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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.jmol.api.JmolSimpleViewer
org.jmol.api.JmolViewer
org.jmol.viewer.Viewer
public class Viewer
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()
|
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,
boolean isLoadVariable)
|
(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) 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)
|
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()
|
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()
|
private java.lang.String |
getFileNameFromDialog(java.lang.String fileName,
int quality)
|
(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)
|
java.lang.String |
getFunctionCalls(java.lang.String selectedFunction)
|
(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()
|
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()
|
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 rotAxis,
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 |
(package private) void |
repaint()
|
(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)
|
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 |
viewerNotifyRepaintDone()
|
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 |
---|
private java.awt.Component display
private Graphics3D g3d
private JmolAdapter modelAdapter
private CommandHistory commandHistory
private ColorManager colorManager
ScriptCompiler compiler
java.util.Hashtable definedAtomSets
private MinimizerInterface minimizer
private SmilesMatcherInterface smilesMatcher
private SymmetryInterface symmetry
ScriptEvaluator eval
private AnimationManager animationManager
private DataManager dataManager
private FileManager fileManager
private ModelManager modelManager
private ModelSet modelSet
public MouseManager mouseManager
private PickingManager pickingManager
private RepaintManager repaintManager
private ScriptManager scriptManager
private SelectionManager selectionManager
private StateManager stateManager
private StateManager.GlobalSettings global
private StatusManager statusManager
private TempArray tempManager
private TransformManager transformManager
private java.lang.String strJavaVendor
private java.lang.String strJavaVersion
private java.lang.String strOSName
private java.lang.String htmlName
private java.lang.String fullName
private java.lang.String syncId
private java.lang.String appletDocumentBase
private java.lang.String appletCodeBase
private boolean jvm11orGreater
private boolean jvm12orGreater
private boolean jvm14orGreater
private boolean isSilent
private boolean isApplet
private boolean isPreviewOnly
boolean autoExit
boolean haveDisplay
private boolean isPrintOnly
private boolean mustRender
private boolean isCmdLine_c_or_C_Option
private boolean listCommands
private boolean isCmdLine_C_Option
private boolean useCommandThread
private boolean isSignedApplet
private boolean isDataOnly
private boolean mouseEnabled
private boolean noneSelected
private static final int FILE_STATUS_NOT_LOADED
private static final int FILE_STATUS_ZAPPED
private static final int FILE_STATUS_CREATING_MODELSET
private static final int FILE_STATUS_MODELSET_CREATED
private static final int FILE_STATUS_MODELS_DELETED
static final java.lang.String STATE_VERSION_STAMP
public static java.lang.Object testData
public static java.lang.Object testData2
java.util.BitSet bsFrameOffsets
javax.vecmath.Point3f[] frameOffsets
boolean wasInMotion
int motionEventNumber
private boolean refreshing
private boolean axesAreTainted
final java.awt.Dimension dimScreen
private int maximumSize
private float imageFontScaling
private boolean antialiasDisplay
java.lang.String interruptScript
int scriptIndex
boolean isScriptQueued
int hoverAtomIndex
java.lang.String hoverText
public static final int CURSOR_DEFAULT
public static final int CURSOR_HAND
public static final int CURSOR_CROSSHAIR
public static final int CURSOR_MOVE
public static final int CURSOR_WAIT
private int currentCursor
int prevFrame
private java.lang.String language
boolean frankOn
private boolean scriptEditorVisible
JmolAppConsoleInterface appConsole
JmolScriptEditorInterface scriptEditor
JmolPopup jmolpopup
java.lang.String menuStructure
boolean isTainted
private boolean creatingImage
public static final java.lang.String SYNC_GRAPHICS_MESSAGE
public static final java.lang.String SYNC_NO_GRAPHICS_MESSAGE
private java.lang.String errorMessage
private java.lang.String errorMessageUntranslated
private int currentShapeID
private java.lang.String currentShapeState
Constructor Detail |
---|
public Viewer(java.awt.Component display, JmolAdapter modelAdapter)
Method Detail |
---|
protected void finalize() throws java.lang.Throwable
finalize
in class java.lang.Object
java.lang.Throwable
public JmolAdapter getModelAdapter()
getModelAdapter
in class JmolViewer
MinimizerInterface getMinimizer(boolean createNew)
SmilesMatcherInterface getSmilesMatcher()
public SymmetryInterface getSymmetry()
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)
private void clearModelDependentObjects()
StateManager.GlobalSettings getGlobalSettings()
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)
display
- either DisplayPanel or WrappedAppletmodelAdapter
- the model readerfullName
- or nulldocumentBase
- or nullcodeBase
- or nullcommandOptions
- or nullstatusListener
- or null
public static JmolViewer allocateViewer(java.awt.Component display, JmolAdapter modelAdapter)
display
- modelAdapter
-
public boolean isApplet()
isApplet
in class JmolViewer
boolean isPreviewOnly()
public void setAppletContext(java.lang.String fullName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions)
setAppletContext
in class JmolViewer
public boolean isDataOnly()
public static java.lang.String getJmolVersion()
public java.lang.String getExportDriverList()
private static int getJmolVersionInt()
java.lang.String getHtmlName()
boolean mustRenderFlag()
static int getLogLevel()
public java.awt.Component getDisplay()
getDisplay
in class JmolViewer
public boolean handleOldJvm10Event(java.awt.Event e)
handleOldJvm10Event
in class JmolViewer
void reset()
public void homePosition()
homePosition
in class JmolViewer
java.util.Hashtable getAppletInfo()
void initialize()
java.lang.String listSavedStates()
public void saveOrientation(java.lang.String saveName)
public boolean restoreOrientation(java.lang.String saveName, float timeSeconds)
public void restoreRotation(java.lang.String saveName, float timeSeconds)
void saveModelOrientation()
public StateManager.Orientation getOrientation()
void restoreModelOrientation(int modelIndex)
void restoreModelRotation(int modelIndex)
void saveBonds(java.lang.String saveName)
boolean restoreBonds(java.lang.String saveName)
void saveState(java.lang.String saveName)
public java.lang.String getSavedState(java.lang.String saveName)
void saveStructure(java.lang.String saveName)
java.lang.String getSavedStructure(java.lang.String saveName)
public void saveCoordinates(java.lang.String saveName, java.util.BitSet bsSelected)
