeModel()
voidinvertSelected(Point3f pt, BitSet bs)
voidinvertSelected(Point3f pt, Point4f plane)
voidinvertSelection()
booleanisAnimationOn()
booleanisApplet()
booleanisInPosition(Point3f pt, float degrees)
booleanisInSelectionSubset(int atomIndex)
booleanisJmolDataFrame(int modelIndex)
booleanisJmolDataFrame()
booleanisJmolVariable(String key)
booleanisJvm12orGreater()
booleanisPreviewOnly()
booleanisRangeSelected()
booleanisScriptExecuting()
booleanisSelected(int atomIndex)
booleanisSignedApplet()
booleanisTrajectory(int modelIndex)
booleanisVibrationOn()
booleanisWindowCentered()
StringlistSavedStates()
voidloadData(int type, String name, String coordinateData)
voidloadInline(String strModel)
voidloadInline(String strModel, boolean isAppend)
voidloadInline(String strModel, char newLine)
booleanloadInline(String strModel, char newLine, boolean isAppend)
voidloadInline(String[] arrayModels)
voidloadInline(String[] arrayModels, boolean isAppend)
voidloadShape(int shapeID)
int[]makeConnections(float minDistance, float maxDistance, short order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds)
booleanmodelHasVibrationVectors(int modelIndex)
booleanmodelSetHasVibrationVectors()
voidmove(Vector3f dRot, float dZoom, Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps)
voidmoveTo(float floatSecondsTotal, Point3f center, Point3f pt, float degrees, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth)
voidmoveTo(float floatSecondsTotal, Matrix3f rotationMatrix, Point3f center, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth)
voidmoveUpdate(float floatSecondsTotal)
booleanmustRenderFlag()
voidnavigate(int keyWhere, int modifiers)
voidnavigate(float timeSeconds, Point3f[] path, float[] theta, int indexStart, int indexEnd)
voidnavigate(float timeSeconds, Point3f center)
voidnavigate(float timeSeconds, Point3f[][] pathGuide)
voidnavigate(float timeSeconds, Vector3f rotAxis, float degrees)
voidnavTranslate(float timeSeconds, Point3f center)
voidnavTranslatePercent(float timeSeconds, float x, float y)
voidnotifyMinimizationStatus()
voidopenClientFile(String fullPathName, String fileName, Object clientFile)
voidopenDOM(Object DOMNode)
voidopenFile(String name)
voidopenFile(String name, Hashtable htParams, String loadScript, boolean isAppend)
voidopenFiles(String modelName, String[] names)
voidopenFiles(String modelName, String[] names, String loadScript, boolean isAppend)
voidopenReader(String fullPathName, String name, Reader reader)
Opens the file, given the reader. name is a text name of the file ... to be displayed in the window no need to pass a BufferedReader ...
voidopenStringInline(String strModel)
booleanopenStringInline(String strModel, Hashtable htParams, boolean isAppend)
voidopenStringsInline(String[] arrayModels, Hashtable htParams, boolean isAppend)
voidpauseAnimation()
voidpauseScriptExecution()
voidpopHoldRepaint()
voidpopupMenu(int x, int y)
voidpushHoldRepaint()
voidrebond()
voidrefresh(int mode, String strWhy)
initiate a repaint/update sequence if it has not already been requested. invoked whenever any operation causes changes that require new rendering.
voidrefreshMeasures()
voidreleaseScreenImage()
StringremoveCommand()
Removes one command from the command history
voidremoveSelectionListener(JmolSelectionListener listener)
voidremoveUserVariable(String key)
voidrender()
voidrender1(Graphics g, Image img, int x, int y)
voidrenderScreenImage(Graphics g, Dimension size, Rectangle clip)
voidrepaint()
voidrepaintView()
voidreportSelection(String msg)
voidrequestRepaintAndWait()
voidreset()
voidresetAromatic()
voidresizeImage(int width, int height, boolean isImageWrite, boolean isGenerator, boolean isReset)
booleanrestoreBonds(String saveName)
voidrestoreModelOrientation(int modelIndex)
voidrestoreModelRotation(int modelIndex)
booleanrestoreOrientation(String saveName, float timeSeconds)
voidrestoreRotation(String saveName, float timeSeconds)
booleanrestoreSelection(String saveName)
voidresumeAnimation()
voidresumeScriptExecution()
voidreverseAnimation()
voidrewindAnimation()
voidrotateAboutPointsInternal(Point3f point1, Point3f point2, float nDegrees, float endDegrees, boolean isSpin, BitSet bsSelected)
voidrotateAtoms(Matrix3f mNew, Matrix3f matrixRotate, boolean fullMolecule, Point3f center, boolean isInternal, BitSet bsAtoms)
voidrotateAxisAngleAtCenter(Point3f rotCenter, Vector3f rotAxis, float degrees, float endDegrees, boolean isSpin, BitSet bsSelected)
voidrotateFront()
voidrotateMolecule(int deltaX, int deltaY)
voidrotatePoint(Point3f pt, Point3f ptRot)
voidrotateX(float angleRadians)
voidrotateX(int angleDegrees)
voidrotateXYBy(int xDelta, int yDelta)
voidrotateY(float angleRadians)
voidrotateY(int angleDegrees)
voidrotateZ(float angleRadians)
voidrotateZBy(int zDelta)
voidsaveBonds(String saveName)
voidsaveCoordinates(String saveName, BitSet bsSelected)
voidsaveModelOrientation()
voidsaveOrientation(String saveName)
voidsaveSelection(String saveName)
voidsaveState(String saveName)
voidsaveStructure(String saveName)
floatscaleToPerspective(int z, float sizeAngstroms)
shortscaleToScreen(int z, int milliAngstroms)
Stringscript(String strScript)
StringscriptCheck(String strScript)
voidscriptEcho(String strEcho)
voidscriptError(String msg)
voidscriptStatus(String strStatus)
StringscriptWait(String strScript)
ObjectscriptWaitStatus(String strScript, String statusList)
voidselect(BitSet bs, boolean isQuiet)
voidselectAll()
voidselectBonds(BitSet bs)
voidselectRectangle(Rectangle rect, int modifiers)
voidsetAllowRotateSelected(boolean TF)
static voidsetAmbientPercent(int ambientPercent)
voidsetAnimationDirection(int direction)
voidsetAnimationFps(int fps)
voidsetAnimationLast()
voidsetAnimationNext()
voidsetAnimationOn(boolean animationOn)
voidsetAnimationPrevious()
voidsetAnimationRange(int modelIndex1, int modelIndex2)
voidsetAnimationReplayMode(int replay, float firstFrameDelay, float lastFrameDelay)
voidsetAntialias(int mode, boolean TF)
voidsetAppendNew(boolean value)
voidsetAppletContext(String fullName, URL documentBase, URL codeBase, String commandOptions)
voidsetApplySymmetryToBonds(boolean TF)
voidsetAtomCoord(int atomIndex, float x, float y, float z)
voidsetAtomCoord(BitSet bs, int tokType, Object xyzValues)
voidsetAtomCoordRelative(int atomIndex, float x, float y, float z)
voidsetAtomCoordRelative(Point3f offset)
voidsetAtomProperty(BitSet bs, int tok, int iValue, float fValue, float[] values)
voidsetAutoBond(boolean TF)
voidsetAxesModeMolecular(boolean TF)
voidsetAxesModeUnitCell(boolean TF)
voidsetAxesOrientationRasmol(boolean TF)
voidsetAxesScale(float scale)
voidsetBackgroundImage(String fileName, Image image)
voidsetBackgroundModelIndex(int modelIndex)
voidsetBondTolerance(float bondTolerance)
voidsetBooleanProperty(String key, boolean value)
booleansetBooleanProperty(String key, boolean value, boolean defineNew)
voidsetBoundBox(Point3f pt1, Point3f pt2, boolean byCorner)
voidsetCenterAt(String relativeTo, Point3f pt)
voidsetCenterBitSet(BitSet bsCenter, boolean doScale)
voidsetCenterSelected()
voidsetColorBackground(String colorName)
BitSetsetConformation()
BitSetsetConformation(int conformationIndex)
voidsetCurrentColorRange(String label)
voidsetCurrentColorRange(float[] data, BitSet bs)
voidsetCurrentColorRange(float min, float max)
voidsetCurrentModelIndex(int modelIndex)
voidsetCurrentModelIndex(int modelIndex, boolean clearBackground)
voidsetCurrentUnitCellOffset(int offset)
voidsetCurrentUnitCellOffset(Point3f pt)
voidsetCursor(int cursor)
voidsetData(String type, Object[] data, int atomCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)
voidsetDebugScript(boolean debugScript)
voidsetDefaultColors(String colorScheme)
voidsetDefaultDrawArrowScale(float scale)
voidsetDefaultLattice(Point3f ptLattice)
voidsetDefaults(String type)
voidsetDefaultVdw(String mode)
static voidsetDiffusePercent(int diffusePercent)
voidsetDynamicMeasurements(boolean TF)
voidsetEchoStateActive(boolean TF)
voidsetElementArgb(int elementNumber, int argb)
voidsetFileInfo(String[] fileInfo)
voidsetFloatProperty(String key, float value)
booleansetFloatProperty(String key, float value, boolean isInt)
voidsetFormalCharges(int formalCharge)
voidsetFrameTitle(int modelIndex, String title)
voidsetFrameTitle(String title)
voidsetFrameVariables(int firstModelIndex, int lastModelIndex)
voidsetFrankOn(boolean TF)
voidsetImageFontScaling(int width, int height)
voidsetInMotion(boolean inMotion)
voidsetIntProperty(String key, int value)
voidsetIntProperty(String key, int value, boolean defineNew)
voidsetJmolDataFrame(String type, int modelIndex, int dataIndex)
voidsetJmolDefaults()
voidsetJmolStatusListener(JmolStatusListener jmolStatusListener)
voidsetLabel(String strLabel)
voidsetListVariable(String name, Token value)
voidsetMarBond(short marBond)
voidsetMaximumSize(int x)
voidsetMeasureDistanceUnits(String units)
voidsetMeasurementFormats(String strFormat)
voidsetMenu(String fileOrText, boolean isFile)
voidsetMinBondDistance(float minBondDistance)
voidsetMinimizer(MinimizerInterface minimizer)
voidsetModelVisibility()
voidsetModeMouse(int modeMouse)
voidsetNavigationDepthPercent(float timeSec, float percent)
voidsetNavigationMode(boolean TF)
voidsetNewRotationCenter(Point3f center)
voidsetNoneSelected(boolean noneSelected)
voidsetObjectArgb(String name, int argb)
voidsetObjectColor(String name, String colorName)
voidsetObjectMad(int iShape, String name, int mad)
voidsetPdbConectBonding(boolean isAuto)
voidsetPendingMeasurement(MeasurementPending measurementPending)
voidsetPercentVdwAtom(int percentVdwAtom)
voidsetPerspectiveDepth(boolean perspectiveDepth)
voidsetPerspectiveModel(int mode)
voidsetPickingMode(String mode)
voidsetPickingStyle(String style)
voidsetPropertyColorScheme(String scheme, boolean isOverloaded)
voidsetProteinType(byte iType, BitSet bs)
voidsetRasmolDefaults()
voidsetRefreshing(boolean TF)
voidsetRotationRadius(float angstroms, boolean doAll)
voidsetRubberbandArgb(int argb)
voidsetScreenDimension(Dimension dim)
voidsetSelectionHalos(boolean TF)
voidsetSelectionSet(BitSet set)
voidsetSelectionSubset(BitSet subset)
voidsetShapeProperty(int shapeID, String propertyName, Object value)
voidsetShapeProperty(int shapeID, String propertyName, Object value, BitSet bs)
voidsetShapePropertyArgb(int shapeID, String propertyName, int argb)
voidsetShapeSize(int shapeID, int size)
voidsetShapeSize(int shapeID, int size, BitSet bsAtoms)
voidsetShowAxes(boolean value)
voidsetShowBbcage(boolean value)
voidsetShowHydrogens(boolean TF)
voidsetShowMeasurements(boolean TF)
voidsetShowUnitCell(boolean value)
voidsetSlabDepthInternal(boolean isDepth)
static voidsetSpecular(boolean specular)
static voidsetSpecularExponent(int specularExponent)
static voidsetSpecularPercent(int specularPercent)
static voidsetSpecularPower(int specularPower)
voidsetSpin(String key, int value)
voidsetSpinOn(boolean spinOn)
voidsetStatusAtomHovered(int atomIndex, String info)
voidsetStatusAtomPicked(int atomIndex, String info)
voidsetStatusFileLoaded(int ptLoad, String fullPathName, String fileName, String modelName, String strError)
voidsetStatusFileNotLoaded(String fullPathName, String errorMsg)
voidsetStatusFrameChanged(int frameNo)
voidsetStatusMeasurePicked(int iatom, String strMeasure)
voidsetStatusMeasuring(String status, int count, String strMeasure)
voidsetStatusResized(int width, int height)
voidsetStatusScriptStarted(int iscript, String script)
voidsetStereoMode(int stereoMode, String state)
voidsetStereoMode(int[] twoColors, String state)
voidsetStrandCount(int type, int value)
voidsetStringProperty(String key, String value)
voidsetSync()
voidsetSyncDriver(int mode)
voidsetSyncTarget(int mode, boolean TF)
voidsetTainted(boolean TF)
voidsetTaintedAtoms(BitSet bs, byte type)
voidsetTrajectory(int modelIndex)
voidsetTrajectory(BitSet bsModels)
voidsetTransformManagerDefaults()
static voidsetUserScale(int[] scale)
voidsetVectorScale(float scale)
voidsetVibrationOff()
voidsetVibrationPeriod(float period)
voidsetVibrationScale(float scale)
voidsetVisualRange(float angstroms)
voidshowConsole(boolean showConsole)
voidshowMeasurement(int[] atomCountPlusIndices, boolean isON)
booleanshowModelSetDownload()
voidshowParameter(String key, boolean ifNotSet, int nMax)
voidshowString(String str)
voidshowUrl(String urlString)
voidslabByPixels(int pixels)
voidslabDepthByPixels(int pixels)
voidslabInternal(Point4f plane, boolean isDepth)
voidslabReset()
voidslabToPercent(int percentSlab)
voidstartSpinningAxis(int atomIndex1, int atomIndex2, boolean isClockwise)
voidstartSpinningAxis(Point3f pt1, Point3f pt2, boolean isClockwise)
voidsyncScript(String script, String applet)
voidtoCartesian(Point3f pt)
voidtoFractional(Point3f pt)
voidtoggleMeasurement(int[] atomCountPlusIndices, String strFormat)
voidtogglePickingLabel(BitSet bs)
voidtoUnitCell(Point3f pt, Point3f offset)
Point3itransformPoint(Point3f pointAngstroms)
Point3itransformPoint(Point3f pointAngstroms, Vector3f vibrationVector)
voidtransformPoint(Point3f pointAngstroms, Point3i pointScreen)
voidtransformPoint(Point3f pointAngstroms, Point3f pointScreen)
voidtransformPointNoClip(Point3f pointAngstroms, Point3f pt)
voidtransformPoints(Point3f[] pointsAngstroms, Point3i[] pointsScreens)
voidtransformVector(Vector3f vectorAngstroms, Vector3f vectorTransformed)
voidtranslateToXPercent(float percent)
voidtranslateToYPercent(float percent)
voidtranslateToZPercent(float percent)
voidtranslateXYBy(int xDelta, int yDelta)
voidunsetProperty(String name)
voidunTransformPoint(Point3f pointScreen, Point3f pointAngstroms)
booleanuseMinimizationThread()
booleanusingScriptQueue()
voidwriteTextFile(String file, String data)
voidzap(boolean notify, boolean resetUndo)
voidzap(String msg)
voidzoomBy(int pixels)
voidzoomByFactor(float factor)
intzValueFromPercent(int zPercent)

