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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 ActionManager |
actionManager
|
private java.util.List |
actionStates
|
private java.util.List |
actionStatesRedo
|
private AnimationManager |
animationManager
|
private boolean |
antialiasDisplay
|
(package private) JmolAppConsoleInterface |
appConsole
|
private java.lang.String |
appletCodeBase
|
private java.lang.String |
appletContext
|
private java.lang.String |
appletDocumentBase
|
boolean |
autoExit
|
private boolean |
axesAreTainted
|
(package private) java.util.BitSet |
bsFrameOffsets
|
private java.util.BitSet |
bsRotateBranch
|
private ColorManager |
colorManager
|
private CommandHistory |
commandHistory
|
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
|
static int |
CURSOR_ZOOM
|
private DataManager |
dataManager
|
java.util.Hashtable |
definedAtomSets
|
(package private) java.awt.Dimension |
dimScreen
|
private java.awt.Component |
display
|
(package private) boolean |
displayLoadErrors
|
private java.lang.String |
errorMessage
|
private java.lang.String |
errorMessageUntranslated
|
(package private) ScriptEvaluator |
eval
|
private java.lang.Object |
executor
|
private static int |
FILE_STATUS_CREATING_MODELSET
|
private FileManager |
fileManager
|
(package private) javax.vecmath.Point3f[] |
frameOffsets
|
private boolean |
frankOn
|
private java.lang.String |
fullName
|
private Graphics3D |
g3d
|
private StateManager.GlobalSettings |
global
|
boolean |
haveDisplay
|
(package private) int |
hoverAtomIndex
|
(package private) boolean |
hoverEnabled
|
(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 |
isKiosk
|
(package private) boolean |
isParallel
|
private boolean |
isPreviewOnly
|
private boolean |
isPrintOnly
|
(package private) boolean |
isScriptQueued
|
private boolean |
isSignedApplet
|
private boolean |
isSignedAppletLocal
|
private boolean |
isSilent
|
(package private) boolean |
isTainted
|
(package private) JmolPopup |
jmolpopup
|
private java.lang.String |
language
|
private int |
lastUndoRedo
|
private boolean |
listCommands
|
private java.lang.String |
logFile
|
private java.lang.String |
logFilePath
|
private static int |
MAX_ACTION_UNDO
|
private int |
maximumSize
|
private MinimizerInterface |
minimizer
|
private JmolAdapter |
modelAdapter
|
(package private) JmolModelKitInterface |
modelkit
|
private ModelManager |
modelManager
|
private ModelSet |
modelSet
|
(package private) int |
motionEventNumber
|
private boolean |
mouseEnabled
|
private MouseManager14 |
mouseManager
|
private boolean |
movingSelected
|
private boolean |
multiTouch
|
private boolean |
mustRender
|
private boolean |
noneSelected
|
static int |
nProcessors
|
(package private) int |
prevFrame
|
private double |
privateKey
|
private RadiusData |
rd
|
private boolean |
refreshing
|
private RepaintManager |
repaintManager
|
private int |
rotateBondIndex
|
private int |
rotatePrev1
|
private int |
rotatePrev2
|
(package private) JmolScriptEditorInterface |
scriptEditor
|
private boolean |
scriptEditorVisible
|
(package private) int |
scriptIndex
|
private ScriptManager |
scriptManager
|
private SelectionManager |
selectionManager
|
private ShapeManager |
shapeManager
|
private boolean |
showSelected
|
private SmilesMatcherInterface |
smilesMatcher
|
static java.lang.String |
STATE_VERSION_STAMP
|
private StateManager |
stateManager
|
private int |
stateScriptVersionInt
|
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
|
private TransformManager |
transformManager
|
private boolean |
useCommandThread
|
(package private) boolean |
wasInMotion
|
Fields inherited from class org.jmol.api.JmolViewer |
---|
menuStructure |
Constructor Summary | |
---|---|
private |
Viewer(java.awt.Component display,
JmolAdapter modelAdapter,
java.lang.String commandOptions)
|
Method Summary | |
---|---|
(package private) void |
actionRotateBond(int deltaX,
int deltaY,
int x,
int y)
|
void |
addCommand(java.lang.String command)
Adds one or more commands to the command history |
void |
addFunction(ScriptFunction f)
|
java.util.BitSet |
addHydrogens(java.util.BitSet bsAtoms,
boolean asScript,
boolean isSilent)
|
java.util.BitSet |
addHydrogensInline(java.util.BitSet bsAtoms,
java.util.List vConnections,
javax.vecmath.Point3f[] pts)
|
void |
addSelectionListener(JmolSelectionListener listener)
|
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)
|
ModelCollection.StateScript |
addStateScript(java.lang.String script,
boolean addFrameNumber,
boolean postDefinitions)
|
void |
addUnitCellOffset(javax.vecmath.Point3f pt)
|
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)
|
boolean |
allowMultiTouch()
|
(package private) boolean |
allowRotateSelected()
|
(package private) void |
appendLoadStates(java.lang.StringBuffer commands)
|
boolean |
areAxesTainted()
|
void |
assignAromaticBonds()
|
void |
assignAtom(int atomIndex,
javax.vecmath.Point3f pt,
java.lang.String type)
|
void |
assignBond(int bondIndex,
char type)
|
void |
assignConnect(int index,
int index2)
|
void |
autoCalculate(int tokProperty)
|
int |
autoHbond(java.util.BitSet bsFrom,
java.util.BitSet bsTo)
|
void |
bindAction(java.lang.String desc,
java.lang.String name,
javax.vecmath.Point3f range1,
javax.vecmath.Point3f range2)
|
void |
calcBoundBoxDimensions(java.util.BitSet bs,
float scale)
|
float |
calcRotationRadius(java.util.BitSet bs)
|
(package private) float |
calcRotationRadius(javax.vecmath.Point3f center)
|
void |
calcSelectedGroupsCount()
|
void |
calcSelectedMoleculesCount()
|
void |
calcSelectedMonomersCount()
|
javax.vecmath.Vector3f |
calculateMolecularDipole()
|
java.lang.String |
calculatePointGroup()
|
void |
calculateStraightness()
|
java.lang.String |
calculateStructures(java.util.BitSet bsAtoms,
boolean asDSSP,
boolean setStructure)
|
int |
calculateStruts(java.util.BitSet bs1,
java.util.BitSet bs2)
|
javax.vecmath.Point3f[] |
calculateSurface(java.util.BitSet bsSelected,
float envelopeRadius)
|
java.lang.String |
cd(java.lang.String dir)
|
(package private) void |
centerAt(int x,
int y,
javax.vecmath.Point3f pt)
|
boolean |
checkAutoBondLegacy()
|
void |
checkCoordinatesChanged()
|
boolean |
checkHalt(java.lang.String str,
boolean isInterrupt)
|
private void |
checkMinimization()
|
(package private) Token |
checkObjectClicked(int x,
int y,
int modifiers)
|
(package private) void |
checkObjectDragged(int prevX,
int prevY,
int x,
int y,
int action)
|
(package private) boolean |
checkObjectHovered(int x,
int y)
|
boolean |
checkPrivateKey(double privateKey)
Simple method to ensure that the image creator (which writes files) was in fact opened by this viewer and not by some manipulation of the applet. |
boolean |
checkResume(java.lang.String str)
|
private java.lang.String |
checkScriptExecution(java.lang.String strScript,
boolean isInterrupt)
|
boolean |
checkStepping(java.lang.String str)
|
private boolean |
checkUndo(java.lang.String str)
|
void |
clearAllMeasurements()
|
private void |
clearAtomSets()
|
void |
clearBfactorRange()
|
(package private) void |
clearClickCount()
|
void |
clearConsole()
|
void |
clearFunctions()
|
void |
clearMeasurements()
|
(package private) void |
