org.jmol.viewer
Class Viewer

java.lang.Object
  extended by org.jmol.api.JmolSimpleViewer
      extended by org.jmol.api.JmolViewer
          extended by org.jmol.viewer.Viewer
All Implemented Interfaces:
AtomDataServer

public class Viewer
extends JmolViewer
implements AtomDataServer


Field Summary
private  AnimationManager animationManager
           
private  boolean antialiasDisplay
           
(package private)  JmolAppConsoleInterface appConsole
           
private  java.lang.String appletCodeBase
           
private  java.lang.String appletDocumentBase
           
(package private)  boolean autoExit
           
private  boolean axesAreTainted
           
(package private)  java.util.BitSet bsFrameOffsets
           
private  ColorManager colorManager
           
private  CommandHistory commandHistory
           
(package private)  ScriptCompiler compiler
           
private  boolean creatingImage
           
private  int currentCursor
           
private  int currentShapeID
           
private  java.lang.String currentShapeState
           
static int CURSOR_CROSSHAIR
           
static int CURSOR_DEFAULT
           
static int CURSOR_HAND
           
static int CURSOR_MOVE
           
static int CURSOR_WAIT
           
private  DataManager dataManager
           
(package private)  java.util.Hashtable definedAtomSets
           
(package private)  java.awt.Dimension dimScreen
           
private  java.awt.Component display
           
private  java.lang.String errorMessage
           
private  java.lang.String errorMessageUntranslated
           
(package private)  ScriptEvaluator eval
           
private static int FILE_STATUS_CREATING_MODELSET
           
private static int FILE_STATUS_MODELS_DELETED
           
private static int FILE_STATUS_MODELSET_CREATED
           
private static int FILE_STATUS_NOT_LOADED
           
private static int FILE_STATUS_ZAPPED
           
private  FileManager fileManager
           
(package private)  javax.vecmath.Point3f[] frameOffsets
           
(package private)  boolean frankOn
           
private  java.lang.String fullName
           
private  Graphics3D g3d
           
private  StateManager.GlobalSettings global
           
(package private)  boolean haveDisplay
           
(package private)  int hoverAtomIndex
           
(package private)  java.lang.String hoverText
           
private  java.lang.String htmlName
           
private  float imageFontScaling
           
(package private)  java.lang.String interruptScript
           
private  boolean isApplet
           
private  boolean isCmdLine_C_Option
           
private  boolean isCmdLine_c_or_C_Option
           
private  boolean isDataOnly
           
private  boolean isPreviewOnly
           
private  boolean isPrintOnly
           
(package private)  boolean isScriptQueued
           
private  boolean isSignedApplet
           
private  boolean isSilent
           
(package private)  boolean isTainted
           
(package private)  JmolPopup jmolpopup
           
private  boolean jvm11orGreater
           
private  boolean jvm12orGreater
           
private  boolean jvm14orGreater
           
private  java.lang.String language
           
private  boolean listCommands
           
private  int maximumSize
           
(package private)  java.lang.String menuStructure
           
private  MinimizerInterface minimizer
           
private  JmolAdapter modelAdapter
           
private  ModelManager modelManager
           
private  ModelSet modelSet
           
(package private)  int motionEventNumber
           
private  boolean mouseEnabled
           
 MouseManager mouseManager
           
private  boolean mustRender
           
private  boolean noneSelected
           
private  PickingManager pickingManager
           
(package private)  int prevFrame
           
private  boolean refreshing
           
private  RepaintManager repaintManager
           
(package private)  JmolScriptEditorInterface scriptEditor
           
private  boolean scriptEditorVisible
           
(package private)  int scriptIndex
           
private  ScriptManager scriptManager
           
private  SelectionManager selectionManager
           
private  SmilesMatcherInterface smilesMatcher
           
(package private) static java.lang.String STATE_VERSION_STAMP
           
private  StateManager stateManager
           
private  StatusManager statusManager
           
private  java.lang.String strJavaVendor
           
private  java.lang.String strJavaVersion
           
private  java.lang.String strOSName
           
private  SymmetryInterface symmetry
           
static java.lang.String SYNC_GRAPHICS_MESSAGE
           
static java.lang.String SYNC_NO_GRAPHICS_MESSAGE
           
private  java.lang.String syncId
           
private  TempArray tempManager
           
static java.lang.Object testData
           
static java.lang.Object testData2
           
private  TransformManager transformManager
           
private  boolean useCommandThread
           
(package private)  boolean wasInMotion
           
 
Constructor Summary
Viewer(java.awt.Component display, JmolAdapter modelAdapter)
           
 
Method Summary
(package private)  void addCommand(java.lang.String command)
          Adds one or more commands to the command history
(package private)  void addFunction(ScriptFunction f)
           
(package private)  void addLoadScript(java.lang.String script)
           
 void addSelectionListener(JmolSelectionListener listener)
           
(package private)  ModelCollection.StateScript addStateScript(java.lang.String script1, java.util.BitSet bsBonds, java.util.BitSet bsAtoms1, java.util.BitSet bsAtoms2, java.lang.String script2, boolean addFrameNumber, boolean postDefinitions)
           
(package private)  ModelCollection.StateScript addStateScript(java.lang.String script, boolean addFrameNumber, boolean postDefinitions)
           
static JmolViewer allocateViewer(java.awt.Component display, JmolAdapter modelAdapter)
          Deprecated.  
static JmolViewer allocateViewer(java.awt.Component display, JmolAdapter modelAdapter, java.lang.String fullName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions, JmolStatusListener statusListener)
          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)
           
 javax.vecmath.Point3f[] allocTempPoints(int size)
           
 javax.vecmath.Point3i[] allocTempScreens(int size)
           
(package private)  boolean allowRotateSelected()
           
 boolean areAxesTainted()
           
(package private)  void assignAromaticBonds()
           
(package private)  void atomPicked(int atomIndex, Point3fi ptClicked, int modifiers, boolean isDoubleClick)
           
 void autoCalculate(int tokProperty)
           
(package private)  int autoHbond(java.util.BitSet bsBonds)
           
(package private)  int autoHbond(java.util.BitSet bsFrom, java.util.BitSet bsTo, java.util.BitSet bsBonds, float maxXYDistance, float minAttachedAngle)
           
(package private)  void calcBoundBoxDimensions(java.util.BitSet bs)
           
 float calcRotationRadius(java.util.BitSet bs)
           
(package private)  float calcRotationRadius(javax.vecmath.Point3f center)
           
(package private)  void calcSelectedGroupsCount()
           
(package private)  void calcSelectedMoleculesCount()
           
(package private)  void calcSelectedMonomersCount()
           
 javax.vecmath.Vector3f calculateMolecularDipole()
           
(package private)  java.lang.String calculatePointGroup()
           
 void calculateStraightness()
           
(package private)  void calculateStructures(java.util.BitSet bsAtoms)
           
 javax.vecmath.Point3f[] calculateSurface(java.util.BitSet bsSelected, float envelopeRadius)
           
(package private)  java.lang.String cd(java.lang.String dir)
           
 boolean checkHalt(java.lang.String str)
           
(package private)  Point3fi checkObjectClicked(int x, int y, int modifiers)
           
(package private)  void checkObjectDragged(int prevX, int prevY, int x, int y, int modifiers)
           
(package private)  boolean checkObjectHovered(int x, int y)
           
 boolean checkResume(java.lang.String str)
           
private  java.lang.String checkScriptExecution(java.lang.String strScript)
           
 boolean checkStepping(java.lang.String str)
           
(package private)  void clearAllMeasurements()
           
private  void clearAtomSets()
           
(package private)  void clearBfactorRange()
           
(package private)  void clearClickCount()
           
(package private)  void clearConsole()
           
(package private)  void clearFunctions()
           
 void clearMeasurements()
           
private  void clearModelDependentObjects()
           
 void clearScriptQueue()
           
 void clearSelection()
           
 void clearShapes()
           
 java.lang.String clipImage(java.lang.String text)
           
private  java.lang.String createAtomDataSet(int tokType, java.lang.Object atomSetCollection)
           
 java.lang.String createImage(java.lang.String fileName, java.lang.String type, java.lang.Object text_or_bytes, int quality, int width, int height)
          general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface
(package private)  java.lang.String createImage(java.lang.String fileName, java.lang.String type, java.lang.Object text_or_bytes, int quality, int width, int height, java.util.BitSet bsFrames)
          from eval write command only includes option to write set of files
private  java.lang.String createModelSet(java.lang.String fullPathName, java.lang.String fileName, java.lang.Object atomSetCollection, boolean isAppend)
           
(package private)  java.lang.String createModelSetAndReturnError(boolean isAppend)
           
private  java.lang.String createModelSetInline(java.lang.String strModel, java.util.Hashtable htParams, boolean isAppend, boolean createModelSet)
           
(package private)  void deallocateReaderThreads()
           
(package private)  void defineMeasurement(java.util.Vector monitorExpressions, float[] rangeMinMax, boolean isDelete, boolean isAll, boolean isAllConnected, boolean isOn, boolean isOff, java.lang.String strFormat)
           
 int deleteAtoms(java.util.BitSet bs, boolean fullModels)
           
 void deleteMeasurement(int i)
           
(package private)  void deleteMeasurement(int[] atomCountPlusIndices)
           
 void deleteModelAtoms(int firstAtomIndex, int nAtoms, java.util.BitSet bsDeleted)
           
(package private)  void depthByPixels(int pixels)
           
(package private)  void depthToPercent(int percentDepth)
           
 java.lang.String dialogAsk(java.lang.String type, java.lang.String fileName)
           
(package private)  void display(java.util.BitSet bs, boolean isQuiet)
           
(package private)  void echoMessage(java.lang.String msg)
           
 java.lang.String evalFile(java.lang.String strFilename)
           
 java.lang.String evalString(java.lang.String strScript)
           
 java.lang.String evalStringQuiet(java.lang.String strScript)
           
(package private)  java.lang.String evalStringQuiet(java.lang.String strScript, boolean isQuiet, boolean allowSyncScript)
           
 java.lang.Object evalStringWaitStatus(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList)
           
(package private)  java.lang.Object evalStringWaitStatus(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)
           
 java.lang.Object evaluateExpression(java.lang.Object stringOrTokens)
           
(package private)  void exitJmol()
           
 void fillAtomData(AtomData atomData, int mode)
           
protected  void finalize()
           
(package private)  void finalizeTransformParameters()
           
 int findNearestAtomIndex(int x, int y)
           
 java.lang.String formatText(java.lang.String text0)
           
(package private)  boolean frankClicked(int x, int y)
           
 void freeTempBytes(byte[] tempBytes)
           
 void freeTempPoints(javax.vecmath.Point3f[] tempPoints)
           
 void freeTempScreens(javax.vecmath.Point3i[] tempScreens)
           
 float[][] functionXY(java.lang.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.
(package private)  float[][][] functionXYZ(java.lang.String functionName, int nX, int nY, int nZ)
           
 java.lang.String generateOutput(java.lang.String type, java.lang.String fileName, int width, int height)
           
(package private)  java.util.Vector getAllAtomInfo(java.lang.Object atomExpression)
           
(package private)  java.util.Vector getAllBondInfo(java.lang.Object atomExpression)
           
 java.util.Hashtable getAllChainInfo(java.lang.Object atomExpression)
           
(package private)  boolean getAllowEmbeddedScripts()
           
 java.util.Hashtable getAllPolymerInfo(java.lang.Object atomExpression)
           
(package private)  java.lang.String getAllSettings(java.lang.String prefix)
           
 java.lang.String getAltLocListInModel(int modelIndex)
           
(package private) static int getAmbientPercent()
           
(package private)  int getAnimationDirection()
           
 int getAnimationFps()
           
(package private)  java.util.Hashtable getAnimationInfo()
           
(package private)  int getAnimationReplayMode()
           
 boolean getAppendNew()
           
(package private)  java.util.Hashtable getAppletInfo()
           
 boolean getApplySymmetryToBonds()
           
 int getAtomArgb(int i)
           
 java.util.BitSet getAtomBits(int tokType, java.lang.Object specInfo)
           
(package private)  java.util.BitSet getAtomBitSet(java.lang.Object atomExpression)
           
(package private)  java.util.Vector getAtomBitSetVector(java.lang.Object atomExpression)
           
(package private)  java.lang.String getAtomChain(int i)
           
 int getAtomCount()
           
 int getAtomCountInModel(int modelIndex)
           
(package private)  float[] getAtomicCharges()
           
 void getAtomIdentityInfo(int atomIndex, java.util.Hashtable info)
           
(package private)  int getAtomIndexFromAtomNumber(int atomNumber)
           
(package private)  int[] getAtomIndices(java.util.BitSet bs)
           
 java.lang.String getAtomInfo(int atomIndex)
           
 java.lang.String getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
           
 int getAtomModelIndex(int i)
           
 java.lang.String getAtomName(int i)
           
 int getAtomNumber(int i)
           
private  boolean getAtomPicking()
           
 javax.vecmath.Point3f getAtomPoint3f(int i)
           
 float getAtomRadius(int i)
           
(package private)  java.util.BitSet getAtomsConnected(float min, float max, int intType, java.util.BitSet bs)
           
(package private)  java.lang.String getAtomSequenceCode(int i)
           
 javax.vecmath.Point3f getAtomSetCenter(java.util.BitSet bs)
           
(package private)  java.util.BitSet getAtomsWithin(float distance, java.util.BitSet bs, boolean isWithinModelSet)
           
(package private)  java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point3f coord)
           
(package private)  java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point4f plane)
           
 float getAtomVdwRadius(int i)
           
(package private)  float getAtomX(int i)
           
(package private)  float getAtomY(int i)
           
(package private)  float getAtomZ(int i)
           
 boolean getAutoBond()
           
(package private)  boolean getAutoFps()
           
 java.util.Hashtable getAuxiliaryInfo(java.lang.Object atomExpression)
           
(package private)  javax.vecmath.Point3f getAverageAtomPoint()
           
 int getAxesMode()
           
 boolean getAxesOrientationRasmol()
           
 float getAxesScale()
           
 void getAxisAngle(javax.vecmath.AxisAngle4f axisAngle)
           
 javax.vecmath.Point3f[] getAxisPoints()
           
 int getBackgroundArgb()
           
 int getBackgroundModelIndex()
           
(package private)  java.util.BitSet getBitSetSelection()
           
 java.util.BitSet getBitSetTrajectories()
           
 int getBondArgb1(int i)
           
 int getBondArgb2(int i)
           
 int getBondCount()
          For use in setting a for() construct max value
 int getBondCountInModel(int modelIndex)
          from JmolPopup.udateModelSetComputedMenu
 int getBondModelIndex(int i)
           
 short getBondOrder(int i)
           
 boolean getBondPicking()
           
 javax.vecmath.Point3f getBondPoint3f1(int i)
           
 javax.vecmath.Point3f getBondPoint3f2(int i)
           
 float getBondRadius(int i)
           
 boolean getBondSelectionModeOr()
           
(package private)  java.util.BitSet getBondsForSelectedAtoms(java.util.BitSet bsAtoms)
           
 float getBondTolerance()
           
 boolean getBooleanProperty(java.lang.String key)
           
 boolean getBooleanProperty(java.lang.String key, boolean doICare)
           
 javax.vecmath.Point3f getBoundBoxCenter()
           
 int getBoundBoxCenterX()
           
 int getBoundBoxCenterY()
           
 java.lang.String getBoundBoxCommand(boolean withOptions)
           
 javax.vecmath.Vector3f getBoundBoxCornerVector()
           
(package private)  java.util.Hashtable getBoundBoxInfo()
           
 java.util.BitSet getBoundBoxModels()
           
(package private)  BoxInfo getBoxInfo(java.util.BitSet bs)
           
(package private)  java.util.BitSet getBranchBitSet(int atomIndex, int atomIndexNot)
           
 java.io.BufferedInputStream getBufferedInputStream(java.lang.String fullPathName)
           
(package private)  java.lang.Object getBufferedReaderOrErrorMessageFromName(java.lang.String name, java.lang.String[] fullPathNameReturn, boolean isBinary)
           
 float getCameraDepth()
           
 boolean getCartoonRocketFlag()
           
 boolean getChainCaseSensitive()
           
 int getChainCount()
           
 int getChainCountInModel(int modelIndex)
           
 int getChainCountInModel(int modelIndex, boolean countWater)
           
 java.lang.String getChimeInfo(int tok)
           
 java.util.Hashtable getCifData(int modelIndex)
           
(package private)  java.util.BitSet getClickableSet()
           
 java.lang.String getClientAtomStringProperty(java.lang.Object clientAtom, java.lang.String propertyName)
           
(package private)  java.lang.Object getClientFile()
           
(package private)  short getColix(java.lang.Object object)
           
 int getColixArgb(short colix)
           
 short getColixAtomPalette(Atom atom, byte pid)
           
 short getColixBackgroundContrast()
           
 short getColixBondPalette(Bond bond, byte pid)
           
 short getColixForPropertyValue(float val)
           
 short getColixRubberband()
           
(package private)  javax.vecmath.Point3f getColorPointForPropertyValue(float val)
           
 int[] getColorSchemeArray(java.lang.String colorScheme)
           
 java.lang.String getColorSchemeList(java.lang.String colorScheme, boolean ifDefault)
           
 java.lang.String getCoordinateState(java.util.BitSet bsSelected)
           
 float[] getCurrentColorRange()
           
 java.lang.Object getCurrentFileAsBytes()
           
 java.lang.String getCurrentFileAsString()
           
 int getCurrentModelIndex()
           
 float getCurrentSolventProbeRadius()
           
