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org::jmol::viewer::Viewer Class Reference

Inheritance diagram for org::jmol::viewer::Viewer:
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List of all members.

Public Member Functions

void addCommand (String command)
void addFunction (ScriptFunction f)
BitSet addHydrogens (BitSet bsAtoms, boolean asScript, boolean isSilent)
BitSet addHydrogensInline (BitSet bsAtoms, List vConnections, Point3f[] pts) throws Exception
void addSelectionListener (JmolSelectionListener listener)
StateScript addStateScript (String script, boolean addFrameNumber, boolean postDefinitions)
StateScript addStateScript (String script1, BitSet bsBonds, BitSet bsAtoms1, BitSet bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)
void addUnitCellOffset (Point3f pt)
byte[] allocTempBytes (int size)
Point3f[] allocTempPoints (int size)
Point3i[] allocTempScreens (int size)
boolean allowMultiTouch ()
boolean areAxesTainted ()
void assignAromaticBonds ()
void assignAtom (int atomIndex, Point3f pt, String type)
void assignBond (int bondIndex, char type)
void assignConnect (int index, int index2)
void autoCalculate (int tokProperty)
int autoHbond (BitSet bsFrom, BitSet bsTo)
void bindAction (String desc, String name, Point3f range1, Point3f range2)
void calcBoundBoxDimensions (BitSet bs, float scale)
float calcRotationRadius (BitSet bs)
void calcSelectedGroupsCount ()
void calcSelectedMoleculesCount ()
void calcSelectedMonomersCount ()
Vector3f calculateMolecularDipole ()
String calculatePointGroup ()
void calculateStraightness ()
String calculateStructures (BitSet bsAtoms, boolean asDSSP, boolean setStructure)
int calculateStruts (BitSet bs1, BitSet bs2)
Point3f[] calculateSurface (BitSet bsSelected, float envelopeRadius)
String cd (String dir)
boolean checkAutoBondLegacy ()
void checkCoordinatesChanged ()
boolean checkHalt (String str, boolean isInterrupt)
boolean checkPrivateKey (double privateKey)
boolean checkResume (String str)
boolean checkStepping (String str)
void clearAllMeasurements ()
void clearBfactorRange ()
void clearConsole ()
void clearFunctions ()
void clearMeasurements ()
void clearScriptQueue ()
void clearSelection ()
void clearShapeRenderers ()
void clearTimeout (String name)
String clipImage (String text)
void connect (float[][] connections)
String createImage (String fileName, String type, Object text_or_bytes, int quality, int width, int height, BitSet bsFrames, String[] fullPath)
Object createImage (String fileName, String type, Object text_or_bytes, int quality, int width, int height)
Object createImage (String fileName, String type, Object text_or_bytes, int quality, int width, int height, String[] fullPath)
int deleteAtoms (BitSet bs, boolean fullModels)
void deleteBonds (BitSet bsDeleted)
void deleteMeasurement (int i)
void deleteModelAtoms (int firstAtomIndex, int nAtoms, BitSet bsDeleted)
void deleteSavedState (String saveName)
void deleteShapeAtoms (Object[] value, BitSet bs)
void depthToPercent (int percentDepth)
String dialogAsk (String type, String fileName)
void display (BitSet bs, boolean isQuiet)
boolean eval (ScriptContext context, ShapeManager shapeManager)
String evalFile (String strFilename)
String evalString (String strScript)
String evalStringQuiet (String strScript)
Object evalStringWaitStatus (String returnType, String strScript, String statusList)
Object evaluateExpression (Object stringOrTokens)
void excludeAtoms (BitSet bs, boolean ignoreSubset)
void exitJmol ()
void fillAtomData (AtomData atomData, int mode)
int findNearestAtomIndex (int x, int y)
int findNearestAtomIndex (int x, int y, boolean mustBeMovable)
String fixInlineString (String strModel, char newLine)
String formatText (String text0)
boolean frankClicked (int x, int y)
boolean frankClickedModelKit (int x, int y)
void freeTempBytes (byte[] tempBytes)
void freeTempPoints (Point3f[] tempPoints)
void freeTempScreens (Point3i[] tempScreens)
float[][] functionXY (String functionName, int nX, int nY)
float[][][] functionXYZ (String functionName, int nX, int nY, int nZ)
String generateOutput (String type, String[] fileName, int width, int height)
Point3f[] getAdditionalHydrogens (BitSet bsAtoms, boolean doAll, boolean justCarbon, List vConnections)
Hashtable getAllChainInfo (Object atomExpression)
boolean getAllowEmbeddedScripts ()
boolean getAllowGestures ()
Hashtable getAllPolymerInfo (Object atomExpression)
String getAllSettings (String prefix)
String getAltLocListInModel (int modelIndex)
int getAnimationFps ()
boolean getAppendNew ()
boolean getApplySymmetryToBonds ()
int getAtomArgb (int i)
BitSet getAtomBits (int tokType, Object specInfo)
BitSet getAtomBitSet (Object atomExpression)
int getAtomCount ()
int getAtomCountInModel (int modelIndex)
Quaternion[] getAtomGroupQuaternions (BitSet bsAtoms, int nMax)
float[] getAtomicCharges ()
float[] getAtomicPotentials (boolean isMep, BitSet bsSelected, BitSet bsIgnore, String fileName)
void getAtomIdentityInfo (int atomIndex, Hashtable info)
int getAtomIndexFromAtomNumber (int atomNumber)
int[] getAtomIndices (BitSet bs)
String getAtomInfo (int atomOrPointIndex)
String getAtomInfoXYZ (int atomIndex, boolean useChimeFormat)
int getAtomModelIndex (int i)
String getAtomName (int i)
int getAtomNumber (int i)
Point3f getAtomPoint3f (int i)
List getAtomPointVector (BitSet bs)
Quaternion getAtomQuaternion (int i)
float getAtomRadius (int i)
BitSet getAtomsConnected (float min, float max, int intType, BitSet bs)
Point3f getAtomSetCenter (BitSet bs)