clearMinimization()
|
private void |
clearModelDependentObjects()
|
void |
clearScriptQueue()
|
void |
clearSelection()
|
void |
clearShapeRenderers()
|
void |
clearTimeout(java.lang.String name)
|
java.lang.String |
clipImage(java.lang.String text)
|
void |
connect(float[][] connections)
|
java.lang.Object |
createImage(java.lang.String fileName,
java.lang.String type,
java.lang.Object text_or_bytes,
int quality,
int width,
int height)
|
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,
java.lang.String[] fullPath)
from eval write command only includes option to write set of files |
java.lang.Object |
createImage(java.lang.String fileName,
java.lang.String type,
java.lang.Object text_or_bytes,
int quality,
int width,
int height,
java.lang.String[] fullPath)
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 |
private java.lang.Object |
createImage(java.lang.String fileName,
java.lang.String type,
java.lang.Object text_or_bytes,
int quality,
int width,
int height,
java.lang.String[] fullPath,
boolean doCheck)
|
private java.lang.String |
createModelSetAndReturnError(java.lang.Object atomSetCollection,
boolean isAppend,
java.lang.StringBuffer loadScript)
finally(!) we are ready to create the "model set" from the "atom set collection" |
int |
deleteAtoms(java.util.BitSet bs,
boolean fullModels)
|
void |
deleteBonds(java.util.BitSet bsDeleted)
|
void |
deleteMeasurement(int i)
|
void |
deleteModelAtoms(int firstAtomIndex,
int nAtoms,
java.util.BitSet bsDeleted)
|
void |
deleteSavedState(java.lang.String saveName)
|
void |
deleteShapeAtoms(java.lang.Object[] value,
java.util.BitSet bs)
|
(package private) void |
depthByPixels(int pixels)
|
void |
depthToPercent(int percentDepth)
|
java.lang.String |
dialogAsk(java.lang.String type,
java.lang.String fileName)
|
void |
display(java.util.BitSet bs,
boolean isQuiet)
|
(package private) void |
echoMessage(java.lang.String msg)
|
boolean |
eval(ScriptContext context,
ShapeManager shapeManager)
|
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)
|
void |
excludeAtoms(java.util.BitSet bs,
boolean ignoreSubset)
|
void |
exitJmol()
|
void |
fillAtomData(AtomData atomData,
int mode)
|
protected void |
finalize()
|
(package private) void |
finalizeTransformParameters()
|
(package private) java.util.BitSet |
findAtomsInRectangle(java.awt.Rectangle rect)
|
int |
findNearestAtomIndex(int x,
int y)
|
int |
findNearestAtomIndex(int x,
int y,
boolean mustBeMovable)
|
java.lang.String |
fixInlineString(java.lang.String strModel,
char newLine)
|
java.lang.String |
formatText(java.lang.String text0)
|
boolean |
frankClicked(int x,
int y)
|
boolean |
frankClickedModelKit(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. |
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)
|
javax.vecmath.Point3f[] |
getAdditionalHydrogens(java.util.BitSet bsAtoms,
boolean doAll,
boolean justCarbon,
java.util.List vConnections)
|
(package private) java.util.List |
getAllAtomInfo(java.lang.Object atomExpression)
|
(package private) java.util.List |
getAllBondInfo(java.lang.Object atomExpression)
|
java.util.Hashtable |
getAllChainInfo(java.lang.Object atomExpression)
|
boolean |
getAllowEmbeddedScripts()
|
boolean |
getAllowGestures()
|
java.util.Hashtable |
getAllPolymerInfo(java.lang.Object atomExpression)
|
java.lang.String |
getAllSettings(java.lang.String prefix)
|
java.lang.String |
getAltLocListInModel(int modelIndex)
|
(package private) int |
getAnimationDirection()
|
int |
getAnimationFps()
|
(package private) java.util.Hashtable |
getAnimationInfo()
|
(package private) int |
getAnimationReplayMode()
|
boolean |
getAppendNew()
|
(package private) java.lang.String |
getAppletContext()
|
(package private) java.util.Hashtable |
getAppletInfo()
|
boolean |
getApplySymmetryToBonds()
|
int |
getAtomArgb(int i)
|
java.util.BitSet |
getAtomBits(int tokType,
java.lang.Object specInfo)
|
java.util.BitSet |
getAtomBitSet(java.lang.Object atomExpression)
|
(package private) java.util.BitSet |
getAtomBitSet(ScriptEvaluator eval,
java.lang.Object atomExpression)
|
(package private) java.util.List |
getAtomBitSetVector(java.lang.Object atomExpression)
|
(package private) java.lang.String |
getAtomChain(int i)
|
int |
getAtomCount()
|
int |
getAtomCountInModel(int modelIndex)
|
Quaternion[] |
getAtomGroupQuaternions(java.util.BitSet bsAtoms,
int nMax)
|
float[] |
getAtomicCharges()
|
float[] |
getAtomicPotentials(boolean isMep,
java.util.BitSet bsSelected,
java.util.BitSet bsIgnore,
java.lang.String fileName)
|
(package private) void |
getAtomicPropertyState(java.lang.StringBuffer commands,
byte type,
java.util.BitSet bs,
java.lang.String name,
float[] data)
|
void |
getAtomIdentityInfo(int atomIndex,
java.util.Hashtable info)
|
int |
getAtomIndexFromAtomNumber(int atomNumber)
|
int[] |
getAtomIndices(java.util.BitSet bs)
|
java.lang.String |
getAtomInfo(int atomOrPointIndex)
|
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)
|
java.util.List |
getAtomPointVector(java.util.BitSet bs)
|
Quaternion |
getAtomQuaternion(int i)
|
float |
getAtomRadius(int i)
|
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)
|
private java.lang.Object |
getAtomSetCollection(java.lang.String fileName,
boolean isAppend,
java.util.Hashtable htParams,
java.lang.StringBuffer loadScript)
|
float |
getAtomShapeValue(int tok,
Group group,
int atomIndex)
|
java.util.BitSet |
getAtomsWithin(float distance,
java.util.BitSet bs,
boolean withinAllModels)
|
java.util.BitSet |
getAtomsWithin(float distance,
javax.vecmath.Point3f coord)
|
java.util.BitSet |
getAtomsWithin(float distance,
javax.vecmath.Point4f plane)
|
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 |
getBfactor100Hi()
|
java.lang.String |
getBindingInfo(java.lang.String qualifiers)
|
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)
|
int |
getBondOrder(int i)
|
boolean |
getBondPicking()
|
javax.vecmath.Point3f |
getBondPoint3f1(int i)
|
javax.vecmath.Point3f |
getBondPoint3f2(int i)
|
float |
getBondRadius(int i)
|
boolean |
getBondSelectionModeOr()
|
java.util.BitSet |
getBondsForSelectedAtoms(java.util.BitSet bsAtoms)
|
float |
getBondTolerance()
|
boolean |
getBooleanProperty(java.lang.String key)
|
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()
|
javax.vecmath.Point3f[] |
getBoundBoxVertices()
|
BoxInfo |
getBoxInfo(java.util.BitSet bs,
float scale)
|
java.util.BitSet |
getBranchBitSet(int atomIndex,
int atomIndexNot)
|
java.io.BufferedInputStream |
getBufferedInputStream(java.lang.String fullPathName)
|
java.lang.Object |
getBufferedReaderOrErrorMessageFromName(java.lang.String name,
java.lang.String[] fullPathNameReturn,
boolean isBinary)
|
javax.vecmath.Point3f[] |
getCameraFactors()
|
boolean |
getCartoonBaseEdgesFlag()
|
boolean |
getCartoonRocketFlag()
|
javax.vecmath.Point3f[][] |
getCenterAndPoints(java.util.List atomSets,
boolean addCenter)
|
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)
|
java.util.BitSet |
getClickableSet()
|
(package private) short |
getColix(java.lang.Object object)
|
short |
getColixAtomPalette(Atom atom,
byte pid)
|
short |
getColixBackgroundContrast()
|
short |
getColixBondPalette(Bond bond,
byte pid)
|
short |
getColixForPropertyValue(float val)