 SymmetryInterface getCurrentUnitCell()
           
 int getCursorX()
           
 int getCursorY()
           
(package private)  java.lang.Object[] getData(java.lang.String type)
           
 java.lang.String getData(java.lang.String atomExpression, java.lang.String type)
           
 float[] getDataFloat(java.lang.String label)
           
 float getDataFloat(java.lang.String label, int atomIndex)
           
(package private)  float[][] getDataFloat2D(java.lang.String label)
           
(package private)  float[][][] getDataFloat3D(java.lang.String label)
           
(package private)  java.lang.String getDataSeparator()
           
(package private)  boolean getDebugScript()
           
(package private)  java.lang.String getDefaultDirectory()
           
 float getDefaultDrawArrowScale()
           
(package private)  javax.vecmath.Point3f getDefaultLattice()
           
(package private)  java.lang.String getDefaultLoadScript()
           
 short getDefaultMadAtom()
           
 java.lang.String getDefaultMeasurementLabel(int nPoints)
           
(package private)  float getDefaultTranslucent()
           
(package private)  java.lang.String getDefaultVdw(int iMode)
           
(package private)  int getDelayMaximum()
           
 java.util.BitSet getDeletedAtoms()
           
(package private) static int getDiffusePercent()
           
 float getDipoleScale()
           
(package private)  boolean getDisablePopupMenu()
           
 java.awt.Component getDisplay()
           
 boolean getDisplayCellParameters()
           
 int getDisplayModelIndex()
           
 int getDotDensity()
           
 boolean getDotsSelectedOnlyFlag()
           
 boolean getDotSurfaceFlag()
           
 boolean getDrawHover()
           
 boolean getDrawPicking()
           
 boolean getDynamicMeasurements()
           
 boolean getEchoStateActive()
           
(package private)  int getElementNumber(int i)
           
 java.util.BitSet getElementsPresentBitSet(int modelIndex)
           
(package private)  java.lang.String getElementSymbol(int i)
           
 java.lang.String getErrorMessage()
           
 java.lang.String getErrorMessageUntranslated()
           
 java.lang.String getExportDriverList()
           
(package private)  JmolAdapter getExportJmolAdapter()
          This is the method that should be used to extract the model data from Jmol.
 java.lang.Object getFileAsBytes(java.lang.String pathName)
           
(package private)  java.lang.Object getFileAsImage(java.lang.String pathName, java.util.Hashtable htParams)
           
 java.lang.String getFileAsString(java.lang.String name)
           
 boolean getFileAsString(java.lang.String[] data, int nBytesMax, boolean doSpecialLoad)
           
 java.lang.String getFileAsString(java.lang.String name, int nBytesMax, boolean doSpecialLoad)
           
(package private)  java.lang.Object getFileData()
           
(package private)  java.lang.String getFileHeader()
           
(package private)  java.lang.String[] getFileInfo()
           
 java.lang.String getFileName()
           
(package private)  Font3D getFont3D(java.lang.String fontFace, java.lang.String fontStyle, float fontSize)
           
 boolean getFontCaching()
           
 boolean getFontScaling()
           
 boolean getForceAutoBond()
           
 java.util.BitSet getFrameOffsets()
           
 java.lang.String getFrameTitle()
           
(package private)  java.lang.String getFrameTitle(int modelIndex)
           
 java.lang.String getFullPath(java.lang.String name)
           
 java.lang.String getFullPathName()
           
(package private)  ScriptFunction getFunction(java.lang.String name)
           
(package private)  java.util.Hashtable getFunctions(boolean isLocal)
           
(package private)  StateManager.GlobalSettings getGlobalSettings()
           
 Graphics3D getGraphics3D()
           
(package private)  boolean getGreyscaleRendering()
           
 int getGroupCount()
           
 int getGroupCountInModel(int modelIndex)
           
 boolean getHbondsBackbone()
           
 boolean getHbondsSolid()
           
(package private)  java.lang.Object getHelixData(java.util.BitSet bs, int tokType)
           
 int getHelixStep()
           
(package private)  void getHelp(java.lang.String what)
           
 int getHermiteLevel()
           
 java.util.Hashtable getHeteroList(int modelIndex)
           
 java.lang.String getHexColorFromIndex(short colix)
           
(package private)  java.util.BitSet getHiddenSet()
           
(package private)  boolean getHideNameInPopup()
           
 boolean getHighResolution()
           
(package private)  int getHoverDelay()
           
(package private)  java.lang.String getHtmlName()
           
 java.lang.String getHybridizationAndAxes(int atomIndex, javax.vecmath.Vector3f z, javax.vecmath.Vector3f x, java.lang.String lcaoType, boolean hybridizationCompatible)
           
private  java.awt.Image getImage(boolean isDouble)
           
 java.lang.Object getImageAs(java.lang.String type, int quality, int width, int height, java.lang.String fileName, java.io.OutputStream os)
           
 float getImageFontScaling()
           
 char getInlineChar()
           
 boolean getInMotion()
           
(package private)  java.lang.String getInterruptScript()
           
(package private)  boolean getIsosurfacePropertySmoothing()
           
 java.lang.String getJavaVendor()
           
 java.lang.String getJavaVersion()
           
(package private)  int getJmolDataFrameIndex(int modelIndex, java.lang.String type)
           
 int getJmolDataSourceFrame(int modelIndex)
           
(package private)  java.lang.String getJmolFrameType(int modelIndex)
           
static java.lang.String getJmolVersion()
           
private static int getJmolVersionInt()
           
 boolean getJustifyMeasurements()
           
 java.lang.String getLanguage()
           
(package private)  java.lang.String getLoadFormat()
           
(package private)  java.lang.String getLoadState()
           
(package private) static int getLogLevel()
           
 short getMadBond()
           
 short getMarBond()
           
(package private)  javax.vecmath.Matrix3f getMatrixRotate()
           
 javax.vecmath.Matrix4f getMatrixtransform()
           
(package private)  float getMaxZoomPercent()
           
 boolean getMeasureAllModelsFlag()
           
 java.lang.String getMeasureDistanceUnits()
           
 int getMeasurementCount()
           
 int[] getMeasurementCountPlusIndices(int i)
           
(package private)  java.util.Vector getMeasurementInfo()
           
 java.lang.String getMeasurementInfoAsString()
           
 java.lang.String getMeasurementStringValue(int i)
           
(package private)  java.lang.String getMenu(java.lang.String type)
           
 java.util.Hashtable getMessageQueue()
           
(package private)  boolean getMessageStyleChime()
           
 float getMinBondDistance()
           
 java.lang.String getMinimizationInfo()
           
(package private)  MinimizerInterface getMinimizer(boolean createNew)
           
 JmolAdapter getModelAdapter()
           
 java.util.BitSet getModelAtomBitSet(int modelIndex, boolean asCopy)
           
 java.util.Hashtable getModelAuxiliaryInfo(int modelIndex)
           
 java.lang.Object getModelAuxiliaryInfo(int modelIndex, java.lang.String keyName)
           
 java.util.BitSet getModelBitSet(java.util.BitSet atomList, boolean allTrajectories)
           
 int getModelCount()
           
 javax.vecmath.Vector3f getModelDipole()
           
(package private)  java.lang.String getModelExtract(java.lang.Object atomExpression)
           
 java.lang.String getModelFileInfo()
           
(package private)  java.lang.String getModelFileInfoAll()
           
private  java.lang.String getModelFileName(int modelIndex)
           
 int getModelFileNumber(int modelIndex)
           
 java.util.Hashtable getModelInfo(java.lang.Object atomExpression)
           
(package private)  java.lang.String getModelInfoAsString()
           
 java.lang.String getModelName(int modelIndex)
           
 int getModelNumber(int modelIndex)
           
 java.lang.String getModelNumberDotted(int modelIndex)
           
(package private)  int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
           
 java.util.Properties getModelProperties(int modelIndex)
           
 java.lang.String getModelProperty(int modelIndex, java.lang.String propertyName)
           
 ModelSet getModelSet()
           
 java.util.Hashtable getModelSetAuxiliaryInfo()
           
 java.lang.Object getModelSetAuxiliaryInfo(java.lang.String strKey)
           
 java.lang.String getModelSetFileName()
           
 java.lang.String getModelSetName()
           
 java.lang.String getModelSetPathName()
           
 java.util.Properties getModelSetProperties()
           
 java.lang.String getModelSetProperty(java.lang.String strProp)
           
 java.lang.String getModelSetTypeName()
           
private  java.lang.String getModelTitle(int modelIndex)
           
 byte getModeMultipleBond()
           
 java.lang.String getMoInfo(int modelIndex)
           
(package private)  java.util.Vector getMoleculeInfo(java.lang.Object atomExpression)
           
 int getMotionEventNumber()
           
(package private)  java.lang.String getMoveToText(float timespan)
           
 boolean getNavigateSurface()
           
 javax.vecmath.Point3f getNavigationCenter()
           
 float getNavigationDepthPercent()
           
 boolean getNavigationMode()
           
 javax.vecmath.Point3f getNavigationOffset()
           
(package private)  float getNavigationOffsetPercent(char XorY)
           
(package private)  boolean getNavigationPeriodic()
           
(package private)  float getNavigationSpeed()
           
(package private)  boolean getNavOn()
           
(package private)  java.lang.Boolean getNoneSelected()
           
(package private)  int getObjectArgb(int objId)
           
 short getObjectColix(int objId)
           
 int getObjectMad(int objId)
           
 java.lang.String getObjectState(java.lang.String name)
           
 java.lang.String getOperatingSystemName()
           
 StateManager.Orientation getOrientation()
           
(package private)  java.util.Hashtable getOrientationInfo()
           
 java.lang.String getOrientationText(int type)
           
(package private)  ScriptVariable getOrSetNewVariable(java.lang.String key, boolean doSet)
           
 java.lang.Object getParameter(java.lang.String key)
           
(package private)  java.lang.Object getParameterEscaped(java.lang.String key)
           
 float[] getPartialCharges()
           
 java.lang.String getPdbData(java.util.BitSet bs)
           
(package private)  java.lang.String getPdbData(int modelIndex, java.lang.String type)
           
(package private)  java.lang.String getPDBHeader()
           
 boolean getPdbLoadInfo(int type)
           
(package private)  MeasurementPending getPendingMeasurement()
           
 int getPercentVdwAtom()
           
 boolean getPerspectiveDepth()
           
 int getPickingMode()
           
(package private)  int getPickingSpinRate()
           
(package private)  int getPickingStyle()
           
 java.lang.String getPointGroupAsString(boolean asDraw, java.lang.String type, int index, float scale)
           
 java.util.Hashtable getPointGroupInfo(java.lang.Object atomExpression)
           
 float getPointGroupTolerance(int type)
           
 int getPolymerCount()
           
 int getPolymerCountInModel(int modelIndex)
           
 javax.vecmath.Point3f[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
           
(package private)  void getPolymerPointsAndVectors(java.util.BitSet bs, java.util.Vector vList)
           
 java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
           
 java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.String paramInfo)
           
 java.lang.String getPropertyColorScheme()
           
(package private)  java.lang.String getProteinStructureState()
           
 char getQuaternionFrame()
           
(package private)  boolean getRasmolHeteroSetting()
           
(package private)  boolean getRasmolHydrogenSetting()
           
(package private)  boolean getRefreshing()
           
 int getRibbonAspectRatio()
           
 boolean getRibbonBorder()
           
 boolean getRocketBarrelFlag()
           
(package private)  void getRotation(javax.vecmath.Matrix3f matrixRotation)
           
 javax.vecmath.Point3f getRotationCenter()
           
(package private)  Quaternion getRotationQuaternion()
           
 float getRotationRadius()
           
(package private)  java.awt.Rectangle getRubberBandSelection()
           
(package private)  java.lang.String getSavedCoordinates(java.lang.String saveName)
           
 java.lang.String getSavedState(java.lang.String saveName)
           
(package private)  java.lang.String getSavedStructure(java.lang.String saveName)
           
 float getScalePixelsPerAngstrom(boolean asAntialiased)
           
 int getScreenDim()
           
 int getScreenHeight()
           
 java.awt.Image getScreenImage()
           
 int getScreenWidth()
           
(package private)  int getScriptDelay()
           
(package private)  boolean getSelectAllModels()
           
 int getSelectionCount()
           
 boolean getSelectionHaloEnabled()
           
 java.util.BitSet getSelectionSet()
           
 java.util.BitSet getSelectionSubset()
           
(package private)  java.util.BitSet getSequenceBits(java.lang.String specInfo, java.util.BitSet bs)
           
 java.lang.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;
 Shape getShape(int i)
           
 java.lang.String getShapeErrorState()
           
(package private)  int getShapeIdFromObjectName(java.lang.String objectName)
           
 java.util.Hashtable getShapeInfo()
           
 java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName)
           
(package private)  java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName, int index)
           
 boolean getShapeProperty(int shapeType, java.lang.String propertyName, java.lang.Object[] data)
           
(package private)  int getShapePropertyAsInt(int shapeID, java.lang.String propertyName)
           
 float getSheetSmoothing()
           
 boolean getShowAxes()
           
 boolean getShowBbcage()
           
 boolean getShowFrank()
           
 boolean getShowHiddenSelectionHalos()
           
 boolean getShowHydrogens()
           
 boolean getShowMeasurementLabels()
           
 boolean getShowMeasurements()
           
 boolean getShowMultipleBonds()
           
 boolean getShowNavigationPoint()
           
 boolean getShowUnitCell()
           
 boolean getSlabEnabled()
           
 boolean getSmartAromatic()
           
(package private)  SmilesMatcherInterface getSmilesMatcher()
           
(package private)  boolean getSolventOn()
           
(package private)  float getSolventProbeRadius()
           
 java.util.Hashtable getSpaceGroupInfo(java.lang.String spaceGroup)
           
(package private)  boolean getSpecular()
           
(package private) static int getSpecularPercent()
           
(package private)  java.lang.String getSpecularState()
           
(package private)  boolean getSpinOn()
           
(package private)  java.lang.String getSpinState()
           
 boolean getSsbondsBackbone()
           
 java.lang.String getStandardLabelFormat()
           
 java.lang.String getStateInfo()
           
 java.lang.String getStateInfo(java.lang.String type)
           
(package private)  java.lang.Object getStatusChanged(java.lang.String statusNameList)
           
private  java.awt.Image getStereoImage(int stereoMode)
           
 int getStrandCount(int type)
           
 java.lang.String getStructureState()
           
(package private)  int getSurfaceDistanceMax()
           
 SymmetryInterface getSymmetry()
           
 java.lang.Object getSymmetryInfo(java.util.BitSet bsAtoms, java.lang.String xyz, int op, javax.vecmath.Point3f pt, java.lang.String id, int type)
           
(package private)  java.lang.String getSymmetryInfoAsString()
           
(package private)  java.util.BitSet getTaintedAtoms(byte type)
           
 boolean getTestFlag1()
           
 boolean getTestFlag2()
           
 boolean getTestFlag3()
           
 boolean getTestFlag4()
           
 boolean getTraceAlpha()
           
(package private)  java.lang.String getTrajectoryInfo()
           
(package private)  java.lang.String getTransformText()
           
 java.lang.String getTranslationScript()
           
 float getTranslationXPercent()
           
 float getTranslationYPercent()
           
(package private)  float getTranslationZPercent()
           
 java.lang.String getUnitCellInfoText()
           
 javax.vecmath.Matrix4f getUnscaledTransformMatrix()
           
 boolean getUseNumberLocalization()
           
 int getVanderwaalsMar(int i)
           
 int getVanderwaalsMar(int i, int iMode)
           
(package private)  java.lang.String getVariableList()
           
 float getVectorScale()
           
(package private)  float getVibrationPeriod()
           
(package private)  float getVibrationScale()
           
 javax.vecmath.Vector3f getVibrationVector(int atomIndex)
           
 java.util.BitSet getVisibleFramesBitSet()
           
(package private)  java.util.BitSet getVisibleSet()
           
 boolean getWireframeRotation()
           
 AtomIndexIterator getWithinAtomSetIterator(int atomIndex, float distance, java.util.BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)
           
 AtomIndexIterator getWithinModelIterator(Atom atom, float distance)
           
 boolean getZeroBasedXyzRasmol()
           
(package private)  boolean getZoomEnabled()
           
(package private)  boolean getZoomLarge()
           
 int getZoomPercent()
           
 float getZoomPercentFloat()
           
(package private)  float getZoomSetting()
           
(package private)  boolean getZShade()
           
 void haltScriptExecution()
           
 void handleError(java.lang.Error er, boolean doClear)
           
 boolean handleOldJvm10Event(java.awt.Event e)
           
 boolean hasCalculatedHBonds(java.util.BitSet bsAtoms)
           
(package private)  boolean haveFileSet()
           
 boolean haveFrame()
           
(package private)  boolean haveModelSet()
           
 boolean havePartialCharges()
           
(package private)  void hide(java.util.BitSet bs, boolean isQuiet)
           
(package private)  void hideMeasurements(boolean isOFF)
           
 void homePosition()
           
(package private)  void hoverOff()
           
(package private)  void hoverOn(int atomIndex, int modifiers)
           
 void hoverOn(int x, int y, java.lang.String text)
           
(package private)  void initialize()
           
private  void initializeModel()
           
(package private)  void invertSelected(javax.vecmath.Point3f pt, java.util.BitSet bs)
           