Field Detail

antialiasDisplay

private boolean antialiasDisplay

appletCodeBase

private String appletCodeBase

appletDocumentBase

private String appletDocumentBase

autoExit

private boolean autoExit

axesAreTainted

private boolean axesAreTainted

checking

boolean checking

checkScriptOnly

private boolean checkScriptOnly

colorManager

private ColorManager colorManager

commandHistory

private CommandHistory commandHistory

compiler

private Compiler compiler

creatingImage

private boolean creatingImage

currentCursor

private int currentCursor

CURSOR_CROSSHAIR

public static final int CURSOR_CROSSHAIR

CURSOR_DEFAULT

public static final int CURSOR_DEFAULT

CURSOR_HAND

public static final int CURSOR_HAND

CURSOR_MOVE

public static final int CURSOR_MOVE

CURSOR_WAIT

public static final int CURSOR_WAIT

dataManager

private DataManager dataManager

dimScreen

final Dimension dimScreen

display

private Component display

eval

private Eval eval

evalVariables

private Hashtable evalVariables

fileManager

private FileManager fileManager

fileOpenCheck

private boolean fileOpenCheck

frankOn

boolean frankOn

fullName

private String fullName

g3d

private Graphics3D g3d

global

private StateManager.GlobalSettings global

haveDisplay

private boolean haveDisplay

hoverAtomIndex

int hoverAtomIndex

hoverText

String hoverText

htmlName

private String htmlName

imageFontScaling

private float imageFontScaling

interruptScript

String interruptScript

isApplet

private boolean isApplet

isPreviewOnly

private boolean isPreviewOnly

isScriptQueued

boolean isScriptQueued

isSignedApplet

private boolean isSignedApplet

isSilent

private boolean isSilent

isTainted

boolean isTainted

jvm11orGreater

private boolean jvm11orGreater

jvm12orGreater

private boolean jvm12orGreater

jvm14orGreater

private boolean jvm14orGreater

listCommands

private boolean listCommands

maximumSize

private int maximumSize

minimizer

private MinimizerInterface minimizer

modelAdapter

private JmolAdapter modelAdapter

modelManager

private ModelManager modelManager

modelSet

private ModelSet modelSet

motionEventNumber

int motionEventNumber

mouseManager

public MouseManager mouseManager

mustRender

private boolean mustRender

noneSelected

private boolean noneSelected

pickingManager

private PickingManager pickingManager

prevFrame

int prevFrame

refreshing

private boolean refreshing

repaintManager

private RepaintManager repaintManager

scriptIndex

int scriptIndex

scriptManager

private ScriptManager scriptManager

selectionManager

private SelectionManager selectionManager

stateManager

private StateManager stateManager

statusManager

private StatusManager statusManager

strJavaVendor

private String strJavaVendor

strJavaVersion

private String strJavaVersion

strOSName

private String strOSName

syncId

private String syncId

STATE_VERSION_STAMP

static final String STATE_VERSION_STAMP

tempManager

private TempArray tempManager

testData

public static Object testData

testData2

public static Object testData2

transformManager

private TransformManager transformManager

useCommandThread

private boolean useCommandThread

wasInMotion

boolean wasInMotion

writeInfo

private String writeInfo

Constructor Detail

Viewer

public Viewer(Component display, JmolAdapter modelAdapter)