|
short |
getColixRubberband()
|
int |
getColorArgbOrGray(short colix)
|
ColorEncoder |
getColorEncoder(java.lang.String colorScheme)
|
javax.vecmath.Point3f |
getColorPointForPropertyValue(float val)
|
java.lang.String |
getColorSchemeList(java.lang.String colorScheme)
|
java.util.BitSet |
getConformation(int iModel,
int conformationIndex,
boolean doSet)
|
java.util.Hashtable |
getContextVariables()
|
java.lang.String |
getCoordinateState(java.util.BitSet bsSelected)
|
float[] |
getCurrentColorRange()
|
java.lang.String |
getCurrentFileAsString()
|
int |
getCurrentModelIndex()
|
float |
getCurrentSolventProbeRadius()
|
SymmetryInterface |
getCurrentUnitCell()
|
int |
getCursor()
|
int |
getCursorX()
|
int |
getCursorY()
|
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)
|
float[][] |
getDataFloat2D(java.lang.String label)
|
float[][][] |
getDataFloat3D(java.lang.String label)
|
(package private) java.lang.String |
getDataSeparator()
|
boolean |
getDebugScript()
|
(package private) java.lang.String |
getDefaultDirectory()
|
float |
getDefaultDrawArrowScale()
|
javax.vecmath.Point3f |
getDefaultLattice()
|
java.lang.String |
getDefaultLoadFilter()
|
java.lang.String |
getDefaultLoadScript()
|
java.lang.String |
getDefaultMeasurementLabel(int nPoints)
|
RadiusData |
getDefaultRadiusData()
|
boolean |
getDefaultStructureDSSP()
|
float |
getDefaultTranslucent()
|
java.lang.String |
getDefaultVdwTypeNameOrData(int iMode)
|
int |
getDelayMaximum()
|
java.util.BitSet |
getDeletedAtoms()
|
float |
getDipoleScale()
|
(package private) boolean |
getDisablePopupMenu()
|
java.awt.Component |
getDisplay()
|
boolean |
getDisplayCellParameters()
|
int |
getDisplayModelIndex()
|
int |
getDotDensity()
|
int |
getDotScale()
|
boolean |
getDotsSelectedOnlyFlag()
|
boolean |
getDotSurfaceFlag()
|
boolean |
getDragSelected()
|
boolean |
getDrawHover()
|
boolean |
getDrawPicking()
|
boolean |
getDynamicMeasurements()
|
boolean |
getEchoStateActive()
|
java.lang.String[] |
getElectronDensityLoadInfo()
|
(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.Object |
getExecutor()
|
java.lang.String |
getExportDriverList()
|
java.lang.Object |
getFileAsBytes(java.lang.String pathName,
java.io.OutputStream os)
|
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()
|
java.lang.String[] |
getFileInfo()
|
java.lang.String |
getFileName()
|
private java.lang.String |
getFileNameFromDialog(java.lang.String fileName,
int quality)
|
java.lang.String |
getFilePath(java.lang.String name,
boolean asShortName)
|
Font3D |
getFont3D(java.lang.String fontFace,
java.lang.String fontStyle,
float fontSize)
|
boolean |
getFontCaching()
|
boolean |
getFontScaling()
|
boolean |
getForceAutoBond()
|
boolean |
getFractionalRelative()
|
java.util.BitSet |
getFrameOffsets()
|
java.lang.String |
getFrameTitle()
|
int |
getFrontPlane()
|
java.lang.String |
getFullPathName()
|
java.lang.String[] |
getFullPathNameOrError(java.lang.String filename)
|
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)
|
java.util.BitSet |
getGroupsWithin(int nResidues,
java.util.BitSet bs)
|
float |
getHbondsAngleMin()
|
boolean |
getHbondsBackbone()
|
float |
getHbondsDistanceMax()
|
boolean |
getHbondsRasmol()
|
boolean |
getHbondsSolid()
|
java.lang.Object |
getHelixData(java.util.BitSet bs,
int tokType)
|
int |
getHelixStep()
|
void |
getHelp(java.lang.String what)
|
int |
getHermiteLevel()
|
java.util.Hashtable |
getHeteroList(int modelIndex)
|
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)
|
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)
|
(package private) java.lang.Object |
getImageAs(java.lang.String type,
int quality,
int width,
int height,
java.lang.String fileName,
java.io.OutputStream os,
java.lang.String comment)
|
float |
getImageFontScaling()
|
char |
getInlineChar()
|
static void |
getInlineData(java.lang.StringBuffer loadScript,
java.lang.String strModel,
boolean isAppend)
|
boolean |
getInMotion()
|
java.lang.String |
getInterruptScript()
|
boolean |
getIsosurfacePropertySmoothing()
|
java.lang.String |
getJavaVendor()
|
java.lang.String |
getJavaVersion()
|
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()
|
boolean |
getJustifyMeasurements()
|
java.lang.String |
getLanguage()
|
float |
getLoadAtomDataTolerance()
|
(package private) java.lang.String |
getLoadState()
|
java.lang.String |
getLogFile()
|
boolean |
getLogGestures()
|
short |
getMadBond()
|
short |
getMarBond()
|
(package private) javax.vecmath.Matrix3f |
getMatrixRotate()
|
javax.vecmath.Matrix4f |
getMatrixtransform()
|
float |
getMaxZoomPercent()
|
boolean |
getMeasureAllModelsFlag()
|
java.lang.String |
getMeasureDistanceUnits()
|
int |
getMeasurementCount()
|
int[] |
getMeasurementCountPlusIndices(int i)
|
(package private) java.util.List |
getMeasurementInfo()
|
java.lang.String |
getMeasurementInfoAsString()
|
java.lang.String |
getMeasurementStringValue(int i)
|
java.lang.String |
getMenu(java.lang.String type)
|
(package private) java.lang.String |
getMenuName(int i)
|
java.util.Hashtable |
getMessageQueue()
|
boolean |
getMessageStyleChime()
|
float |
getMinBondDistance()
|
java.lang.String |
getMinimizationInfo()
|
MinimizerInterface |
getMinimizer(boolean createNew)
|
JmolAdapter |
getModelAdapter()
|
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)
|
java.lang.String |
getModelCml(java.util.BitSet bs,
int nAtomsMax,
boolean addBonds)
|
int |
getModelCount()
|
javax.vecmath.Vector3f |
getModelDipole()
|
java.lang.String |
getModelExtract(java.lang.Object atomExpression,
boolean doTransform,
boolean asSDF,
boolean asV3000)
|
java.lang.String |
getModelFileInfo()
|
java.lang.String |
getModelFileInfoAll()
|
java.lang.String |
getModelFileName(int modelIndex)
|
int |
getModelFileNumber(int modelIndex)
|
java.util.Hashtable |
getModelInfo(java.lang.Object atomExpression)
|
java.lang.String |
getModelInfoAsString()
|
boolean |
getModelkitMode()
|
(package private) java.util.BitSet |
getModelKitStateBitSet(java.util.BitSet bs,
java.util.BitSet bsDeleted)
|
java.lang.String |
getModelName(int modelIndex)
|
int |
getModelNumber(int modelIndex)
|
java.lang.String |
getModelNumberDotted(int modelIndex)
|
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)
|
java.util.BitSet |
getModelUndeletedAtomsBitSet(java.util.BitSet bsModels)
|
java.util.BitSet |
getModelUndeletedAtomsBitSet(int modelIndex)
|
SymmetryInterface |
getModelUnitCell(int modelIndex)
|
byte |
getModeMultipleBond()
|
java.lang.String |
getMoInfo(int modelIndex)
|
java.util.BitSet |
getMoleculeBitSet(int atomIndex)
|
(package private) java.util.List |
getMoleculeInfo(java.lang.Object atomExpression)
|
int |
getMotionEventNumber()
|
java.util.BitSet |
getMotionFixedAtoms()
|
boolean |
getMouseEnabled()
|
java.lang.Object |
getMouseInfo()
|
(package private) java.lang.String |
getMoveToText(float timespan)
|
float |
getMultipleBondRadiusFactor()
|
float |
getMultipleBondSpacing()
|
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()
|
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,
java.lang.String name)
|
ScriptVariable |
getOrSetNewVariable(java.lang.String key,
boolean doSet)
|
java.io.OutputStream |