(package private)  void invertSelected(javax.vecmath.Point3f pt, javax.vecmath.Point4f plane)
           
(package private)  void invertSelection()
           
(package private)  boolean isAnimationOn()
           
 boolean isApplet()
           
 boolean isDataOnly()
           
(package private)  boolean isFunction(java.lang.String name)
           
(package private)  boolean isInPosition(javax.vecmath.Vector3f axis, float degrees)
           
(package private)  boolean isInSelectionSubset(int atomIndex)
           
 boolean isJmolDataFrame()
           
 boolean isJmolDataFrame(int modelIndex)
           
(package private)  boolean isJmolVariable(java.lang.String key)
           
 boolean isJvm12orGreater()
           
 boolean isNavigating()
           
(package private)  boolean isPreviewOnly()
           
 boolean isRangeSelected()
           
(package private)  boolean isRepaintPending()
           
(package private)  boolean isScriptEditorVisible()
           
 boolean isScriptExecuting()
           
 boolean isSelected(int atomIndex)
           
 boolean isSignedApplet()
           
(package private)  boolean isTrajectory(int modelIndex)
           
 boolean isVibrationOn()
           
(package private)  boolean isWindowCentered()
           
(package private)  java.lang.String jsEval(java.lang.String strEval)
           
(package private)  java.lang.String listSavedStates()
           
(package private)  java.lang.String loadAtomDataAndReturnError(int tokType)
           
 java.lang.String loadInline(java.lang.String strModel)
           
 java.lang.String loadInline(java.lang.String[] arrayModels)
           
 java.lang.String loadInline(java.lang.String[] arrayModels, boolean isAppend)
           
 java.lang.String loadInline(java.lang.String strModel, boolean isAppend)
           
 java.lang.String loadInline(java.lang.String strModel, char newLine)
           
(package private)  java.lang.String loadInline(java.lang.String strModel, char newLine, boolean isAppend)
           
 void loadShape(int shapeID)
           
(package private)  int[] makeConnections(float minDistance, float maxDistance, short order, int connectOperation, java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsBonds, boolean isBonds)
           
 boolean modelHasVibrationVectors(int modelIndex)
           
(package private)  boolean modelSetHasVibrationVectors()
           
(package private)  void move(javax.vecmath.Vector3f dRot, float dZoom, javax.vecmath.Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps)
           
(package private)  void moveSelected(int deltaX, int deltaY, int x, int y, boolean isTranslation)
           
(package private)  void moveTo(float floatSecondsTotal, javax.vecmath.Point3f center, javax.vecmath.Matrix3f rotationMatrix, float zoom, float xTrans, float yTrans, float rotationRadius, javax.vecmath.Point3f navCenter, float xNav, float yNav, float navDepth)
           
(package private)  void moveTo(float floatSecondsTotal, javax.vecmath.Point3f center, javax.vecmath.Vector3f pt, float degrees, float zoom, float xTrans, float yTrans, float rotationRadius, javax.vecmath.Point3f navCenter, float xNav, float yNav, float navDepth)
           
private  void moveUpdate(float floatSecondsTotal)
           
(package private)  boolean mustRenderFlag()
           
 void navigate(float timeSeconds, javax.vecmath.Point3f center)
           
(package private)  void navigate(float timeSeconds, javax.vecmath.Point3f[][] pathGuide)
           
(package private)  void navigate(float timeSeconds, javax.vecmath.Point3f[] path, float[] theta, int indexStart, int indexEnd)
           
 void navigate(float timeSeconds, javax.vecmath.Vector3f rotAxis, float degrees)
           
(package private)  void navigate(int keyWhere, int modifiers)
           
(package private)  void navigateSurface(float timeSeconds, java.lang.String name)
           
(package private)  void navTranslate(float timeSeconds, javax.vecmath.Point3f center)
           
(package private)  void navTranslatePercent(float timeSeconds, float x, float y)
           
(package private)  void notifyError(java.lang.String errType, java.lang.String errMsg, java.lang.String errMsgUntranslated)
           
 void notifyMinimizationStatus()
           
 void openClientFile(java.lang.String fullPathName, java.lang.String fileName, java.lang.Object clientFile)
          Deprecated.  
 java.lang.String openDOM(java.lang.Object DOMNode)
           
 java.lang.String openFile(java.lang.String fileName)
          for JmolSimpleViewer -- external applications only
(package private)  void openFile(java.lang.String fileName, java.util.Hashtable htParams, java.lang.String loadScript, boolean isAppend)
           
 void openFileAsynchronously(java.lang.String fileName)
           
 java.lang.String openFiles(java.lang.String modelName, java.lang.String[] fileNames)
           
(package private)  java.lang.String openFiles(java.lang.String modelName, java.lang.String[] fileNames, java.lang.String loadScript, boolean isAppend, java.util.Hashtable htParams)
           
 java.lang.String openReader(java.lang.String fullPathName, java.lang.String fileName, java.io.Reader reader)
          Opens the file, given the reader.
 java.lang.String openStringInline(java.lang.String strModel)
           
private  java.lang.String openStringsInline(java.lang.String[] arrayModels, java.util.Hashtable htParams, boolean isAppend)
           
(package private)  void pauseAnimation()
           
 void pauseScriptExecution()
           
 void popHoldRepaint()
           
(package private)  void popHoldRepaint(java.lang.String why)
           
(package private)  void popupMenu(int x, int y)
           
 void pushHoldRepaint()
           
(package private)  void pushHoldRepaint(java.lang.String why)
           
 void rebond()
           
 void refresh(int mode, java.lang.String strWhy)
          initiate a repaint/update sequence if it has not already been requested.
 void refreshMeasures()
           
 void releaseScreenImage()
           
(package private)  java.lang.String removeCommand()
          Removes one command from the command history
 void removeSelectionListener(JmolSelectionListener listener)
           
(package private)  void removeUserVariable(java.lang.String key)
           
private  void render()
           
private  void render1(java.awt.Graphics g, java.awt.Image img, int x, int y)
           
 void renderScreenImage(java.awt.Graphics g, java.awt.Dimension size, java.awt.Rectangle clip)
           
 void renderScreenImage(java.awt.Graphics gLeft, java.awt.Graphics gRight, java.awt.Dimension size, java.awt.Rectangle clip)
          an added class for rendering stereo in two independent applets
 void repaintView()
           
(package private)  void reportSelection(java.lang.String msg)
           
(package private)  void requestRepaintAndWait()
           
(package private)  void reset()
           
(package private)  void resetAromatic()
           
private  void resizeImage(int width, int height, boolean isImageWrite, boolean isGenerator, boolean isReset)
           
(package private)  boolean restoreBonds(java.lang.String saveName)
           
(package private)  void restoreModelOrientation(int modelIndex)
           
(package private)  void restoreModelRotation(int modelIndex)
           
 boolean restoreOrientation(java.lang.String saveName, float timeSeconds)
           
 void restoreRotation(java.lang.String saveName, float timeSeconds)
           
(package private)  boolean restoreSelection(java.lang.String saveName)
           
(package private)  void resumeAnimation()
           
 void resumeScriptExecution()
           
(package private)  void reverseAnimation()
           
(package private)  void rewindAnimation()
           
(package private)  void rotateAboutPointsInternal(javax.vecmath.Point3f point1, javax.vecmath.Point3f point2, float degrees, float endDegrees, boolean isSpin, java.util.BitSet bsSelected)
           
(package private)  void rotateAtoms(javax.vecmath.Matrix3f mNew, javax.vecmath.Matrix3f matrixRotate, boolean fullMolecule, javax.vecmath.Point3f center, boolean isInternal, java.util.BitSet bsAtoms)
           
(package private)  void rotateAxisAngleAtCenter(javax.vecmath.Point3f rotCenter, javax.vecmath.Vector3f rotAxis, float degrees, float endDegrees, boolean isSpin, java.util.BitSet bsSelected)
           
 void rotateFront()
           
(package private)  void rotateMolecule(int deltaX, int deltaY)
           
 void rotatePoint(javax.vecmath.Point3f pt, javax.vecmath.Point3f ptRot)
           
 void rotateX(float angleRadians)
           
 void rotateX(int angleDegrees)
           
(package private)  void rotateXYBy(int xDelta, int yDelta)
           
 void rotateY(float angleRadians)
           
 void rotateY(int angleDegrees)
           
 void rotateZ(float angleRadians)
           
(package private)  void rotateZBy(int zDelta)
           
(package private)  void saveBonds(java.lang.String saveName)
           
 void saveCoordinates(java.lang.String saveName, java.util.BitSet bsSelected)
           
(package private)  void saveModelOrientation()
           
 void saveOrientation(java.lang.String saveName)
           
(package private)  void saveSelection(java.lang.String saveName)
           
(package private)  void saveState(java.lang.String saveName)
           
(package private)  void saveStructure(java.lang.String saveName)
           
 float scaleToPerspective(int z, float sizeAngstroms)
           
 short scaleToScreen(int z, int milliAngstroms)
           
 java.lang.String script(java.lang.String strScript)
           
 java.lang.Object scriptCheck(java.lang.String strScript)
           
private  java.lang.Object scriptCheck(java.lang.String strScript, boolean returnContext)
           
 void scriptEcho(java.lang.String strEcho)
           
(package private)  void scriptStatus(java.lang.String strStatus)
           
(package private)  void scriptStatus(java.lang.String strStatus, java.lang.String statusMessage)
           
(package private)  void scriptStatus(java.lang.String strStatus, java.lang.String statusMessage, int msWalltime, java.lang.String strErrorMessageUntranslated)
           
 java.lang.String scriptWait(java.lang.String strScript)
           
 java.lang.Object scriptWaitStatus(java.lang.String strScript, java.lang.String statusList)
           
(package private)  void select(java.util.BitSet bs, boolean isQuiet)
           
 void selectAll()
           
(package private)  void selectBonds(java.util.BitSet bs)
           
(package private)  void selectRectangle(java.awt.Rectangle rect, int modifiers)
           
(package private)  void setAllowRotateSelected(boolean TF)
           
private static void setAmbientPercent(int ambientPercent)
           
(package private)  void setAnimationDirection(int direction)
           
 void setAnimationFps(int fps)
           
(package private)  void setAnimationLast()
           
(package private)  void setAnimationNext()
           
(package private)  void setAnimationOn(boolean animationOn)
           
(package private)  void setAnimationPrevious()
           
(package private)  void setAnimationRange(int modelIndex1, int modelIndex2)
           
(package private)  void setAnimationReplayMode(int replay, float firstFrameDelay, float lastFrameDelay)
           
private  void setAntialias(int mode, boolean TF)
           
(package private)  void setAppendNew(boolean value)
           
 void setAppletContext(java.lang.String fullName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions)
           
(package private)  void setApplySymmetryToBonds(boolean TF)
           
(package private)  void setAtomCoord(java.util.BitSet bs, int tokType, java.lang.Object xyzValues)
           
 void setAtomCoord(int atomIndex, float x, float y, float z)
           
 void setAtomCoordRelative(int atomIndex, float x, float y, float z)
           
(package private)  void setAtomCoordRelative(javax.vecmath.Point3f offset)
           
(package private)  void setAtomData(int type, java.lang.String name, java.lang.String coordinateData)
           
(package private)  void setAtomProperty(java.util.BitSet bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
           
 void setAutoBond(boolean TF)
           
private  void setAxesModeMolecular(boolean TF)
           
(package private)  void setAxesModeUnitCell(boolean TF)
           
 void setAxesOrientationRasmol(boolean TF)
           
(package private)  void setAxesScale(float scale)
           
(package private)  void setBackgroundImage(java.lang.String fileName, java.awt.Image image)
           
(package private)  void setBackgroundModelIndex(int modelIndex)
           
 void setBondTolerance(float bondTolerance)
           
 void setBooleanProperty(java.lang.String key, boolean value)
           
(package private)  boolean setBooleanProperty(java.lang.String key, boolean value, boolean defineNew)
           
(package private)  void setBoundBox(javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, boolean byCorner)
           
(package private)  void setCenterAt(java.lang.String relativeTo, javax.vecmath.Point3f pt)
           
(package private)  void setCenterBitSet(java.util.BitSet bsCenter, boolean doScale)
           
 void setCenterSelected()
           
 void setColorBackground(java.lang.String colorName)
           
 java.util.BitSet setConformation()
           
 java.util.BitSet setConformation(int conformationIndex)
           
(package private)  void setCurrentColorRange(float[] data, java.util.BitSet bs)
           
 void setCurrentColorRange(float min, float max)
           
(package private)  void setCurrentColorRange(java.lang.String label)
           
(package private)  void setCurrentModelIndex(int modelIndex)
           
 void setCurrentModelIndex(int modelIndex, boolean clearBackground)
           
(package private)  void setCurrentUnitCellOffset(int offset)
           
(package private)  void setCurrentUnitCellOffset(javax.vecmath.Point3f pt)
           
 void setCursor(int cursor)
           
 void setData(java.lang.String type, java.lang.Object[] data, int atomCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)
           
 void setDebugScript(boolean debugScript)
           
private  void setDefaultColors(java.lang.String colorScheme)
           
 void setDefaultDrawArrowScale(float scale)
           
(package private)  void setDefaultLattice(javax.vecmath.Point3f ptLattice)
           
private  void setDefaults(java.lang.String type)
           
(package private)  void setDefaultVdw(java.lang.String mode)
           
private static void setDiffusePercent(int diffusePercent)
           
(package private)  void setDynamicMeasurements(boolean TF)
           
(package private)  void setEchoStateActive(boolean TF)
           
(package private)  void setElementArgb(int elementNumber, int argb)
           
private  java.lang.String setErrorMessage(java.lang.String errMsg)
           
private  java.lang.String setErrorMessage(java.lang.String errMsg, java.lang.String errMsgUntranslated)
           
(package private)  void setFileInfo(java.lang.String[] fileInfo)
           
private  void setFileLoadStatus(int ptLoad, java.lang.String fullPathName, java.lang.String fileName, java.lang.String modelName, java.lang.String strError)
           
 void setFloatProperty(java.lang.String key, float value)
           
private  boolean setFloatProperty(java.lang.String key, float value, boolean isInt)
           
(package private)  void setFormalCharges(int formalCharge)
           
(package private)  void setFrameOffset(int modelIndex)
           
 void setFrameOffsets(java.util.BitSet bsAtoms)
           
(package private)  void setFrameTitle(int modelIndex, java.lang.String title)
           
(package private)  void setFrameTitle(java.lang.String title)
           
(package private)  void setFrameVariables(int firstModelIndex, int lastModelIndex)
           
 void setFrankOn(boolean TF)
           
private  void setImageFontScaling(int width, int height)
           
(package private)  void setInMotion(boolean inMotion)
           
 void setIntProperty(java.lang.String key, int value)
           
private  void setIntProperty(java.lang.String key, int value, boolean defineNew)
           
 void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
           
(package private)  void setJmolDataFrame(java.lang.String type, int modelIndex, int dataIndex)
           
 void setJmolDefaults()
           
 void setJmolStatusListener(JmolStatusListener jmolStatusListener)
           
(package private)  void setLabel(java.lang.String strLabel)
           
private  void setLanguage(java.lang.String value)
           
private  java.util.Hashtable setLoadParameters(java.util.Hashtable htParams)
           
 void setMarBond(short marBond)
           
private  void setMaximumSize(int x)
           
(package private)  void setMeasureDistanceUnits(java.lang.String units)
           
(package private)  void setMeasurementFormats(java.lang.String strFormat)
           
(package private)  void setMenu(java.lang.String fileOrText, boolean isFile)
           
 void setMeshCreator(java.lang.Object meshCreator)
          an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer viewer = applet.getViewer(); viewer.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.
 void setMinBondDistance(float minBondDistance)
           
(package private)  void setModelVisibility()
           
 void setModeMouse(int modeMouse)
           
 void setMouseEnabled(boolean TF)
           
(package private)  void setNavigationDepthPercent(float timeSec, float percent)
           
private  void setNavigationMode(boolean TF)
           
(package private)  void setNavOn(boolean navOn)
           
(package private)  void setNavXYZ(float x, float y, float z)
           
(package private)  void setNewRotationCenter(javax.vecmath.Point3f center)
           
(package private)  void setNoneSelected(boolean noneSelected)
           
(package private)  void setObjectArgb(java.lang.String name, int argb)
           
(package private)  void setObjectColor(java.lang.String name, java.lang.String colorName)
           
(package private)  void setObjectMad(int iShape, java.lang.String name, int mad)
           
(package private)  void setPdbConectBonding(boolean isAuto)
           
(package private)  void setPendingMeasurement(MeasurementPending measurementPending)
           
 void setPercentVdwAtom(int percentVdwAtom)
           
 void setPerspectiveDepth(boolean perspectiveDepth)
           
private  void setPerspectiveModel(int mode)
           
private  void setPickingMode(java.lang.String mode)
           
private  void setPickingStyle(java.lang.String style)
           
 void setPropertyColorScheme(java.lang.String scheme, boolean isOverloaded)
           
private  void setPropertyError(java.lang.String msg)
           
(package private)  void setProteinType(byte iType, java.util.BitSet bs)
           
 void setRasmolDefaults()
           
(package private)  void setRefreshing(boolean TF)
           
(package private)  void setRotationRadius(float angstroms, boolean doAll)
           
(package private)  void setRubberbandArgb(int argb)
           
 void setScreenDimension(java.awt.Dimension dim)
           
 void setSelectionHalos(boolean TF)
           
 void setSelectionSet(java.util.BitSet set)
           