float getAtomShapeValue (int tok, Group group, int atomIndex)
BitSet getAtomsWithin (float distance, Point4f plane)
BitSet getAtomsWithin (float distance, Point3f coord)
BitSet getAtomsWithin (float distance, BitSet bs, boolean withinAllModels)
boolean getAutoBond ()
Hashtable getAuxiliaryInfo (Object atomExpression)
int getAxesMode ()
boolean getAxesOrientationRasmol ()
float getAxesScale ()
void getAxisAngle (AxisAngle4f axisAngle)
Point3f[] getAxisPoints ()
int getBackgroundArgb ()
int getBfactor100Hi ()
String getBindingInfo (String qualifiers)
BitSet getBitSetTrajectories ()
int getBondArgb1 (int i)
int getBondArgb2 (int i)
int getBondCount ()
int getBondCountInModel (int modelIndex)
int getBondModelIndex (int i)
int getBondOrder (int i)
boolean getBondPicking ()
Point3f getBondPoint3f1 (int i)
Point3f getBondPoint3f2 (int i)
float getBondRadius (int i)
boolean getBondSelectionModeOr ()
BitSet getBondsForSelectedAtoms (BitSet bsAtoms)
float getBondTolerance ()
boolean getBooleanProperty (String key, boolean doICare)
boolean getBooleanProperty (String key)
Point3f getBoundBoxCenter ()
int getBoundBoxCenterX ()
int getBoundBoxCenterY ()
String getBoundBoxCommand (boolean withOptions)
Vector3f getBoundBoxCornerVector ()
BitSet getBoundBoxModels ()
Point3f[] getBoundBoxVertices ()
BoxInfo getBoxInfo (BitSet bs, float scale)
BitSet getBranchBitSet (int atomIndex, int atomIndexNot)
BufferedInputStream getBufferedInputStream (String fullPathName)
Object getBufferedReaderOrErrorMessageFromName (String name, String[] fullPathNameReturn, boolean isBinary)
Point3f[] getCameraFactors ()
boolean getCartoonBaseEdgesFlag ()
boolean getCartoonRocketFlag ()
Point3f[][] getCenterAndPoints (List atomSets, boolean addCenter)
boolean getChainCaseSensitive ()
int getChainCount ()
int getChainCountInModel (int modelIndex, boolean countWater)
int getChainCountInModel (int modelIndex)
String getChimeInfo (int tok)
Hashtable getCifData (int modelIndex)
BitSet getClickableSet ()
short getColixAtomPalette (Atom atom, byte pid)
short getColixBackgroundContrast ()
short getColixBondPalette (Bond bond, byte pid)
short getColixForPropertyValue (float val)
short getColixRubberband ()
int getColorArgbOrGray (short colix)
ColorEncoder getColorEncoder (String colorScheme)
Point3f getColorPointForPropertyValue (float val)
String getColorSchemeList (String colorScheme)
BitSet getConformation (int iModel, int conformationIndex, boolean doSet)
Hashtable getContextVariables ()
String getCoordinateState (BitSet bsSelected)
float[] getCurrentColorRange ()
String getCurrentFileAsString ()
int getCurrentModelIndex ()
float getCurrentSolventProbeRadius ()
SymmetryInterface getCurrentUnitCell ()
int getCursor ()
int getCursorX ()
int getCursorY ()
String getData (String atomExpression, String type)
Object[] getData (String type)
float[] getDataFloat (String label)
float getDataFloat (String label, int atomIndex)
float[][] getDataFloat2D (String label)
float[][][] getDataFloat3D (String label)
boolean getDebugScript ()
float getDefaultDrawArrowScale ()
Point3f getDefaultLattice ()
String getDefaultLoadFilter ()
String getDefaultLoadScript ()
String getDefaultMeasurementLabel (int nPoints)
RadiusData getDefaultRadiusData ()
boolean getDefaultStructureDSSP ()
float getDefaultTranslucent ()
String getDefaultVdwTypeNameOrData (int iMode)
int getDelayMaximum ()
BitSet getDeletedAtoms ()
float getDipoleScale ()
Component getDisplay ()
boolean getDisplayCellParameters ()
int getDisplayModelIndex ()
int getDotDensity ()
int getDotScale ()
boolean getDotsSelectedOnlyFlag ()
boolean getDotSurfaceFlag ()
boolean getDragSelected ()
boolean getDrawHover ()
boolean getDrawPicking ()
boolean getDynamicMeasurements ()
boolean getEchoStateActive ()
String[] getElectronDensityLoadInfo ()
BitSet getElementsPresentBitSet (int modelIndex)
String getErrorMessage ()
String getErrorMessageUntranslated ()
Object getExecutor ()
String getExportDriverList ()
Object getFileAsBytes (String pathName, OutputStream os)
Object getFileAsImage (String pathName, Hashtable htParams)
String getFileAsString (String name)
String getFileAsString (String name, int nBytesMax, boolean doSpecialLoad)
boolean getFileAsString (String[] data, int nBytesMax, boolean doSpecialLoad)
String[] getFileInfo ()
String getFileName ()
String getFilePath (String name, boolean asShortName)
Font3D getFont3D (String fontFace, String fontStyle, float fontSize)
boolean getFontCaching ()
boolean getFontScaling ()
boolean getForceAutoBond ()
boolean getFractionalRelative ()
BitSet getFrameOffsets ()
String getFrameTitle ()
int getFrontPlane ()
String getFullPathName ()
String[] getFullPathNameOrError (String filename)
ScriptFunction getFunction (String name)
String getFunctionCalls (String selectedFunction)
Graphics3D getGraphics3D ()
int getGroupCount ()
int getGroupCountInModel (int modelIndex)
BitSet getGroupsWithin (int nResidues, BitSet bs)
float getHbondsAngleMin ()
boolean getHbondsBackbone ()
float getHbondsDistanceMax ()
boolean getHbondsRasmol ()
boolean getHbondsSolid ()
Object getHelixData (BitSet bs, int tokType)
int getHelixStep ()
void getHelp (String what)
int getHermiteLevel ()
Hashtable getHeteroList (int modelIndex)
BitSet getHiddenSet ()
boolean getHighResolution ()
String getHybridizationAndAxes (int atomIndex, Vector3f z, Vector3f x, String lcaoType)
Object getImageAs (String type, int quality, int width, int height, String fileName, OutputStream os)
float getImageFontScaling ()
char getInlineChar ()