Method Detail

addCommand

void addCommand(String command)
Adds one or more commands to the command history

Parameters: command the command to add

addLoadScript

void addLoadScript(String script)

addSelectionListener

public void addSelectionListener(JmolSelectionListener listener)

addStateScript

void addStateScript(String script, boolean addFrameNumber, boolean postDefinitions)

addStateScript

void addStateScript(String script1, BitSet bsBonds, BitSet bsAtoms1, BitSet bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)

allocateViewer

public static JmolViewer allocateViewer(Component display, JmolAdapter modelAdapter)
NOTE: for APPLICATION AND APPLET call setModeMouse(JmolConstants.MOUSE_NONE); before setting viewer=null in order to remove references to display window in listeners and hoverWatcher This is the main access point for creating an application or applet viewer. After allocation it is MANDATORY that one of the next commands is either viewer.evalString("ZAP"); or at least: viewer.setAppletContext("",null,null,"") One or the other of these is necessary to establish the first modelset, which might be required by one or more later evaluated commands or file loadings.

Parameters: display either DisplayPanel or WrappedApplet modelAdapter the model reader

Returns: a viewer instance

allocTempBytes

public byte[] allocTempBytes(int size)

allocTempPoints

public Point3f[] allocTempPoints(int size)

allocTempScreens

public Point3i[] allocTempScreens(int size)

allowRotateSelected

boolean allowRotateSelected()

areAxesTainted

public boolean areAxesTainted()

assignAromaticBonds

void assignAromaticBonds()

atomPicked

void atomPicked(int atomIndex, Point3f ptClicked, int modifiers)

autoHbond

int autoHbond(BitSet bsBonds)

autoHbond

int autoHbond(BitSet bsFrom, BitSet bsTo, BitSet bsBonds)

calcBoundBoxDimensions

void calcBoundBoxDimensions(BitSet bs)

calcRotationRadius

float calcRotationRadius(Point3f center)

calcRotationRadius

public float calcRotationRadius(BitSet bs)

calcSelectedGroupsCount

void calcSelectedGroupsCount()

calcSelectedMoleculesCount

void calcSelectedMoleculesCount()

calcSelectedMonomersCount

void calcSelectedMonomersCount()

calculateMolecularDipole

public Vector3f calculateMolecularDipole()

calculatePointGroup

String calculatePointGroup()

calculateStraightness

public void calculateStraightness()

calculateStructures

void calculateStructures(BitSet bsAtoms)

calculateSurface

public Point3f[] calculateSurface(BitSet bsSelected, float envelopeRadius)

checkHalt

public boolean checkHalt(String strScript)

checkObjectClicked

Point3f checkObjectClicked(int x, int y, int modifiers)

checkObjectDragged

void checkObjectDragged(int prevX, int prevY, int deltaX, int deltaY, int modifiers)

checkObjectHovered

boolean checkObjectHovered(int x, int y)

checkResume

public boolean checkResume(String strScript)

clear

private void clear()

clearAllMeasurements

void clearAllMeasurements()

clearBfactorRange

void clearBfactorRange()

clearClickCount

void clearClickCount()

clearConsole

void clearConsole()

clearMeasurements

public void clearMeasurements()

clearMinimization

private void clearMinimization()

clearScriptQueue

public void clearScriptQueue()

clearSelection

public void clearSelection()

createImage

private void createImage(String type_name)

Parameters: type_name TYPE:filename\twidth\theight\tquality

createImage

public String createImage(String file, String type, Object text_or_bytes, int quality, int width, int height)

defineMeasurement

void defineMeasurement(Vector monitorExpressions, float[] rangeMinMax, boolean isDelete, boolean isAll, boolean isAllConnected, boolean isOn, boolean isOff, String strFormat)

deleteAtoms

public int deleteAtoms(BitSet bs, boolean fullModels)

deleteMeasurement

public void deleteMeasurement(int i)

deleteMeasurement

void deleteMeasurement(int[] atomCountPlusIndices)

depthByPixels

void depthByPixels(int pixels)

depthToPercent

void depthToPercent(int percentDepth)

dialogAsk

public String dialogAsk(String type, String fileName)

display

void display(BitSet bs, boolean isQuiet)

echoMessage

void echoMessage(String msg)

eval

String eval(String strEval)

evalFile

public String evalFile(String strFilename)

evalString

public String evalString(String strScript)

evalStringQuiet

public String evalStringQuiet(String strScript)

evalStringQuiet

private String evalStringQuiet(String strScript, boolean isQuiet, boolean allowSyncScript)

evalStringWaitStatus

public Object evalStringWaitStatus(String returnType, String strScript, String statusList)

evalStringWaitStatus

Object evalStringWaitStatus(String returnType, String strScript, String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)

evaluateExpression

public Object evaluateExpression(Object stringOrTokens)

fillAtomData

public void fillAtomData(AtomData atomData, int mode)

finalize

protected void finalize()

finalizeTransformParameters

void finalizeTransformParameters()

findNearestAtomIndex

int findNearestAtomIndex(int x, int y)

formatText

public String formatText(String text0)

frankClicked

boolean frankClicked(int x, int y)

freeTempBytes

public void freeTempBytes(byte[] tempBytes)

freeTempPoints

public void freeTempPoints(Point3f[] tempPoints)

freeTempScreens

public void freeTempScreens(Point3i[] tempScreens)

functionXY

public float[][] functionXY(String functionName, int nX, int nY)
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. Otherwise it reads the values using individual function calls, which each return Double. If the functionName begins with "file:" then data are read from a file specified after the colon. The sign of nX is not relevant in that case. The file may contain mixed numeric and non-numeric values; the non-numeric values will be skipped by Parser.parseFloatArray

Parameters: functionName nX nY

Returns: nX by nY array of floating values

generateOutput

public String generateOutput(String type, String fileName, int width, int height)

getAllAtomInfo

Vector getAllAtomInfo(Object atomExpression)

getAllBondInfo

Vector getAllBondInfo(Object atomExpression)

getAllChainInfo

public Hashtable getAllChainInfo(Object atomExpression)

getAllowEmbeddedScripts

boolean getAllowEmbeddedScripts()

getAllPolymerInfo

public Hashtable getAllPolymerInfo(Object atomExpression)

getAllSettings

String getAllSettings(String prefix)

getAltLocListInModel

public String getAltLocListInModel(int modelIndex)

getAmbientPercent

static int getAmbientPercent()

getAnimationDirection

int getAnimationDirection()

getAnimationFps

public int getAnimationFps()

getAnimationInfo

Hashtable getAnimationInfo()

getAnimationReplayMode

int getAnimationReplayMode()

getAppendNew

public boolean getAppendNew()

getAppletInfo

Hashtable getAppletInfo()

getApplySymmetryToBonds

public boolean getApplySymmetryToBonds()

getAtomArgb

public int getAtomArgb(int i)

getAtomBits

public BitSet getAtomBits(int tokType, Object specInfo)

getAtomBitSet

BitSet getAtomBitSet(Object atomExpression)

getAtomBitSetVector

Vector getAtomBitSetVector(Object atomExpression)

getAtomChain

String getAtomChain(int i)

getAtomCount

public int getAtomCount()

getAtomCountInModel

public int getAtomCountInModel(int modelIndex)

getAtomIdentityInfo

public void getAtomIdentityInfo(int atomIndex, Hashtable info)

getAtomIndexFromAtomNumber

int getAtomIndexFromAtomNumber(int atomNumber)

getAtomIndices

int[] getAtomIndices(BitSet bs)

getAtomInfo

public String getAtomInfo(int atomIndex)

getAtomInfoXYZ

public String getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)

getAtomModelIndex

public int getAtomModelIndex(int i)

getAtomName

public String getAtomName(int i)

getAtomNumber

public int getAtomNumber(int i)

getAtomPicking

private boolean getAtomPicking()

getAtomPoint3f

public Point3f getAtomPoint3f(int i)

getAtomRadius

public float getAtomRadius(int i)

getAtomsConnected

BitSet getAtomsConnected(float min, float max, int intType, BitSet bs)

getAtomsWithin

BitSet getAtomsWithin(float distance, Point3f coord)

getAtomsWithin

BitSet getAtomsWithin(float distance, Point4f plane)

getAtomsWithin

BitSet getAtomsWithin(float distance, BitSet bs, boolean isWithinModelSet)

getAtomSequenceCode

String getAtomSequenceCode(int i)

getAtomSetCenter

public Point3f getAtomSetCenter(BitSet bs)

getAtomVdwRadius

public float getAtomVdwRadius(int i)

getAtomX

float getAtomX(int i)

getAtomY

float getAtomY(int i)

getAtomZ

float getAtomZ(int i)

getAutoBond

public boolean getAutoBond()

getAutoFps

boolean getAutoFps()

getAuxiliaryInfo

public Hashtable getAuxiliaryInfo(Object atomExpression)

getAverageAtomPoint

Point3f getAverageAtomPoint()

getAwtComponent

public Component getAwtComponent()

getAxesMode

public int getAxesMode()

getAxesOrientationRasmol

public boolean getAxesOrientationRasmol()

getAxesScale

public float getAxesScale()

getAxisAngle

void getAxisAngle(AxisAngle4f axisAngle)

getAxisPoints

public Point3f[] getAxisPoints()

getBackgroundArgb

public int getBackgroundArgb()

getBackgroundModelIndex

public int getBackgroundModelIndex()

getBitSetSelection

BitSet getBitSetSelection()

getBitSetTrajectories

public BitSet getBitSetTrajectories()

getBondArgb1

public int getBondArgb1(int i)

getBondArgb2

public int getBondArgb2(int i)

getBondCount

public int getBondCount()
For use in setting a for() construct max value

Returns: used size of the bonds array;

getBondCountInModel

public int getBondCountInModel(int modelIndex)
from JmolPopup.udateModelSetComputedMenu