(package private)  void setSelectionSubset(java.util.BitSet subset)
           
 void setShapeErrorState(int shapeID, java.lang.String state)
           
 void setShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object value)
           
(package private)  void setShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs)
           
(package private)  void setShapePropertyArgb(int shapeID, java.lang.String propertyName, int argb)
           
 void setShapeSize(int shapeID, int size, java.util.BitSet bsAtoms)
           
(package private)  void setShapeSize(int shapeID, int size, float fsize)
           
 void setShapeSize(int shapeID, int size, float fsize, java.util.BitSet bsAtoms)
           
 void setShowAxes(boolean value)
           
 void setShowBbcage(boolean value)
           
 void setShowHydrogens(boolean TF)
           
 void setShowMeasurements(boolean TF)
           
 void setShowUnitCell(boolean value)
           
(package private)  void setSlabDepthInternal(boolean isDepth)
           
private static void setSpecular(boolean specular)
           
private static void setSpecularExponent(int specularExponent)
           
private static void setSpecularPercent(int specularPercent)
           
private static void setSpecularPower(int specularPower)
           
(package private)  void setSpin(java.lang.String key, int value)
           
(package private)  void setSpinOn(boolean spinOn)
           
 void setStatusAtomHovered(int atomIndex, java.lang.String info)
           
 void setStatusAtomPicked(int atomIndex, java.lang.String info)
           
(package private)  void setStatusFrameChanged(int frameNo)
           
 void setStatusMeasuring(java.lang.String status, int intInfo, java.lang.String strMeasure)
           
 void setStatusResized(int width, int height)
           
(package private)  void setStereoMode(int[] twoColors, int stereoMode, float degrees)
           
private  void setStrandCount(int type, int value)
           
 void setStringProperty(java.lang.String key, java.lang.String value)
           
(package private)  void setSync()
           
(package private)  void setSyncDriver(int mode)
           
private  void setSyncTarget(int mode, boolean TF)
           
(package private)  void setTainted(boolean TF)
           
 void setTaintedAtoms(java.util.BitSet bs, byte type)
           
 void setTrajectory(java.util.BitSet bsModels)
           
(package private)  void setTrajectory(int modelIndex)
           
 void setTransformManager(TransformManager transformManager)
          for an external application
private  void setTransformManagerDefaults()
           
static void setUserScale(int[] scale)
           
(package private)  ScriptVariable setUserVariable(java.lang.String name, ScriptVariable value)
           
 void setVectorScale(float scale)
           
(package private)  void setVibrationOff()
           
 void setVibrationPeriod(float period)
           
 void setVibrationScale(float scale)
           
 void setVisualRange(float angstroms)
           
(package private)  void showConsole(boolean showConsole)
           
(package private)  void showEditor(java.lang.String[] file_text)
           
 void showMeasurement(int[] atomCountPlusIndices, boolean isON)
           
(package private)  void showMessage(java.lang.String s)
           
 boolean showModelSetDownload()
           
(package private)  void showParameter(java.lang.String key, boolean ifNotSet, int nMax)
           
 void showString(java.lang.String str, boolean isPrint)
           
 void showUrl(java.lang.String urlString)
           
(package private)  void slabByPixels(int pixels)
           
(package private)  void slabDepthByPixels(int pixels)
           
(package private)  void slabInternal(javax.vecmath.Point4f plane, boolean isDepth)
           
(package private)  void slabReset()
           
(package private)  void slabToPercent(int percentSlab)
           
 void startSpinningAxis(javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, boolean isClockwise)
           
 void stepScriptExecution()
           
private  void stopAnimationThreads()
           
 void syncScript(java.lang.String script, java.lang.String applet)
           
(package private)  void toCartesian(javax.vecmath.Point3f pt)
           
(package private)  void toFractional(javax.vecmath.Point3f pt)
           
(package private)  void toggleMeasurement(int[] atomCountPlusIndices, java.lang.String strFormat)
           
(package private)  void togglePickingLabel(java.util.BitSet bs)
           
(package private)  void toUnitCell(javax.vecmath.Point3f pt, javax.vecmath.Point3f offset)
           
 javax.vecmath.Point3i transformPoint(javax.vecmath.Point3f pointAngstroms)
           
 void transformPoint(javax.vecmath.Point3f pointAngstroms, javax.vecmath.Point3f pointScreen)
           
 void transformPoint(javax.vecmath.Point3f pointAngstroms, javax.vecmath.Point3i pointScreen)
           
 javax.vecmath.Point3i transformPoint(javax.vecmath.Point3f pointAngstroms, javax.vecmath.Vector3f vibrationVector)
           
 void transformPointNoClip(javax.vecmath.Point3f pointAngstroms, javax.vecmath.Point3f pt)
           
 void transformPoints(javax.vecmath.Point3f[] pointsAngstroms, javax.vecmath.Point3i[] pointsScreens)
           
 void transformVector(javax.vecmath.Vector3f vectorAngstroms, javax.vecmath.Vector3f vectorTransformed)
           
(package private)  void translate(char xyz, float x, char type)
           
(package private)  void translateXYBy(int xDelta, int yDelta)
           
 float unscaleToScreen(int z, int screenDistance)
           
(package private)  void unsetProperty(java.lang.String name)
           
 void unTransformPoint(javax.vecmath.Point3f pointScreen, javax.vecmath.Point3f pointAngstroms)
           
 boolean useMinimizationThread()
           
(package private)  boolean usingScriptQueue()
           
 void writeTextFile(java.lang.String fileName, java.lang.String data)
           
 void zap(boolean notify, boolean resetUndo)
           
private  void zap(java.lang.String msg)
           
(package private)  void zoomBy(int pixels)
           
(package private)  void zoomByFactor(float factor)
           
 int zValueFromPercent(int zPercent)
           
 
Methods inherited from class org.jmol.api.JmolViewer
checkOption
 
Methods inherited from class org.jmol.api.JmolSimpleViewer
allocateSimpleViewer
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

display

private java.awt.Component display

g3d

private Graphics3D g3d

modelAdapter

private JmolAdapter modelAdapter

commandHistory

private CommandHistory commandHistory

colorManager

private ColorManager colorManager

compiler

ScriptCompiler compiler

definedAtomSets

java.util.Hashtable definedAtomSets

minimizer

private MinimizerInterface minimizer

smilesMatcher

private SmilesMatcherInterface smilesMatcher

symmetry

private SymmetryInterface symmetry

eval

ScriptEvaluator eval

animationManager

private AnimationManager animationManager

dataManager

private DataManager dataManager

fileManager

private FileManager fileManager

modelManager

private ModelManager modelManager

modelSet

private ModelSet modelSet

mouseManager

public MouseManager mouseManager

pickingManager

private PickingManager pickingManager

repaintManager

private RepaintManager repaintManager

scriptManager

private ScriptManager scriptManager

selectionManager

private SelectionManager selectionManager

stateManager

private StateManager stateManager

global

private StateManager.GlobalSettings global

statusManager

private StatusManager statusManager

tempManager

private TempArray tempManager

transformManager

private TransformManager transformManager

strJavaVendor

private java.lang.String strJavaVendor

strJavaVersion

private java.lang.String strJavaVersion

strOSName

private java.lang.String strOSName

htmlName

private java.lang.String htmlName

fullName

private java.lang.String fullName

syncId

private java.lang.String syncId

appletDocumentBase

private java.lang.String appletDocumentBase

appletCodeBase

private java.lang.String appletCodeBase

jvm11orGreater

private boolean jvm11orGreater

jvm12orGreater

private boolean jvm12orGreater

jvm14orGreater

private boolean jvm14orGreater

isSilent

private boolean isSilent

isApplet

private boolean isApplet

isPreviewOnly

private boolean isPreviewOnly

autoExit

boolean autoExit

haveDisplay

boolean haveDisplay

isPrintOnly

private boolean isPrintOnly

mustRender

private boolean mustRender

isCmdLine_c_or_C_Option

private boolean isCmdLine_c_or_C_Option

listCommands

private boolean listCommands

isCmdLine_C_Option

private boolean isCmdLine_C_Option

useCommandThread

private boolean useCommandThread

isSignedApplet

private boolean isSignedApplet

isDataOnly

private boolean isDataOnly

mouseEnabled

private boolean mouseEnabled

noneSelected

private boolean noneSelected

FILE_STATUS_NOT_LOADED

private static final int FILE_STATUS_NOT_LOADED
See Also:
Constant Field Values

FILE_STATUS_ZAPPED

private static final int FILE_STATUS_ZAPPED
See Also:
Constant Field Values

FILE_STATUS_CREATING_MODELSET

private static final int FILE_STATUS_CREATING_MODELSET
See Also:
Constant Field Values

FILE_STATUS_MODELSET_CREATED

private static final int FILE_STATUS_MODELSET_CREATED
See Also:
Constant Field Values

FILE_STATUS_MODELS_DELETED

private static final int FILE_STATUS_MODELS_DELETED
See Also:
Constant Field Values

STATE_VERSION_STAMP

static final java.lang.String STATE_VERSION_STAMP
See Also:
Constant Field Values

testData

public static java.lang.Object testData

testData2

public static java.lang.Object testData2

bsFrameOffsets

java.util.BitSet bsFrameOffsets

frameOffsets

javax.vecmath.Point3f[] frameOffsets

wasInMotion

boolean wasInMotion

motionEventNumber

int motionEventNumber

refreshing

private boolean refreshing

axesAreTainted

private boolean axesAreTainted

dimScreen

final java.awt.Dimension dimScreen

maximumSize

private int maximumSize

imageFontScaling

private float imageFontScaling

antialiasDisplay

private boolean antialiasDisplay

interruptScript

java.lang.String interruptScript

scriptIndex

int scriptIndex

isScriptQueued

boolean isScriptQueued

hoverAtomIndex

int hoverAtomIndex

hoverText

java.lang.String hoverText

CURSOR_DEFAULT

public static final int CURSOR_DEFAULT
See Also:
Constant Field Values

CURSOR_HAND

public static final int CURSOR_HAND
See Also:
Constant Field Values

CURSOR_CROSSHAIR

public static final int CURSOR_CROSSHAIR
See Also:
Constant Field Values

CURSOR_MOVE

public static final int CURSOR_MOVE
See Also:
Constant Field Values

CURSOR_WAIT

public static final int CURSOR_WAIT
See Also:
Constant Field Values

currentCursor

private int currentCursor

prevFrame

int prevFrame

language

private java.lang.String language

frankOn

boolean frankOn

scriptEditorVisible

private boolean scriptEditorVisible

appConsole

JmolAppConsoleInterface appConsole

scriptEditor

JmolScriptEditorInterface scriptEditor

jmolpopup

JmolPopup jmolpopup

menuStructure

java.lang.String menuStructure

isTainted

boolean isTainted

creatingImage

private boolean creatingImage

SYNC_GRAPHICS_MESSAGE

public static final java.lang.String SYNC_GRAPHICS_MESSAGE
See Also:
Constant Field Values

SYNC_NO_GRAPHICS_MESSAGE

public static final java.lang.String SYNC_NO_GRAPHICS_MESSAGE
See Also:
Constant Field Values

errorMessage

private java.lang.String errorMessage

errorMessageUntranslated

private java.lang.String errorMessageUntranslated

currentShapeID

private int currentShapeID

currentShapeState

private java.lang.String currentShapeState
Constructor Detail

Viewer

public Viewer(java.awt.Component display,
              JmolAdapter modelAdapter)
Method Detail

finalize

protected void finalize()
                 throws java.lang.Throwable
Overrides:
finalize in class java.lang.Object
Throws:
java.lang.Throwable

getModelAdapter

public JmolAdapter getModelAdapter()
Specified by:
getModelAdapter in class JmolViewer

getMinimizer

MinimizerInterface getMinimizer(boolean createNew)

getSmilesMatcher

SmilesMatcherInterface getSmilesMatcher()

getSymmetry

public SymmetryInterface getSymmetry()

getSymmetryInfo

public java.lang.Object getSymmetryInfo(java.util.BitSet bsAtoms,
                                        java.lang.String xyz,
                                        int op,
                                        javax.vecmath.Point3f pt,
                                        java.lang.String id,
                                        int type)

clearModelDependentObjects

private void clearModelDependentObjects()

getGlobalSettings

StateManager.GlobalSettings getGlobalSettings()

allocateViewer

public static JmolViewer allocateViewer(java.awt.Component display,
                                        JmolAdapter modelAdapter,
                                        java.lang.String fullName,
                                        java.net.URL documentBase,
                                        java.net.URL codeBase,
                                        java.lang.String commandOptions,
                                        JmolStatusListener statusListener)
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.

Parameters:
display - either DisplayPanel or WrappedApplet
modelAdapter - the model reader
fullName - or null
documentBase - or null
codeBase - or null
commandOptions - or null
statusListener - or null
Returns:
a viewer instance

allocateViewer

public static JmolViewer allocateViewer(java.awt.Component display,
                                        JmolAdapter modelAdapter)
Deprecated. 

deprecated because setAppletContext needs to be invoked as well.

Parameters:
display -
modelAdapter -
Returns:
a viewer instance

isApplet

public boolean isApplet()
Specified by:
isApplet in class JmolViewer

isPreviewOnly

boolean isPreviewOnly()

setAppletContext

public void setAppletContext(java.lang.String fullName,
                             java.net.URL documentBase,
                             java.net.URL codeBase,
                             java.lang.String commandOptions)
Specified by:
setAppletContext in class JmolViewer

isDataOnly

public boolean isDataOnly()

getJmolVersion

public static java.lang.String getJmolVersion()

getExportDriverList

public java.lang.String getExportDriverList()

getJmolVersionInt

private static int getJmolVersionInt()

getHtmlName

java.lang.String getHtmlName()

mustRenderFlag

boolean mustRenderFlag()

getLogLevel

static int getLogLevel()

getDisplay

public java.awt.Component getDisplay()
Specified by:
getDisplay in class JmolViewer

handleOldJvm10Event

public boolean handleOldJvm10Event(java.awt.Event e)
Specified by:
handleOldJvm10Event in class JmolViewer

reset

void reset()

homePosition

public void homePosition()
Specified by:
homePosition in class JmolViewer

getAppletInfo

java.util.Hashtable getAppletInfo()

initialize

void initialize()

listSavedStates

java.lang.String listSavedStates()

saveOrientation

public void saveOrientation(java.lang.String saveName)

restoreOrientation

public boolean restoreOrientation(java.lang.String saveName,
                                  float timeSeconds)

restoreRotation

public void restoreRotation(java.lang.String saveName,
                            float timeSeconds)

saveModelOrientation

void saveModelOrientation()

getOrientation

public StateManager.Orientation getOrientation()

restoreModelOrientation

void restoreModelOrientation(int modelIndex)

restoreModelRotation

void restoreModelRotation(int modelIndex)

saveBonds

void saveBonds(java.lang.String saveName)

restoreBonds

boolean restoreBonds(java.lang.String saveName)

saveState

void saveState(java.lang.String saveName)

getSavedState

public java.lang.String getSavedState(java.lang.String saveName)

saveStructure

void saveStructure(java.lang.String saveName)

getSavedStructure

java.lang.String getSavedStructure(java.lang.String saveName)

saveCoordinates

public void saveCoordinates(java.lang.String saveName,
                            java.util.BitSet bsSelected)

getSavedCoordinates

java.lang.String getSavedCoordinates(java.lang.String saveName)

saveSelection

void saveSelection(java.lang.String saveName)

restoreSelection

boolean restoreSelection(java.lang.String saveName)

getMatrixtransform

public javax.vecmath.Matrix4f getMatrixtransform()

getRotationQuaternion

Quaternion getRotationQuaternion()

getRotationRadius

public float getRotationRadius()
Specified by:
getRotationRadius in class JmolViewer

setRotationRadius

void setRotationRadius(float angstroms,
                       boolean doAll)

getRotationCenter

public javax.vecmath.Point3f getRotationCenter()

setCenterAt

void setCenterAt(java.lang.String relativeTo,
                 javax.vecmath.Point3f pt)

setCenterBitSet

void setCenterBitSet(java.util.BitSet bsCenter,
                     boolean doScale)

setNewRotationCenter

void setNewRotationCenter(javax.vecmath.Point3f center)

getNavigationCenter

public javax.vecmath.Point3f getNavigationCenter()

getNavigationDepthPercent

public float getNavigationDepthPercent()

navigate

void navigate(int keyWhere,
              int modifiers)

getNavigationOffset

public javax.vecmath.Point3f getNavigationOffset()

getNavigationOffsetPercent

float getNavigationOffsetPercent(char XorY)

isNavigating

public boolean isNavigating()

isInPosition

boolean isInPosition(javax.vecmath.Vector3f axis,
                     float degrees)

move

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

moveTo

void moveTo(float floatSecondsTotal,
            javax.vecmath.Point3f center,
            javax.vecmath.Vector3f pt,
            float degrees,
            float zoom,
            float xTrans,
            float yTrans,
            float rotationRadius,
            javax.vecmath.Point3f navCenter,
            float xNav,
            float yNav,
            float navDepth)

moveTo

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

moveUpdate

private void moveUpdate(float floatSecondsTotal)

getMoveToText

java.lang.String getMoveToText(float timespan)

navigate

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

navigate

public void navigate(float timeSeconds,
                     javax.vecmath.Point3f center)