java.lang.String getSavedCoordinates(java.lang.String saveName)
void saveSelection(java.lang.String saveName)
boolean restoreSelection(java.lang.String saveName)
public javax.vecmath.Matrix4f getMatrixtransform()
Quaternion getRotationQuaternion()
public float getRotationRadius()
getRotationRadius
in class JmolViewer
void setRotationRadius(float angstroms, boolean doAll)
public javax.vecmath.Point3f getRotationCenter()
void setCenterAt(java.lang.String relativeTo, javax.vecmath.Point3f pt)
void setCenterBitSet(java.util.BitSet bsCenter, boolean doScale)
void setNewRotationCenter(javax.vecmath.Point3f center)
public javax.vecmath.Point3f getNavigationCenter()
public float getNavigationDepthPercent()
void navigate(int keyWhere, int modifiers)
public javax.vecmath.Point3f getNavigationOffset()
float getNavigationOffsetPercent(char XorY)
public boolean isNavigating()
boolean isInPosition(javax.vecmath.Vector3f axis, float degrees)
void move(javax.vecmath.Vector3f dRot, float dZoom, javax.vecmath.Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps)
void moveTo(float floatSecondsTotal, javax.vecmath.Point3f center, javax.vecmath.Vector3f rotAxis, float degrees, float zoom, float xTrans, float yTrans, float rotationRadius, javax.vecmath.Point3f navCenter, float xNav, float yNav, float navDepth)
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)
private void moveUpdate(float floatSecondsTotal)
java.lang.String getMoveToText(float timespan)
void navigate(float timeSeconds, javax.vecmath.Point3f[] path, float[] theta, int indexStart, int indexEnd)
public void navigate(float timeSeconds, javax.vecmath.Point3f center)
void navigate(float timeSeconds, javax.vecmath.Point3f[][] pathGuide)
void navigateSurface(float timeSeconds, java.lang.String name)
public void navigate(float timeSeconds, javax.vecmath.Vector3f rotAxis, float degrees)
void navTranslate(float timeSeconds, javax.vecmath.Point3f center)
void navTranslatePercent(float timeSeconds, float x, float y)
public void setMouseEnabled(boolean TF)
void zoomBy(int pixels)
void zoomByFactor(float factor)
void rotateXYBy(int xDelta, int yDelta)
void rotateZBy(int zDelta)
void rotateMolecule(int deltaX, int deltaY)
void translateXYBy(int xDelta, int yDelta)
public void rotateFront()
rotateFront
in class JmolViewer
public void rotateX(float angleRadians)
rotateX
in class JmolViewer
public void rotateY(float angleRadians)
rotateY
in class JmolViewer
public void rotateZ(float angleRadians)
rotateZ
in class JmolViewer
public void rotateX(int angleDegrees)
rotateX
in class JmolViewer
public void rotateY(int angleDegrees)
rotateY
in class JmolViewer
void translate(char xyz, float x, char type)
public float getTranslationXPercent()
public float getTranslationYPercent()
float getTranslationZPercent()
public java.lang.String getTranslationScript()
public int getZoomPercent()
getZoomPercent
in class JmolViewer
float getZoomSetting()
public float getZoomPercentFloat()
getZoomPercentFloat
in class JmolViewer
float getMaxZoomPercent()
void slabReset()
boolean getZoomEnabled()
public boolean getSlabEnabled()
void slabByPixels(int pixels)
void depthByPixels(int pixels)
void slabDepthByPixels(int pixels)
void slabToPercent(int percentSlab)
void slabInternal(javax.vecmath.Point4f plane, boolean isDepth)
void depthToPercent(int percentDepth)
void setSlabDepthInternal(boolean isDepth)
public int zValueFromPercent(int zPercent)
public javax.vecmath.Matrix4f getUnscaledTransformMatrix()
getUnscaledTransformMatrix
in class JmolViewer
void finalizeTransformParameters()
public void rotatePoint(javax.vecmath.Point3f pt, javax.vecmath.Point3f ptRot)
public javax.vecmath.Point3i transformPoint(javax.vecmath.Point3f pointAngstroms)
public javax.vecmath.Point3i transformPoint(javax.vecmath.Point3f pointAngstroms, javax.vecmath.Vector3f vibrationVector)
public void transformPoint(javax.vecmath.Point3f pointAngstroms, javax.vecmath.Point3i pointScreen)
public void transformPointNoClip(javax.vecmath.Point3f pointAngstroms, javax.vecmath.Point3f pt)
public void transformPoint(javax.vecmath.Point3f pointAngstroms, javax.vecmath.Point3f pointScreen)
public void transformPoints(javax.vecmath.Point3f[] pointsAngstroms, javax.vecmath.Point3i[] pointsScreens)
public void transformVector(javax.vecmath.Vector3f vectorAngstroms, javax.vecmath.Vector3f vectorTransformed)
public void unTransformPoint(javax.vecmath.Point3f pointScreen, javax.vecmath.Point3f pointAngstroms)
public float getScalePixelsPerAngstrom(boolean asAntialiased)
public short scaleToScreen(int z, int milliAngstroms)
public float unscaleToScreen(int z, int screenDistance)
public float scaleToPerspective(int z, float sizeAngstroms)
void setSpin(java.lang.String key, int value)
java.lang.String getSpinState()
void setSpinOn(boolean spinOn)
boolean getSpinOn()
void setNavOn(boolean navOn)
boolean getNavOn()
void setNavXYZ(float x, float y, float z)
public java.lang.String getOrientationText(int type)
java.util.Hashtable getOrientationInfo()
javax.vecmath.Matrix3f getMatrixRotate()
public void getAxisAngle(javax.vecmath.AxisAngle4f axisAngle)
java.lang.String getTransformText()
void getRotation(javax.vecmath.Matrix3f matrixRotation)
private void setDefaultColors(java.lang.String colorScheme)
float getDefaultTranslucent()
public int getColixArgb(short colix)
void setRubberbandArgb(int argb)
public short getColixRubberband()
void setElementArgb(int elementNumber, int argb)
public float getVectorScale()
public void setVectorScale(float scale)
setVectorScale
in class JmolViewer
public float getDefaultDrawArrowScale()
public void setDefaultDrawArrowScale(float scale)
float getVibrationScale()
float getVibrationPeriod()
public boolean isVibrationOn()
public void setVibrationScale(float scale)
setVibrationScale
in class JmolViewer
void setVibrationOff()
public void setVibrationPeriod(float period)
setVibrationPeriod
in class JmolViewer
void setObjectColor(java.lang.String name, java.lang.String colorName)
void setObjectArgb(java.lang.String name, int argb)
void setBackgroundImage(java.lang.String fileName, java.awt.Image image)
int getObjectArgb(int objId)
public short getObjectColix(int objId)
public java.lang.String getObjectState(java.lang.String name)
public void setColorBackground(java.lang.String colorName)
setColorBackground
in class JmolViewer
public int getBackgroundArgb()
getBackgroundArgb
in class JmolViewer
void setObjectMad(int iShape, java.lang.String name, int mad)
public int getObjectMad(int objId)
public void setPropertyColorScheme(java.lang.String scheme, boolean isOverloaded)
public java.lang.String getPropertyColorScheme()
public short getColixBackgroundContrast()
java.lang.String getSpecularState()
private static void setSpecular(boolean specular)
boolean getSpecular()
private static void setSpecularPower(int specularPower)
private static void setSpecularExponent(int specularExponent)
private static void setAmbientPercent(int ambientPercent)