Parameters: modelIndex the model of interest or -1 for all

Returns: the actual number of connections

getBondModelIndex

public int getBondModelIndex(int i)

getBondOrder

public short getBondOrder(int i)

getBondPicking

public boolean getBondPicking()

getBondPoint3f1

public Point3f getBondPoint3f1(int i)

getBondPoint3f2

public Point3f getBondPoint3f2(int i)

getBondRadius

public float getBondRadius(int i)

getBondsForSelectedAtoms

BitSet getBondsForSelectedAtoms(BitSet bsAtoms)

getBondSelectionModeOr

public boolean getBondSelectionModeOr()

getBondTolerance

public float getBondTolerance()

getBooleanProperty

public boolean getBooleanProperty(String key)

getBooleanProperty

public boolean getBooleanProperty(String key, boolean doICare)

Parameters: key doICare true if you want an error message if it doesn't exist

Returns: the boolean property mth 2005 06 24 and/or these property names should be interned strings so that we can just do == comparisions between strings

getBoundBoxCenter

public Point3f getBoundBoxCenter()

getBoundBoxCenterX

public int getBoundBoxCenterX()

getBoundBoxCenterY

public int getBoundBoxCenterY()

getBoundBoxCommand

public String getBoundBoxCommand(boolean withOptions)

getBoundBoxCornerVector

public Vector3f getBoundBoxCornerVector()

getBoundBoxInfo

Hashtable getBoundBoxInfo()

getBoundBoxModels

public BitSet getBoundBoxModels()

getBoxInfo

BoxInfo getBoxInfo(BitSet bs)

getBranchBitSet

BitSet getBranchBitSet(int atomIndex, int atomIndexNot)

getBufferedReaderForString

Object getBufferedReaderForString(String string)

getBufferedReaderOrErrorMessageFromName

Object getBufferedReaderOrErrorMessageFromName(String name, String[] fullPathNameReturn, boolean isBinary)

getCartoonRocketFlag

public boolean getCartoonRocketFlag()

getChainCaseSensitive

public boolean getChainCaseSensitive()

getChainCount

public int getChainCount()

getChainCountInModel

public int getChainCountInModel(int modelIndex)

getChainCountInModel

public int getChainCountInModel(int modelIndex, boolean countWater)

getChimeInfo

public String getChimeInfo(int tok)

getClickableSet

BitSet getClickableSet()

getClientAtomStringProperty

public String getClientAtomStringProperty(Object clientAtom, String propertyName)

getClientFile

Object getClientFile()

getColix

short getColix(Object object)

getColixArgb

public int getColixArgb(short colix)

getColixAtomPalette

public short getColixAtomPalette(Atom atom, byte pid)

getColixBackgroundContrast

public short getColixBackgroundContrast()

getColixForPropertyValue

public short getColixForPropertyValue(float val)

getColixRubberband

public short getColixRubberband()

getColorPointForPropertyValue

Point3f getColorPointForPropertyValue(float val)

getColorSchemeArray

public int[] getColorSchemeArray(String colorScheme)

getColorSchemeList

public String getColorSchemeList(String colorScheme, boolean ifDefault)

getCompiler

Compiler getCompiler()

getCoordinateState

public String getCoordinateState(BitSet bsSelected)

getCurrentColorRange

public float[] getCurrentColorRange()

getCurrentFileAsBytes

public Object getCurrentFileAsBytes()

getCurrentFileAsString

public String getCurrentFileAsString()

getCurrentModelIndex

public int getCurrentModelIndex()

getCurrentSolventProbeRadius

public float getCurrentSolventProbeRadius()

getCurrentUnitCell

public SymmetryInterface getCurrentUnitCell()

getCurrentUnitCellOffset

Point3f getCurrentUnitCellOffset()

getCursorX

public int getCursorX()

getCursorY

public int getCursorY()

getData

Object[] getData(String type)

getData

public String getData(String atomExpression, String type)

getDataFloat

float[] getDataFloat(String label)

getDataFloat

public float getDataFloat(String label, int atomIndex)

getDataFloat2D

float[][] getDataFloat2D(String label)

getDataSeparator

String getDataSeparator()

getDebugScript

boolean getDebugScript()

getDefaultDirectory

String getDefaultDirectory()

getDefaultDrawArrowScale

public float getDefaultDrawArrowScale()

getDefaultLattice

Point3f getDefaultLattice()

getDefaultLoadScript

String getDefaultLoadScript()

getDefaultMadAtom

public short getDefaultMadAtom()

getDefaultMeasurementLabel

public String getDefaultMeasurementLabel(int nPoints)

getDefaultTranslucent

float getDefaultTranslucent()

getDefaultVdw

String getDefaultVdw(int iMode)

getDelayMaximum

int getDelayMaximum()

getDeletedAtoms

public BitSet getDeletedAtoms()

getDiffusePercent

static int getDiffusePercent()

getDipoleScale

public float getDipoleScale()

getDisablePopupMenu

boolean getDisablePopupMenu()

getDisplayCellParameters

public boolean getDisplayCellParameters()

getDisplayModelIndex

public int getDisplayModelIndex()

getDotDensity

public int getDotDensity()

getDotsSelectedOnlyFlag

public boolean getDotsSelectedOnlyFlag()

getDotSurfaceFlag

public boolean getDotSurfaceFlag()

getDrawHover

public boolean getDrawHover()

getDrawPicking

public boolean getDrawPicking()

getDynamicMeasurements

public boolean getDynamicMeasurements()

getEchoStateActive

public boolean getEchoStateActive()

getElementNumber

int getElementNumber(int i)

getElementsPresentBitSet

public BitSet getElementsPresentBitSet(int modelIndex)

getElementSymbol

String getElementSymbol(int i)

getEvalVariables

Hashtable getEvalVariables()

getExportDriverList

public String getExportDriverList()

getExportJmolAdapter

JmolAdapter getExportJmolAdapter()
This is the method that should be used to extract the model data from Jmol. Note that the API provided by JmolAdapter is used to import data into Jmol and to export data out of Jmol. When exporting, a few of the methods in JmolAdapter do not make sense. openBufferedReader(...) Others may be implemented in the future, but are not currently all pdb specific things Just pass in null for the methods that want a clientFile. The main methods to use are getFrameCount(null) -> currently always returns 1 getAtomCount(null, 0) getAtomIterator(null, 0) getBondIterator(null, 0) The AtomIterator and BondIterator return Objects as unique IDs to identify the atoms. atomIterator.getAtomUid() bondIterator.getAtomUid1() & bondIterator.getAtomUid2() The ExportJmolAdapter will return the 0-based atom index as a boxed Integer. That means that you can cast the results to get a zero-based atom index int atomIndex = ((Integer)atomIterator.getAtomUid()).intValue(); ... int bondedAtom1 = ((Integer)bondIterator.getAtomUid1()).intValue(); int bondedAtom2 = ((Integer)bondIterator.getAtomUid2()).intValue(); post questions to jmol-developers@lists.sf.net