boolean getInMotion ()
String getInterruptScript ()
boolean getIsosurfacePropertySmoothing ()
String getJavaVendor ()
String getJavaVersion ()
int getJmolDataFrameIndex (int modelIndex, String type)
int getJmolDataSourceFrame (int modelIndex)
boolean getJustifyMeasurements ()
String getLanguage ()
float getLoadAtomDataTolerance ()
String getLogFile ()
boolean getLogGestures ()
short getMadBond ()
short getMarBond ()
Matrix4f getMatrixtransform ()
float getMaxZoomPercent ()
boolean getMeasureAllModelsFlag ()
String getMeasureDistanceUnits ()
int getMeasurementCount ()
int[] getMeasurementCountPlusIndices (int i)
String getMeasurementInfoAsString ()
String getMeasurementStringValue (int i)
String getMenu (String type)
Hashtable getMessageQueue ()
boolean getMessageStyleChime ()
float getMinBondDistance ()
String getMinimizationInfo ()
MinimizerInterface getMinimizer (boolean createNew)
JmolAdapter getModelAdapter ()
Object getModelAuxiliaryInfo (int modelIndex, String keyName)
Hashtable getModelAuxiliaryInfo (int modelIndex)
BitSet getModelBitSet (BitSet atomList, boolean allTrajectories)
String getModelCml (BitSet bs, int nAtomsMax, boolean addBonds)
int getModelCount ()
Vector3f getModelDipole ()
String getModelExtract (Object atomExpression, boolean doTransform, boolean asSDF, boolean asV3000)
String getModelFileInfo ()
String getModelFileInfoAll ()
String getModelFileName (int modelIndex)
int getModelFileNumber (int modelIndex)
Hashtable getModelInfo (Object atomExpression)
String getModelInfoAsString ()
boolean getModelkitMode ()
String getModelName (int modelIndex)
int getModelNumber (int modelIndex)
String getModelNumberDotted (int modelIndex)
int getModelNumberIndex (int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
Properties getModelProperties (int modelIndex)
String getModelProperty (int modelIndex, String propertyName)
ModelSet getModelSet ()
Object getModelSetAuxiliaryInfo (String strKey)
Hashtable getModelSetAuxiliaryInfo ()
String getModelSetFileName ()
String getModelSetName ()
String getModelSetPathName ()
Properties getModelSetProperties ()
String getModelSetProperty (String strProp)
String getModelSetTypeName ()
BitSet getModelUndeletedAtomsBitSet (BitSet bsModels)
BitSet getModelUndeletedAtomsBitSet (int modelIndex)
SymmetryInterface getModelUnitCell (int modelIndex)
byte getModeMultipleBond ()
String getMoInfo (int modelIndex)
BitSet getMoleculeBitSet (int atomIndex)
int getMotionEventNumber ()
BitSet getMotionFixedAtoms ()
boolean getMouseEnabled ()
Object getMouseInfo ()
float getMultipleBondRadiusFactor ()
float getMultipleBondSpacing ()
boolean getNavigateSurface ()
Point3f getNavigationCenter ()
float getNavigationDepthPercent ()
boolean getNavigationMode ()
Point3f getNavigationOffset ()
Boolean getNoneSelected ()
short getObjectColix (int objId)
int getObjectMad (int objId)
String getObjectState (String name)
String getOperatingSystemName ()
Orientation getOrientation ()
String getOrientationText (int type, String name)
ScriptVariable getOrSetNewVariable (String key, boolean doSet)
OutputStream getOutputStream (String localName, String[] fullPath)
Object getParameter (String key)
Object getParameterEscaped (String key)
float[] getPartialCharges ()
String getPdbData (BitSet bs, OutputStringBuffer sb)
String getPdbData (int modelIndex, String type, Object[] parameters)
String getPDBHeader ()
int getPercentVdwAtom ()
boolean getPerspectiveDepth ()
int getPickingMode ()
List getPlaneIntersection (int type, Point4f plane, float scale, int flags)
String getPointGroupAsString (boolean asDraw, String type, int index, float scale)
Hashtable getPointGroupInfo (Object atomExpression)
float getPointGroupTolerance (int type)
int getPolymerCount ()
int getPolymerCountInModel (int modelIndex)
Point3f[] getPolymerLeadMidPoints (int modelIndex, int polymerIndex)
void getPolymerPointsAndVectors (BitSet bs, List vList)
boolean getPreserveState ()
Object getProperty (String returnType, String infoType, String paramInfo)
Object getProperty (String returnType, String infoType, Object paramInfo)
String getPropertyColorScheme ()
String getProteinStructureState ()
char getQuaternionFrame ()
boolean getRasmolSetting (int tok)
boolean getRefreshing ()
int getRepaintWait ()
int getRibbonAspectRatio ()
boolean getRibbonBorder ()
boolean getRocketBarrelFlag ()
Point3f getRotationCenter ()
Quaternion getRotationQuaternion ()
float getRotationRadius ()
String getSavedCoordinates (String saveName)
String getSavedOrienationText (String name)
String getSavedState (String saveName)
String getSavedStructure (String saveName)
float getScalePixelsPerAngstrom (boolean asAntialiased)
int getScreenDim ()
int getScreenHeight ()
Image getScreenImage ()
Image getScreenImage (Graphics g)
int getScreenWidth ()
int getScriptDelay ()
AtomIndexIterator getSelectedAtomIterator (BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)
int getSelectionCount ()
boolean getSelectionHaloEnabled ()
BitSet getSelectionSet (boolean includeDeleted)
BitSet getSelectionSubset ()
BitSet getSequenceBits (String specInfo, BitSet bs)
String getSetHistory (int howFarBack)
String getShapeErrorState ()
Hashtable getShapeInfo ()
ShapeManager getShapeManager ()
Object getShapeProperty (int shapeType, String propertyName)
boolean getShapeProperty (int shapeType, String propertyName, Object[] data)
Object getShapeProperty (int shapeType, String propertyName, int index)
void getShapeState (StringBuffer commands, boolean isAll)
float getSheetSmoothing ()