static int getAmbientPercent()
private static void setDiffusePercent(int diffusePercent)
static int getDiffusePercent()
private static void setSpecularPercent(int specularPercent)
static int getSpecularPercent()
public short getColixAtomPalette(Atom atom, byte pid)
public short getColixBondPalette(Bond bond, byte pid)
public int[] getColorSchemeArray(java.lang.String colorScheme)
public java.lang.String getColorSchemeList(java.lang.String colorScheme, boolean ifDefault)
public static void setUserScale(int[] scale)
public short getColixForPropertyValue(float val)
javax.vecmath.Point3f getColorPointForPropertyValue(float val)
void select(java.util.BitSet bs, boolean isQuiet)
void selectBonds(java.util.BitSet bs)
void hide(java.util.BitSet bs, boolean isQuiet)
void display(java.util.BitSet bs, boolean isQuiet)
java.util.BitSet getHiddenSet()
public boolean isSelected(int atomIndex)
boolean isInSelectionSubset(int atomIndex)
void reportSelection(java.lang.String msg)
public javax.vecmath.Point3f getAtomSetCenter(java.util.BitSet bs)
private void clearAtomSets()
public void selectAll()
selectAll
in class JmolViewer
void setNoneSelected(boolean noneSelected)
java.lang.Boolean getNoneSelected()
public void clearSelection()
clearSelection
in class JmolViewer
public void setSelectionSet(java.util.BitSet set)
setSelectionSet
in class JmolViewer
void setSelectionSubset(java.util.BitSet subset)
public java.util.BitSet getSelectionSubset()
void invertSelection()
public java.util.BitSet getSelectionSet()
public int getSelectionCount()
getSelectionCount
in class JmolViewer
void setFormalCharges(int formalCharge)
public void addSelectionListener(JmolSelectionListener listener)
addSelectionListener
in class JmolViewer
public void removeSelectionListener(JmolSelectionListener listener)
removeSelectionListener
in class JmolViewer
java.util.BitSet getAtomBitSet(java.lang.Object atomExpression)
java.util.Vector getAtomBitSetVector(java.lang.Object atomExpression)
public void setModeMouse(int modeMouse)
setModeMouse
in class JmolViewer
java.awt.Rectangle getRubberBandSelection()
public int getCursorX()
public int getCursorY()
java.lang.String getDefaultDirectory()
public java.io.BufferedInputStream getBufferedInputStream(java.lang.String fullPathName)
getBufferedInputStream
in interface AtomDataServer
java.lang.Object getBufferedReaderOrErrorMessageFromName(java.lang.String name, java.lang.String[] fullPathNameReturn, boolean isBinary)
void addLoadScript(java.lang.String script)
private java.util.Hashtable setLoadParameters(java.util.Hashtable htParams)
public java.lang.String openFile(java.lang.String fileName)
openFile
in class JmolSimpleViewer
fileName
-
public void openFileAsynchronously(java.lang.String fileName)
openFileAsynchronously
in class JmolViewer
void openFile(java.lang.String fileName, java.util.Hashtable htParams, java.lang.String loadScript, boolean isAppend)
public java.lang.String openFiles(java.lang.String modelName, java.lang.String[] fileNames)
java.lang.String openFiles(java.lang.String modelName, java.lang.String[] fileNames, java.lang.String loadScript, boolean isAppend, java.util.Hashtable htParams)
public java.lang.String openStringInline(java.lang.String strModel)
openStringInline
in class JmolSimpleViewer
private java.lang.String createModelSetInline(java.lang.String strModel, java.util.Hashtable htParams, boolean isAppend, boolean createModelSet, boolean isLoadVariable)
private java.lang.String openStringsInline(java.lang.String[] arrayModels, java.util.Hashtable htParams, boolean isAppend)
public char getInlineChar()
public java.lang.String loadInline(java.lang.String strModel)
loadInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String strModel, boolean isAppend)
loadInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String strModel, char newLine)
loadInline
in class JmolViewer
java.lang.String loadInline(java.lang.String strModel, char newLine, boolean isAppend)
java.lang.String getDataSeparator()
public java.lang.String loadInline(java.lang.String[] arrayModels)
loadInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String[] arrayModels, boolean isAppend)
loadInline
in class JmolViewer
public boolean getApplySymmetryToBonds()
void setApplySymmetryToBonds(boolean TF)
void setAtomData(int type, java.lang.String name, java.lang.String coordinateData)
public java.lang.String openDOM(java.lang.Object DOMNode)
openDOM
in class JmolSimpleViewer
public java.lang.String openReader(java.lang.String fullPathName, java.lang.String fileName, java.io.Reader reader)
openReader
in class JmolViewer
fullPathName
- fileName
- reader
-
java.lang.String createModelSetAndReturnError(boolean isAppend)
isAppend
-
java.lang.String loadAtomDataAndReturnError(int tokType)
private java.lang.String createAtomDataSet(int tokType, java.lang.Object atomSetCollection)
void deallocateReaderThreads()
public void openClientFile(java.lang.String fullPathName, java.lang.String fileName, java.lang.Object clientFile)
openClientFile
in class JmolViewer
fullPathName
- fileName
- clientFile
- private java.lang.String createModelSet(java.lang.String fullPathName, java.lang.String fileName, java.lang.Object atomSetCollection, boolean isAppend)
fullPathName
- fileName
- atomSetCollection
- isAppend
-
public java.lang.Object getCurrentFileAsBytes()
public java.lang.Object getFileAsBytes(java.lang.String pathName)
public java.lang.String getCurrentFileAsString()
public java.lang.String getFullPathName()
public java.lang.String getFileName()
public java.lang.String getFileAsString(java.lang.String name)
getFileAsString
in class JmolViewer
public java.lang.String getFileAsString(java.lang.String name, int nBytesMax, boolean doSpecialLoad)
public java.lang.String getFullPath(java.lang.String name)
public boolean getFileAsString(java.lang.String[] data, int nBytesMax, boolean doSpecialLoad)
getFileAsString
in class JmolViewer
java.lang.String[] getFileInfo()
void setFileInfo(java.lang.String[] fileInfo)
public void autoCalculate(int tokProperty)
int getSurfaceDistanceMax()
public void calculateStraightness()
public javax.vecmath.Point3f[] calculateSurface(java.util.BitSet bsSelected, float envelopeRadius)
void calculateStructures(java.util.BitSet bsAtoms)
public AtomIndexIterator getWithinModelIterator(Atom atom, float distance)
public AtomIndexIterator getWithinAtomSetIterator(int atomIndex, float distance, java.util.BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)
getWithinAtomSetIterator
in interface AtomDataServer
public void fillAtomData(AtomData atomData, int mode)
fillAtomData
in interface AtomDataServer
ModelCollection.StateScript addStateScript(java.lang.String script, boolean addFrameNumber, boolean postDefinitions)
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)
public boolean getEchoStateActive()
void setEchoStateActive(boolean TF)
public void zap(boolean notify, boolean resetUndo)
private void zap(java.lang.String msg)
void echoMessage(java.lang.String msg)