navigate

void navigate(float timeSeconds,
              javax.vecmath.Point3f[][] pathGuide)

navigateSurface

void navigateSurface(float timeSeconds,
                     java.lang.String name)

navigate

public void navigate(float timeSeconds,
                     javax.vecmath.Vector3f rotAxis,
                     float degrees)

navTranslate

void navTranslate(float timeSeconds,
                  javax.vecmath.Point3f center)

navTranslatePercent

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

setMouseEnabled

public void setMouseEnabled(boolean TF)

zoomBy

void zoomBy(int pixels)

zoomByFactor

void zoomByFactor(float factor)

rotateXYBy

void rotateXYBy(int xDelta,
                int yDelta)

rotateZBy

void rotateZBy(int zDelta)

rotateMolecule

void rotateMolecule(int deltaX,
                    int deltaY)

translateXYBy

void translateXYBy(int xDelta,
                   int yDelta)

rotateFront

public void rotateFront()
Specified by:
rotateFront in class JmolViewer

rotateX

public void rotateX(float angleRadians)
Specified by:
rotateX in class JmolViewer

rotateY

public void rotateY(float angleRadians)
Specified by:
rotateY in class JmolViewer

rotateZ

public void rotateZ(float angleRadians)
Specified by:
rotateZ in class JmolViewer

rotateX

public void rotateX(int angleDegrees)
Specified by:
rotateX in class JmolViewer

rotateY

public void rotateY(int angleDegrees)
Specified by:
rotateY in class JmolViewer

translate

void translate(char xyz,
               float x,
               char type)

getTranslationXPercent

public float getTranslationXPercent()

getTranslationYPercent

public float getTranslationYPercent()

getTranslationZPercent

float getTranslationZPercent()

getTranslationScript

public java.lang.String getTranslationScript()

getZoomPercent

public int getZoomPercent()
Specified by:
getZoomPercent in class JmolViewer

getZoomSetting

float getZoomSetting()

getZoomPercentFloat

public float getZoomPercentFloat()
Specified by:
getZoomPercentFloat in class JmolViewer

getMaxZoomPercent

float getMaxZoomPercent()

slabReset

void slabReset()

getZoomEnabled

boolean getZoomEnabled()

getSlabEnabled

public boolean getSlabEnabled()

slabByPixels

void slabByPixels(int pixels)

depthByPixels

void depthByPixels(int pixels)

slabDepthByPixels

void slabDepthByPixels(int pixels)

slabToPercent

void slabToPercent(int percentSlab)

slabInternal

void slabInternal(javax.vecmath.Point4f plane,
                  boolean isDepth)

depthToPercent

void depthToPercent(int percentDepth)

setSlabDepthInternal

void setSlabDepthInternal(boolean isDepth)

zValueFromPercent

public int zValueFromPercent(int zPercent)

getUnscaledTransformMatrix

public javax.vecmath.Matrix4f getUnscaledTransformMatrix()
Specified by:
getUnscaledTransformMatrix in class JmolViewer

finalizeTransformParameters

void finalizeTransformParameters()

rotatePoint

public void rotatePoint(javax.vecmath.Point3f pt,
                        javax.vecmath.Point3f ptRot)

transformPoint

public javax.vecmath.Point3i transformPoint(javax.vecmath.Point3f pointAngstroms)

transformPoint

public javax.vecmath.Point3i transformPoint(javax.vecmath.Point3f pointAngstroms,
                                            javax.vecmath.Vector3f vibrationVector)

transformPoint

public void transformPoint(javax.vecmath.Point3f pointAngstroms,
                           javax.vecmath.Point3i pointScreen)

transformPointNoClip

public void transformPointNoClip(javax.vecmath.Point3f pointAngstroms,
                                 javax.vecmath.Point3f pt)

transformPoint

public void transformPoint(javax.vecmath.Point3f pointAngstroms,
                           javax.vecmath.Point3f pointScreen)

transformPoints

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

transformVector

public void transformVector(javax.vecmath.Vector3f vectorAngstroms,
                            javax.vecmath.Vector3f vectorTransformed)

unTransformPoint

public void unTransformPoint(javax.vecmath.Point3f pointScreen,
                             javax.vecmath.Point3f pointAngstroms)

getScalePixelsPerAngstrom

public float getScalePixelsPerAngstrom(boolean asAntialiased)

scaleToScreen

public short scaleToScreen(int z,
                           int milliAngstroms)

unscaleToScreen

public float unscaleToScreen(int z,
                             int screenDistance)

scaleToPerspective

public float scaleToPerspective(int z,
                                float sizeAngstroms)

setSpin

void setSpin(java.lang.String key,
             int value)

getSpinState

java.lang.String getSpinState()

setSpinOn

void setSpinOn(boolean spinOn)

getSpinOn

boolean getSpinOn()

setNavOn

void setNavOn(boolean navOn)

getNavOn

boolean getNavOn()

setNavXYZ

void setNavXYZ(float x,
               float y,
               float z)

getOrientationText

public java.lang.String getOrientationText(int type)

getOrientationInfo

java.util.Hashtable getOrientationInfo()

getMatrixRotate

javax.vecmath.Matrix3f getMatrixRotate()

getAxisAngle

public void getAxisAngle(javax.vecmath.AxisAngle4f axisAngle)

getTransformText

java.lang.String getTransformText()

getRotation

void getRotation(javax.vecmath.Matrix3f matrixRotation)

setDefaultColors

private void setDefaultColors(java.lang.String colorScheme)

getDefaultTranslucent

float getDefaultTranslucent()

getColixArgb

public int getColixArgb(short colix)

setRubberbandArgb

void setRubberbandArgb(int argb)

getColixRubberband

public short getColixRubberband()

setElementArgb

void setElementArgb(int elementNumber,
                    int argb)

getVectorScale

public float getVectorScale()

setVectorScale

public void setVectorScale(float scale)
Specified by:
setVectorScale in class JmolViewer

getDefaultDrawArrowScale

public float getDefaultDrawArrowScale()

setDefaultDrawArrowScale

public void setDefaultDrawArrowScale(float scale)

getVibrationScale

float getVibrationScale()

getVibrationPeriod

float getVibrationPeriod()

isVibrationOn

public boolean isVibrationOn()

setVibrationScale

public void setVibrationScale(float scale)
Specified by:
setVibrationScale in class JmolViewer

setVibrationOff

void setVibrationOff()

setVibrationPeriod

public void setVibrationPeriod(float period)
Specified by:
setVibrationPeriod in class JmolViewer

setObjectColor

void setObjectColor(java.lang.String name,
                    java.lang.String colorName)

setObjectArgb

void setObjectArgb(java.lang.String name,
                   int argb)

setBackgroundImage

void setBackgroundImage(java.lang.String fileName,
                        java.awt.Image image)

getObjectArgb

int getObjectArgb(int objId)

getObjectColix

public short getObjectColix(int objId)

getObjectState

public java.lang.String getObjectState(java.lang.String name)

setColorBackground

public void setColorBackground(java.lang.String colorName)
Specified by:
setColorBackground in class JmolViewer

getBackgroundArgb

public int getBackgroundArgb()
Specified by:
getBackgroundArgb in class JmolViewer

setObjectMad

void setObjectMad(int iShape,
                  java.lang.String name,
                  int mad)

getObjectMad

public int getObjectMad(int objId)

setPropertyColorScheme

public void setPropertyColorScheme(java.lang.String scheme,
                                   boolean isOverloaded)

getPropertyColorScheme

public java.lang.String getPropertyColorScheme()

getColixBackgroundContrast

public short getColixBackgroundContrast()

getSpecularState

java.lang.String getSpecularState()

setSpecular

private static void setSpecular(boolean specular)

getSpecular

boolean getSpecular()

setSpecularPower

private static void setSpecularPower(int specularPower)

setSpecularExponent

private static void setSpecularExponent(int specularExponent)

setAmbientPercent

private static void setAmbientPercent(int ambientPercent)

getAmbientPercent

static int getAmbientPercent()

setDiffusePercent

private static void setDiffusePercent(int diffusePercent)

getDiffusePercent

static int getDiffusePercent()

setSpecularPercent

private static void setSpecularPercent(int specularPercent)

getSpecularPercent

static int getSpecularPercent()

getZShade

boolean getZShade()

getColixAtomPalette

public short getColixAtomPalette(Atom atom,
                                 byte pid)

getColixBondPalette

public short getColixBondPalette(Bond bond,
                                 byte pid)

getColorSchemeArray

public int[] getColorSchemeArray(java.lang.String colorScheme)

getColorSchemeList

public java.lang.String getColorSchemeList(java.lang.String colorScheme,
                                           boolean ifDefault)

setUserScale

public static void setUserScale(int[] scale)

getColixForPropertyValue

public short getColixForPropertyValue(float val)

getColorPointForPropertyValue

javax.vecmath.Point3f getColorPointForPropertyValue(float val)

select

void select(java.util.BitSet bs,
            boolean isQuiet)

selectBonds

void selectBonds(java.util.BitSet bs)

hide

void hide(java.util.BitSet bs,
          boolean isQuiet)

display

void display(java.util.BitSet bs,
             boolean isQuiet)

getHiddenSet

java.util.BitSet getHiddenSet()

isSelected

public boolean isSelected(int atomIndex)

isInSelectionSubset

boolean isInSelectionSubset(int atomIndex)

reportSelection

void reportSelection(java.lang.String msg)

getAtomSetCenter

public javax.vecmath.Point3f getAtomSetCenter(java.util.BitSet bs)

clearAtomSets

private void clearAtomSets()

selectAll

public void selectAll()
Specified by:
selectAll in class JmolViewer

setNoneSelected

void setNoneSelected(boolean noneSelected)

getNoneSelected

java.lang.Boolean getNoneSelected()

clearSelection

public void clearSelection()
Specified by:
clearSelection in class JmolViewer

setSelectionSet

public void setSelectionSet(java.util.BitSet set)
Specified by:
setSelectionSet in class JmolViewer

setSelectionSubset

void setSelectionSubset(java.util.BitSet subset)

getSelectionSubset

public java.util.BitSet getSelectionSubset()

invertSelection

void invertSelection()

getSelectionSet

public java.util.BitSet getSelectionSet()

getSelectionCount

public int getSelectionCount()
Specified by:
getSelectionCount in class JmolViewer

setFormalCharges

void setFormalCharges(int formalCharge)

addSelectionListener

public void addSelectionListener(JmolSelectionListener listener)
Specified by:
addSelectionListener in class JmolViewer

removeSelectionListener

public void removeSelectionListener(JmolSelectionListener listener)
Specified by:
removeSelectionListener in class JmolViewer

getAtomBitSet

java.util.BitSet getAtomBitSet(java.lang.Object atomExpression)

getAtomBitSetVector

java.util.Vector getAtomBitSetVector(java.lang.Object atomExpression)

setModeMouse

public void setModeMouse(int modeMouse)
Specified by:
setModeMouse in class JmolViewer

getRubberBandSelection

java.awt.Rectangle getRubberBandSelection()

getCursorX

public int getCursorX()

getCursorY

public int getCursorY()

getDefaultDirectory

java.lang.String getDefaultDirectory()

getBufferedInputStream

public java.io.BufferedInputStream getBufferedInputStream(java.lang.String fullPathName)
Specified by:
getBufferedInputStream in interface AtomDataServer

getBufferedReaderOrErrorMessageFromName

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

addLoadScript

void addLoadScript(java.lang.String script)

setLoadParameters

private java.util.Hashtable setLoadParameters(java.util.Hashtable htParams)

openFile

public java.lang.String openFile(java.lang.String fileName)
for JmolSimpleViewer -- external applications only

Specified by:
openFile in class JmolSimpleViewer
Parameters:
fileName -
Returns:
null or error

openFileAsynchronously

public void openFileAsynchronously(java.lang.String fileName)
Specified by:
openFileAsynchronously in class JmolViewer

openFile

void openFile(java.lang.String fileName,
              java.util.Hashtable htParams,
              java.lang.String loadScript,
              boolean isAppend)

openFiles

public java.lang.String openFiles(java.lang.String modelName,
                                  java.lang.String[] fileNames)

openFiles

java.lang.String openFiles(java.lang.String modelName,
                           java.lang.String[] fileNames,
                           java.lang.String loadScript,
                           boolean isAppend,
                           java.util.Hashtable htParams)

openStringInline

public java.lang.String openStringInline(java.lang.String strModel)
Specified by:
openStringInline in class JmolSimpleViewer

createModelSetInline

private java.lang.String createModelSetInline(java.lang.String strModel,
                                              java.util.Hashtable htParams,
                                              boolean isAppend,
                                              boolean createModelSet)

openStringsInline

private java.lang.String openStringsInline(java.lang.String[] arrayModels,
                                           java.util.Hashtable htParams,
                                           boolean isAppend)

getInlineChar

public char getInlineChar()

loadInline

public java.lang.String loadInline(java.lang.String strModel)
Specified by:
loadInline in class JmolViewer

loadInline

public java.lang.String loadInline(java.lang.String strModel,
                                   boolean isAppend)
Specified by:
loadInline in class JmolViewer

loadInline

public java.lang.String loadInline(java.lang.String strModel,
                                   char newLine)
Specified by:
loadInline in class JmolViewer

loadInline

java.lang.String loadInline(java.lang.String strModel,
                            char newLine,
                            boolean isAppend)

getDataSeparator

java.lang.String getDataSeparator()

loadInline

public java.lang.String loadInline(java.lang.String[] arrayModels)
Specified by:
loadInline in class JmolViewer

loadInline

public java.lang.String loadInline(java.lang.String[] arrayModels,
                                   boolean isAppend)
Specified by:
loadInline in class JmolViewer

getApplySymmetryToBonds

public boolean getApplySymmetryToBonds()

setApplySymmetryToBonds

void setApplySymmetryToBonds(boolean TF)

setAtomData

void setAtomData(int type,
                 java.lang.String name,
                 java.lang.String coordinateData)

openDOM

public java.lang.String openDOM(java.lang.Object DOMNode)
Specified by:
openDOM in class JmolSimpleViewer

openReader

public java.lang.String openReader(java.lang.String fullPathName,
                                   java.lang.String fileName,
                                   java.io.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 -- will close the reader

Specified by:
openReader in class JmolViewer
Parameters:
fullPathName -
fileName -
reader -
Returns:
null or error message

createModelSetAndReturnError

java.lang.String createModelSetAndReturnError(boolean isAppend)
Parameters:
isAppend -
Returns:
errMsg

loadAtomDataAndReturnError

java.lang.String loadAtomDataAndReturnError(int tokType)

createAtomDataSet

private java.lang.String createAtomDataSet(int tokType,
                                           java.lang.Object atomSetCollection)

deallocateReaderThreads

void deallocateReaderThreads()

openClientFile

public void openClientFile(java.lang.String fullPathName,
                           java.lang.String fileName,
                           java.lang.Object clientFile)
Deprecated. 

deprecated -- this method does not actually open the file

Specified by:
openClientFile in class JmolViewer
Parameters:
fullPathName -
fileName -
clientFile -

createModelSet

private java.lang.String createModelSet(java.lang.String fullPathName,
                                        java.lang.String fileName,
                                        java.lang.Object atomSetCollection,
                                        boolean isAppend)
Parameters:
fullPathName -
fileName -
atomSetCollection -
isAppend -
Returns:
null or error message

getCurrentFileAsBytes

public java.lang.Object getCurrentFileAsBytes()

getFileAsBytes

public java.lang.Object getFileAsBytes(java.lang.String pathName)

getCurrentFileAsString

public java.lang.String getCurrentFileAsString()

getFullPathName

public java.lang.String getFullPathName()

getFileName

public java.lang.String getFileName()

getFileAsString

public java.lang.String getFileAsString(java.lang.String name)
Specified by:
getFileAsString in class JmolViewer

getFileAsString

public java.lang.String getFileAsString(java.lang.String name,
                                        int nBytesMax,
                                        boolean doSpecialLoad)

getFullPath

public java.lang.String getFullPath(java.lang.String name)

getFileAsString

public boolean getFileAsString(java.lang.String[] data,
                               int nBytesMax,
                               boolean doSpecialLoad)
Specified by:
getFileAsString in class JmolViewer

getFileInfo

java.lang.String[] getFileInfo()

setFileInfo

void setFileInfo(java.lang.String[] fileInfo)

autoCalculate

public void autoCalculate(int tokProperty)

getSurfaceDistanceMax

int getSurfaceDistanceMax()

calculateStraightness

public void calculateStraightness()

calculateSurface

public javax.vecmath.Point3f[] calculateSurface(java.util.BitSet bsSelected,
                                                float envelopeRadius)

calculateStructures

void calculateStructures(java.util.BitSet bsAtoms)

getWithinModelIterator

public AtomIndexIterator getWithinModelIterator(Atom atom,
                                                float distance)

getWithinAtomSetIterator

public AtomIndexIterator getWithinAtomSetIterator(int atomIndex,
                                                  float distance,
                                                  java.util.BitSet bsSelected,
                                                  boolean isGreaterOnly,
                                                  boolean modelZeroBased)
Specified by:
getWithinAtomSetIterator in interface AtomDataServer

fillAtomData

public void fillAtomData(AtomData atomData,
                         int mode)
Specified by:
fillAtomData in interface AtomDataServer

addStateScript

ModelCollection.StateScript addStateScript(java.lang.String script,
                                           boolean addFrameNumber,
                                           boolean postDefinitions)

addStateScript

ModelCollection.StateScript addStateScript(java.lang.String script1,
                                           java.util.BitSet bsBonds,
                                           java.util.BitSet bsAtoms1,
                                           java.util.BitSet bsAtoms2,
                                           java.lang.String script2,
                                           boolean addFrameNumber,
                                           boolean postDefinitions)

getEchoStateActive

public boolean getEchoStateActive()

setEchoStateActive

void setEchoStateActive(boolean TF)

zap

public void zap(boolean notify,
                boolean resetUndo)

zap

private void zap(java.lang.String msg)

echoMessage

void echoMessage(java.lang.String msg)

getMinimizationInfo

public java.lang.String getMinimizationInfo()

useMinimizationThread

public boolean useMinimizationThread()

initializeModel

private void initializeModel()

getModelSetName

public java.lang.String getModelSetName()
Specified by:
getModelSetName in class JmolViewer

getModelSetFileName

public java.lang.String getModelSetFileName()
Specified by:
getModelSetFileName in class JmolViewer

getUnitCellInfoText

public java.lang.String getUnitCellInfoText()

getSpaceGroupInfo

public java.util.Hashtable getSpaceGroupInfo(java.lang.String spaceGroup)

getPolymerPointsAndVectors

void getPolymerPointsAndVectors(java.util.BitSet bs,
                                java.util.Vector vList)

getModelSetProperty

public java.lang.String getModelSetProperty(java.lang.String strProp)

getModelSetAuxiliaryInfo

public java.lang.Object getModelSetAuxiliaryInfo(java.lang.String strKey)

getModelSetPathName

public java.lang.String getModelSetPathName()
Specified by:
getModelSetPathName in class JmolViewer

getModelSetTypeName

public java.lang.String getModelSetTypeName()

haveFrame

public boolean haveFrame()
Specified by:
haveFrame in class JmolViewer

haveModelSet

boolean haveModelSet()

clearBfactorRange

void clearBfactorRange()

getHybridizationAndAxes

public java.lang.String getHybridizationAndAxes(int atomIndex,
                                                javax.vecmath.Vector3f z,
                                                javax.vecmath.Vector3f x,
                                                java.lang.String lcaoType,
                                                boolean hybridizationCompatible)

getModelAtomBitSet

public java.util.BitSet getModelAtomBitSet(int modelIndex,
                                           boolean asCopy)

getModelBitSet

public java.util.BitSet getModelBitSet(java.util.BitSet atomList,
                                       boolean allTrajectories)

getClientFile

java.lang.Object getClientFile()

getClientAtomStringProperty

public java.lang.String getClientAtomStringProperty(java.lang.Object clientAtom,
                                                    java.lang.String propertyName)