getOutputStream(java.lang.String localName,
java.lang.String[] fullPath)
|
java.lang.Object |
getParameter(java.lang.String key)
|
java.lang.Object |
getParameterEscaped(java.lang.String key)
|
float[] |
getPartialCharges()
|
java.lang.String |
getPdbData(java.util.BitSet bs,
OutputStringBuffer sb)
|
java.lang.String |
getPdbData(int modelIndex,
java.lang.String type,
java.lang.Object[] parameters)
|
java.lang.String |
getPDBHeader()
|
(package private) MeasurementPending |
getPendingMeasurement()
|
int |
getPercentVdwAtom()
|
boolean |
getPerspectiveDepth()
|
int |
getPickingMode()
|
(package private) int |
getPickingSpinRate()
|
java.util.List |
getPlaneIntersection(int type,
javax.vecmath.Point4f plane,
float scale,
int flags)
|
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)
|
void |
getPolymerPointsAndVectors(java.util.BitSet bs,
java.util.List vList)
|
boolean |
getPreserveState()
This flag if set FALSE: 1) turns UNDO off for the application 2) turns history off 3) prevents saving of inlinedata for later LOAD "" commands 4) turns off the saving of changed atom properties 5) does not guarantee accurate state representation 6) disallows generation of the state It is useful in situations such as web sites where memory is an issue and there is no need for such. |
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()
|
java.lang.String |
getProteinStructureState()
|
char |
getQuaternionFrame()
|
boolean |
getRasmolSetting(int tok)
|
boolean |
getRefreshing()
|
int |
getRepaintWait()
|
int |
getRibbonAspectRatio()
|
boolean |
getRibbonBorder()
|
boolean |
getRocketBarrelFlag()
|
(package private) int |
getRotateBondIndex()
|
(package private) void |
getRotation(javax.vecmath.Matrix3f matrixRotation)
|
javax.vecmath.Point3f |
getRotationCenter()
|
Quaternion |
getRotationQuaternion()
|
float |
getRotationRadius()
|
(package private) java.awt.Rectangle |
getRubberBandSelection()
|
java.lang.String |
getSavedCoordinates(java.lang.String saveName)
|
java.lang.String |
getSavedOrienationText(java.lang.String name)
|
java.lang.String |
getSavedState(java.lang.String saveName)
|
java.lang.String |
getSavedStructure(java.lang.String saveName)
|
float |
getScalePixelsPerAngstrom(boolean asAntialiased)
|
int |
getScreenDim()
|
int |
getScreenHeight()
|
java.awt.Image |
getScreenImage(java.awt.Graphics g)
|
int |
getScreenWidth()
|
int |
getScriptDelay()
|
(package private) boolean |
getSelectAllModels()
|
AtomIndexIterator |
getSelectedAtomIterator(java.util.BitSet bsSelected,
boolean isGreaterOnly,
boolean modelZeroBased)
|
int |
getSelectionCount()
|
boolean |
getSelectionHaloEnabled()
|
java.util.BitSet |
getSelectionSet(boolean includeDeleted)
|
java.util.BitSet |
getSelectionSubset()
|
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; |
java.lang.String |
getShapeErrorState()
|
java.util.Hashtable |
getShapeInfo()
|
ShapeManager |
getShapeManager()
|
java.lang.Object |
getShapeProperty(int shapeType,
java.lang.String propertyName)
|
java.lang.Object |
getShapeProperty(int shapeType,
java.lang.String propertyName,
int index)
|
boolean |
getShapeProperty(int shapeType,
java.lang.String propertyName,
java.lang.Object[] data)
|
private int |
getShapePropertyAsInt(int shapeID,
java.lang.String propertyName)
|
void |
getShapeState(java.lang.StringBuffer commands,
boolean isAll)
|
float |
getSheetSmoothing()
|
boolean |
getShowAxes()
|
boolean |
getShowBbcage()
|
boolean |
getShowFrank()
|
boolean |
getShowHiddenSelectionHalos()
|
boolean |
getShowHydrogens()
|
boolean |
getShowMeasurementLabels()
|
boolean |
getShowMeasurements()
|
boolean |
getShowMultipleBonds()
|
boolean |
getShowNavigationPoint()
|
boolean |
getShowUnitCell()
|
boolean |
getSlabByAtom()
|
boolean |
getSlabByMolecule()
|
boolean |
getSlabEnabled()
|
int |
getSmallMoleculeMaxAtoms()
|
boolean |
getSmartAromatic()
|
java.util.BitSet |
getSmartsMatch(java.lang.String smarts,
java.util.BitSet bsSelected)
|
java.lang.String |
getSmiles(int index1,
int index2,
java.util.BitSet bsSelected,
boolean isBioSmiles,
boolean allowUnmatchedRings,
boolean addCrossLinks,
boolean addComment)
returns the SMILES string for a sequence or atom set |
SmilesMatcherInterface |
getSmilesMatcher()
|
(package private) boolean |
getSolventOn()
|
float |
getSolventProbeRadius()
|
java.util.Hashtable |
getSpaceGroupInfo(java.lang.String spaceGroup)
|
java.lang.String |
getSpecularState()
|
(package private) boolean |
getSpinOn()
|
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.util.List |
getStatusChanged(java.lang.String statusNameList)
|
private java.awt.Image |
getStereoImage(int stereoMode)
|
int |
getStrandCount(int type)
|
java.lang.String |
getStructureState()
|
float |
getStrutDefaultRadius()
|
float |
getStrutLengthMaximum()
|
boolean |
getStrutsMultiple()
|
int |
getStrutSpacingMinimum()
|
(package private) int |
getSurfaceDistanceMax()
|
SymmetryInterface |
getSymmetry()
|
java.lang.Object |
getSymmetryInfo(java.util.BitSet bsAtoms,
java.lang.String xyz,
int op,
javax.vecmath.Point3f pt,
javax.vecmath.Point3f pt2,
java.lang.String id,
int type)
|
java.lang.String |
getSymmetryInfoAsString()
|
java.lang.String |
getSymmetryOperation(java.lang.String spaceGroup,
int symop,
javax.vecmath.Point3f pt1,
javax.vecmath.Point3f pt2,
boolean labelOnly)
|
java.util.BitSet |
getTaintedAtoms(byte type)
|
boolean |
getTestFlag1()
|
boolean |
getTestFlag2()
|
boolean |
getTestFlag3()
|
boolean |
getTestFlag4()
|
boolean |
getTraceAlpha()
|
java.lang.String |
getTrajectoryInfo()
|
java.lang.String |
getTransformText()
|
java.lang.String |
getTranslationScript()
|
float |
getTranslationXPercent()
|
float |
getTranslationYPercent()
|
(package private) float |
getTranslationZPercent()
|
float |
getUnitCellInfo(int infoType)
|
java.lang.String |
getUnitCellInfoText()
|
javax.vecmath.Matrix4f |
getUnscaledTransformMatrix()
|
boolean |
getUseNumberLocalization()
|
int |
getVanderwaalsMar(int i)
|
int |
getVanderwaalsMar(int i,
int iType)
|
java.lang.String |
getVariableList()
|
float |
getVectorScale()
|
float |
getVibrationPeriod()
|
(package private) float |
getVibrationScale()
|
javax.vecmath.Vector3f |
getVibrationVector(int atomIndex)
|
java.util.BitSet |
getVisibleFramesBitSet()
|
java.util.BitSet |
getVisibleSet()
|
float |
getVolume(java.util.BitSet bs,
java.lang.String type)
|
boolean |
getWireframeRotation()
|
java.lang.String |
getWrappedState(boolean isImage)
|
java.lang.String |
getZapName()
|
boolean |
getZeroBasedXyzRasmol()
|
boolean |
getZoomEnabled()
|
(package private) boolean |
getZoomLarge()
|
int |
getZoomPercent()
|
float |
getZoomPercentFloat()
|
float |
getZoomSetting()
|
void |
haltScriptExecution()
|
void |
handleError(java.lang.Error er,
boolean doClear)
|
boolean |
handleOldJvm10Event(java.awt.Event e)
|
boolean |
hasCalculatedHBonds(java.util.BitSet bsAtoms)
|
boolean |
hasFocus()
|
boolean |
haveFileSet()
|
boolean |
haveFrame()
|
(package private) boolean |
haveModelKit()
|
(package private) boolean |
haveModelSet()
|
boolean |
havePartialCharges()
|
void |
hide(java.util.BitSet bs,
boolean isQuiet)
|
void |
highlight(java.util.BitSet bs)
|
void |
highlightBond(int index,
boolean isHover)
|
void |