boolean getShowAxes ()
boolean getShowBbcage ()
boolean getShowFrank ()
boolean getShowHiddenSelectionHalos ()
boolean getShowHydrogens ()
boolean getShowMeasurementLabels ()
boolean getShowMeasurements ()
boolean getShowMultipleBonds ()
boolean getShowNavigationPoint ()
boolean getShowUnitCell ()
boolean getSlabByAtom ()
boolean getSlabByMolecule ()
boolean getSlabEnabled ()
int getSmallMoleculeMaxAtoms ()
boolean getSmartAromatic ()
BitSet getSmartsMatch (String smarts, BitSet bsSelected)
String getSmiles (int index1, int index2, BitSet bsSelected, boolean isBioSmiles, boolean allowUnmatchedRings, boolean addCrossLinks, boolean addComment)
SmilesMatcherInterface getSmilesMatcher ()
float getSolventProbeRadius ()
Hashtable getSpaceGroupInfo (String spaceGroup)
String getSpecularState ()
String getSpinState ()
boolean getSsbondsBackbone ()
String getStandardLabelFormat ()
String getStateInfo (String type)
String getStateInfo ()
int getStrandCount (int type)
String getStructureState ()
float getStrutDefaultRadius ()
float getStrutLengthMaximum ()
boolean getStrutsMultiple ()
int getStrutSpacingMinimum ()
SymmetryInterface getSymmetry ()
Object getSymmetryInfo (BitSet bsAtoms, String xyz, int op, Point3f pt, Point3f pt2, String id, int type)
String getSymmetryInfoAsString ()
String getSymmetryOperation (String spaceGroup, int symop, Point3f pt1, Point3f pt2, boolean labelOnly)
BitSet getTaintedAtoms (byte type)
boolean getTestFlag1 ()
boolean getTestFlag2 ()
boolean getTestFlag3 ()
boolean getTestFlag4 ()
boolean getTraceAlpha ()
String getTrajectoryInfo ()
String getTransformText ()
String getTranslationScript ()
float getTranslationXPercent ()
float getTranslationYPercent ()
float getUnitCellInfo (int infoType)
String getUnitCellInfoText ()
Matrix4f getUnscaledTransformMatrix ()
boolean getUseNumberLocalization ()
int getVanderwaalsMar (int i)
int getVanderwaalsMar (int i, int iType)
String getVariableList ()
float getVectorScale ()
float getVibrationPeriod ()
Vector3f getVibrationVector (int atomIndex)
BitSet getVisibleFramesBitSet ()
BitSet getVisibleSet ()
float getVolume (BitSet bs, String type)
boolean getWireframeRotation ()
String getWrappedState (boolean isImage)
String getZapName ()
boolean getZeroBasedXyzRasmol ()
boolean getZoomEnabled ()
int getZoomPercent ()
float getZoomPercentFloat ()
float getZoomSetting ()
void haltScriptExecution ()
void handleError (Error er, boolean doClear)
boolean handleOldJvm10Event (Event e)
boolean hasCalculatedHBonds (BitSet bsAtoms)
boolean hasFocus ()
boolean haveFileSet ()
boolean haveFrame ()
boolean havePartialCharges ()
void hide (BitSet bs, boolean isQuiet)
void highlight (BitSet bs)
void highlightBond (int index, boolean isHover)
void homePosition ()
void hoverOn (int x, int y, String text)
void initialize ()
void invertAtomCoord (Point3f pt, BitSet bs)
void invertAtomCoord (Point4f plane, BitSet bs)
void invertSelected (Point3f pt, Point4f plane, int iAtom, BitSet invAtoms)
void invertSelection ()
boolean isApplet ()
boolean isAtomSelected (int atomIndex)
boolean isBound (int action, int gesture)
boolean isDataOnly ()
boolean isFunction (String name)
boolean isHoverEnabled ()
boolean isInPosition (Vector3f axis, float degrees)
boolean isJmolDataFrame ()
boolean isJmolDataFrame (int modelIndex)
boolean isJmolVariable (String key)
boolean isModelKitMode ()
boolean isNavigating ()
boolean isParallel ()
boolean isPdbSequential ()
boolean isPreviewOnly ()
boolean isRangeSelected ()
boolean isScriptEditorVisible ()
boolean isScriptExecuting ()
boolean isSelected (int atomIndex)
boolean isSignedApplet ()
boolean isTrajectory (int modelIndex)
boolean isVibrationOn ()
boolean isWindowCentered ()
String jsEval (String strEval)
String listSavedStates ()
String loadInline (String strModel)
String loadInline (String strModel, char newLine)
String loadInline (List arrayData, boolean isAppend)
String loadInline (String strModel, char newLine, boolean isAppend, Hashtable htParams)
String loadInline (String[] arrayModels, boolean isAppend)
String loadInline (String[] arrayModels)
String loadInline (String strModel, boolean isAppend)
String loadModelFromFile (String fullPathName, String fileName, String[] fileNames, Object reader, boolean isAppend, Hashtable htParams, StringBuffer loadScript, int tokType)
void loadShape (int shapeID)
void log (String data)
boolean logCommands ()
int[] makeConnections (float minDistance, float maxDistance, int order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds, float energy)
boolean menuEnabled ()
void mergeShapes (Shape[] newShapes)
void minimize (int steps, float crit, BitSet bsSelected, BitSet bsFixed, float rangeFixed, boolean addHydrogen, boolean isSilent, boolean asScript)
boolean modelHasVibrationVectors (int modelIndex)
void move (Vector3f dRot, float dZoom, Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps)
void moveSelected (int deltaX, int deltaY, int x, int y, BitSet bsSelected, boolean isTranslation)
void moveTo (float floatSecondsTotal, Point3f center, Vector3f rotAxis, float degrees, Matrix3f rotationMatrix, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth)
void navigate (float timeSeconds, Point3f[] path, float[] theta, int indexStart, int indexEnd)
void navigate (float timeSeconds, Point3f center)
void navigate (float timeSeconds, Point3f[][] pathGuide)
void navigate (float timeSeconds, Vector3f rotAxis, float degrees)
void navigateSurface (float timeSeconds, String name)