Returns: A JmolAdapter

getFileAsImage

Object getFileAsImage(String pathName, Hashtable htParams)

getFileAsString

public String getFileAsString(String name)

getFileAsString

boolean getFileAsString(String[] data)

getFileHeader

String getFileHeader()

getFileInfo

String[] getFileInfo()

getFileName

public String getFileName()

getFont3D

Font3D getFont3D(String fontFace, String fontStyle, float fontSize)

getFontScaling

public boolean getFontScaling()

getForceAutoBond

public boolean getForceAutoBond()

getFrameRenderer

public FrameRenderer getFrameRenderer()

getFrameTitle

String getFrameTitle(int modelIndex)

getFrameTitle

public String getFrameTitle()

getFullPathName

public String getFullPathName()

getGlobalSettings

StateManager.GlobalSettings getGlobalSettings()

getGraphics3D

public Graphics3D getGraphics3D()

getGreyscaleRendering

boolean getGreyscaleRendering()

getGroupCount

public int getGroupCount()

getGroupCountInModel

public int getGroupCountInModel(int modelIndex)

getHbondsBackbone

public boolean getHbondsBackbone()

getHbondsSolid

public boolean getHbondsSolid()

getHelp

void getHelp(String what)

getHermiteLevel

public int getHermiteLevel()

getHeteroList

public Hashtable getHeteroList(int modelIndex)

getHexColorFromIndex

public String getHexColorFromIndex(short colix)

getHiddenSet

BitSet getHiddenSet()

getHideNameInPopup

boolean getHideNameInPopup()

getHighResolution

public boolean getHighResolution()

getHoverDelay

int getHoverDelay()

getHtmlName

String getHtmlName()

getHybridizationAndAxes

public String getHybridizationAndAxes(int atomIndex, Vector3f z, Vector3f x, String lcaoType, boolean hybridizationCompatible)

getImage

private Image getImage(boolean isDouble)

getImageFontScaling

public float getImageFontScaling()

getInlineChar

public char getInlineChar()

getInMotion

public boolean getInMotion()

getInterruptScript

String getInterruptScript()

getIsosurfacePropertySmoothing

boolean getIsosurfacePropertySmoothing()

getJavaVendor

public String getJavaVendor()

getJavaVersion

public String getJavaVersion()

getJmolDataFrameIndex

int getJmolDataFrameIndex(int modelIndex, String type)

getJmolDataSourceFrame

public int getJmolDataSourceFrame(int modelIndex)

getJmolFrameType

String getJmolFrameType(int modelIndex)

getJmolVersion

public static String getJmolVersion()

getJmolVersionInt

private static int getJmolVersionInt()

getJpeg

public Object getJpeg(int quality, boolean asString)

Parameters: quality asString

Returns: base64-encoded or binary version of the image

getJustifyMeasurements

public boolean getJustifyMeasurements()

getListVariable

Object getListVariable(String name, Object value)

getLoadFormat

String getLoadFormat()

getLoadState

String getLoadState()

getLogLevel

static int getLogLevel()

getMadBond

public short getMadBond()

getMarBond

public short getMarBond()

getMatrixRotate

Matrix3f getMatrixRotate()

getMatrixtransform

public Matrix4f getMatrixtransform()

getMaxZoomPercent

float getMaxZoomPercent()

getMeasureAllModelsFlag

public boolean getMeasureAllModelsFlag()

getMeasureDistanceUnits

public String getMeasureDistanceUnits()

getMeasurementCount

public int getMeasurementCount()

getMeasurementCountPlusIndices

public int[] getMeasurementCountPlusIndices(int i)

getMeasurementInfo

Vector getMeasurementInfo()

getMeasurementInfoAsString

public String getMeasurementInfoAsString()

getMeasurementStringValue

public String getMeasurementStringValue(int i)

getMenu

String getMenu(String type)

getMessageQueue

public Hashtable getMessageQueue()

getMessageStyleChime

boolean getMessageStyleChime()

getMinBondDistance

public float getMinBondDistance()

getMinimizationInfo

public String getMinimizationInfo()

getMinimizer

public MinimizerInterface getMinimizer()

getModelAtomBitSet

public BitSet getModelAtomBitSet(int modelIndex, boolean asCopy)

getModelAuxiliaryInfo

public Hashtable getModelAuxiliaryInfo(int modelIndex)

getModelAuxiliaryInfo

public Object getModelAuxiliaryInfo(int modelIndex, String keyName)

getModelBitSet

public BitSet getModelBitSet(BitSet atomList)

getModelCount

public int getModelCount()

getModelDipole

public Vector3f getModelDipole()

getModelExtract

String getModelExtract(Object atomExpression)

getModelFileInfo

public String getModelFileInfo()

getModelFileInfoAll

String getModelFileInfoAll()

getModelFileName

private String getModelFileName(int modelIndex)

getModelFileNumber

public int getModelFileNumber(int modelIndex)

getModelInfo

public Hashtable getModelInfo(Object atomExpression)

getModelInfoAsString

String getModelInfoAsString()

getModelName

public String getModelName(int modelIndex)

getModelNumber

public int getModelNumber(int modelIndex)

getModelNumberDotted

public String getModelNumberDotted(int modelIndex)

getModelNumberIndex

int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)

getModelProperties

public Properties getModelProperties(int modelIndex)

getModelProperty

public String getModelProperty(int modelIndex, String propertyName)

getModelSet

public ModelSet getModelSet()

getModelSetAuxiliaryInfo

public Object getModelSetAuxiliaryInfo(String strKey)

getModelSetAuxiliaryInfo

public Hashtable getModelSetAuxiliaryInfo()

getModelSetFileName

public String getModelSetFileName()

getModelSetName

public String getModelSetName()

getModelSetPathName

public String getModelSetPathName()

getModelSetProperties

public Properties getModelSetProperties()

getModelSetProperty

public String getModelSetProperty(String strProp)

getModelSetTypeName

public String getModelSetTypeName()

getModelTitle

private String getModelTitle(int modelIndex)

getModeMultipleBond

public byte getModeMultipleBond()

getMoleculeInfo

Vector getMoleculeInfo(Object atomExpression)

getMotionEventNumber

public int getMotionEventNumber()

getMoveToText

String getMoveToText(float timespan)

getNavigating

public boolean getNavigating()

getNavigationCenter

Point3f getNavigationCenter()

getNavigationCentered

public boolean getNavigationCentered()

getNavigationDepthPercent

float getNavigationDepthPercent()

getNavigationMode

boolean getNavigationMode()

getNavigationOffset

public Point3f getNavigationOffset()

getNavigationOffsetPercent

float getNavigationOffsetPercent(char XorY)

getNavigationPeriodic

boolean getNavigationPeriodic()

getNavigationSpeed

float getNavigationSpeed()

getNoneSelected

Boolean getNoneSelected()

getObjectArgb

int getObjectArgb(int objId)

getObjectColix

public short getObjectColix(int objId)

getObjectMad

public int getObjectMad(int objId)

getObjectState

public String getObjectState(String name)

getOpenFileError

public String getOpenFileError()
misnamed -- really this opens the file, gets the data, and returns error or null

Returns: errorMsg

getOpenFileError

String getOpenFileError(boolean isAppend)
the opener for Jmol

Parameters: isAppend

Returns: errorMsg

getOperatingSystemName

public String getOperatingSystemName()

getOrientationInfo

Hashtable getOrientationInfo()

getOrientationText

String getOrientationText(int type)

getParameter

public Object getParameter(String key)

getParameterEscaped

Object getParameterEscaped(String key)

getPartialCharges

public float[] getPartialCharges()

getPdbData

public String getPdbData(BitSet bs)

getPdbData

String getPdbData(int modelIndex, String type)

getPdbLoadInfo

public boolean getPdbLoadInfo(int type)

getPDBHeader

String getPDBHeader()

getPendingMeasurement

MeasurementPending getPendingMeasurement()

getPercentVdwAtom

public int getPercentVdwAtom()

getPerspectiveDepth

public boolean getPerspectiveDepth()

getPickingMode

public int getPickingMode()

getPickingSpinRate

int getPickingSpinRate()

getPickingStyle

int getPickingStyle()

getPointGroupAsString

public String getPointGroupAsString(boolean asDraw, String type, int index, float scale)

getPointGroupInfo

public Hashtable getPointGroupInfo(Object atomExpression)

getPointGroupTolerance

public float getPointGroupTolerance(int type)

getPolymerCount

public int getPolymerCount()

getPolymerCountInModel

public int getPolymerCountInModel(int modelIndex)

getPolymerLeadMidPoints

public Point3f[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)

getPolymerPointsAndVectors

void getPolymerPointsAndVectors(BitSet bs, Vector vList)

getProperty

public Object getProperty(String returnType, String infoType, String paramInfo)

getProperty

public Object getProperty(String returnType, String infoType, Object paramInfo)

getPropertyColorScheme

public String getPropertyColorScheme()

getProteinStructureState

String getProteinStructureState()

getQuaternionFrame

public char getQuaternionFrame()

getRasmolHeteroSetting

boolean getRasmolHeteroSetting()

getRasmolHydrogenSetting

boolean getRasmolHydrogenSetting()

getRefreshing

boolean getRefreshing()

getRibbonAspectRatio

public int getRibbonAspectRatio()

getRibbonBorder

public boolean getRibbonBorder()

getRocketBarrelFlag

public boolean getRocketBarrelFlag()

getRotation

void getRotation(Matrix3f matrixRotation)

getRotationCenter

public Point3f getRotationCenter()

getRotationRadius

public float getRotationRadius()

getRubberBandSelection

Rectangle getRubberBandSelection()

getSavedCoordinates

String getSavedCoordinates(String saveName)

getSavedState

public String getSavedState(String saveName)

getSavedStructure

String getSavedStructure(String saveName)

getScalePixelsPerAngstrom

public float getScalePixelsPerAngstrom()

getScreenDim

public int getScreenDim()

getScreenHeight

public int getScreenHeight()

getScreenImage

public Image getScreenImage()

getScreenWidth

public int getScreenWidth()

getScriptDelay

int getScriptDelay()

getSelectAllModels

boolean getSelectAllModels()

getSelectionCount

public int getSelectionCount()

getSelectionHaloEnabled

public boolean getSelectionHaloEnabled()

getSelectionSet

public BitSet getSelectionSet()

getSelectionSubset

public BitSet getSelectionSubset()

getSequenceBits

BitSet getSequenceBits(String specInfo, BitSet bs)

getSetHistory

public String getSetHistory(int howFarBack)
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;