homePosition()
|
(package private) void |
hoverOff()
|
(package private) void |
hoverOn(int atomIndex,
int action)
|
void |
hoverOn(int x,
int y,
java.lang.String text)
|
void |
initialize()
|
private void |
initializeModel()
|
void |
invertAtomCoord(javax.vecmath.Point3f pt,
java.util.BitSet bs)
|
void |
invertAtomCoord(javax.vecmath.Point4f plane,
java.util.BitSet bs)
|
void |
invertSelected(javax.vecmath.Point3f pt,
javax.vecmath.Point4f plane,
int iAtom,
java.util.BitSet invAtoms)
|
void |
invertSelection()
|
(package private) boolean |
isAnimationOn()
|
boolean |
isApplet()
|
(package private) boolean |
isAtomAssignable(int i)
|
(package private) boolean |
isAtomPDB(int i)
|
boolean |
isAtomSelected(int atomIndex)
|
boolean |
isBound(int action,
int gesture)
|
boolean |
isDataOnly()
|
boolean |
isFunction(java.lang.String name)
|
boolean |
isHoverEnabled()
|
boolean |
isInPosition(javax.vecmath.Vector3f axis,
float degrees)
|
(package private) boolean |
isInSelectionSubset(int atomIndex)
|
boolean |
isJmolDataFrame()
|
boolean |
isJmolDataFrame(int modelIndex)
|
boolean |
isJmolVariable(java.lang.String key)
|
(package private) boolean |
isKiosk()
|
boolean |
isModelKitMode()
|
boolean |
isNavigating()
|
boolean |
isParallel()
|
boolean |
isPdbSequential()
|
boolean |
isPreviewOnly()
|
boolean |
isRangeSelected()
|
(package private) boolean |
isRepaintPending()
|
boolean |
isScriptEditorVisible()
|
boolean |
isScriptExecuting()
|
boolean |
isSelected(int atomIndex)
|
boolean |
isSignedApplet()
|
(package private) boolean |
isStereoDouble()
|
boolean |
isTrajectory(int modelIndex)
|
boolean |
isVibrationOn()
|
boolean |
isWindowCentered()
|
private void |
jmolTest()
|
java.lang.String |
jsEval(java.lang.String strEval)
|
java.lang.String |
listSavedStates()
|
private java.lang.String |
loadAtomDataAndReturnError(java.lang.Object atomSetCollection,
int tokType)
or just apply the data to the current model set |
java.lang.String |
loadInline(java.util.List arrayData,
boolean isAppend)
does not preserver state, intentionally! |
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)
|
java.lang.String |
loadInline(java.lang.String strModel,
char newLine,
boolean isAppend,
java.util.Hashtable htParams)
|
java.lang.String |
loadModelFromFile(java.lang.String fullPathName,
java.lang.String fileName,
java.lang.String[] fileNames,
java.lang.Object reader,
boolean isAppend,
java.util.Hashtable htParams,
java.lang.StringBuffer loadScript,
int tokType)
Used by the ScriptEvaluator LOAD command to open one or more files. |
void |
loadShape(int shapeID)
|
void |
log(java.lang.String data)
|
boolean |
logCommands()
|
int[] |
makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
boolean isBonds,
float energy)
|
boolean |
menuEnabled()
|
void |
mergeShapes(Shape[] newShapes)
|
void |
minimize(int steps,
float crit,
java.util.BitSet bsSelected,
java.util.BitSet bsFixed,
float rangeFixed,
boolean addHydrogen,
boolean isSilent,
boolean asScript)
|
boolean |
modelHasVibrationVectors(int modelIndex)
|
(package private) boolean |
modelSetHasVibrationVectors()
|
void |
move(javax.vecmath.Vector3f dRot,
float dZoom,
javax.vecmath.Vector3f dTrans,
float dSlab,
float floatSecondsTotal,
int fps)
|
(package private) void |
moveAtomWithHydrogens(int atomIndex,
int deltaX,
int deltaY,
java.util.BitSet bsAtoms)
|
void |
moveSelected(int deltaX,
int deltaY,
int x,
int y,
java.util.BitSet bsSelected,
boolean isTranslation)
|
void |
moveTo(float floatSecondsTotal,
javax.vecmath.Point3f center,
javax.vecmath.Vector3f rotAxis,
float degrees,
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)
|
(package private) boolean |
mustRenderFlag()
|
void |
navigate(float timeSeconds,
javax.vecmath.Point3f center)
|
void |
navigate(float timeSeconds,
javax.vecmath.Point3f[][] pathGuide)
|
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)
|
void |
navigateSurface(float timeSeconds,
java.lang.String name)
|
void |
navTranslate(float timeSeconds,
javax.vecmath.Point3f center)
|
void |
navTranslatePercent(float timeSeconds,
float x,
float y)
|
void |
notifyError(java.lang.String errType,
java.lang.String errMsg,
java.lang.String errMsgUntranslated)
|
void |
notifyMinimizationStatus()
|
int |
notifyMouseClicked(int x,
int y,
int action,
int mode)
|
void |
notifyViewerRepaintDone()
|
java.lang.String |
openDOM(java.lang.Object DOMNode)
applet DOM method -- does not preserve state |
java.lang.String |
openFile(java.lang.String fileName)
for JmolSimpleViewer -- external applications only |
void |
openFileAsynchronously(java.lang.String fileName)
opens a file as a model, a script, or a surface via the creation of a script that is queued \t at the beginning disallows script option - used by JmolFileDropper and JmolPanel file-open actions - sets up a script to load the file |
java.lang.String |
openFiles(java.lang.String[] fileNames)
for JmolSimpleViewer -- external applications only |
java.lang.String |
openReader(java.lang.String fullPathName,
java.lang.String fileName,
java.io.Reader reader)
Opens the file, given an already-created reader. |
java.lang.String |
openStringInline(java.lang.String strModel)
|
private java.lang.String |
openStringInline(java.lang.String strModel,
java.util.Hashtable htParams,
boolean isAppend)
|
private java.lang.String |
openStringsInline(java.lang.String[] arrayModels,
java.util.Hashtable htParams,
boolean isAppend)
|
void |
pauseScriptExecution()
|
void |
popHoldRepaint()
|
void |
popHoldRepaint(java.lang.String why)
|
(package private) void |
popupMenu(int x,
int y,
char type)
|
java.lang.String |
prompt(java.lang.String label,
java.lang.String data,
java.lang.String[] list,
boolean asButtons)
|
void |
pushHoldRepaint()
|
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(boolean andStopMinimization)
|
void |
releaseScreenImage()
|
java.lang.String |
removeCommand()
Removes one command from the command history |
void |
removeSelectionListener(JmolSelectionListener listener)
|
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)
|
void |
requestRepaintAndWait()
|
void |
reset(boolean includingSpin)
|
void |
resetAromatic()
|
void |
resetBioshapes(java.util.BitSet bsAllAtoms)
|
void |
resetError()
|
void |
resetShapes()
|
private void |
resizeImage(int width,
int height,
boolean isImageWrite,
boolean isExport,
boolean isReset)
|
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)
|
boolean |
restoreSelection(java.lang.String saveName)
|
void |
resumeScriptExecution()
|
void |
rotateAboutPointsInternal(javax.vecmath.Point3f point1,
javax.vecmath.Point3f point2,
float degreesPerSecond,
float endDegrees,
boolean isSpin,
java.util.BitSet bsSelected,
javax.vecmath.Vector3f translation,
java.util.List finalPoints)
|
(package private) void |
rotateArcBall(int x,
int y,
float factor)
|
(package private) void |
rotateAtoms(javax.vecmath.Matrix3f mNew,
javax.vecmath.Matrix3f matrixRotate,
boolean fullMolecule,
javax.vecmath.Point3f center,
boolean isInternal,
java.util.BitSet bsAtoms)
|
void |
rotateAxisAngleAtCenter(javax.vecmath.Point3f rotCenter,
javax.vecmath.Vector3f rotAxis,
float degreesPerSecond,
float endDegrees,
boolean isSpin,
java.util.BitSet bsSelected)
|
void |