void navTranslate (float timeSeconds, Point3f center)
void navTranslatePercent (float timeSeconds, float x, float y)
void notifyError (String errType, String errMsg, String errMsgUntranslated)
void notifyMinimizationStatus ()
int notifyMouseClicked (int x, int y, int action, int mode)
void notifyViewerRepaintDone ()
String openDOM (Object DOMNode)
String openFile (String fileName)
void openFileAsynchronously (String fileName)
String openFiles (String[] fileNames)
String openReader (String fullPathName, String fileName, Reader reader)
String openStringInline (String strModel)
 (unnecessarily) many inline versions
void pauseScriptExecution ()
void popHoldRepaint ()
void popHoldRepaint (String why)
String prompt (String label, String data, String[] list, boolean asButtons)
void pushHoldRepaint ()
void pushHoldRepaint (String why)
void rebond ()
void refresh (int mode, String strWhy)
void refreshMeasures (boolean andStopMinimization)
void releaseScreenImage ()
String removeCommand ()
void removeSelectionListener (JmolSelectionListener listener)
void removeUserVariable (String key)
void renderScreenImage (Graphics g, Dimension size, Rectangle clip)
void renderScreenImage (Graphics gLeft, Graphics gRight, Dimension size, Rectangle clip)
void requestRepaintAndWait ()
void reset (boolean includingSpin)
void resetAromatic ()
void resetBioshapes (BitSet bsAllAtoms)
void resetError ()
void resetShapes ()
boolean restoreBonds (String saveName)
boolean restoreOrientation (String saveName, float timeSeconds)
void restoreRotation (String saveName, float timeSeconds)
boolean restoreSelection (String saveName)
void resumeScriptExecution ()
void rotateAboutPointsInternal (Point3f point1, Point3f point2, float degreesPerSecond, float endDegrees, boolean isSpin, BitSet bsSelected, Vector3f translation, List finalPoints)
void rotateAxisAngleAtCenter (Point3f rotCenter, Vector3f rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BitSet bsSelected)
void rotateFront ()
void rotatePoint (Point3f pt, Point3f ptRot)
void rotateX (float angleRadians)
void rotateX (int angleDegrees)
void rotateY (int angleDegrees)
void rotateY (float angleRadians)
void rotateZ (float angleRadians)
void rotateZBy (int zDelta, int x, int y)
void saveBonds (String saveName)
void saveCoordinates (String saveName, BitSet bsSelected)
void saveOrientation (String saveName)
void saveSelection (String saveName)
void saveState (String saveName)
void saveStructure (String saveName)
float scaleToPerspective (int z, float sizeAngstroms)
short scaleToScreen (int z, int milliAngstroms)
String script (String strScript)
synchronized Object scriptCheck (String strScript)
void scriptEcho (String strEcho)
void scriptStatus (String strStatus)
void scriptStatus (String strStatus, String statusMessage)
void scriptStatus (String strStatus, String statusMessage, int msWalltime, String strErrorMessageUntranslated)
String scriptWait (String strScript)
Object scriptWaitStatus (String strScript, String statusList)
void select (BitSet bs, boolean isQuiet)
void selectAll ()
void selectBonds (BitSet bs)
void setAnimation (int tok)
void setAnimationDirection (int direction)
void setAnimationFps (int fps)
void setAnimationOn (boolean animationOn)
void setAnimationRange (int modelIndex1, int modelIndex2)
void setAnimationReplayMode (int replay, float firstFrameDelay, float lastFrameDelay)
void setAppendNew (boolean value)
synchronized void setAppletContext (String fullName, URL documentBase, URL codeBase, String commandOptions)
void setAtomCoord (int atomIndex, float x, float y, float z)
void setAtomCoord (BitSet bs, int tokType, Object xyzValues)
void setAtomCoordRelative (int atomIndex, float x, float y, float z)
void setAtomCoordRelative (Tuple3f offset, BitSet bs)
void setAtomData (int type, String name, String coordinateData, boolean isDefault)
void setAtomLabel (String value, int i)
void setAtomProperty (BitSet bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)
void setAutoBond (boolean TF)
void setAxesOrientationRasmol (boolean TF)
void setBackgroundImage (String fileName, Image image)
void setBackgroundModelIndex (int modelIndex)
void setBondTolerance (float bondTolerance)
void setBooleanProperty (String key, boolean value)
void setBoundBox (Point3f pt1, Point3f pt2, boolean byCorner, float scale)
void setCenterAt (String relativeTo, Point3f pt)
void setCenterBitSet (BitSet bsCenter, boolean doScale)
void setCenterSelected ()
void setColorBackground (String colorName)
BitSet setConformation ()
void setCurrentColorRange (float min, float max)
void setCurrentColorRange (String label)
void setCurrentColorRange (float[] data, BitSet bs)
void setCurrentModelIndex (int modelIndex, boolean clearBackground)
void setCurrentModelIndex (int modelIndex)
void setCurrentUnitCellOffset (int ijk)
void setCurrentUnitCellOffset (Point3f pt)
void setCursor (int cursor)
void setData (String type, Object[] data, int atomCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)
void setDebugScript (boolean debugScript)
void setDefaultLattice (Point3f ptLattice)
void setEchoStateActive (boolean TF)
void setElementArgb (int elementNumber, int argb)
void setFileInfo (String[] fileInfo)
void setFloatProperty (String key, float value)
boolean setFloatProperty (String key, int tok, float value, boolean isInt)
void setFocus ()
void setFormalCharges (int formalCharge)
void setFrameOffsets (BitSet bsAtoms)
void setFrameTitle (String title)
void setFrameTitle (int modelIndex, String title)
void setFrankOn (boolean TF)