public java.lang.String getMinimizationInfo()
public boolean useMinimizationThread()
private void initializeModel()
public java.lang.String getModelSetName()
getModelSetName
in class JmolViewer
public java.lang.String getModelSetFileName()
getModelSetFileName
in class JmolViewer
public java.lang.String getUnitCellInfoText()
public java.util.Hashtable getSpaceGroupInfo(java.lang.String spaceGroup)
void getPolymerPointsAndVectors(java.util.BitSet bs, java.util.Vector vList)
public java.lang.String getModelSetProperty(java.lang.String strProp)
public java.lang.Object getModelSetAuxiliaryInfo(java.lang.String strKey)
public java.lang.String getModelSetPathName()
getModelSetPathName
in class JmolViewer
public java.lang.String getModelSetTypeName()
public boolean haveFrame()
haveFrame
in class JmolViewer
boolean haveModelSet()
void clearBfactorRange()
public java.lang.String getHybridizationAndAxes(int atomIndex, javax.vecmath.Vector3f z, javax.vecmath.Vector3f x, java.lang.String lcaoType, boolean hybridizationCompatible)
public java.util.BitSet getModelAtomBitSet(int modelIndex, boolean asCopy)
public java.util.BitSet getModelBitSet(java.util.BitSet atomList, boolean allTrajectories)
public java.lang.String getClientAtomStringProperty(java.lang.Object clientAtom, java.lang.String propertyName)
public ModelSet getModelSet()
public java.lang.String getBoundBoxCommand(boolean withOptions)
void setBoundBox(javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, boolean byCorner)
public javax.vecmath.Point3f getBoundBoxCenter()
javax.vecmath.Point3f getAverageAtomPoint()
void calcBoundBoxDimensions(java.util.BitSet bs)
BoxInfo getBoxInfo(java.util.BitSet bs)
float calcRotationRadius(javax.vecmath.Point3f center)
public float calcRotationRadius(java.util.BitSet bs)
public javax.vecmath.Vector3f getBoundBoxCornerVector()
java.util.Hashtable getBoundBoxInfo()
public java.util.BitSet getBoundBoxModels()
public int getBoundBoxCenterX()
public int getBoundBoxCenterY()
public int getModelCount()
getModelCount
in class JmolViewer
java.lang.String getModelInfoAsString()
java.lang.String getSymmetryInfoAsString()
public java.util.Properties getModelSetProperties()
getModelSetProperties
in class JmolViewer
public java.util.Hashtable getModelSetAuxiliaryInfo()
getModelSetAuxiliaryInfo
in class JmolViewer
public int getModelNumber(int modelIndex)
getModelNumber
in class JmolViewer
public int getModelFileNumber(int modelIndex)
public java.lang.String getModelNumberDotted(int modelIndex)
getModelNumberDotted
in class JmolViewer
public java.lang.String getModelName(int modelIndex)
getModelName
in class JmolViewer
public java.util.Properties getModelProperties(int modelIndex)
getModelProperties
in class JmolViewer
public java.lang.String getModelProperty(int modelIndex, java.lang.String propertyName)
getModelProperty
in class JmolViewer
public java.lang.String getModelFileInfo()
java.lang.String getModelFileInfoAll()
public java.util.Hashtable getModelAuxiliaryInfo(int modelIndex)
getModelAuxiliaryInfo
in class JmolViewer
public java.lang.Object getModelAuxiliaryInfo(int modelIndex, java.lang.String keyName)
getModelAuxiliaryInfo
in class JmolViewer
int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
boolean modelSetHasVibrationVectors()
public boolean modelHasVibrationVectors(int modelIndex)
modelHasVibrationVectors
in class JmolViewer
public int getChainCount()
getChainCount
in class JmolViewer
public int getChainCountInModel(int modelIndex)
getChainCountInModel
in class JmolViewer
public int getChainCountInModel(int modelIndex, boolean countWater)
public int getGroupCount()
getGroupCount
in class JmolViewer
public int getGroupCountInModel(int modelIndex)
getGroupCountInModel
in class JmolViewer
public int getPolymerCount()
getPolymerCount
in class JmolViewer
public int getPolymerCountInModel(int modelIndex)
getPolymerCountInModel
in class JmolViewer
public int getAtomCount()
getAtomCount
in class JmolViewer
public int getAtomCountInModel(int modelIndex)
getAtomCountInModel
in class JmolViewer
public int getBondCount()
getBondCount
in class JmolViewer
public int getBondCountInModel(int modelIndex)
getBondCountInModel
in class JmolViewer
modelIndex
- the model of interest or -1 for all
java.util.BitSet getBondsForSelectedAtoms(java.util.BitSet bsAtoms)
boolean frankClicked(int x, int y)
public int findNearestAtomIndex(int x, int y)
findNearestAtomIndex
in class JmolViewer
void selectRectangle(java.awt.Rectangle rect, int modifiers)
void toCartesian(javax.vecmath.Point3f pt)
void toUnitCell(javax.vecmath.Point3f pt, javax.vecmath.Point3f offset)
void toFractional(javax.vecmath.Point3f pt)
public void setCenterSelected()
setCenterSelected
in class JmolViewer
public void setBondTolerance(float bondTolerance)
setBondTolerance
in class JmolViewer
public float getBondTolerance()
getBondTolerance
in class JmolViewer
public void setMinBondDistance(float minBondDistance)
setMinBondDistance
in class JmolViewer
public float getMinBondDistance()
getMinBondDistance
in class JmolViewer
int[] getAtomIndices(java.util.BitSet bs)
public java.util.BitSet getAtomBits(int tokType, java.lang.Object specInfo)
java.util.BitSet getSequenceBits(java.lang.String specInfo, java.util.BitSet bs)
java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point3f coord)
java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point4f plane)
java.util.BitSet getAtomsWithin(float distance, java.util.BitSet bs, boolean isWithinModelSet)
java.util.BitSet getAtomsConnected(float min, float max, int intType, java.util.BitSet bs)
java.util.BitSet getBranchBitSet(int atomIndex, int atomIndexNot)
int getAtomIndexFromAtomNumber(int atomNumber)
public java.util.BitSet getElementsPresentBitSet(int modelIndex)
getElementsPresentBitSet
in class JmolViewer
public java.util.Hashtable getHeteroList(int modelIndex)
getHeteroList
in class JmolViewer
java.util.BitSet getVisibleSet()
java.util.BitSet getClickableSet()
void calcSelectedGroupsCount()
void calcSelectedMonomersCount()
void calcSelectedMoleculesCount()
java.lang.String getFileHeader()
java.lang.Object getFileData()
public java.util.Hashtable getCifData(int modelIndex)
java.lang.String getPDBHeader()
public java.util.Hashtable getModelInfo(java.lang.Object atomExpression)
public java.util.Hashtable getAuxiliaryInfo(java.lang.Object atomExpression)
public java.util.Hashtable getShapeInfo()
int getShapeIdFromObjectName(java.lang.String objectName)
java.util.Vector getAllAtomInfo(java.lang.Object atomExpression)
java.util.Vector getAllBondInfo(java.lang.Object atomExpression)
java.util.Vector getMoleculeInfo(java.lang.Object atomExpression)
public java.lang.String getChimeInfo(int tok)
public java.util.Hashtable getAllChainInfo(java.lang.Object atomExpression)
public java.util.Hashtable getAllPolymerInfo(java.lang.Object atomExpression)
public java.lang.String getStateInfo()
getStateInfo
in class JmolViewer
public java.lang.String getStateInfo(java.lang.String type)