rotateFront()
|
(package private) void |
rotateMolecule(float deltaX,
float deltaY,
java.util.BitSet bsSelected)
|
void |
rotatePoint(javax.vecmath.Point3f pt,
javax.vecmath.Point3f ptRot)
|
void |
rotateX(float angleRadians)
|
void |
rotateX(int angleDegrees)
|
(package private) void |
rotateXYBy(float xDelta,
float yDelta)
|
void |
rotateY(float angleRadians)
|
void |
rotateY(int angleDegrees)
|
void |
rotateZ(float angleRadians)
|
void |
rotateZBy(int zDelta,
int x,
int y)
|
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)
|
void |
saveSelection(java.lang.String saveName)
|
void |
saveState(java.lang.String saveName)
|
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)
|
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)
|
java.lang.String |
scriptWait(java.lang.String strScript)
|
java.lang.Object |
scriptWaitStatus(java.lang.String strScript,
java.lang.String statusList)
|
void |
select(java.util.BitSet bs,
boolean isQuiet)
|
void |
selectAll()
|
void |
selectBonds(java.util.BitSet bs)
|
(package private) void |
setAllowRotateSelected(boolean TF)
|
void |
setAnimation(int tok)
|
void |
setAnimationDirection(int direction)
|
void |
setAnimationFps(int fps)
|
void |
setAnimationOn(boolean animationOn)
|
void |
setAnimationRange(int modelIndex1,
int modelIndex2)
|
void |
setAnimationReplayMode(int replay,
float firstFrameDelay,
float lastFrameDelay)
|
private void |
setAntialias(int mode,
boolean TF)
|
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)
|
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)
|
void |
setAtomCoordRelative(javax.vecmath.Tuple3f offset,
java.util.BitSet bs)
|
void |
setAtomData(int type,
java.lang.String name,
java.lang.String coordinateData,
boolean isDefault)
|
void |
setAtomLabel(java.lang.String value,
int i)
|
private void |
setAtomPickingOption(java.lang.String option)
|
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)
|
void |
setBackgroundImage(java.lang.String fileName,
java.awt.Image image)
|
void |
setBackgroundModelIndex(int modelIndex)
|
private void |
setBondPickingOption(java.lang.String option)
|
void |
setBondTolerance(float bondTolerance)
|
void |
setBooleanProperty(java.lang.String key,
boolean value)
|
private boolean |
setBooleanProperty(java.lang.String key,
int tok,
boolean value,
boolean defineNew)
|
void |
setBoundBox(javax.vecmath.Point3f pt1,
javax.vecmath.Point3f pt2,
boolean byCorner,
float scale)
|
void |
setCenterAt(java.lang.String relativeTo,
javax.vecmath.Point3f pt)
|
void |
setCenterBitSet(java.util.BitSet bsCenter,
boolean doScale)
|
void |
setCenterSelected()
|
void |
setColorBackground(java.lang.String colorName)
|
java.util.BitSet |
setConformation()
|
void |
setCurrentColorRange(float[] data,
java.util.BitSet bs)
|
void |
setCurrentColorRange(float min,
float max)
|
void |
setCurrentColorRange(java.lang.String label)
|
void |
setCurrentModelIndex(int modelIndex)
|
void |
setCurrentModelIndex(int modelIndex,
boolean clearBackground)
|
void |
setCurrentUnitCellOffset(int ijk)
|
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(boolean isRasmol)
|
void |
setDefaultLattice(javax.vecmath.Point3f ptLattice)
|
private void |
setDefaults(java.lang.String type)
|
(package private) void |
setDefaultVdw(java.lang.String type)
|
(package private) void |
setDynamicMeasurements(boolean TF)
|
void |
setEchoStateActive(boolean TF)
|
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)
|
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)
|
boolean |
setFloatProperty(java.lang.String key,
int tok,
float value,
boolean isInt)
|
void |
setFocus()
|
void |
setFormalCharges(int formalCharge)
|
(package private) void |
setFrameOffset(int modelIndex)
|
void |
setFrameOffsets(java.util.BitSet bsAtoms)
|
void |
setFrameTitle(int modelIndex,
java.lang.String title)
|
void |
setFrameTitle(java.lang.String title)
|
(package private) void |
setFrameVariables(int firstModelIndex,
int lastModelIndex)
|
void |
setFrankOn(boolean TF)
|
void |
setHoverLabel(java.lang.String strLabel)
|
(package private) void |
setInMotion(boolean inMotion)
|
void |
setIntProperty(java.lang.String key,
int value)
|
void |
setIntProperty(java.lang.String key,
int tok,
int value)
|
void |
setIteratorForAtom(AtomIndexIterator iterator,
int atomIndex,
float distance)
|
void |
setIteratorForPoint(AtomIndexIterator iterator,
int modelIndex,
javax.vecmath.Point3f pt,
float distance)
|
void |
setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
|
void |
setJmolDataFrame(java.lang.String type,
int modelIndex,
int dataIndex)
|
void |
setJmolDefaults()
|
void |
setJmolStatusListener(JmolStatusListener jmolStatusListener)
|
java.lang.Object |
setLoadFormat(java.lang.String name,
char type,
boolean withPrefix)
|
private java.util.Hashtable |
setLoadParameters(java.util.Hashtable htParams,
boolean isAppend)
|
private java.lang.String |
setLogFile(java.lang.String value)
|
void |
setMarBond(short marBond)
|
private void |
setMaximumSize(int x)
|
void |
setMeasureDistanceUnits(java.lang.String units)
|
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)
|
private void |
setModelKitMode(boolean value)
|
void |
setModelVisibility()
|
void |
setModeMouse(int modeMouse)
|
void |
setMotionFixedAtoms(java.util.BitSet bs)
|
void |
setMouseEnabled(boolean TF)
|
void |
setNavigationDepthPercent(float timeSec,
float percent)
|
private void |
setNavigationMode(boolean TF)
|
void |
setNavOn(boolean navOn)
|
void |
setNavXYZ(float x,
float y,
float z)
|
void |
setNewRotationCenter(javax.vecmath.Point3f center)
|
void |
setNoneSelected(boolean noneSelected)
|
void |
setObjectArgb(java.lang.String name,
int argb)
|
(package private) void |
setObjectColor(java.lang.String name,
java.lang.String colorName)
|
void |
setObjectMad(int iShape,
java.lang.String name,
int mad)
|
boolean |
setParallel(boolean TF)
|
void |
setPdbConectBonding(boolean isAuto)
|
(package private) void |
setPendingMeasurement(MeasurementPending measurementPending)
|
void |
setPercentVdwAtom(int value)
|
void |
setPerspectiveDepth(boolean perspectiveDepth)
|
private void |
setPerspectiveModel(int mode)
|
(package private) void |
setPickingMode(java.lang.String strMode,
int pickingMode)
|
(package private) void |
setPickingStyle(java.lang.String style,
int pickingStyle)
|
void |
setPropertyColorScheme(java.lang.String scheme,
boolean isTranslucent,
boolean isOverloaded)
|
void |
setProteinType(byte iType,
java.util.BitSet bs)
|
void |
setRasmolDefaults()
|
private void |
setRefreshing(boolean TF)
|
(package private) void |
setRotateBondIndex(int index)
|
(package private) void |
setRotationMatrix(javax.vecmath.Matrix3f rotationMatrix)
|
void |
setRotationRadius(float angstroms,
boolean doAll)
|
void |
setRubberbandArgb(int argb)
|
void |
setScreenDimension(java.awt.Dimension dim)
|
private void |
setScriptQueue(boolean TF)
|
void |
setSelectedAtom(int atomIndex,
boolean TF)
|
void |
setSelectionHalos(boolean TF)
|
void |
setSelectionSet(java.util.BitSet set)
|
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)
|
void |
setShapeSize(int shapeID,
int mad,
java.util.BitSet bsSelected)
|
void |
setShapeSize(int shapeID,
RadiusData rd,
java.util.BitSet bsAtoms)
|