Parameters: howFarBack number of lines (-1 for next line)

Returns: one or more lines of command history

getShapeIdFromObjectName

int getShapeIdFromObjectName(String objectName)

getShapeInfo

public Hashtable getShapeInfo()

getShapeProperty

public Object getShapeProperty(int shapeType, String propertyName)

getShapeProperty

Object getShapeProperty(int shapeType, String propertyName, int index)

getShapePropertyAsInt

int getShapePropertyAsInt(int shapeID, String propertyName)

getSheetSmoothing

public float getSheetSmoothing()

getShowAxes

public boolean getShowAxes()

getShowBbcage

public boolean getShowBbcage()

getShowFrank

public boolean getShowFrank()

getShowHiddenSelectionHalos

public boolean getShowHiddenSelectionHalos()

getShowHydrogens

public boolean getShowHydrogens()

getShowMeasurementLabels

public boolean getShowMeasurementLabels()

getShowMeasurements

public boolean getShowMeasurements()

getShowMultipleBonds

public boolean getShowMultipleBonds()

getShowNavigationPoint

public boolean getShowNavigationPoint()

getShowUnitCell

public boolean getShowUnitCell()

getSlabEnabled

public boolean getSlabEnabled()

getSmartAromatic

public boolean getSmartAromatic()

getSolventOn

boolean getSolventOn()

getSolventProbeRadius

float getSolventProbeRadius()

getSpaceGroupInfoText

public String getSpaceGroupInfoText(String spaceGroup)

getSpecular

boolean getSpecular()

getSpecularPercent

static int getSpecularPercent()

getSpecularState

String getSpecularState()

getSpinFps

float getSpinFps()

getSpinOn

boolean getSpinOn()

getSpinState

String getSpinState()

getSpinX

float getSpinX()

getSpinY

float getSpinY()

getSpinZ

float getSpinZ()

getSsbondsBackbone

public boolean getSsbondsBackbone()

getStandardLabelFormat

public String getStandardLabelFormat()

getStateInfo

public String getStateInfo()

getStateInfo

public String getStateInfo(String type)

getStatusChanged

Object getStatusChanged(String statusNameList)

getStereoDegrees

float getStereoDegrees()

getStereoImage

private Image getStereoImage(int stereoMode)

getStereoMode

int getStereoMode()

getStrandCount

public int getStrandCount(int type)

getStructureState

public String getStructureState()

getSurfaceDistanceMax

int getSurfaceDistanceMax()

getSymmetryInfoAsString

String getSymmetryInfoAsString()

getTaintedAtoms

BitSet getTaintedAtoms(byte type)

getTestFlag1

public boolean getTestFlag1()

getTestFlag2

public boolean getTestFlag2()

getTestFlag3

public boolean getTestFlag3()

getTestFlag4

public boolean getTestFlag4()

getTraceAlpha

public boolean getTraceAlpha()

getTrajectoryInfo

String getTrajectoryInfo()

getTransformText

String getTransformText()

getTranslationScript

String getTranslationScript()

getTranslationXPercent

float getTranslationXPercent()

getTranslationYPercent

float getTranslationYPercent()

getTranslationZPercent

float getTranslationZPercent()

getUnitCellInfoText

public String getUnitCellInfoText()

getUnscaledTransformMatrix

public Matrix4f getUnscaledTransformMatrix()

getUseNumberLocalization

public boolean getUseNumberLocalization()

getVanderwaalsMar

public int getVanderwaalsMar(int i)

getVanderwaalsMar

public int getVanderwaalsMar(int i, int iMode)

getVectorScale

public float getVectorScale()

getVibrationCoord

float getVibrationCoord(int atomIndex, char c)

getVibrationPeriod

float getVibrationPeriod()

getVibrationScale

float getVibrationScale()

getVibrationVector

public Vector3f getVibrationVector(int atomIndex)

getVisibleFramesBitSet

public BitSet getVisibleFramesBitSet()

getVisibleSet

BitSet getVisibleSet()

getWireframeRotation

public boolean getWireframeRotation()

getWithinAtomSetIterator

public AtomIndexIterator getWithinAtomSetIterator(int atomIndex, float distance, BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)

getWithinModelIterator

public AtomIndexIterator getWithinModelIterator(Atom atom, float distance)

getZeroBasedXyzRasmol

public boolean getZeroBasedXyzRasmol()

getZoomEnabled

boolean getZoomEnabled()

getZoomLarge

boolean getZoomLarge()

getZoomPercent

public int getZoomPercent()

getZoomPercentFloat

public float getZoomPercentFloat()

getZoomSetting

float getZoomSetting()

getZShade

boolean getZShade()

haltScriptExecution

public void haltScriptExecution()

handleOldJvm10Event

public boolean handleOldJvm10Event(Event e)

hasCalculatedHBonds

public boolean hasCalculatedHBonds(BitSet bsAtoms)

haveFileSet

boolean haveFileSet()

haveFrame

public boolean haveFrame()

haveModelSet

boolean haveModelSet()

havePartialCharges

public boolean havePartialCharges()

hide

void hide(BitSet bs, boolean isQuiet)

hideMeasurements

void hideMeasurements(boolean isOFF)

homePosition

public void homePosition()

hoverOff

void hoverOff()

hoverOn

public void hoverOn(int atomIndex)

hoverOn

public void hoverOn(int x, int y, String text)

initialize

void initialize()

initializeModel

private void initializeModel()

invertSelected

void invertSelected(Point3f pt, BitSet bs)

invertSelected

void invertSelected(Point3f pt, Point4f plane)

invertSelection

void invertSelection()

isAnimationOn

boolean isAnimationOn()

isApplet

public boolean isApplet()

isInPosition

boolean isInPosition(Point3f pt, float degrees)

isInSelectionSubset

boolean isInSelectionSubset(int atomIndex)

isJmolDataFrame

public boolean isJmolDataFrame(int modelIndex)

isJmolDataFrame

public boolean isJmolDataFrame()

isJmolVariable

boolean isJmolVariable(String key)

isJvm12orGreater

public boolean isJvm12orGreater()

isPreviewOnly

boolean isPreviewOnly()

isRangeSelected

public boolean isRangeSelected()

isScriptExecuting

public boolean isScriptExecuting()

isSelected

public boolean isSelected(int atomIndex)

isSignedApplet

public boolean isSignedApplet()

isTrajectory

boolean isTrajectory(int modelIndex)

isVibrationOn

public boolean isVibrationOn()

isWindowCentered

boolean isWindowCentered()

listSavedStates

String listSavedStates()

loadData

void loadData(int type, String name, String coordinateData)

loadInline

public void loadInline(String strModel)

loadInline

public void loadInline(String strModel, boolean isAppend)

loadInline

public void loadInline(String strModel, char newLine)

loadInline

boolean loadInline(String strModel, char newLine, boolean isAppend)

loadInline

public void loadInline(String[] arrayModels)

loadInline

public void loadInline(String[] arrayModels, boolean isAppend)

loadShape

public void loadShape(int shapeID)

makeConnections

int[] makeConnections(float minDistance, float maxDistance, short order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds)

modelHasVibrationVectors

public boolean modelHasVibrationVectors(int modelIndex)

modelSetHasVibrationVectors

boolean modelSetHasVibrationVectors()

move

void move(Vector3f dRot, float dZoom, Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps)

moveTo

void moveTo(float floatSecondsTotal, Point3f center, Point3f pt, float degrees, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth)

moveTo

void moveTo(float floatSecondsTotal, Matrix3f rotationMatrix, Point3f center, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth)

moveUpdate

private void moveUpdate(float floatSecondsTotal)

mustRenderFlag

boolean mustRenderFlag()

navigate

void navigate(int keyWhere, int modifiers)

navigate

void navigate(float timeSeconds, Point3f[] path, float[] theta, int indexStart, int indexEnd)

navigate

void navigate(float timeSeconds, Point3f center)

navigate

void navigate(float timeSeconds, Point3f[][] pathGuide)

navigate

void navigate(float timeSeconds, Vector3f rotAxis, float degrees)

navTranslate

void navTranslate(float timeSeconds, Point3f center)

navTranslatePercent

void navTranslatePercent(float timeSeconds, float x, float y)

notifyMinimizationStatus

public void notifyMinimizationStatus()

openClientFile

public void openClientFile(String fullPathName, String fileName, Object clientFile)

openDOM

public void openDOM(Object DOMNode)

openFile

public void openFile(String name)

openFile

void openFile(String name, Hashtable htParams, String loadScript, boolean isAppend)

openFiles

public void openFiles(String modelName, String[] names)

openFiles

void openFiles(String modelName, String[] names, String loadScript, boolean isAppend)

openReader

public void openReader(String fullPathName, String name, Reader reader)
Opens the file, given the reader. name is a text name of the file ... to be displayed in the window no need to pass a BufferedReader ... ... the FileManager will wrap a buffer around it DO NOT USE IN JMOL -- THIS METHOD IS ONLY HERE BECAUSE IT IS PART OF THE LEGACY INTERFACE IF USED BY ANOTHER APPLICATION, YOU ARE RESPONSIBLE FOR CLOSING THE READER