void setHoverLabel (String strLabel)
void setIntProperty (String key, int tok, int value)
void setIntProperty (String key, int value)
void setIteratorForAtom (AtomIndexIterator iterator, int atomIndex, float distance)
void setIteratorForAtom (AtomIndexIterator iterator, int atomIndex, float distance)
void setIteratorForPoint (AtomIndexIterator iter, int modelIndex, Point3f pt, float maxDistance)
void setIteratorForPoint (AtomIndexIterator iterator, int modelIndex, Point3f pt, float distance)
void setJmolCallbackListener (JmolCallbackListener jmolCallbackListener)
void setJmolDataFrame (String type, int modelIndex, int dataIndex)
void setJmolDefaults ()
void setJmolStatusListener (JmolStatusListener jmolStatusListener)
Object setLoadFormat (String name, char type, boolean withPrefix)
void setMarBond (short marBond)
void setMeasureDistanceUnits (String units)
void setMenu (String fileOrText, boolean isFile)
void setMeshCreator (Object meshCreator)
void setMinBondDistance (float minBondDistance)
void setModelVisibility ()
void setModeMouse (int modeMouse)
void setMotionFixedAtoms (BitSet bs)
void setMouseEnabled (boolean TF)
void setNavigationDepthPercent (float timeSec, float percent)
void setNavOn (boolean navOn)
void setNavXYZ (float x, float y, float z)
void setNewRotationCenter (Point3f center)
void setNoneSelected (boolean noneSelected)
void setObjectArgb (String name, int argb)
void setObjectMad (int iShape, String name, int mad)
boolean setParallel (boolean TF)
void setPdbConectBonding (boolean isAuto)
void setPercentVdwAtom (int value)
void setPerspectiveDepth (boolean perspectiveDepth)
void setPropertyColorScheme (String scheme, boolean isTranslucent, boolean isOverloaded)
void setProteinType (byte iType, BitSet bs)
void setRasmolDefaults ()
void setRotationRadius (float angstroms, boolean doAll)
void setRubberbandArgb (int argb)
void setScreenDimension (Dimension dim)
void setSelectedAtom (int atomIndex, boolean TF)
void setSelectionHalos (boolean TF)
void setSelectionSet (BitSet set)
void setSelectionSubset (BitSet subset)
void setShapeErrorState (int shapeID, String state)
void setShapeProperty (int shapeID, String propertyName, Object value)
void setShapeSize (int shapeID, RadiusData rd, BitSet bsAtoms)
void setShapeSize (int shapeID, int mad, BitSet bsSelected)
void setShowAxes (boolean value)
void setShowBbcage (boolean value)
void setShowHydrogens (boolean TF)
void setShowMeasurements (boolean TF)
void setShowUnitCell (boolean value)
void setSlabDepthInternal (boolean isDepth)
void setSmilesString (String s)
void setSpin (String key, int value)
void setSpinOn (boolean spinOn)
void setStateScriptVersion (String version)
void setStatusAtomHovered (int atomIndex, String info)
void setStatusAtomPicked (int atomIndex, String info)
void setStatusMeasuring (String status, int intInfo, String strMeasure, float value)
void setStatusResized (int width, int height)
void setStereoMode (int[] twoColors, int stereoMode, float degrees)
void setStringProperty (String key, int tok, String value)
void setStringProperty (String key, String value)
void setTainted (boolean TF)
void setTaintedAtoms (BitSet bs, byte type)
void setTimeout (String name, int mSec, String script)
void setTrajectory (BitSet bsModels)
void setTransformManager (TransformManager transformManager)
void setUserScale (int[] scale)
ScriptVariable setUserVariable (String name, ScriptVariable value)
void setVectorScale (float scale)
void setVibrationOff ()
void setVibrationPeriod (float period)
void setVibrationScale (float scale)
void showConsole (boolean showConsole)
void showMessage (String s)
boolean showModelSetDownload ()
void showParameter (String key, boolean ifNotSet, int nMax)
void showString (String str, boolean isPrint)
String showTimeout (String name)
void showUrl (String urlString)
void slabInternal (Point4f plane, boolean isDepth)
void slabReset ()
void slabToPercent (int percentSlab)
void spinXYBy (int xDelta, int yDelta, float speed)
void startSpinningAxis (Point3f pt1, Point3f pt2, boolean isClockwise)
void stepScriptExecution ()
void stopMotion ()
String streamFileData (String fileName, String type, String type2, int modelIndex, Object[] parameters)
void syncScript (String script, String applet)
void toCartesian (Point3f pt, boolean asAbsolute)
void toFractional (Point3f pt, boolean asAbsolute)
void togglePickingLabel (BitSet bs)
void toUnitCell (Point3f pt, Point3f offset)
BitSet transformAtoms (boolean firstPass)
Point3i transformPoint (Point3f pointAngstroms, Vector3f vibrationVector)
void transformPoint (Point3f pointAngstroms, Point3f pointScreen)
Point3i transformPoint (Point3f pointAngstroms)
void transformPoint (Point3f pointAngstroms, Point3i pointScreen)
void transformPointNoClip (Point3f pointAngstroms, Point3f pt)
void transformPoints (Point3f[] pointsAngstroms, Point3i[] pointsScreens)
void transformVector (Vector3f vectorAngstroms, Vector3f vectorTransformed)
void translate (char xyz, float x, char type, BitSet bsAtoms)
void translateXYBy (int xDelta, int yDelta)
void unBindAction (String desc, String name)
float unscaleToScreen (float z, float screenDistance)
void unsetProperty (String name)
void unTransformPoint (Point3f pointScreen, Point3f pointAngstroms)
boolean useMinimizationThread ()
boolean usingScriptQueue ()
boolean waitForMoveTo ()
String writeCurrentFile (OutputStream os)
void writeTextFile (String fileName, String data)
void zap (boolean notify, boolean resetUndo, boolean zapModelKit)
int zValueFromPercent (int zPercent)