void |
setShowAxes(boolean value)
|
void |
setShowBbcage(boolean value)
|
void |
setShowHydrogens(boolean TF)
|
void |
setShowMeasurements(boolean TF)
|
void |
setShowUnitCell(boolean value)
|
void |
setSlabDepthInternal(boolean isDepth)
|
void |
setSmilesString(java.lang.String s)
|
void |
setSpin(java.lang.String key,
int value)
|
void |
setSpinOn(boolean spinOn)
|
void |
setStateScriptVersion(java.lang.String version)
|
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,
float value)
|
void |
setStatusResized(int width,
int height)
|
void |
setStereoMode(int[] twoColors,
int stereoMode,
float degrees)
|
private void |
setStrandCount(int type,
int value)
|
void |
setStringProperty(java.lang.String key,
int tok,
java.lang.String 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)
|
void |
setTainted(boolean TF)
|
void |
setTaintedAtoms(java.util.BitSet bs,
byte type)
|
void |
setTimeout(java.lang.String name,
int mSec,
java.lang.String script)
|
void |
setTrajectory(java.util.BitSet bsModels)
|
(package private) void |
setTrajectory(int modelIndex)
|
void |
setTransformManager(TransformManager transformManager)
for an external application |
private void |
setTransformManagerDefaults()
|
void |
setUserScale(int[] scale)
|
ScriptVariable |
setUserVariable(java.lang.String name,
ScriptVariable value)
|
void |
setVectorScale(float scale)
|
void |
setVibrationOff()
|
void |
setVibrationPeriod(float period)
|
void |
setVibrationScale(float scale)
|
void |
showConsole(boolean showConsole)
|
(package private) void |
showEditor(java.lang.String[] file_text)
|
void |
showMessage(java.lang.String s)
|
boolean |
showModelSetDownload()
|
void |
showParameter(java.lang.String key,
boolean ifNotSet,
int nMax)
|
void |
showString(java.lang.String str,
boolean isPrint)
|
java.lang.String |
showTimeout(java.lang.String name)
|
void |
showUrl(java.lang.String urlString)
|
(package private) void |
slabByPixels(int pixels)
|
(package private) void |
slabDepthByPixels(int pixels)
|
void |
slabInternal(javax.vecmath.Point4f plane,
boolean isDepth)
|
void |
slabReset()
|
void |
slabToPercent(int percentSlab)
|
void |
spinXYBy(int xDelta,
int yDelta,
float speed)
|
void |
startSpinningAxis(javax.vecmath.Point3f pt1,
javax.vecmath.Point3f pt2,
boolean isClockwise)
|
void |
stepScriptExecution()
|
private void |
stopAnimationThreads(java.lang.String fromWhere)
|
(package private) void |
stopMinimization()
|
void |
stopMotion()
|
java.lang.String |
streamFileData(java.lang.String fileName,
java.lang.String type,
java.lang.String type2,
int modelIndex,
java.lang.Object[] parameters)
|
void |
syncScript(java.lang.String script,
java.lang.String applet)
|
void |
toCartesian(javax.vecmath.Point3f pt,
boolean asAbsolute)
absolute or relative to origin of UNITCELL {x y z} |
void |
toFractional(javax.vecmath.Point3f pt,
boolean asAbsolute)
absolute or relative to origin of UNITCELL {x y z} |
void |
togglePickingLabel(java.util.BitSet bs)
|
void |
toUnitCell(javax.vecmath.Point3f pt,
javax.vecmath.Point3f offset)
relative to origin without regard to UNITCELL {x y z} |
java.util.BitSet |
transformAtoms(boolean firstPass)
|
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)
|
void |
translate(char xyz,
float x,
char type,
java.util.BitSet bsAtoms)
|
void |
translateXYBy(int xDelta,
int yDelta)
|
void |
unBindAction(java.lang.String desc,
java.lang.String name)
|
(package private) void |
undoAction(boolean isSave,
int taintedAtom,
int type)
|
float |
unscaleToScreen(float z,
float screenDistance)
|
void |
unsetProperty(java.lang.String name)
|
void |
unTransformPoint(javax.vecmath.Point3f pointScreen,
javax.vecmath.Point3f pointAngstroms)
|
(package private) boolean |
useArcBall()
|
boolean |
useMinimizationThread()
|
boolean |
usingScriptQueue()
|
boolean |
waitForMoveTo()
|
java.lang.String |
writeCurrentFile(java.io.OutputStream os)
|
void |
writeTextFile(java.lang.String fileName,
java.lang.String data)
|
void |
zap(boolean notify,
boolean resetUndo,
boolean zapModelKit)
|
private void |
zap(java.lang.String msg)
|
(package private) void |
zoomBy(int pixels)
|
(package private) void |
zoomByFactor(float factor,
int x,
int y)
|
int |
zValueFromPercent(int zPercent)
|
Methods inherited from class org.jmol.api.JmolViewer |
---|
allocateViewer, checkOption, getBooleanProperty, getScreenImage |
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
public ScriptCompiler compiler
public java.util.Hashtable definedAtomSets
private SymmetryInterface symmetry
private SmilesMatcherInterface smilesMatcher
ScriptEvaluator eval
private AnimationManager animationManager
private DataManager dataManager
private FileManager fileManager
private ActionManager actionManager
private ShapeManager shapeManager
private ModelManager modelManager
private ModelSet modelSet
private MouseManager14 mouseManager
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 java.lang.String logFilePath
private boolean multiTouch
private boolean isSilent
private boolean isApplet
private boolean isPreviewOnly
public boolean haveDisplay
public boolean autoExit
private boolean mustRender
private boolean isPrintOnly
private boolean isCmdLine_C_Option
private boolean isCmdLine_c_or_C_Option
private boolean listCommands
private boolean useCommandThread
private boolean isSignedApplet
private boolean isSignedAppletLocal
private boolean isDataOnly
private java.lang.String appletContext
private boolean mouseEnabled
private boolean noneSelected
private static final int FILE_STATUS_CREATING_MODELSET
public static final java.lang.String STATE_VERSION_STAMP
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
boolean hoverEnabled
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
public static final int CURSOR_ZOOM
private int currentCursor
int prevFrame
private java.lang.String language
private RadiusData rd
private boolean frankOn
private boolean scriptEditorVisible
JmolAppConsoleInterface appConsole
JmolScriptEditorInterface scriptEditor
JmolPopup jmolpopup
JmolModelKitInterface modelkit
boolean isTainted
private boolean movingSelected
private boolean showSelected
private int rotateBondIndex
private int rotatePrev1
private int rotatePrev2
private java.util.BitSet bsRotateBranch
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
private double privateKey
private java.lang.String logFile
private boolean isKiosk
private MinimizerInterface minimizer
private java.lang.Object executor
public static int nProcessors
boolean displayLoadErrors
boolean isParallel
private static final int MAX_ACTION_UNDO
private final java.util.List actionStates
private final java.util.List actionStatesRedo
private int lastUndoRedo
private int stateScriptVersionInt
Constructor Detail |
---|
private Viewer(java.awt.Component display, JmolAdapter modelAdapter, java.lang.String commandOptions)
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
public SymmetryInterface getSymmetry()
public java.lang.Object getSymmetryInfo(java.util.BitSet bsAtoms, java.lang.String xyz, int op, javax.vecmath.Point3f pt, javax.vecmath.Point3f pt2, java.lang.String id, int type)
private void clearModelDependentObjects()
public SmilesMatcherInterface getSmilesMatcher()