Parameters: fullPathName name reader

openStringInline

public void openStringInline(String strModel)

openStringInline

private boolean openStringInline(String strModel, Hashtable htParams, boolean isAppend)

openStringsInline

private void openStringsInline(String[] arrayModels, Hashtable htParams, boolean isAppend)

pauseAnimation

void pauseAnimation()

pauseScriptExecution

public void pauseScriptExecution()

popHoldRepaint

public void popHoldRepaint()

popupMenu

void popupMenu(int x, int y)

pushHoldRepaint

public void pushHoldRepaint()

rebond

public void rebond()

refresh

public void refresh(int mode, String strWhy)
initiate a repaint/update sequence if it has not already been requested. invoked whenever any operation causes changes that require new rendering. The repaint/update sequence will only be invoked if (a) no repaint is already pending and (b) there is no hold flag set in repaintManager. Sequence is as follows: 1) RepaintManager.refresh() checks flags and then calls Viewer.repaint() 2) Viewer.repaint() invokes display.repaint(), provided display is not null (headless) 3) The system responds with an invocation of Jmol.update(Graphics g), which we are routing through Jmol.paint(Graphics g). 4) Jmol.update invokes Viewer.setScreenDimension(size), which makes the necessary changes in parameters for any new window size. 5) Jmol.update invokes Viewer.renderScreenImage(g, size, rectClip) 6) Viewer.renderScreenImage checks object visibility, invokes render1 to do the actual creation of the image pixel map and send it to the screen, and then invokes repaintView() 7) Viewer.repaintView() invokes RepaintManager.repaintDone(), to clear the flags and then use notify() to release any threads holding on wait().

Parameters: mode strWhy

refreshMeasures

public void refreshMeasures()

releaseScreenImage

public void releaseScreenImage()

removeCommand

String removeCommand()
Removes one command from the command history

Returns: command removed

removeSelectionListener

public void removeSelectionListener(JmolSelectionListener listener)

removeUserVariable

void removeUserVariable(String key)

render

private void render()

render1

private void render1(Graphics g, Image img, int x, int y)

renderScreenImage

public void renderScreenImage(Graphics g, Dimension size, Rectangle clip)

repaint

void repaint()

repaintView

public void repaintView()

reportSelection

void reportSelection(String msg)

requestRepaintAndWait

void requestRepaintAndWait()

reset

void reset()

resetAromatic

void resetAromatic()

resizeImage

private void resizeImage(int width, int height, boolean isImageWrite, boolean isGenerator, boolean isReset)

restoreBonds

boolean restoreBonds(String saveName)

restoreModelOrientation

void restoreModelOrientation(int modelIndex)

restoreModelRotation

void restoreModelRotation(int modelIndex)

restoreOrientation

boolean restoreOrientation(String saveName, float timeSeconds)

restoreRotation

public void restoreRotation(String saveName, float timeSeconds)

restoreSelection

boolean restoreSelection(String saveName)

resumeAnimation

void resumeAnimation()

resumeScriptExecution

public void resumeScriptExecution()

reverseAnimation

void reverseAnimation()

rewindAnimation

void rewindAnimation()

rotateAboutPointsInternal

void rotateAboutPointsInternal(Point3f point1, Point3f point2, float nDegrees, float endDegrees, boolean isSpin, BitSet bsSelected)

rotateAtoms

void rotateAtoms(Matrix3f mNew, Matrix3f matrixRotate, boolean fullMolecule, Point3f center, boolean isInternal, BitSet bsAtoms)

rotateAxisAngleAtCenter

void rotateAxisAngleAtCenter(Point3f rotCenter, Vector3f rotAxis, float degrees, float endDegrees, boolean isSpin, BitSet bsSelected)

rotateFront

public void rotateFront()

rotateMolecule

void rotateMolecule(int deltaX, int deltaY)

rotatePoint

public void rotatePoint(Point3f pt, Point3f ptRot)

rotateX

public void rotateX(float angleRadians)

rotateX

public void rotateX(int angleDegrees)

rotateXYBy

void rotateXYBy(int xDelta, int yDelta)

rotateY

public void rotateY(float angleRadians)

rotateY

public void rotateY(int angleDegrees)

rotateZ

public void rotateZ(float angleRadians)

rotateZBy

void rotateZBy(int zDelta)

saveBonds

void saveBonds(String saveName)

saveCoordinates

public void saveCoordinates(String saveName, BitSet bsSelected)

saveModelOrientation

void saveModelOrientation()

saveOrientation

void saveOrientation(String saveName)

saveSelection

void saveSelection(String saveName)

saveState

void saveState(String saveName)

saveStructure

void saveStructure(String saveName)

scaleToPerspective

public float scaleToPerspective(int z, float sizeAngstroms)

scaleToScreen

public short scaleToScreen(int z, int milliAngstroms)

script

public String script(String strScript)

scriptCheck

public String scriptCheck(String strScript)

scriptEcho

public void scriptEcho(String strEcho)

scriptError

private void scriptError(String msg)

scriptStatus

void scriptStatus(String strStatus)

scriptWait

public String scriptWait(String strScript)

scriptWaitStatus

public Object scriptWaitStatus(String strScript, String statusList)

select

void select(BitSet bs, boolean isQuiet)

selectAll

public void selectAll()

selectBonds

void selectBonds(BitSet bs)

selectRectangle

void selectRectangle(Rectangle rect, int modifiers)

setAllowRotateSelected

void setAllowRotateSelected(boolean TF)

setAmbientPercent

private static void setAmbientPercent(int ambientPercent)

setAnimationDirection

void setAnimationDirection(int direction)

setAnimationFps

public void setAnimationFps(int fps)

setAnimationLast

void setAnimationLast()

setAnimationNext

void setAnimationNext()

setAnimationOn

void setAnimationOn(boolean animationOn)

setAnimationPrevious

void setAnimationPrevious()

setAnimationRange

void setAnimationRange(int modelIndex1, int modelIndex2)

setAnimationReplayMode

void setAnimationReplayMode(int replay, float firstFrameDelay, float lastFrameDelay)

setAntialias

private void setAntialias(int mode, boolean TF)

setAppendNew

void setAppendNew(boolean value)

setAppletContext

public void setAppletContext(String fullName, URL documentBase, URL codeBase, String commandOptions)

setApplySymmetryToBonds

void setApplySymmetryToBonds(boolean TF)

setAtomCoord

public void setAtomCoord(int atomIndex, float x, float y, float z)

setAtomCoord

void setAtomCoord(BitSet bs, int tokType, Object xyzValues)

setAtomCoordRelative

public void setAtomCoordRelative(int atomIndex, float x, float y, float z)

setAtomCoordRelative

void setAtomCoordRelative(Point3f offset)

setAtomProperty

void setAtomProperty(BitSet bs, int tok, int iValue, float fValue, float[] values)

setAutoBond

public void setAutoBond(boolean TF)

setAxesModeMolecular

private void setAxesModeMolecular(boolean TF)

setAxesModeUnitCell

void setAxesModeUnitCell(boolean TF)

setAxesOrientationRasmol

public void setAxesOrientationRasmol(boolean TF)

setAxesScale

void setAxesScale(float scale)

setBackgroundImage

void setBackgroundImage(String fileName, Image image)

setBackgroundModelIndex

void setBackgroundModelIndex(int modelIndex)

setBondTolerance

public void setBondTolerance(float bondTolerance)

setBooleanProperty

public void setBooleanProperty(String key, boolean value)

setBooleanProperty

boolean setBooleanProperty(String key, boolean value, boolean defineNew)

setBoundBox

void setBoundBox(Point3f pt1, Point3f pt2, boolean byCorner)

setCenterAt

void setCenterAt(String relativeTo, Point3f pt)

setCenterBitSet

void setCenterBitSet(BitSet bsCenter, boolean doScale)

setCenterSelected

public void setCenterSelected()

setColorBackground

public void setColorBackground(String colorName)

setConformation

public BitSet setConformation()

setConformation

public BitSet setConformation(int conformationIndex)

setCurrentColorRange

void setCurrentColorRange(String label)

setCurrentColorRange

void setCurrentColorRange(float[] data, BitSet bs)

setCurrentColorRange

public void setCurrentColorRange(float min, float max)

setCurrentModelIndex

void setCurrentModelIndex(int modelIndex)

setCurrentModelIndex

public void setCurrentModelIndex(int modelIndex, boolean clearBackground)

setCurrentUnitCellOffset

void setCurrentUnitCellOffset(int offset)

setCurrentUnitCellOffset

void setCurrentUnitCellOffset(Point3f pt)

setCursor

public void setCursor(int cursor)

setData

public void setData(String type, Object[] data, int atomCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)

setDebugScript

public void setDebugScript(boolean debugScript)

setDefaultColors

private void setDefaultColors(String colorScheme)

setDefaultDrawArrowScale

public void setDefaultDrawArrowScale(float scale)

setDefaultLattice

void setDefaultLattice(Point3f ptLattice)

setDefaults

private void setDefaults(String type)

setDefaultVdw

void setDefaultVdw(String mode)

setDiffusePercent

private static void setDiffusePercent(int diffusePercent)

setDynamicMeasurements

void setDynamicMeasurements(boolean TF)