public java.lang.String getStructureState()
java.lang.String getProteinStructureState()
public java.lang.String getCoordinateState(java.util.BitSet bsSelected)
void setCurrentColorRange(java.lang.String label)
void setCurrentColorRange(float[] data, java.util.BitSet bs)
public void setCurrentColorRange(float min, float max)
public float[] getCurrentColorRange()
public void setData(java.lang.String type, java.lang.Object[] data, int atomCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)
java.lang.Object[] getData(java.lang.String type)
public float[] getDataFloat(java.lang.String label)
float[][] getDataFloat2D(java.lang.String label)
public float[][][] getDataFloat3D(java.lang.String label)
public float getDataFloat(java.lang.String label, int atomIndex)
public java.lang.String getAltLocListInModel(int modelIndex)
getAltLocListInModel
in class JmolViewer
public java.util.BitSet setConformation()
public java.util.BitSet setConformation(int conformationIndex)
int autoHbond(java.util.BitSet bsBonds)
int autoHbond(java.util.BitSet bsFrom, java.util.BitSet bsTo, java.util.BitSet bsBonds, float maxXYDistance, float minAttachedAngle)
public boolean hasCalculatedHBonds(java.util.BitSet bsAtoms)
public boolean havePartialCharges()
havePartialCharges
in class JmolViewer
public SymmetryInterface getCurrentUnitCell()
void setCurrentUnitCellOffset(int offset)
void setCurrentUnitCellOffset(javax.vecmath.Point3f pt)
public java.lang.String getDefaultMeasurementLabel(int nPoints)
public int getMeasurementCount()
getMeasurementCount
in class JmolViewer
public java.lang.String getMeasurementStringValue(int i)
getMeasurementStringValue
in class JmolViewer
java.util.Vector getMeasurementInfo()
public java.lang.String getMeasurementInfoAsString()
public int[] getMeasurementCountPlusIndices(int i)
getMeasurementCountPlusIndices
in class JmolViewer
void setPendingMeasurement(MeasurementPending measurementPending)
MeasurementPending getPendingMeasurement()
void clearAllMeasurements()
public void clearMeasurements()
clearMeasurements
in class JmolViewer
public boolean getJustifyMeasurements()
void setMeasurementFormats(java.lang.String strFormat)
void defineMeasurement(java.util.Vector monitorExpressions, float[] rangeMinMax, boolean isDelete, boolean isAll, boolean isAllConnected, boolean isOn, boolean isOff, java.lang.String strFormat)
public void deleteMeasurement(int i)
deleteMeasurement
in class JmolViewer
void deleteMeasurement(int[] atomCountPlusIndices)
public void showMeasurement(int[] atomCountPlusIndices, boolean isON)
void hideMeasurements(boolean isOFF)
void toggleMeasurement(int[] atomCountPlusIndices, java.lang.String strFormat)
void setAnimationDirection(int direction)
void reverseAnimation()
int getAnimationDirection()
java.util.Hashtable getAnimationInfo()
public void setAnimationFps(int fps)
setAnimationFps
in class JmolViewer
public int getAnimationFps()
getAnimationFps
in class JmolViewer
void setAnimationReplayMode(int replay, float firstFrameDelay, float lastFrameDelay)
int getAnimationReplayMode()
void setAnimationOn(boolean animationOn)
void resumeAnimation()
void pauseAnimation()
void setAnimationRange(int modelIndex1, int modelIndex2)
public java.util.BitSet getVisibleFramesBitSet()
boolean isAnimationOn()
void setAnimationNext()
void setAnimationPrevious()
void setAnimationLast()
void rewindAnimation()
void setCurrentModelIndex(int modelIndex)
void setTrajectory(int modelIndex)
public void setTrajectory(java.util.BitSet bsModels)
boolean isTrajectory(int modelIndex)
public java.util.BitSet getBitSetTrajectories()
java.lang.String getTrajectoryInfo()
void setFrameOffset(int modelIndex)
public void setFrameOffsets(java.util.BitSet bsAtoms)
public java.util.BitSet getFrameOffsets()
public void setCurrentModelIndex(int modelIndex, boolean clearBackground)
public int getCurrentModelIndex()
public int getDisplayModelIndex()
getDisplayModelIndex
in class JmolViewer
boolean haveFileSet()
void setBackgroundModelIndex(int modelIndex)
public int getBackgroundModelIndex()
void setFrameVariables(int firstModelIndex, int lastModelIndex)
public int getMotionEventNumber()
getMotionEventNumber
in class JmolViewer
void setInMotion(boolean inMotion)
public boolean getInMotion()
public void pushHoldRepaint()
pushHoldRepaint
in class JmolViewer
void pushHoldRepaint(java.lang.String why)
public void popHoldRepaint()
popHoldRepaint
in class JmolViewer
void popHoldRepaint(java.lang.String why)
void setRefreshing(boolean TF)
boolean getRefreshing()
public void refresh(int mode, java.lang.String strWhy)
refresh
in class JmolViewer
mode
- strWhy
- void requestRepaintAndWait()
void setSync()
public void viewerNotifyRepaintDone()
viewerNotifyRepaintDone
in class JmolViewer
public boolean areAxesTainted()
private void setMaximumSize(int x)
public void setScreenDimension(java.awt.Dimension dim)
setScreenDimension
in class JmolViewer
public float getImageFontScaling()
private void resizeImage(int width, int height, boolean isImageWrite, boolean isGenerator, boolean isReset)
public int getScreenWidth()
getScreenWidth
in class JmolViewer
public int getScreenHeight()
getScreenHeight
in class JmolViewer
public int getScreenDim()
public java.lang.String generateOutput(java.lang.String type, java.lang.String fileName, int width, int height)
generateOutput
in class JmolViewer
public void renderScreenImage(java.awt.Graphics gLeft, java.awt.Graphics gRight, java.awt.Dimension size, java.awt.Rectangle clip)
JmolViewer
renderScreenImage
in class JmolViewer
public void renderScreenImage(java.awt.Graphics g, java.awt.Dimension size, java.awt.Rectangle clip)
renderScreenImage
in class JmolSimpleViewer
private java.awt.Image getImage(boolean isDouble)
private void render()
private java.awt.Image getStereoImage(int stereoMode)
private void render1(java.awt.Graphics g, java.awt.Image img, int x, int y)
public java.awt.Image getScreenImage()
getScreenImage
in class JmolViewer
public java.lang.Object getImageAs(java.lang.String type, int quality, int width, int height, java.lang.String fileName, java.io.OutputStream os)
getImageAs
in class JmolViewer
type
- "PNG", "JPG", "JPEG", "JPG64", "PPM", "GIF"quality
- width
- height
- fileName
- os
-
public void releaseScreenImage()
releaseScreenImage
in class JmolViewer
boolean getAllowEmbeddedScripts()
public java.lang.String evalFile(java.lang.String strFilename)
evalFile
in class JmolSimpleViewer
public java.lang.String script(java.lang.String strScript)
script
in class JmolViewer
java.lang.String getInterruptScript()
public java.lang.String evalString(java.lang.String strScript)
evalString
in class JmolSimpleViewer
public java.lang.String evalStringQuiet(java.lang.String strScript)
evalStringQuiet
in class JmolViewer
java.lang.String evalStringQuiet(java.lang.String strScript, boolean isQuiet, boolean allowSyncScript)
private java.lang.String checkScriptExecution(java.lang.String strScript)
boolean usingScriptQueue()
public void clearScriptQueue()