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

getModelSet

public ModelSet getModelSet()

getBoundBoxCommand

public java.lang.String getBoundBoxCommand(boolean withOptions)

setBoundBox

void setBoundBox(javax.vecmath.Point3f pt1,
                 javax.vecmath.Point3f pt2,
                 boolean byCorner)

getBoundBoxCenter

public javax.vecmath.Point3f getBoundBoxCenter()

getAverageAtomPoint

javax.vecmath.Point3f getAverageAtomPoint()

calcBoundBoxDimensions

void calcBoundBoxDimensions(java.util.BitSet bs)

getBoxInfo

BoxInfo getBoxInfo(java.util.BitSet bs)

calcRotationRadius

float calcRotationRadius(javax.vecmath.Point3f center)

calcRotationRadius

public float calcRotationRadius(java.util.BitSet bs)

getBoundBoxCornerVector

public javax.vecmath.Vector3f getBoundBoxCornerVector()

getBoundBoxInfo

java.util.Hashtable getBoundBoxInfo()

getBoundBoxModels

public java.util.BitSet getBoundBoxModels()

getBoundBoxCenterX

public int getBoundBoxCenterX()

getBoundBoxCenterY

public int getBoundBoxCenterY()

getModelCount

public int getModelCount()
Specified by:
getModelCount in class JmolViewer

getModelInfoAsString

java.lang.String getModelInfoAsString()

getSymmetryInfoAsString

java.lang.String getSymmetryInfoAsString()

getModelSetProperties

public java.util.Properties getModelSetProperties()
Specified by:
getModelSetProperties in class JmolViewer

getModelSetAuxiliaryInfo

public java.util.Hashtable getModelSetAuxiliaryInfo()
Specified by:
getModelSetAuxiliaryInfo in class JmolViewer

getModelNumber

public int getModelNumber(int modelIndex)
Specified by:
getModelNumber in class JmolViewer

getModelFileNumber

public int getModelFileNumber(int modelIndex)

getModelNumberDotted

public java.lang.String getModelNumberDotted(int modelIndex)
Specified by:
getModelNumberDotted in class JmolViewer

getModelName

public java.lang.String getModelName(int modelIndex)
Specified by:
getModelName in class JmolViewer

getModelProperties

public java.util.Properties getModelProperties(int modelIndex)
Specified by:
getModelProperties in class JmolViewer

getModelProperty

public java.lang.String getModelProperty(int modelIndex,
                                         java.lang.String propertyName)
Specified by:
getModelProperty in class JmolViewer

getModelFileInfo

public java.lang.String getModelFileInfo()

getModelFileInfoAll

java.lang.String getModelFileInfoAll()

getModelAuxiliaryInfo

public java.util.Hashtable getModelAuxiliaryInfo(int modelIndex)
Specified by:
getModelAuxiliaryInfo in class JmolViewer

getModelAuxiliaryInfo

public java.lang.Object getModelAuxiliaryInfo(int modelIndex,
                                              java.lang.String keyName)
Specified by:
getModelAuxiliaryInfo in class JmolViewer

getModelNumberIndex

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

modelSetHasVibrationVectors

boolean modelSetHasVibrationVectors()

modelHasVibrationVectors

public boolean modelHasVibrationVectors(int modelIndex)
Specified by:
modelHasVibrationVectors in class JmolViewer

getChainCount

public int getChainCount()
Specified by:
getChainCount in class JmolViewer

getChainCountInModel

public int getChainCountInModel(int modelIndex)
Specified by:
getChainCountInModel in class JmolViewer

getChainCountInModel

public int getChainCountInModel(int modelIndex,
                                boolean countWater)

getGroupCount

public int getGroupCount()
Specified by:
getGroupCount in class JmolViewer

getGroupCountInModel

public int getGroupCountInModel(int modelIndex)
Specified by:
getGroupCountInModel in class JmolViewer

getPolymerCount

public int getPolymerCount()
Specified by:
getPolymerCount in class JmolViewer

getPolymerCountInModel

public int getPolymerCountInModel(int modelIndex)
Specified by:
getPolymerCountInModel in class JmolViewer

getAtomCount

public int getAtomCount()
Specified by:
getAtomCount in class JmolViewer

getAtomCountInModel

public int getAtomCountInModel(int modelIndex)
Specified by:
getAtomCountInModel in class JmolViewer

getBondCount

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

Specified by:
getBondCount in class JmolViewer
Returns:
used size of the bonds array;

getBondCountInModel

public int getBondCountInModel(int modelIndex)
from JmolPopup.udateModelSetComputedMenu

Specified by:
getBondCountInModel in class JmolViewer
Parameters:
modelIndex - the model of interest or -1 for all
Returns:
the actual number of connections

getBondsForSelectedAtoms

java.util.BitSet getBondsForSelectedAtoms(java.util.BitSet bsAtoms)

frankClicked

boolean frankClicked(int x,
                     int y)

findNearestAtomIndex

public int findNearestAtomIndex(int x,
                                int y)
Specified by:
findNearestAtomIndex in class JmolViewer

selectRectangle

void selectRectangle(java.awt.Rectangle rect,
                     int modifiers)

toCartesian

void toCartesian(javax.vecmath.Point3f pt)

toUnitCell

void toUnitCell(javax.vecmath.Point3f pt,
                javax.vecmath.Point3f offset)

toFractional

void toFractional(javax.vecmath.Point3f pt)

setCenterSelected

public void setCenterSelected()
Specified by:
setCenterSelected in class JmolViewer

setBondTolerance

public void setBondTolerance(float bondTolerance)
Specified by:
setBondTolerance in class JmolViewer

getBondTolerance

public float getBondTolerance()
Specified by:
getBondTolerance in class JmolViewer

setMinBondDistance

public void setMinBondDistance(float minBondDistance)
Specified by:
setMinBondDistance in class JmolViewer

getMinBondDistance

public float getMinBondDistance()
Specified by:
getMinBondDistance in class JmolViewer

getAtomIndices

int[] getAtomIndices(java.util.BitSet bs)

getAtomBits

public java.util.BitSet getAtomBits(int tokType,
                                    java.lang.Object specInfo)

getSequenceBits

java.util.BitSet getSequenceBits(java.lang.String specInfo,
                                 java.util.BitSet bs)

getAtomsWithin

java.util.BitSet getAtomsWithin(float distance,
                                javax.vecmath.Point3f coord)

getAtomsWithin

java.util.BitSet getAtomsWithin(float distance,
                                javax.vecmath.Point4f plane)

getAtomsWithin

java.util.BitSet getAtomsWithin(float distance,
                                java.util.BitSet bs,
                                boolean isWithinModelSet)

getAtomsConnected

java.util.BitSet getAtomsConnected(float min,
                                   float max,
                                   int intType,
                                   java.util.BitSet bs)

getBranchBitSet

java.util.BitSet getBranchBitSet(int atomIndex,
                                 int atomIndexNot)

getAtomIndexFromAtomNumber

int getAtomIndexFromAtomNumber(int atomNumber)

getElementsPresentBitSet

public java.util.BitSet getElementsPresentBitSet(int modelIndex)
Specified by:
getElementsPresentBitSet in class JmolViewer

getHeteroList

public java.util.Hashtable getHeteroList(int modelIndex)
Specified by:
getHeteroList in class JmolViewer

getVisibleSet

java.util.BitSet getVisibleSet()

getClickableSet

java.util.BitSet getClickableSet()

calcSelectedGroupsCount

void calcSelectedGroupsCount()

calcSelectedMonomersCount

void calcSelectedMonomersCount()

calcSelectedMoleculesCount

void calcSelectedMoleculesCount()

getFileHeader

java.lang.String getFileHeader()

getFileData

java.lang.Object getFileData()

getCifData

public java.util.Hashtable getCifData(int modelIndex)

getPDBHeader

java.lang.String getPDBHeader()

getModelInfo

public java.util.Hashtable getModelInfo(java.lang.Object atomExpression)

getAuxiliaryInfo

public java.util.Hashtable getAuxiliaryInfo(java.lang.Object atomExpression)

getShapeInfo

public java.util.Hashtable getShapeInfo()

getShapeIdFromObjectName

int getShapeIdFromObjectName(java.lang.String objectName)

getAllAtomInfo

java.util.Vector getAllAtomInfo(java.lang.Object atomExpression)

getAllBondInfo

java.util.Vector getAllBondInfo(java.lang.Object atomExpression)

getMoleculeInfo

java.util.Vector getMoleculeInfo(java.lang.Object atomExpression)

getChimeInfo

public java.lang.String getChimeInfo(int tok)

getAllChainInfo

public java.util.Hashtable getAllChainInfo(java.lang.Object atomExpression)

getAllPolymerInfo

public java.util.Hashtable getAllPolymerInfo(java.lang.Object atomExpression)

getStateInfo

public java.lang.String getStateInfo()
Specified by:
getStateInfo in class JmolViewer

getStateInfo

public java.lang.String getStateInfo(java.lang.String type)

getStructureState

public java.lang.String getStructureState()

getProteinStructureState

java.lang.String getProteinStructureState()

getCoordinateState

public java.lang.String getCoordinateState(java.util.BitSet bsSelected)

setCurrentColorRange

void setCurrentColorRange(java.lang.String label)

setCurrentColorRange

void setCurrentColorRange(float[] data,
                          java.util.BitSet bs)

setCurrentColorRange

public void setCurrentColorRange(float min,
                                 float max)

getCurrentColorRange

public float[] getCurrentColorRange()

setData

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

getData

java.lang.Object[] getData(java.lang.String type)

getDataFloat

public float[] getDataFloat(java.lang.String label)

getDataFloat2D

float[][] getDataFloat2D(java.lang.String label)

getDataFloat3D

float[][][] getDataFloat3D(java.lang.String label)

getDataFloat

public float getDataFloat(java.lang.String label,
                          int atomIndex)

getAltLocListInModel

public java.lang.String getAltLocListInModel(int modelIndex)
Specified by:
getAltLocListInModel in class JmolViewer

setConformation

public java.util.BitSet setConformation()

setConformation

public java.util.BitSet setConformation(int conformationIndex)

autoHbond

int autoHbond(java.util.BitSet bsBonds)

autoHbond

int autoHbond(java.util.BitSet bsFrom,
              java.util.BitSet bsTo,
              java.util.BitSet bsBonds,
              float maxXYDistance,
              float minAttachedAngle)

hasCalculatedHBonds

public boolean hasCalculatedHBonds(java.util.BitSet bsAtoms)

havePartialCharges

public boolean havePartialCharges()
Specified by:
havePartialCharges in class JmolViewer

getCurrentUnitCell

public SymmetryInterface getCurrentUnitCell()

setCurrentUnitCellOffset

void setCurrentUnitCellOffset(int offset)

setCurrentUnitCellOffset

void setCurrentUnitCellOffset(javax.vecmath.Point3f pt)

getDefaultMeasurementLabel

public java.lang.String getDefaultMeasurementLabel(int nPoints)

getMeasurementCount

public int getMeasurementCount()
Specified by:
getMeasurementCount in class JmolViewer

getMeasurementStringValue

public java.lang.String getMeasurementStringValue(int i)
Specified by:
getMeasurementStringValue in class JmolViewer

getMeasurementInfo

java.util.Vector getMeasurementInfo()

getMeasurementInfoAsString

public java.lang.String getMeasurementInfoAsString()

getMeasurementCountPlusIndices

public int[] getMeasurementCountPlusIndices(int i)
Specified by:
getMeasurementCountPlusIndices in class JmolViewer

setPendingMeasurement

void setPendingMeasurement(MeasurementPending measurementPending)

getPendingMeasurement

MeasurementPending getPendingMeasurement()

clearAllMeasurements

void clearAllMeasurements()

clearMeasurements

public void clearMeasurements()
Specified by:
clearMeasurements in class JmolViewer

getJustifyMeasurements

public boolean getJustifyMeasurements()

setMeasurementFormats

void setMeasurementFormats(java.lang.String strFormat)

defineMeasurement

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

deleteMeasurement

public void deleteMeasurement(int i)
Specified by:
deleteMeasurement in class JmolViewer

deleteMeasurement

void deleteMeasurement(int[] atomCountPlusIndices)

showMeasurement

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

hideMeasurements

void hideMeasurements(boolean isOFF)

toggleMeasurement

void toggleMeasurement(int[] atomCountPlusIndices,
                       java.lang.String strFormat)

setAnimationDirection

void setAnimationDirection(int direction)

reverseAnimation

void reverseAnimation()

getAnimationDirection

int getAnimationDirection()

getAnimationInfo

java.util.Hashtable getAnimationInfo()

setAnimationFps

public void setAnimationFps(int fps)
Specified by:
setAnimationFps in class JmolViewer

getAnimationFps

public int getAnimationFps()
Specified by:
getAnimationFps in class JmolViewer

setAnimationReplayMode

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

getAnimationReplayMode

int getAnimationReplayMode()

setAnimationOn

void setAnimationOn(boolean animationOn)

resumeAnimation

void resumeAnimation()

pauseAnimation

void pauseAnimation()

setAnimationRange

void setAnimationRange(int modelIndex1,
                       int modelIndex2)

getVisibleFramesBitSet

public java.util.BitSet getVisibleFramesBitSet()

isAnimationOn

boolean isAnimationOn()

setAnimationNext

void setAnimationNext()

setAnimationPrevious

void setAnimationPrevious()

setAnimationLast

void setAnimationLast()

rewindAnimation

void rewindAnimation()

setCurrentModelIndex

void setCurrentModelIndex(int modelIndex)

setTrajectory

void setTrajectory(int modelIndex)

setTrajectory

public void setTrajectory(java.util.BitSet bsModels)

isTrajectory

boolean isTrajectory(int modelIndex)

getBitSetTrajectories

public java.util.BitSet getBitSetTrajectories()

getTrajectoryInfo

java.lang.String getTrajectoryInfo()

setFrameOffset

void setFrameOffset(int modelIndex)

setFrameOffsets

public void setFrameOffsets(java.util.BitSet bsAtoms)

getFrameOffsets

public java.util.BitSet getFrameOffsets()

setCurrentModelIndex

public void setCurrentModelIndex(int modelIndex,
                                 boolean clearBackground)

getCurrentModelIndex

public int getCurrentModelIndex()

getDisplayModelIndex

public int getDisplayModelIndex()
Specified by:
getDisplayModelIndex in class JmolViewer

haveFileSet

boolean haveFileSet()

setBackgroundModelIndex

void setBackgroundModelIndex(int modelIndex)

getBackgroundModelIndex

public int getBackgroundModelIndex()

setFrameVariables

void setFrameVariables(int firstModelIndex,
                       int lastModelIndex)

getMotionEventNumber

public int getMotionEventNumber()
Specified by:
getMotionEventNumber in class JmolViewer

setInMotion

void setInMotion(boolean inMotion)

getInMotion

public boolean getInMotion()

pushHoldRepaint

public void pushHoldRepaint()
Specified by:
pushHoldRepaint in class JmolViewer

pushHoldRepaint

void pushHoldRepaint(java.lang.String why)

popHoldRepaint

public void popHoldRepaint()
Specified by:
popHoldRepaint in class JmolViewer

popHoldRepaint

void popHoldRepaint(java.lang.String why)

setRefreshing

void setRefreshing(boolean TF)

getRefreshing

boolean getRefreshing()

refresh

public void refresh(int mode,
                    java.lang.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().