setEchoStateActive

void setEchoStateActive(boolean TF)

setElementArgb

void setElementArgb(int elementNumber, int argb)

setFileInfo

void setFileInfo(String[] fileInfo)

setFloatProperty

public void setFloatProperty(String key, float value)

setFloatProperty

private boolean setFloatProperty(String key, float value, boolean isInt)

setFormalCharges

void setFormalCharges(int formalCharge)

setFrameTitle

void setFrameTitle(int modelIndex, String title)

setFrameTitle

void setFrameTitle(String title)

setFrameVariables

void setFrameVariables(int firstModelIndex, int lastModelIndex)

setFrankOn

public void setFrankOn(boolean TF)

setImageFontScaling

private void setImageFontScaling(int width, int height)

setInMotion

void setInMotion(boolean inMotion)

setIntProperty

public void setIntProperty(String key, int value)

setIntProperty

private void setIntProperty(String key, int value, boolean defineNew)

setJmolDataFrame

void setJmolDataFrame(String type, int modelIndex, int dataIndex)

setJmolDefaults

public void setJmolDefaults()

setJmolStatusListener

public void setJmolStatusListener(JmolStatusListener jmolStatusListener)

setLabel

void setLabel(String strLabel)

setListVariable

void setListVariable(String name, Token value)

setMarBond

public void setMarBond(short marBond)

setMaximumSize

private void setMaximumSize(int x)

setMeasureDistanceUnits

void setMeasureDistanceUnits(String units)

setMeasurementFormats

void setMeasurementFormats(String strFormat)

setMenu

void setMenu(String fileOrText, boolean isFile)

setMinBondDistance

public void setMinBondDistance(float minBondDistance)

setMinimizer

public void setMinimizer(MinimizerInterface minimizer)

setModelVisibility

void setModelVisibility()

setModeMouse

public void setModeMouse(int modeMouse)

setNavigationDepthPercent

void setNavigationDepthPercent(float timeSec, float percent)

setNavigationMode

private void setNavigationMode(boolean TF)

setNewRotationCenter

void setNewRotationCenter(Point3f center)

setNoneSelected

void setNoneSelected(boolean noneSelected)

setObjectArgb

void setObjectArgb(String name, int argb)

setObjectColor

void setObjectColor(String name, String colorName)

setObjectMad

void setObjectMad(int iShape, String name, int mad)

setPdbConectBonding

void setPdbConectBonding(boolean isAuto)

setPendingMeasurement

void setPendingMeasurement(MeasurementPending measurementPending)

setPercentVdwAtom

public void setPercentVdwAtom(int percentVdwAtom)

setPerspectiveDepth

public void setPerspectiveDepth(boolean perspectiveDepth)

setPerspectiveModel

private void setPerspectiveModel(int mode)

setPickingMode

private void setPickingMode(String mode)

setPickingStyle

private void setPickingStyle(String style)

setPropertyColorScheme

public void setPropertyColorScheme(String scheme, boolean isOverloaded)

setProteinType

void setProteinType(byte iType, BitSet bs)

setRasmolDefaults

public void setRasmolDefaults()

setRefreshing

void setRefreshing(boolean TF)

setRotationRadius

void setRotationRadius(float angstroms, boolean doAll)

setRubberbandArgb

void setRubberbandArgb(int argb)

setScreenDimension

public void setScreenDimension(Dimension dim)

setSelectionHalos

public void setSelectionHalos(boolean TF)

setSelectionSet

public void setSelectionSet(BitSet set)

setSelectionSubset

void setSelectionSubset(BitSet subset)

setShapeProperty

public void setShapeProperty(int shapeID, String propertyName, Object value)

setShapeProperty

void setShapeProperty(int shapeID, String propertyName, Object value, BitSet bs)

setShapePropertyArgb

void setShapePropertyArgb(int shapeID, String propertyName, int argb)

setShapeSize

void setShapeSize(int shapeID, int size)

setShapeSize

public void setShapeSize(int shapeID, int size, BitSet bsAtoms)

setShowAxes

public void setShowAxes(boolean value)

setShowBbcage

public void setShowBbcage(boolean value)

setShowHydrogens

public void setShowHydrogens(boolean TF)

setShowMeasurements

public void setShowMeasurements(boolean TF)

setShowUnitCell

public void setShowUnitCell(boolean value)

setSlabDepthInternal

void setSlabDepthInternal(boolean isDepth)

setSpecular

private static void setSpecular(boolean specular)

setSpecularExponent

private static void setSpecularExponent(int specularExponent)

setSpecularPercent

private static void setSpecularPercent(int specularPercent)

setSpecularPower

private static void setSpecularPower(int specularPower)

setSpin

void setSpin(String key, int value)

setSpinOn

void setSpinOn(boolean spinOn)

setStatusAtomHovered

public void setStatusAtomHovered(int atomIndex, String info)

setStatusAtomPicked

public void setStatusAtomPicked(int atomIndex, String info)

setStatusFileLoaded

void setStatusFileLoaded(int ptLoad, String fullPathName, String fileName, String modelName, String strError)

setStatusFileNotLoaded

private void setStatusFileNotLoaded(String fullPathName, String errorMsg)

setStatusFrameChanged

void setStatusFrameChanged(int frameNo)

setStatusMeasurePicked

public void setStatusMeasurePicked(int iatom, String strMeasure)

setStatusMeasuring

public void setStatusMeasuring(String status, int count, String strMeasure)

setStatusResized

public void setStatusResized(int width, int height)

setStatusScriptStarted

void setStatusScriptStarted(int iscript, String script)

setStereoMode

void setStereoMode(int stereoMode, String state)

setStereoMode

void setStereoMode(int[] twoColors, String state)

setStrandCount

private void setStrandCount(int type, int value)

setStringProperty

public void setStringProperty(String key, String value)

setSync

void setSync()

setSyncDriver

void setSyncDriver(int mode)

setSyncTarget

private void setSyncTarget(int mode, boolean TF)

setTainted

void setTainted(boolean TF)

setTaintedAtoms

public void setTaintedAtoms(BitSet bs, byte type)

setTrajectory

void setTrajectory(int modelIndex)

setTrajectory

public void setTrajectory(BitSet bsModels)

setTransformManagerDefaults

private void setTransformManagerDefaults()

setUserScale

public static void setUserScale(int[] scale)

setVectorScale

public void setVectorScale(float scale)

setVibrationOff

void setVibrationOff()

setVibrationPeriod

public void setVibrationPeriod(float period)

setVibrationScale

public void setVibrationScale(float scale)

setVisualRange

public void setVisualRange(float angstroms)

showConsole

void showConsole(boolean showConsole)

showMeasurement

public void showMeasurement(int[] atomCountPlusIndices, boolean isON)

showModelSetDownload

public boolean showModelSetDownload()

showParameter

void showParameter(String key, boolean ifNotSet, int nMax)

showString

public void showString(String str)

showUrl

public void showUrl(String urlString)

slabByPixels

void slabByPixels(int pixels)

slabDepthByPixels

void slabDepthByPixels(int pixels)

slabInternal

void slabInternal(Point4f plane, boolean isDepth)

slabReset

void slabReset()

slabToPercent

void slabToPercent(int percentSlab)

startSpinningAxis

public void startSpinningAxis(int atomIndex1, int atomIndex2, boolean isClockwise)

startSpinningAxis

public void startSpinningAxis(Point3f pt1, Point3f pt2, boolean isClockwise)

syncScript

public void syncScript(String script, String applet)

toCartesian

void toCartesian(Point3f pt)

toFractional

void toFractional(Point3f pt)

toggleMeasurement

void toggleMeasurement(int[] atomCountPlusIndices, String strFormat)

togglePickingLabel

void togglePickingLabel(BitSet bs)

toUnitCell

void toUnitCell(Point3f pt, Point3f offset)

transformPoint

public Point3i transformPoint(Point3f pointAngstroms)

transformPoint

public Point3i transformPoint(Point3f pointAngstroms, Vector3f vibrationVector)

transformPoint

public void transformPoint(Point3f pointAngstroms, Point3i pointScreen)

transformPoint

public void transformPoint(Point3f pointAngstroms, Point3f pointScreen)

transformPointNoClip

public void transformPointNoClip(Point3f pointAngstroms, Point3f pt)

transformPoints

public void transformPoints(Point3f[] pointsAngstroms, Point3i[] pointsScreens)

transformVector

public void transformVector(Vector3f vectorAngstroms, Vector3f vectorTransformed)

translateToXPercent

void translateToXPercent(float percent)

translateToYPercent

void translateToYPercent(float percent)

translateToZPercent

void translateToZPercent(float percent)

translateXYBy

void translateXYBy(int xDelta, int yDelta)

unsetProperty

void unsetProperty(String name)

unTransformPoint

public void unTransformPoint(Point3f pointScreen, Point3f pointAngstroms)

useMinimizationThread

public boolean useMinimizationThread()

usingScriptQueue

boolean usingScriptQueue()

writeTextFile

public void writeTextFile(String file, String data)

zap

public void zap(boolean notify, boolean resetUndo)

zap

private void zap(String msg)

zoomBy

void zoomBy(int pixels)

zoomByFactor

void zoomByFactor(float factor)

zValueFromPercent

public int zValueFromPercent(int zPercent)