public boolean checkResume(java.lang.String str)
public boolean checkStepping(java.lang.String str)
public boolean checkHalt(java.lang.String str)
checkHalt
in class JmolViewer
public java.lang.String scriptWait(java.lang.String strScript)
scriptWait
in class JmolViewer
public java.lang.Object scriptWaitStatus(java.lang.String strScript, java.lang.String statusList)
scriptWaitStatus
in class JmolViewer
public java.lang.Object evalStringWaitStatus(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList)
java.lang.Object evalStringWaitStatus(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)
void exitJmol()
private java.lang.Object scriptCheck(java.lang.String strScript, boolean returnContext)
public java.lang.Object scriptCheck(java.lang.String strScript)
scriptCheck
in class JmolViewer
public boolean isScriptExecuting()
isScriptExecuting
in class JmolViewer
public void haltScriptExecution()
haltScriptExecution
in class JmolViewer
public void resumeScriptExecution()
public void stepScriptExecution()
public void pauseScriptExecution()
java.lang.String getDefaultLoadScript()
java.lang.String getLoadFormat()
public java.lang.String getStandardLabelFormat()
public int getRibbonAspectRatio()
public float getSheetSmoothing()
public boolean getSsbondsBackbone()
public boolean getHbondsBackbone()
public boolean getHbondsSolid()
public void setMarBond(short marBond)
setMarBond
in class JmolViewer
void hoverOn(int atomIndex, int modifiers)
int getHoverDelay()
public void hoverOn(int x, int y, java.lang.String text)
void hoverOff()
void setLabel(java.lang.String strLabel)
void togglePickingLabel(java.util.BitSet bs)
java.util.BitSet getBitSetSelection()
public void clearShapes()
public void loadShape(int shapeID)
void setShapeSize(int shapeID, int size, float fsize)
public void setShapeSize(int shapeID, int size, java.util.BitSet bsAtoms)
public void setShapeSize(int shapeID, int size, float fsize, java.util.BitSet bsAtoms)
public void setShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object value)
void setShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs)
public java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName)
public boolean getShapeProperty(int shapeType, java.lang.String propertyName, java.lang.Object[] data)
java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName, int index)
int getShapePropertyAsInt(int shapeID, java.lang.String propertyName)
short getColix(java.lang.Object object)
boolean getRasmolHydrogenSetting()
boolean getRasmolHeteroSetting()
boolean getDebugScript()
public void setDebugScript(boolean debugScript)
setDebugScript
in class JmolViewer
void atomPicked(int atomIndex, Point3fi ptClicked, int modifiers, boolean isDoubleClick)
void clearClickCount()
public void setCursor(int cursor)
private void setPickingMode(java.lang.String mode)
public int getPickingMode()
public boolean getDrawPicking()
public boolean getBondPicking()
private boolean getAtomPicking()
private void setPickingStyle(java.lang.String style)
int getPickingStyle()
public boolean getDrawHover()
public java.lang.String getAtomInfo(int atomIndex)
getAtomInfo
in class JmolViewer
public java.lang.String getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
public void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
setJmolCallbackListener
in class JmolViewer
public void setJmolStatusListener(JmolStatusListener jmolStatusListener)
setJmolStatusListener
in class JmolViewer
public java.util.Hashtable getMessageQueue()
java.lang.Object getStatusChanged(java.lang.String statusNameList)
void popupMenu(int x, int y)
java.lang.String getMenu(java.lang.String type)
void setMenu(java.lang.String fileOrText, boolean isFile)
void setStatusFrameChanged(int frameNo)
public void scriptEcho(java.lang.String strEcho)
void notifyError(java.lang.String errType, java.lang.String errMsg, java.lang.String errMsgUntranslated)
java.lang.String jsEval(java.lang.String strEval)
public void setStatusAtomHovered(int atomIndex, java.lang.String info)
private void setFileLoadStatus(int ptLoad, java.lang.String fullPathName, java.lang.String fileName, java.lang.String modelName, java.lang.String strError)
public void setStatusMeasuring(java.lang.String status, int intInfo, java.lang.String strMeasure)
public void notifyMinimizationStatus()
public void setStatusAtomPicked(int atomIndex, java.lang.String info)
public void setStatusResized(int width, int height)
void scriptStatus(java.lang.String strStatus)
void scriptStatus(java.lang.String strStatus, java.lang.String statusMessage)
void scriptStatus(java.lang.String strStatus, java.lang.String statusMessage, int msWalltime, java.lang.String strErrorMessageUntranslated)
private java.lang.String getModelTitle(int modelIndex)
private java.lang.String getModelFileName(int modelIndex)
public java.lang.String dialogAsk(java.lang.String type, java.lang.String fileName)
int getScriptDelay()
public void showUrl(java.lang.String urlString)
showUrl
in class JmolViewer
public void setMeshCreator(java.lang.Object meshCreator)
meshCreator
- void showConsole(boolean showConsole)
void clearConsole()
java.lang.Object getParameterEscaped(java.lang.String key)
public java.lang.Object getParameter(java.lang.String key)
getParameter
in class JmolViewer
ScriptVariable getOrSetNewVariable(java.lang.String key, boolean doSet)
ScriptVariable setUserVariable(java.lang.String name, ScriptVariable value)
void unsetProperty(java.lang.String name)
java.lang.String getVariableList()
public boolean getBooleanProperty(java.lang.String key)
getBooleanProperty
in class JmolViewer
public boolean getBooleanProperty(java.lang.String key, boolean doICare)
getBooleanProperty
in class JmolViewer
key
- doICare
- true if you want an error message if it doesn't exist
public void setStringProperty(java.lang.String key, java.lang.String value)
setStringProperty
in class JmolViewer
public java.lang.String getLanguage()
private void setLanguage(java.lang.String value)
private void setPropertyError(java.lang.String msg)
void removeUserVariable(java.lang.String key)
boolean isJmolVariable(java.lang.String key)
public void setFloatProperty(java.lang.String key, float value)
setFloatProperty
in class JmolViewer
private boolean setFloatProperty(java.lang.String key, float value, boolean isInt)
public void setIntProperty(java.lang.String key, int value)
setIntProperty
in class JmolViewer
private void setIntProperty(java.lang.String key, int value, boolean defineNew)
int getDelayMaximum()
public void setBooleanProperty(java.lang.String key, boolean value)
setBooleanProperty
in class JmolViewer
boolean setBooleanProperty(java.lang.String key, boolean value, boolean defineNew)
public boolean getPdbLoadInfo(int type)
boolean getSelectAllModels()
boolean getMessageStyleChime()
public boolean getFontCaching()
public boolean getFontScaling()
void showParameter(java.lang.String key, boolean ifNotSet, int nMax)
public void showString(java.lang.String str, boolean isPrint)