Specified by:
refresh in class JmolViewer
Parameters:
mode -
strWhy -

requestRepaintAndWait

void requestRepaintAndWait()

setSync

void setSync()

repaintView

public void repaintView()
Specified by:
repaintView in class JmolViewer

areAxesTainted

public boolean areAxesTainted()

setMaximumSize

private void setMaximumSize(int x)

setScreenDimension

public void setScreenDimension(java.awt.Dimension dim)
Specified by:
setScreenDimension in class JmolViewer

getImageFontScaling

public float getImageFontScaling()

resizeImage

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

getScreenWidth

public int getScreenWidth()
Specified by:
getScreenWidth in class JmolViewer

getScreenHeight

public int getScreenHeight()
Specified by:
getScreenHeight in class JmolViewer

getScreenDim

public int getScreenDim()

generateOutput

public java.lang.String generateOutput(java.lang.String type,
                                       java.lang.String fileName,
                                       int width,
                                       int height)
Specified by:
generateOutput in class JmolViewer

renderScreenImage

public void renderScreenImage(java.awt.Graphics gLeft,
                              java.awt.Graphics gRight,
                              java.awt.Dimension size,
                              java.awt.Rectangle clip)
Description copied from class: JmolViewer
an added class for rendering stereo in two independent applets

Specified by:
renderScreenImage in class JmolViewer

renderScreenImage

public void renderScreenImage(java.awt.Graphics g,
                              java.awt.Dimension size,
                              java.awt.Rectangle clip)
Specified by:
renderScreenImage in class JmolSimpleViewer

getImage

private java.awt.Image getImage(boolean isDouble)

render

private void render()

getStereoImage

private java.awt.Image getStereoImage(int stereoMode)

render1

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

getScreenImage

public java.awt.Image getScreenImage()
Specified by:
getScreenImage in class JmolViewer

getImageAs

public java.lang.Object getImageAs(java.lang.String type,
                                   int quality,
                                   int width,
                                   int height,
                                   java.lang.String fileName,
                                   java.io.OutputStream os)
Specified by:
getImageAs in class JmolViewer
Parameters:
type - "PNG", "JPG", "JPEG", "JPG64", "PPM", "GIF"
quality -
width -
height -
fileName -
os -
Returns:
base64-encoded or binary version of the image

releaseScreenImage

public void releaseScreenImage()
Specified by:
releaseScreenImage in class JmolViewer

getAllowEmbeddedScripts

boolean getAllowEmbeddedScripts()

evalFile

public java.lang.String evalFile(java.lang.String strFilename)
Specified by:
evalFile in class JmolSimpleViewer

script

public java.lang.String script(java.lang.String strScript)
Specified by:
script in class JmolViewer

getInterruptScript

java.lang.String getInterruptScript()

evalString

public java.lang.String evalString(java.lang.String strScript)
Specified by:
evalString in class JmolSimpleViewer

evalStringQuiet

public java.lang.String evalStringQuiet(java.lang.String strScript)
Specified by:
evalStringQuiet in class JmolViewer

evalStringQuiet

java.lang.String evalStringQuiet(java.lang.String strScript,
                                 boolean isQuiet,
                                 boolean allowSyncScript)

checkScriptExecution

private java.lang.String checkScriptExecution(java.lang.String strScript)

usingScriptQueue

boolean usingScriptQueue()

clearScriptQueue

public void clearScriptQueue()

checkResume

public boolean checkResume(java.lang.String str)

checkStepping

public boolean checkStepping(java.lang.String str)

checkHalt

public boolean checkHalt(java.lang.String str)
Specified by:
checkHalt in class JmolViewer

scriptWait

public java.lang.String scriptWait(java.lang.String strScript)
Specified by:
scriptWait in class JmolViewer

scriptWaitStatus

public java.lang.Object scriptWaitStatus(java.lang.String strScript,
                                         java.lang.String statusList)
Specified by:
scriptWaitStatus in class JmolViewer

evalStringWaitStatus

public java.lang.Object evalStringWaitStatus(java.lang.String returnType,
                                             java.lang.String strScript,
                                             java.lang.String statusList)

evalStringWaitStatus

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

exitJmol

void exitJmol()

scriptCheck

private java.lang.Object scriptCheck(java.lang.String strScript,
                                     boolean returnContext)

scriptCheck

public java.lang.Object scriptCheck(java.lang.String strScript)
Specified by:
scriptCheck in class JmolViewer

isScriptExecuting

public boolean isScriptExecuting()
Specified by:
isScriptExecuting in class JmolViewer

haltScriptExecution

public void haltScriptExecution()
Specified by:
haltScriptExecution in class JmolViewer

resumeScriptExecution

public void resumeScriptExecution()

stepScriptExecution

public void stepScriptExecution()

pauseScriptExecution

public void pauseScriptExecution()

getDefaultLoadScript

java.lang.String getDefaultLoadScript()

getLoadFormat

java.lang.String getLoadFormat()

getStandardLabelFormat

public java.lang.String getStandardLabelFormat()

getRibbonAspectRatio

public int getRibbonAspectRatio()

getSheetSmoothing

public float getSheetSmoothing()

getSsbondsBackbone

public boolean getSsbondsBackbone()

getHbondsBackbone

public boolean getHbondsBackbone()

getHbondsSolid

public boolean getHbondsSolid()

setMarBond

public void setMarBond(short marBond)
Specified by:
setMarBond in class JmolViewer

hoverOn

void hoverOn(int atomIndex,
             int modifiers)

getHoverDelay

int getHoverDelay()

hoverOn

public void hoverOn(int x,
                    int y,
                    java.lang.String text)

hoverOff

void hoverOff()

setLabel

void setLabel(java.lang.String strLabel)

togglePickingLabel

void togglePickingLabel(java.util.BitSet bs)

getBitSetSelection

java.util.BitSet getBitSetSelection()

clearShapes

public void clearShapes()

loadShape

public void loadShape(int shapeID)

setShapeSize

void setShapeSize(int shapeID,
                  int size,
                  float fsize)

setShapeSize

public void setShapeSize(int shapeID,
                         int size,
                         java.util.BitSet bsAtoms)

setShapeSize

public void setShapeSize(int shapeID,
                         int size,
                         float fsize,
                         java.util.BitSet bsAtoms)

setShapeProperty

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

setShapeProperty

void setShapeProperty(int shapeID,
                      java.lang.String propertyName,
                      java.lang.Object value,
                      java.util.BitSet bs)

setShapePropertyArgb

void setShapePropertyArgb(int shapeID,
                          java.lang.String propertyName,
                          int argb)

getShapeProperty

public java.lang.Object getShapeProperty(int shapeType,
                                         java.lang.String propertyName)

getShapeProperty

public boolean getShapeProperty(int shapeType,
                                java.lang.String propertyName,
                                java.lang.Object[] data)

getShapeProperty

java.lang.Object getShapeProperty(int shapeType,
                                  java.lang.String propertyName,
                                  int index)

getShapePropertyAsInt

int getShapePropertyAsInt(int shapeID,
                          java.lang.String propertyName)

getColix

short getColix(java.lang.Object object)

getRasmolHydrogenSetting

boolean getRasmolHydrogenSetting()

getRasmolHeteroSetting

boolean getRasmolHeteroSetting()

getDebugScript

boolean getDebugScript()

setDebugScript

public void setDebugScript(boolean debugScript)
Specified by:
setDebugScript in class JmolViewer

atomPicked

void atomPicked(int atomIndex,
                Point3fi ptClicked,
                int modifiers,
                boolean isDoubleClick)

clearClickCount

void clearClickCount()

setCursor

public void setCursor(int cursor)

setPickingMode

private void setPickingMode(java.lang.String mode)

getPickingMode

public int getPickingMode()

getDrawPicking

public boolean getDrawPicking()

getBondPicking

public boolean getBondPicking()

getAtomPicking

private boolean getAtomPicking()

setPickingStyle

private void setPickingStyle(java.lang.String style)

getPickingStyle

int getPickingStyle()

getDrawHover

public boolean getDrawHover()

getAtomInfo

public java.lang.String getAtomInfo(int atomIndex)
Specified by:
getAtomInfo in class JmolViewer

getAtomInfoXYZ

public java.lang.String getAtomInfoXYZ(int atomIndex,
                                       boolean useChimeFormat)

setJmolCallbackListener

public void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
Specified by:
setJmolCallbackListener in class JmolViewer

setJmolStatusListener

public void setJmolStatusListener(JmolStatusListener jmolStatusListener)
Specified by:
setJmolStatusListener in class JmolViewer

getMessageQueue

public java.util.Hashtable getMessageQueue()

getStatusChanged

java.lang.Object getStatusChanged(java.lang.String statusNameList)

popupMenu

void popupMenu(int x,
               int y)

getMenu

java.lang.String getMenu(java.lang.String type)

setMenu

void setMenu(java.lang.String fileOrText,
             boolean isFile)

setStatusFrameChanged

void setStatusFrameChanged(int frameNo)

scriptEcho

public void scriptEcho(java.lang.String strEcho)

notifyError

void notifyError(java.lang.String errType,
                 java.lang.String errMsg,
                 java.lang.String errMsgUntranslated)

jsEval

java.lang.String jsEval(java.lang.String strEval)

setStatusAtomHovered

public void setStatusAtomHovered(int atomIndex,
                                 java.lang.String info)

setFileLoadStatus

private void setFileLoadStatus(int ptLoad,
                               java.lang.String fullPathName,
                               java.lang.String fileName,
                               java.lang.String modelName,
                               java.lang.String strError)

setStatusMeasuring

public void setStatusMeasuring(java.lang.String status,
                               int intInfo,
                               java.lang.String strMeasure)

notifyMinimizationStatus

public void notifyMinimizationStatus()

setStatusAtomPicked

public void setStatusAtomPicked(int atomIndex,
                                java.lang.String info)

setStatusResized

public void setStatusResized(int width,
                             int height)

scriptStatus

void scriptStatus(java.lang.String strStatus)

scriptStatus

void scriptStatus(java.lang.String strStatus,
                  java.lang.String statusMessage)

scriptStatus

void scriptStatus(java.lang.String strStatus,
                  java.lang.String statusMessage,
                  int msWalltime,
                  java.lang.String strErrorMessageUntranslated)

getModelTitle

private java.lang.String getModelTitle(int modelIndex)

getModelFileName

private java.lang.String getModelFileName(int modelIndex)

dialogAsk

public java.lang.String dialogAsk(java.lang.String type,
                                  java.lang.String fileName)

getScriptDelay

int getScriptDelay()

showUrl

public void showUrl(java.lang.String urlString)
Specified by:
showUrl in class JmolViewer

setMeshCreator

public void setMeshCreator(java.lang.Object meshCreator)
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer viewer = applet.getViewer(); viewer.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.

Parameters:
meshCreator -

showConsole

void showConsole(boolean showConsole)

clearConsole

void clearConsole()

getParameterEscaped

java.lang.Object getParameterEscaped(java.lang.String key)

getParameter

public java.lang.Object getParameter(java.lang.String key)
Specified by:
getParameter in class JmolViewer

getOrSetNewVariable

ScriptVariable getOrSetNewVariable(java.lang.String key,
                                   boolean doSet)

setUserVariable

ScriptVariable setUserVariable(java.lang.String name,
                               ScriptVariable value)

unsetProperty

void unsetProperty(java.lang.String name)

getVariableList

java.lang.String getVariableList()

getBooleanProperty

public boolean getBooleanProperty(java.lang.String key)
Specified by:
getBooleanProperty in class JmolViewer

getBooleanProperty

public boolean getBooleanProperty(java.lang.String key,
                                  boolean doICare)
Specified by:
getBooleanProperty in class JmolViewer
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

setStringProperty

public void setStringProperty(java.lang.String key,
                              java.lang.String value)
Specified by:
setStringProperty in class JmolViewer

getLanguage

public java.lang.String getLanguage()

setLanguage

private void setLanguage(java.lang.String value)

setPropertyError

private void setPropertyError(java.lang.String msg)

removeUserVariable

void removeUserVariable(java.lang.String key)

isJmolVariable

boolean isJmolVariable(java.lang.String key)

setFloatProperty

public void setFloatProperty(java.lang.String key,
                             float value)
Specified by:
setFloatProperty in class JmolViewer

setFloatProperty

private boolean setFloatProperty(java.lang.String key,
                                 float value,
                                 boolean isInt)

setIntProperty

public void setIntProperty(java.lang.String key,
                           int value)
Specified by:
setIntProperty in class JmolViewer

setIntProperty

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

getDelayMaximum

int getDelayMaximum()

setBooleanProperty

public void setBooleanProperty(java.lang.String key,
                               boolean value)
Specified by:
setBooleanProperty in class JmolViewer

setBooleanProperty

boolean setBooleanProperty(java.lang.String key,
                           boolean value,
                           boolean defineNew)

getPdbLoadInfo

public boolean getPdbLoadInfo(int type)

getSelectAllModels

boolean getSelectAllModels()

getMessageStyleChime

boolean getMessageStyleChime()

getFontCaching

public boolean getFontCaching()

getFontScaling

public boolean getFontScaling()

showParameter

void showParameter(java.lang.String key,
                   boolean ifNotSet,
                   int nMax)

showString

public void showString(java.lang.String str,
                       boolean isPrint)

getAllSettings

java.lang.String getAllSettings(java.lang.String prefix)

getDotSurfaceFlag

public boolean getDotSurfaceFlag()

getDotsSelectedOnlyFlag

public boolean getDotsSelectedOnlyFlag()

getDotDensity

public int getDotDensity()

isRangeSelected

public boolean isRangeSelected()

getIsosurfacePropertySmoothing

boolean getIsosurfacePropertySmoothing()

getWireframeRotation

public boolean getWireframeRotation()

isWindowCentered

boolean isWindowCentered()

setNavigationDepthPercent

void setNavigationDepthPercent(float timeSec,
                               float percent)

getNavigationSpeed

float getNavigationSpeed()

getShowNavigationPoint

public boolean getShowNavigationPoint()

setVisualRange

public void setVisualRange(float angstroms)

getSolventProbeRadius

float getSolventProbeRadius()

getCurrentSolventProbeRadius

public float getCurrentSolventProbeRadius()

getSolventOn

boolean getSolventOn()

getTestFlag1

public boolean getTestFlag1()

getTestFlag2

public boolean getTestFlag2()

getTestFlag3

public boolean getTestFlag3()

getTestFlag4

public boolean getTestFlag4()

setPerspectiveDepth

public void setPerspectiveDepth(boolean perspectiveDepth)
Specified by:
setPerspectiveDepth in class JmolViewer

setAxesOrientationRasmol

public void setAxesOrientationRasmol(boolean TF)
Specified by:
setAxesOrientationRasmol in class JmolViewer

getAxesOrientationRasmol

public boolean getAxesOrientationRasmol()
Specified by:
getAxesOrientationRasmol in class JmolViewer

setAxesScale

void setAxesScale(float scale)

getAxisPoints

public javax.vecmath.Point3f[] getAxisPoints()

getAxesScale

public float getAxesScale()

setAxesModeMolecular

private void setAxesModeMolecular(boolean TF)

setAxesModeUnitCell

void setAxesModeUnitCell(boolean TF)

getAxesMode

public int getAxesMode()

getDisplayCellParameters

public boolean getDisplayCellParameters()

getPerspectiveDepth

public boolean getPerspectiveDepth()
Specified by:
getPerspectiveDepth in class JmolViewer

setSelectionHalos

public void setSelectionHalos(boolean TF)
Specified by:
setSelectionHalos in class JmolViewer

getSelectionHaloEnabled

public boolean getSelectionHaloEnabled()

getBondSelectionModeOr

public boolean getBondSelectionModeOr()

getChainCaseSensitive

public boolean getChainCaseSensitive()

getRibbonBorder

public boolean getRibbonBorder()

getCartoonRocketFlag

public boolean getCartoonRocketFlag()

getRocketBarrelFlag

public boolean getRocketBarrelFlag()

setStrandCount

private void setStrandCount(int type,
                            int value)

getStrandCount

public int getStrandCount(int type)

getHideNameInPopup

boolean getHideNameInPopup()

getNavigationPeriodic

boolean getNavigationPeriodic()

stopAnimationThreads

private void stopAnimationThreads()

setNavigationMode

private void setNavigationMode(boolean TF)

getNavigationMode

public boolean getNavigationMode()

getNavigateSurface

public boolean getNavigateSurface()

setTransformManager

public void setTransformManager(TransformManager transformManager)
for an external application