Static Public Member Functions

static JmolSimpleViewer allocateSimpleViewer (Component awtComponent, JmolAdapter jmolAdapter)
static JmolViewer allocateViewer (Component awtComponent, JmolAdapter jmolAdapter, String htmlName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener)
static JmolViewer allocateViewer (Component awtComponent, JmolAdapter jmolAdapter)
static JmolViewer allocateViewer (Component display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener)
static boolean checkOption (JmolViewer viewer, String option)
static void getInlineData (StringBuffer loadScript, String strModel, boolean isAppend)
static String getJmolVersion ()

Public Attributes

boolean autoExit = false
ScriptCompiler compiler
Hashtable definedAtomSets
boolean haveDisplay = false
String menuStructure

Static Public Attributes

static final int CURSOR_CROSSHAIR = 2
static final int CURSOR_DEFAULT = 0
static final int CURSOR_HAND = 1
static final int CURSOR_MOVE = 3
static final int CURSOR_WAIT = 4
static final int CURSOR_ZOOM = 5
static int nProcessors = Runtime.getRuntime().availableProcessors()
static final String STATE_VERSION_STAMP = "# Jmol state version "
static final String SYNC_GRAPHICS_MESSAGE = "GET_GRAPHICS"
static final String SYNC_NO_GRAPHICS_MESSAGE = "SET_GRAPHICS_OFF"

Protected Member Functions

void finalize () throws Throwable

Package Functions

void actionRotateBond (int deltaX, int deltaY, int x, int y)
boolean allowRotateSelected ()
void appendLoadStates (StringBuffer commands)
float calcRotationRadius (Point3f center)
void centerAt (int x, int y, Point3f pt)
Token checkObjectClicked (int x, int y, int modifiers)
void checkObjectDragged (int prevX, int prevY, int x, int y, int action)
boolean checkObjectHovered (int x, int y)
void clearClickCount ()
void clearMinimization ()
void depthByPixels (int pixels)
void echoMessage (String msg)
String evalStringQuiet (String strScript, boolean isQuiet, boolean allowSyncScript)
synchronized Object evalStringWaitStatus (String returnType, String strScript, String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)
void finalizeTransformParameters ()
BitSet findAtomsInRectangle (Rectangle rect)
List getAllAtomInfo (Object atomExpression)
List getAllBondInfo (Object atomExpression)
int getAnimationDirection ()
Hashtable getAnimationInfo ()
int getAnimationReplayMode ()
String getAppletContext ()
Hashtable getAppletInfo ()
BitSet getAtomBitSet (ScriptEvaluator eval, Object atomExpression)
List getAtomBitSetVector (Object atomExpression)
String getAtomChain (int i)
void getAtomicPropertyState (StringBuffer commands, byte type, BitSet bs, String name, float[] data)
String getAtomSequenceCode (int i)
boolean getAutoFps ()
Point3f getAverageAtomPoint ()
Hashtable getBoundBoxInfo ()
short getColix (Object object)
String getDataSeparator ()
String getDefaultDirectory ()
boolean getDisablePopupMenu ()
int getElementNumber (int i)
String getElementSymbol (int i)
Object getFileData ()
String getFileHeader ()
StateManager.GlobalSettings getGlobalSettings ()
boolean getGreyscaleRendering ()
boolean getHideNameInPopup ()
int getHoverDelay ()
String getHtmlName ()
Object getImageAs (String type, int quality, int width, int height, String fileName, OutputStream os, String comment)
String getJmolFrameType (int modelIndex)
String getLoadState ()
Matrix3f getMatrixRotate ()
List getMeasurementInfo ()
String getMenuName (int i)
BitSet getModelKitStateBitSet (BitSet bs, BitSet bsDeleted)
List getMoleculeInfo (Object atomExpression)
String getMoveToText (float timespan)
float getNavigationOffsetPercent (char XorY)
boolean getNavigationPeriodic ()
float getNavigationSpeed ()
boolean getNavOn ()
int getObjectArgb (int objId)
Hashtable getOrientationInfo ()
MeasurementPending getPendingMeasurement ()
int getPickingSpinRate ()
int getRotateBondIndex ()
void getRotation (Matrix3f matrixRotation)
Rectangle getRubberBandSelection ()
boolean getSelectAllModels ()
boolean getSolventOn ()
boolean getSpinOn ()
List getStatusChanged (String statusNameList)
int getSurfaceDistanceMax ()
float getTranslationZPercent ()
float getVibrationScale ()
boolean getZoomLarge ()
boolean haveModelKit ()
boolean haveModelSet ()
void hoverOff ()
void hoverOn (int atomIndex, int action)
boolean isAnimationOn ()
boolean isAtomAssignable (int i)
boolean isAtomPDB (int i)
boolean isInSelectionSubset (int atomIndex)
boolean isKiosk ()
boolean isRepaintPending ()
boolean isStereoDouble ()
boolean modelSetHasVibrationVectors ()
void moveAtomWithHydrogens (int atomIndex, int deltaX, int deltaY, BitSet bsAtoms)
boolean mustRenderFlag ()
void navigate (int keyWhere, int modifiers)
void popupMenu (int x, int y, char type)
void repaint ()
void reportSelection (String msg)
void restoreModelOrientation (int modelIndex)
void restoreModelRotation (int modelIndex)
void rotateArcBall (int x, int y, float factor)
void rotateAtoms (Matrix3f mNew, Matrix3f matrixRotate, boolean fullMolecule, Point3f center, boolean isInternal, BitSet bsAtoms)
void rotateMolecule (float deltaX, float deltaY, BitSet bsSelected)
void rotateXYBy (float xDelta, float yDelta)
void saveModelOrientation ()
void setAllowRotateSelected (boolean TF)
void setApplySymmetryToBonds (boolean TF)
void setAxesModeUnitCell (boolean TF)
void setAxesScale (float scale)
void setDefaultVdw (String type)
void setDynamicMeasurements (boolean TF)
void setFrameOffset (int modelIndex)
void setFrameVariables (int firstModelIndex, int lastModelIndex)
void setInMotion (boolean inMotion)
void setObjectColor (String name, String colorName)
void setPendingMeasurement (MeasurementPending measurementPending)
void setPickingMode (String strMode, int pickingMode)
void setPickingStyle (String style, int pickingStyle)
void setRotateBondIndex (int index)
void setRotationMatrix (Matrix3f rotationMatrix)
void setStatusFrameChanged (int frameNo)
void setSync ()
void setSyncDriver (int mode)
void setTrajectory (int modelIndex)
void showEditor (String[] file_text)
void slabByPixels (int pixels)
void slabDepthByPixels (int pixels)
void stopMinimization ()
void undoAction (boolean isSave, int taintedAtom, int type)
boolean useArcBall ()
void zoomBy (int pixels)
void zoomByFactor (float factor, int x, int y)