java.lang.String getAllSettings(java.lang.String prefix)
public boolean getDotSurfaceFlag()
public boolean getDotsSelectedOnlyFlag()
public int getDotDensity()
public boolean isRangeSelected()
boolean getIsosurfacePropertySmoothing()
public boolean getWireframeRotation()
boolean isWindowCentered()
void setNavigationDepthPercent(float timeSec, float percent)
float getNavigationSpeed()
public boolean getShowNavigationPoint()
public void setVisualRange(float angstroms)
float getSolventProbeRadius()
public float getCurrentSolventProbeRadius()
boolean getSolventOn()
public boolean getTestFlag1()
public boolean getTestFlag2()
public boolean getTestFlag3()
public boolean getTestFlag4()
public void setPerspectiveDepth(boolean perspectiveDepth)
setPerspectiveDepth
in class JmolViewer
public void setAxesOrientationRasmol(boolean TF)
setAxesOrientationRasmol
in class JmolViewer
public boolean getAxesOrientationRasmol()
getAxesOrientationRasmol
in class JmolViewer
void setAxesScale(float scale)
public javax.vecmath.Point3f[] getAxisPoints()
public float getAxesScale()
private void setAxesModeMolecular(boolean TF)
void setAxesModeUnitCell(boolean TF)
public int getAxesMode()
public boolean getDisplayCellParameters()
public boolean getPerspectiveDepth()
getPerspectiveDepth
in class JmolViewer
public void setSelectionHalos(boolean TF)
setSelectionHalos
in class JmolViewer
public boolean getSelectionHaloEnabled()
public boolean getBondSelectionModeOr()
public boolean getChainCaseSensitive()
public boolean getRibbonBorder()
public boolean getCartoonRocketFlag()
public boolean getRocketBarrelFlag()
private void setStrandCount(int type, int value)
public int getStrandCount(int type)
boolean getHideNameInPopup()
boolean getNavigationPeriodic()
private void stopAnimationThreads()
private void setNavigationMode(boolean TF)
public boolean getNavigationMode()
public boolean getNavigateSurface()
public void setTransformManager(TransformManager transformManager)
transformManager
- private void setPerspectiveModel(int mode)
private void setTransformManagerDefaults()
public float getCameraDepth()
boolean getZoomLarge()
public boolean getTraceAlpha()
public int getHermiteLevel()
public boolean getHighResolution()
java.lang.String getLoadState()
public void setAutoBond(boolean TF)
setAutoBond
in class JmolViewer
public boolean getAutoBond()
getAutoBond
in class JmolViewer
int[] makeConnections(float minDistance, float maxDistance, short order, int connectOperation, java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsBonds, boolean isBonds)
public void rebond()
rebond
in class JmolViewer
void setPdbConectBonding(boolean isAuto)
boolean getGreyscaleRendering()
boolean getDisablePopupMenu()
public boolean getForceAutoBond()
public void setPercentVdwAtom(int percentVdwAtom)
setPercentVdwAtom
in class JmolViewer
public int getPercentVdwAtom()
getPercentVdwAtom
in class JmolViewer
public short getDefaultMadAtom()
public short getMadBond()
getMadBond
in class JmolViewer
public short getMarBond()
public byte getModeMultipleBond()
public boolean getShowMultipleBonds()
public void setShowHydrogens(boolean TF)
setShowHydrogens
in class JmolViewer
public boolean getShowHydrogens()
getShowHydrogens
in class JmolViewer
public boolean getShowHiddenSelectionHalos()
public void setShowBbcage(boolean value)
setShowBbcage
in class JmolViewer
public boolean getShowBbcage()
getShowBbcage
in class JmolViewer
public void setShowUnitCell(boolean value)
public boolean getShowUnitCell()
public void setShowAxes(boolean value)
setShowAxes
in class JmolViewer
public boolean getShowAxes()
getShowAxes
in class JmolViewer
public void setFrankOn(boolean TF)
setFrankOn
in class JmolViewer
public boolean getShowFrank()
public boolean isSignedApplet()
public void setShowMeasurements(boolean TF)
setShowMeasurements
in class JmolViewer
public boolean getShowMeasurements()
getShowMeasurements
in class JmolViewer
public boolean getShowMeasurementLabels()
public boolean getMeasureAllModelsFlag()
void setMeasureDistanceUnits(java.lang.String units)
public java.lang.String getMeasureDistanceUnits()
public boolean getUseNumberLocalization()
void setAppendNew(boolean value)
public boolean getAppendNew()
boolean getAutoFps()
public void setRasmolDefaults()
setRasmolDefaults
in class JmolViewer
public void setJmolDefaults()
setJmolDefaults
in class JmolViewer
private void setDefaults(java.lang.String type)
public boolean getZeroBasedXyzRasmol()
private void setAntialias(int mode, boolean TF)
public javax.vecmath.Point3f[] allocTempPoints(int size)
public void freeTempPoints(javax.vecmath.Point3f[] tempPoints)
public javax.vecmath.Point3i[] allocTempScreens(int size)
public void freeTempScreens(javax.vecmath.Point3i[] tempScreens)
public byte[] allocTempBytes(int size)
public void freeTempBytes(byte[] tempBytes)
Font3D getFont3D(java.lang.String fontFace, java.lang.String fontStyle, float fontSize)
public java.lang.String formatText(java.lang.String text0)
java.lang.String getElementSymbol(int i)
int getElementNumber(int i)
public java.lang.String getAtomName(int i)
getAtomName
in class JmolViewer
public int getAtomNumber(int i)
getAtomNumber
in class JmolViewer
float getAtomX(int i)
float getAtomY(int i)
float getAtomZ(int i)
public javax.vecmath.Point3f getAtomPoint3f(int i)
getAtomPoint3f
in class JmolViewer
public float getAtomRadius(int i)
getAtomRadius
in class JmolViewer
public float getAtomVdwRadius(int i)
public int getAtomArgb(int i)
getAtomArgb
in class JmolViewer
java.lang.String getAtomChain(int i)
public int getAtomModelIndex(int i)
getAtomModelIndex
in class JmolViewer
java.lang.String getAtomSequenceCode(int i)
public float getBondRadius(int i)
getBondRadius
in class JmolViewer
public short getBondOrder(int i)
getBondOrder
in class JmolViewer
void assignAromaticBonds()
public boolean getSmartAromatic()
void resetAromatic()
public int getBondArgb1(int i)
getBondArgb1
in class JmolViewer
public int getBondModelIndex(int i)
getBondModelIndex
in class JmolViewer
public int getBondArgb2(int i)
getBondArgb2
in class JmolViewer
public javax.vecmath.Point3f[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
getPolymerLeadMidPoints
in class JmolViewer
void setStereoMode(int[] twoColors, int stereoMode, float degrees)
public boolean isJvm12orGreater()
isJvm12orGreater
in class JmolViewer
public java.lang.String getOperatingSystemName()
getOperatingSystemName
in class JmolViewer
public java.lang.String getJavaVendor()
getJavaVendor
in class JmolViewer
public java.lang.String getJavaVersion()
getJavaVersion
in class JmolViewer
public Graphics3D getGraphics3D()
public boolean showModelSetDownload()
showModelSetDownload
in class JmolViewer
public java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.String paramInfo)
boolean isScriptEditorVisible()
public java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
getProperty
in class JmolSimpleViewer
returnType
- "JSON", "string", "readable", and anything else returns the Java object.