Parameters:
transformManager -

setPerspectiveModel

private void setPerspectiveModel(int mode)

setTransformManagerDefaults

private void setTransformManagerDefaults()

getCameraDepth

public float getCameraDepth()

getZoomLarge

boolean getZoomLarge()

getTraceAlpha

public boolean getTraceAlpha()

getHermiteLevel

public int getHermiteLevel()

getHighResolution

public boolean getHighResolution()

getLoadState

java.lang.String getLoadState()

setAutoBond

public void setAutoBond(boolean TF)
Specified by:
setAutoBond in class JmolViewer

getAutoBond

public boolean getAutoBond()
Specified by:
getAutoBond in class JmolViewer

makeConnections

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

rebond

public void rebond()
Specified by:
rebond in class JmolViewer

setPdbConectBonding

void setPdbConectBonding(boolean isAuto)

getGreyscaleRendering

boolean getGreyscaleRendering()

getDisablePopupMenu

boolean getDisablePopupMenu()

getForceAutoBond

public boolean getForceAutoBond()

setPercentVdwAtom

public void setPercentVdwAtom(int percentVdwAtom)
Specified by:
setPercentVdwAtom in class JmolViewer

getPercentVdwAtom

public int getPercentVdwAtom()
Specified by:
getPercentVdwAtom in class JmolViewer

getDefaultMadAtom

public short getDefaultMadAtom()

getMadBond

public short getMadBond()
Specified by:
getMadBond in class JmolViewer

getMarBond

public short getMarBond()

getModeMultipleBond

public byte getModeMultipleBond()

getShowMultipleBonds

public boolean getShowMultipleBonds()

setShowHydrogens

public void setShowHydrogens(boolean TF)
Specified by:
setShowHydrogens in class JmolViewer

getShowHydrogens

public boolean getShowHydrogens()
Specified by:
getShowHydrogens in class JmolViewer

getShowHiddenSelectionHalos

public boolean getShowHiddenSelectionHalos()

setShowBbcage

public void setShowBbcage(boolean value)
Specified by:
setShowBbcage in class JmolViewer

getShowBbcage

public boolean getShowBbcage()
Specified by:
getShowBbcage in class JmolViewer

setShowUnitCell

public void setShowUnitCell(boolean value)

getShowUnitCell

public boolean getShowUnitCell()

setShowAxes

public void setShowAxes(boolean value)
Specified by:
setShowAxes in class JmolViewer

getShowAxes

public boolean getShowAxes()
Specified by:
getShowAxes in class JmolViewer

setFrankOn

public void setFrankOn(boolean TF)
Specified by:
setFrankOn in class JmolViewer

getShowFrank

public boolean getShowFrank()

isSignedApplet

public boolean isSignedApplet()

setShowMeasurements

public void setShowMeasurements(boolean TF)
Specified by:
setShowMeasurements in class JmolViewer

getShowMeasurements

public boolean getShowMeasurements()
Specified by:
getShowMeasurements in class JmolViewer

getShowMeasurementLabels

public boolean getShowMeasurementLabels()

getMeasureAllModelsFlag

public boolean getMeasureAllModelsFlag()

setMeasureDistanceUnits

void setMeasureDistanceUnits(java.lang.String units)

getMeasureDistanceUnits

public java.lang.String getMeasureDistanceUnits()

getUseNumberLocalization

public boolean getUseNumberLocalization()

setAppendNew

void setAppendNew(boolean value)

getAppendNew

public boolean getAppendNew()

getAutoFps

boolean getAutoFps()

setRasmolDefaults

public void setRasmolDefaults()
Specified by:
setRasmolDefaults in class JmolViewer

setJmolDefaults

public void setJmolDefaults()
Specified by:
setJmolDefaults in class JmolViewer

setDefaults

private void setDefaults(java.lang.String type)

getZeroBasedXyzRasmol

public boolean getZeroBasedXyzRasmol()

setAntialias

private void setAntialias(int mode,
                          boolean TF)

allocTempPoints

public javax.vecmath.Point3f[] allocTempPoints(int size)

freeTempPoints

public void freeTempPoints(javax.vecmath.Point3f[] tempPoints)

allocTempScreens

public javax.vecmath.Point3i[] allocTempScreens(int size)

freeTempScreens

public void freeTempScreens(javax.vecmath.Point3i[] tempScreens)

allocTempBytes

public byte[] allocTempBytes(int size)

freeTempBytes

public void freeTempBytes(byte[] tempBytes)

getFont3D

Font3D getFont3D(java.lang.String fontFace,
                 java.lang.String fontStyle,
                 float fontSize)

formatText

public java.lang.String formatText(java.lang.String text0)

getElementSymbol

java.lang.String getElementSymbol(int i)

getElementNumber

int getElementNumber(int i)

getAtomName

public java.lang.String getAtomName(int i)
Specified by:
getAtomName in class JmolViewer

getAtomNumber

public int getAtomNumber(int i)
Specified by:
getAtomNumber in class JmolViewer

getAtomX

float getAtomX(int i)

getAtomY

float getAtomY(int i)

getAtomZ

float getAtomZ(int i)

getAtomPoint3f

public javax.vecmath.Point3f getAtomPoint3f(int i)
Specified by:
getAtomPoint3f in class JmolViewer

getAtomRadius

public float getAtomRadius(int i)
Specified by:
getAtomRadius in class JmolViewer

getAtomVdwRadius

public float getAtomVdwRadius(int i)

getAtomArgb

public int getAtomArgb(int i)
Specified by:
getAtomArgb in class JmolViewer

getAtomChain

java.lang.String getAtomChain(int i)

getAtomModelIndex

public int getAtomModelIndex(int i)
Specified by:
getAtomModelIndex in class JmolViewer

getAtomSequenceCode

java.lang.String getAtomSequenceCode(int i)

getBondRadius

public float getBondRadius(int i)
Specified by:
getBondRadius in class JmolViewer

getBondOrder

public short getBondOrder(int i)
Specified by:
getBondOrder in class JmolViewer

assignAromaticBonds

void assignAromaticBonds()

getSmartAromatic

public boolean getSmartAromatic()

resetAromatic

void resetAromatic()

getBondArgb1

public int getBondArgb1(int i)
Specified by:
getBondArgb1 in class JmolViewer

getBondModelIndex

public int getBondModelIndex(int i)
Specified by:
getBondModelIndex in class JmolViewer

getBondArgb2

public int getBondArgb2(int i)
Specified by:
getBondArgb2 in class JmolViewer

getPolymerLeadMidPoints

public javax.vecmath.Point3f[] getPolymerLeadMidPoints(int modelIndex,
                                                       int polymerIndex)
Specified by:
getPolymerLeadMidPoints in class JmolViewer

setStereoMode

void setStereoMode(int[] twoColors,
                   int stereoMode,
                   float degrees)

isJvm12orGreater

public boolean isJvm12orGreater()
Specified by:
isJvm12orGreater in class JmolViewer

getOperatingSystemName

public java.lang.String getOperatingSystemName()
Specified by:
getOperatingSystemName in class JmolViewer

getJavaVendor

public java.lang.String getJavaVendor()
Specified by:
getJavaVendor in class JmolViewer

getJavaVersion

public java.lang.String getJavaVersion()
Specified by:
getJavaVersion in class JmolViewer

getGraphics3D

public Graphics3D getGraphics3D()

showModelSetDownload

public boolean showModelSetDownload()
Specified by:
showModelSetDownload in class JmolViewer

getProperty

public java.lang.Object getProperty(java.lang.String returnType,
                                    java.lang.String infoType,
                                    java.lang.String paramInfo)

isScriptEditorVisible

boolean isScriptEditorVisible()

getProperty

public java.lang.Object getProperty(java.lang.String returnType,
                                    java.lang.String infoType,
                                    java.lang.Object paramInfo)
Specified by:
getProperty in class JmolSimpleViewer
Parameters:
returnType - "JSON", "string", "readable", and anything else returns the Java object.
Returns:
property data -- see org.jmol.viewer.PropertyManager.java

showEditor

void showEditor(java.lang.String[] file_text)

getModelExtract

java.lang.String getModelExtract(java.lang.Object atomExpression)

getHexColorFromIndex

public java.lang.String getHexColorFromIndex(short colix)

setModelVisibility

void setModelVisibility()

setFrameTitle

void setFrameTitle(int modelIndex,
                   java.lang.String title)

getFrameTitle

java.lang.String getFrameTitle(int modelIndex)

setTainted

void setTainted(boolean TF)

checkObjectClicked

Point3fi checkObjectClicked(int x,
                            int y,
                            int modifiers)

checkObjectHovered

boolean checkObjectHovered(int x,
                           int y)

checkObjectDragged

void checkObjectDragged(int prevX,
                        int prevY,
                        int x,
                        int y,
                        int modifiers)

rotateAxisAngleAtCenter

void rotateAxisAngleAtCenter(javax.vecmath.Point3f rotCenter,
                             javax.vecmath.Vector3f rotAxis,
                             float degrees,
                             float endDegrees,
                             boolean isSpin,
                             java.util.BitSet bsSelected)

rotateAboutPointsInternal

void rotateAboutPointsInternal(javax.vecmath.Point3f point1,
                               javax.vecmath.Point3f point2,
                               float degrees,
                               float endDegrees,
                               boolean isSpin,
                               java.util.BitSet bsSelected)

getPickingSpinRate

int getPickingSpinRate()

startSpinningAxis

public void startSpinningAxis(javax.vecmath.Point3f pt1,
                              javax.vecmath.Point3f pt2,
                              boolean isClockwise)

getModelDipole

public javax.vecmath.Vector3f getModelDipole()

calculateMolecularDipole

public javax.vecmath.Vector3f calculateMolecularDipole()

getDipoleScale

public float getDipoleScale()

getAtomIdentityInfo

public void getAtomIdentityInfo(int atomIndex,
                                java.util.Hashtable info)

setDefaultLattice

void setDefaultLattice(javax.vecmath.Point3f ptLattice)

getDefaultLattice

javax.vecmath.Point3f getDefaultLattice()

getTaintedAtoms

java.util.BitSet getTaintedAtoms(byte type)

setTaintedAtoms

public void setTaintedAtoms(java.util.BitSet bs,
                            byte type)

getData

public java.lang.String getData(java.lang.String atomExpression,
                                java.lang.String type)
Specified by:
getData in class JmolViewer

evaluateExpression

public java.lang.Object evaluateExpression(java.lang.Object stringOrTokens)

getHelixData

java.lang.Object getHelixData(java.util.BitSet bs,
                              int tokType)

getPdbData

public java.lang.String getPdbData(java.util.BitSet bs)

getPdbData

java.lang.String getPdbData(int modelIndex,
                            java.lang.String type)

isJmolDataFrame

public boolean isJmolDataFrame(int modelIndex)

isJmolDataFrame

public boolean isJmolDataFrame()

getJmolDataFrameIndex

int getJmolDataFrameIndex(int modelIndex,
                          java.lang.String type)

setJmolDataFrame

void setJmolDataFrame(java.lang.String type,
                      int modelIndex,
                      int dataIndex)

setFrameTitle

void setFrameTitle(java.lang.String title)

getFrameTitle

public java.lang.String getFrameTitle()

getJmolFrameType

java.lang.String getJmolFrameType(int modelIndex)

getJmolDataSourceFrame

public int getJmolDataSourceFrame(int modelIndex)

setAtomProperty

void setAtomProperty(java.util.BitSet bs,
                     int tok,
                     int iValue,
                     float fValue,
                     java.lang.String sValue,
                     float[] values,
                     java.lang.String[] list)

setAtomCoord

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

setAtomCoord

void setAtomCoord(java.util.BitSet bs,
                  int tokType,
                  java.lang.Object xyzValues)

setAtomCoordRelative

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

setAtomCoordRelative

void setAtomCoordRelative(javax.vecmath.Point3f offset)

setAllowRotateSelected

void setAllowRotateSelected(boolean TF)

allowRotateSelected

boolean allowRotateSelected()

invertSelected

void invertSelected(javax.vecmath.Point3f pt,
                    java.util.BitSet bs)

invertSelected

void invertSelected(javax.vecmath.Point3f pt,
                    javax.vecmath.Point4f plane)

moveSelected

void moveSelected(int deltaX,
                  int deltaY,
                  int x,
                  int y,
                  boolean isTranslation)

rotateAtoms

void rotateAtoms(javax.vecmath.Matrix3f mNew,
                 javax.vecmath.Matrix3f matrixRotate,
                 boolean fullMolecule,
                 javax.vecmath.Point3f center,
                 boolean isInternal,
                 java.util.BitSet bsAtoms)

refreshMeasures

public void refreshMeasures()

setDynamicMeasurements

void setDynamicMeasurements(boolean TF)

getDynamicMeasurements

public boolean getDynamicMeasurements()

functionXY

public float[][] functionXY(java.lang.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

functionXYZ

float[][][] functionXYZ(java.lang.String functionName,
                        int nX,
                        int nY,
                        int nZ)

getHelp

void getHelp(java.lang.String what)

addCommand

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

Parameters:
command - the command to add

removeCommand

java.lang.String removeCommand()
Removes one command from the command history

Returns:
command removed

getSetHistory

public java.lang.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;

Specified by:
getSetHistory in class JmolViewer
Parameters:
howFarBack - number of lines (-1 for next line)
Returns:
one or more lines of command history

writeTextFile

public void writeTextFile(java.lang.String fileName,
                          java.lang.String data)
Specified by:
writeTextFile in class JmolViewer

clipImage

public java.lang.String clipImage(java.lang.String text)
Specified by:
clipImage in class JmolViewer
Parameters:
text - null here clips image; String clips text
Returns:
"OK" for image or "OK [number of bytes]"

createImage

java.lang.String createImage(java.lang.String fileName,
                             java.lang.String type,
                             java.lang.Object text_or_bytes,
                             int quality,
                             int width,
                             int height,
                             java.util.BitSet bsFrames)
from eval write command only includes option to write set of files

Parameters:
fileName -
type -
text_or_bytes -
quality -
width -
height -
bsFrames -
Returns:
message starting with "OK" or an error message

createImage

public java.lang.String createImage(java.lang.String fileName,
                                    java.lang.String type,
                                    java.lang.Object text_or_bytes,
                                    int quality,
                                    int width,
                                    int height)
general routine for creating an image or writing data to a file passes request to statusManager to pass along to app or applet jmolStatusListener interface

Specified by:
createImage in class JmolViewer
Parameters:
fileName - starts with ? --> use file dialog; null --> to clipboard
type - PNG, JPG, etc.
text_or_bytes - String or byte[] or null if an image
quality - Integer.MIN_VALUE --> not an image
width - image width
height - image height
Returns:
null (canceled) or a message starting with OK or an error message

setImageFontScaling

private void setImageFontScaling(int width,
                                 int height)

setSyncTarget

private void setSyncTarget(int mode,
                           boolean TF)

syncScript

public void syncScript(java.lang.String script,
                       java.lang.String applet)
Specified by:
syncScript in class JmolViewer

setSyncDriver

void setSyncDriver(int mode)

getPartialCharges

public float[] getPartialCharges()

setProteinType

void setProteinType(byte iType,
                    java.util.BitSet bs)

getBondPoint3f1

public javax.vecmath.Point3f getBondPoint3f1(int i)
Specified by:
getBondPoint3f1 in class JmolViewer

getBondPoint3f2

public javax.vecmath.Point3f getBondPoint3f2(int i)
Specified by:
getBondPoint3f2 in class JmolViewer

getVibrationVector

public javax.vecmath.Vector3f getVibrationVector(int atomIndex)

getVanderwaalsMar

public int getVanderwaalsMar(int i)

getVanderwaalsMar

public int getVanderwaalsMar(int i,
                             int iMode)

setDefaultVdw

void setDefaultVdw(java.lang.String mode)

getDefaultVdw

java.lang.String getDefaultVdw(int iMode)

deleteAtoms

public int deleteAtoms(java.util.BitSet bs,
                       boolean fullModels)

deleteModelAtoms

public void deleteModelAtoms(int firstAtomIndex,
                             int nAtoms,
                             java.util.BitSet bsDeleted)

getDeletedAtoms

public java.util.BitSet getDeletedAtoms()

getQuaternionFrame

public char getQuaternionFrame()

getHelixStep

public int getHelixStep()

calculatePointGroup

java.lang.String calculatePointGroup()

getPointGroupInfo

public java.util.Hashtable getPointGroupInfo(java.lang.Object atomExpression)

getPointGroupAsString

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

getPointGroupTolerance

public float getPointGroupTolerance(int type)

getFileAsImage

java.lang.Object getFileAsImage(java.lang.String pathName,
                                java.util.Hashtable htParams)

cd

java.lang.String cd(java.lang.String dir)

setErrorMessage

private java.lang.String setErrorMessage(java.lang.String errMsg)

setErrorMessage

private java.lang.String setErrorMessage(java.lang.String errMsg,
                                         java.lang.String errMsgUntranslated)

getErrorMessage

public java.lang.String getErrorMessage()
Specified by:
getErrorMessage in class JmolViewer

getErrorMessageUntranslated

public java.lang.String getErrorMessageUntranslated()
Specified by:
getErrorMessageUntranslated in class JmolViewer

getShape

public Shape getShape(int i)

setShapeErrorState

public void setShapeErrorState(int shapeID,
                               java.lang.String state)

getShapeErrorState

public java.lang.String getShapeErrorState()

handleError

public void handleError(java.lang.Error er,
                        boolean doClear)

getAtomicCharges

float[] getAtomicCharges()

getFunction

ScriptFunction getFunction(java.lang.String name)

addFunction

void addFunction(ScriptFunction f)

clearFunctions

void clearFunctions()

isFunction

boolean isFunction(java.lang.String name)

getFunctions

java.util.Hashtable getFunctions(boolean isLocal)

showMessage

void showMessage(java.lang.String s)

getMoInfo

public java.lang.String getMoInfo(int modelIndex)

isRepaintPending

boolean isRepaintPending()