Package Attributes

JmolAppConsoleInterface appConsole
BitSet bsFrameOffsets
final Dimension dimScreen = new Dimension()
boolean displayLoadErrors = true
ScriptEvaluator eval
Point3f[] frameOffsets
int hoverAtomIndex = -1
boolean hoverEnabled = true
String hoverText
String interruptScript = ""
boolean isParallel
boolean isScriptQueued = true
boolean isTainted = true
JmolPopup jmolpopup
JmolModelKitInterface modelkit
int motionEventNumber
int prevFrame = Integer.MIN_VALUE
JmolScriptEditorInterface scriptEditor
int scriptIndex
boolean wasInMotion = false

Private Member Functions

void checkMinimization ()
String checkScriptExecution (String strScript, boolean isInterrupt)
boolean checkUndo (String str)
void clearAtomSets ()
void clearModelDependentObjects ()
Object createImage (String fileName, String type, Object text_or_bytes, int quality, int width, int height, String[] fullPath, boolean doCheck)
String createModelSetAndReturnError (Object atomSetCollection, boolean isAppend, StringBuffer loadScript)
boolean getAtomPicking ()
Object getAtomSetCollection (String fileName, boolean isAppend, Hashtable htParams, StringBuffer loadScript)
String getFileNameFromDialog (String fileName, int quality)
Image getImage (boolean isDouble)
String getModelTitle (int modelIndex)
int getShapePropertyAsInt (int shapeID, String propertyName)
Image getStereoImage (int stereoMode)
void initializeModel ()
void jmolTest ()
String loadAtomDataAndReturnError (Object atomSetCollection, int tokType)
void moveUpdate (float floatSecondsTotal)
String openStringInline (String strModel, Hashtable htParams, boolean isAppend)
String openStringsInline (String[] arrayModels, Hashtable htParams, boolean isAppend)
void render ()
void render1 (Graphics g, Image img, int x, int y)
void resizeImage (int width, int height, boolean isImageWrite, boolean isExport, boolean isReset)
Object scriptCheck (String strScript, boolean returnContext)
void setAntialias (int mode, boolean TF)
void setAtomPickingOption (String option)
void setAxesModeMolecular (boolean TF)
void setBondPickingOption (String option)
boolean setBooleanProperty (String key, int tok, boolean value, boolean defineNew)
void setDefaultColors (boolean isRasmol)
void setDefaults (String type)
String setErrorMessage (String errMsg)
String setErrorMessage (String errMsg, String errMsgUntranslated)
void setFileLoadStatus (int ptLoad, String fullPathName, String fileName, String modelName, String strError)
Hashtable setLoadParameters (Hashtable htParams, boolean isAppend)
String setLogFile (String value)
void setMaximumSize (int x)
void setModelKitMode (boolean value)
void setNavigationMode (boolean TF)
void setPerspectiveModel (int mode)
void setRefreshing (boolean TF)
void setScriptQueue (boolean TF)
void setStrandCount (int type, int value)
void setSyncTarget (int mode, boolean TF)
void setTransformManagerDefaults ()
void stopAnimationThreads (String fromWhere)
 Viewer (Component display, JmolAdapter modelAdapter, String commandOptions)
void zap (String msg)

Private Attributes

ActionManager actionManager
final List actionStates = new ArrayList()
final List actionStatesRedo = new ArrayList()
AnimationManager animationManager
boolean antialiasDisplay
String appletCodeBase = ""
String appletContext
String appletDocumentBase = ""
boolean axesAreTainted = false
BitSet bsRotateBranch
ColorManager colorManager
CommandHistory commandHistory = new CommandHistory()
boolean creatingImage
int currentCursor = CURSOR_DEFAULT
int currentShapeID = -1
String currentShapeState
DataManager dataManager
Component display
String errorMessage
String errorMessageUntranslated
Object executor
FileManager fileManager
boolean frankOn = true
String fullName = ""
Graphics3D g3d
StateManager.GlobalSettings global
String htmlName = ""
float imageFontScaling = 1
boolean isApplet = false
boolean isCmdLine_C_Option = false
boolean isCmdLine_c_or_C_Option = false
boolean isDataOnly = false
boolean isKiosk
boolean isPreviewOnly = false
boolean isPrintOnly = false
boolean isSignedApplet = false
boolean isSignedAppletLocal = false
boolean isSilent = false
String language = GT.getLanguage()
int lastUndoRedo = 0
boolean listCommands = false
String logFile = null
String logFilePath = ""
int maximumSize = Integer.MAX_VALUE
MinimizerInterface minimizer
JmolAdapter modelAdapter
ModelManager modelManager
ModelSet modelSet
boolean mouseEnabled = true
MouseManager14 mouseManager
boolean movingSelected
boolean multiTouch = false
boolean mustRender = true
boolean noneSelected
double privateKey = Math.random()
RadiusData rd = new RadiusData()
boolean refreshing = true
RepaintManager repaintManager
int rotateBondIndex = -1
int rotatePrev1 = -1
int rotatePrev2 = -1
boolean scriptEditorVisible
ScriptManager scriptManager
SelectionManager selectionManager
ShapeManager shapeManager
boolean showSelected
SmilesMatcherInterface smilesMatcher
StateManager stateManager
int stateScriptVersionInt
StatusManager statusManager
String strJavaVendor
String strJavaVersion
String strOSName
SymmetryInterface symmetry
String syncId = ""
TempArray tempManager
TransformManager transformManager
boolean useCommandThread = false

Static Private Attributes

static final int FILE_STATUS_CREATING_MODELSET = 2
static final int MAX_ACTION_UNDO = 100

Detailed Description

Definition at line 144 of file Viewer.java.


The documentation for this class was generated from the following file:

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