void showEditor(java.lang.String[] file_text)
java.lang.String getModelExtract(java.lang.Object atomExpression)
public java.lang.String getHexColorFromIndex(short colix)
void setModelVisibility()
void setFrameTitle(int modelIndex, java.lang.String title)
java.lang.String getFrameTitle(int modelIndex)
void setTainted(boolean TF)
Point3fi checkObjectClicked(int x, int y, int modifiers)
boolean checkObjectHovered(int x, int y)
void checkObjectDragged(int prevX, int prevY, int x, int y, int modifiers)
void rotateAxisAngleAtCenter(javax.vecmath.Point3f rotCenter, javax.vecmath.Vector3f rotAxis, float degrees, float endDegrees, boolean isSpin, java.util.BitSet bsSelected)
void rotateAboutPointsInternal(javax.vecmath.Point3f point1, javax.vecmath.Point3f point2, float degrees, float endDegrees, boolean isSpin, java.util.BitSet bsSelected)
int getPickingSpinRate()
public void startSpinningAxis(javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, boolean isClockwise)
public javax.vecmath.Vector3f getModelDipole()
public javax.vecmath.Vector3f calculateMolecularDipole()
public float getDipoleScale()
public void getAtomIdentityInfo(int atomIndex, java.util.Hashtable info)
void setDefaultLattice(javax.vecmath.Point3f ptLattice)
javax.vecmath.Point3f getDefaultLattice()
java.util.BitSet getTaintedAtoms(byte type)
public void setTaintedAtoms(java.util.BitSet bs, byte type)
public java.lang.String getData(java.lang.String atomExpression, java.lang.String type)
getData
in class JmolViewer
public java.lang.Object evaluateExpression(java.lang.Object stringOrTokens)
java.lang.Object getHelixData(java.util.BitSet bs, int tokType)
public java.lang.String getPdbData(java.util.BitSet bs)
java.lang.String getPdbData(int modelIndex, java.lang.String type)
public boolean isJmolDataFrame(int modelIndex)
public boolean isJmolDataFrame()
int getJmolDataFrameIndex(int modelIndex, java.lang.String type)
void setJmolDataFrame(java.lang.String type, int modelIndex, int dataIndex)
void setFrameTitle(java.lang.String title)
public java.lang.String getFrameTitle()
java.lang.String getJmolFrameType(int modelIndex)
public int getJmolDataSourceFrame(int modelIndex)
void setAtomProperty(java.util.BitSet bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
public void setAtomCoord(int atomIndex, float x, float y, float z)
void setAtomCoord(java.util.BitSet bs, int tokType, java.lang.Object xyzValues)
public void setAtomCoordRelative(int atomIndex, float x, float y, float z)
void setAtomCoordRelative(javax.vecmath.Point3f offset)
void setAllowRotateSelected(boolean TF)
boolean allowRotateSelected()
void invertSelected(javax.vecmath.Point3f pt, java.util.BitSet bs)
void invertSelected(javax.vecmath.Point3f pt, javax.vecmath.Point4f plane)
void moveSelected(int deltaX, int deltaY, int x, int y, boolean isTranslation)
void rotateAtoms(javax.vecmath.Matrix3f mNew, javax.vecmath.Matrix3f matrixRotate, boolean fullMolecule, javax.vecmath.Point3f center, boolean isInternal, java.util.BitSet bsAtoms)
public void refreshMeasures()
void setDynamicMeasurements(boolean TF)
public boolean getDynamicMeasurements()
public float[][] functionXY(java.lang.String functionName, int nX, int nY)
functionName
- nX
- nY
-
float[][][] functionXYZ(java.lang.String functionName, int nX, int nY, int nZ)
void getHelp(java.lang.String what)
void addCommand(java.lang.String command)
command
- the command to addjava.lang.String removeCommand()
public java.lang.String getSetHistory(int howFarBack)
getSetHistory
in class JmolViewer
howFarBack
- number of lines (-1 for next line)
public void writeTextFile(java.lang.String fileName, java.lang.String data)
writeTextFile
in class JmolViewer
public java.lang.String clipImage(java.lang.String text)
clipImage
in class JmolViewer
text
- null here clips image; String clips text
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)
fileName
- type
- text_or_bytes
- quality
- width
- height
- bsFrames
-
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)
createImage
in class JmolViewer
fileName
- starts with ? --> use file dialog; null --> to clipboardtype
- PNG, JPG, etc.text_or_bytes
- String or byte[] or null if an imagequality
- Integer.MIN_VALUE --> not an imagewidth
- image widthheight
- image height
private java.lang.String getFileNameFromDialog(java.lang.String fileName, int quality)
private void setImageFontScaling(int width, int height)
private void setSyncTarget(int mode, boolean TF)
public void syncScript(java.lang.String script, java.lang.String applet)
syncScript
in class JmolViewer
void setSyncDriver(int mode)
public float[] getPartialCharges()
void setProteinType(byte iType, java.util.BitSet bs)
public javax.vecmath.Point3f getBondPoint3f1(int i)
getBondPoint3f1
in class JmolViewer
public javax.vecmath.Point3f getBondPoint3f2(int i)
getBondPoint3f2
in class JmolViewer
public javax.vecmath.Vector3f getVibrationVector(int atomIndex)
public int getVanderwaalsMar(int i)
public int getVanderwaalsMar(int i, int iMode)
void setDefaultVdw(java.lang.String mode)
java.lang.String getDefaultVdw(int iMode)
public int deleteAtoms(java.util.BitSet bs, boolean fullModels)
public void deleteModelAtoms(int firstAtomIndex, int nAtoms, java.util.BitSet bsDeleted)
public java.util.BitSet getDeletedAtoms()
public char getQuaternionFrame()
public int getHelixStep()
java.lang.String calculatePointGroup()
public java.util.Hashtable getPointGroupInfo(java.lang.Object atomExpression)
public java.lang.String getPointGroupAsString(boolean asDraw, java.lang.String type, int index, float scale)
public float getPointGroupTolerance(int type)
java.lang.Object getFileAsImage(java.lang.String pathName, java.util.Hashtable htParams)
java.lang.String cd(java.lang.String dir)
private java.lang.String setErrorMessage(java.lang.String errMsg)
private java.lang.String setErrorMessage(java.lang.String errMsg, java.lang.String errMsgUntranslated)
public java.lang.String getErrorMessage()
getErrorMessage
in class JmolViewer
public java.lang.String getErrorMessageUntranslated()
getErrorMessageUntranslated
in class JmolViewer
public Shape getShape(int i)
public void setShapeErrorState(int shapeID, java.lang.String state)
public java.lang.String getShapeErrorState()
public void handleError(java.lang.Error er, boolean doClear)
float[] getAtomicCharges()
ScriptFunction getFunction(java.lang.String name)
void addFunction(ScriptFunction f)
public void clearFunctions()
public boolean isFunction(java.lang.String name)
public java.lang.String getFunctionCalls(java.lang.String selectedFunction)
void showMessage(java.lang.String s)
public java.lang.String getMoInfo(int modelIndex)
boolean isRepaintPending()
void repaint()
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