public java.util.BitSet getSmartsMatch(java.lang.String smarts, java.util.BitSet bsSelected)
getSmartsMatch
in class JmolViewer
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 boolean isApplet()
isApplet
in class JmolViewer
public boolean isPreviewOnly()
java.lang.String getAppletContext()
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()
java.lang.String getHtmlName()
boolean mustRenderFlag()
public java.awt.Component getDisplay()
getDisplay
in class JmolViewer
public boolean handleOldJvm10Event(java.awt.Event e)
handleOldJvm10Event
in class JmolViewer
public void reset(boolean includingSpin)
public void homePosition()
homePosition
in class JmolViewer
java.util.Hashtable getAppletInfo()
public void initialize()
public 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()
public java.lang.String getSavedOrienationText(java.lang.String name)
void restoreModelOrientation(int modelIndex)
void restoreModelRotation(int modelIndex)
public void saveBonds(java.lang.String saveName)
public boolean restoreBonds(java.lang.String saveName)
public void saveState(java.lang.String saveName)
public void deleteSavedState(java.lang.String saveName)
public java.lang.String getSavedState(java.lang.String saveName)
public void saveStructure(java.lang.String saveName)
public java.lang.String getSavedStructure(java.lang.String saveName)
public void saveCoordinates(java.lang.String saveName, java.util.BitSet bsSelected)
public java.lang.String getSavedCoordinates(java.lang.String saveName)
public void saveSelection(java.lang.String saveName)
public boolean restoreSelection(java.lang.String saveName)
public javax.vecmath.Matrix4f getMatrixtransform()
public Quaternion getRotationQuaternion()
public float getRotationRadius()
getRotationRadius
in class JmolViewer
public void setRotationRadius(float angstroms, boolean doAll)
public javax.vecmath.Point3f getRotationCenter()
public void setCenterAt(java.lang.String relativeTo, javax.vecmath.Point3f pt)
public void setCenterBitSet(java.util.BitSet bsCenter, boolean doScale)
public 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()
public boolean isInPosition(javax.vecmath.Vector3f axis, float degrees)
public void move(javax.vecmath.Vector3f dRot, float dZoom, javax.vecmath.Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps)
public boolean waitForMoveTo()
public void stopMotion()
void setRotationMatrix(javax.vecmath.Matrix3f rotationMatrix)
public void moveTo(float floatSecondsTotal, javax.vecmath.Point3f center, javax.vecmath.Vector3f rotAxis, float degrees, 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)
public void navigate(float timeSeconds, javax.vecmath.Point3f[] path, float[] theta, int indexStart, int indexEnd)
public void navigate(float timeSeconds, javax.vecmath.Point3f center)
public void navigate(float timeSeconds, javax.vecmath.Point3f[][] pathGuide)
public void navigateSurface(float timeSeconds, java.lang.String name)
public void navigate(float timeSeconds, javax.vecmath.Vector3f rotAxis, float degrees)
public void navTranslate(float timeSeconds, javax.vecmath.Point3f center)
public void navTranslatePercent(float timeSeconds, float x, float y)
public void setMouseEnabled(boolean TF)
void zoomBy(int pixels)
void zoomByFactor(float factor, int x, int y)
void rotateXYBy(float xDelta, float yDelta)
public void spinXYBy(int xDelta, int yDelta, float speed)
public void rotateZBy(int zDelta, int x, int y)
void rotateMolecule(float deltaX, float deltaY, java.util.BitSet bsSelected)
public void translateXYBy(int xDelta, int yDelta)
void centerAt(int x, int y, javax.vecmath.Point3f pt)
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
public void translate(char xyz, float x, char type, java.util.BitSet bsAtoms)
public float getTranslationXPercent()
public float getTranslationYPercent()
float getTranslationZPercent()
public java.lang.String getTranslationScript()
public int getZoomPercent()
getZoomPercent
in class JmolViewer
public float getZoomSetting()
public float getZoomPercentFloat()
getZoomPercentFloat
in class JmolViewer
public float getMaxZoomPercent()
public void slabReset()
public boolean getZoomEnabled()
public boolean getSlabEnabled()
public boolean getSlabByMolecule()
public boolean getSlabByAtom()
void slabByPixels(int pixels)
void depthByPixels(int pixels)
void slabDepthByPixels(int pixels)
public void slabToPercent(int percentSlab)
public void slabInternal(javax.vecmath.Point4f plane, boolean isDepth)
public void depthToPercent(int percentDepth)
public 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(float z, float screenDistance)
public float scaleToPerspective(int z, float sizeAngstroms)
public void setSpin(java.lang.String key, int value)
public java.lang.String getSpinState()
public void setSpinOn(boolean spinOn)
boolean getSpinOn()
public void setNavOn(boolean navOn)
boolean getNavOn()
public void setNavXYZ(float x, float y, float z)
public java.lang.String getOrientationText(int type, java.lang.String name)
java.util.Hashtable getOrientationInfo()
javax.vecmath.Matrix3f getMatrixRotate()
public void getAxisAngle(javax.vecmath.AxisAngle4f axisAngle)
public java.lang.String getTransformText()
void getRotation(javax.vecmath.Matrix3f matrixRotation)
public float[] getCurrentColorRange()
private void setDefaultColors(boolean isRasmol)
public float getDefaultTranslucent()
public int getColorArgbOrGray(short colix)
public void setRubberbandArgb(int argb)
public short getColixRubberband()
public void setElementArgb(int elementNumber, int argb)
public float getVectorScale()
public void setVectorScale(float scale)
setVectorScale
in class JmolViewer
public float getDefaultDrawArrowScale()
float getVibrationScale()
public float getVibrationPeriod()
public boolean isVibrationOn()
public void setVibrationScale(float scale)
setVibrationScale
in class JmolViewer
public void setVibrationOff()
public void setVibrationPeriod(float period)
setVibrationPeriod
in class JmolViewer
void setObjectColor(java.lang.String name, java.lang.String colorName)
public void setObjectArgb(java.lang.String name, int argb)
public 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
public void setObjectMad(int iShape, java.lang.String name, int mad)
public int getObjectMad(int objId)
public void setPropertyColorScheme(java.lang.String scheme, boolean isTranslucent, boolean isOverloaded)
public java.lang.String getPropertyColorScheme()
public short getColixBackgroundContrast()
public java.lang.String getSpecularState()
public short getColixAtomPalette(Atom atom, byte pid)
public short getColixBondPalette(Bond bond, byte pid)
public java.lang.String getColorSchemeList(java.lang.String colorScheme)
public void setUserScale(int[] scale)
public short getColixForPropertyValue(float val)
public javax.vecmath.Point3f getColorPointForPropertyValue(float val)
public void select(java.util.BitSet bs, boolean isQuiet)
public void setSelectionSet(java.util.BitSet set)
setSelectionSet
in class JmolViewer
public void selectBonds(java.util.BitSet bs)
public void hide(java.util.BitSet bs, boolean isQuiet)
public void display(java.util.BitSet bs, boolean isQuiet)
public 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
public void setNoneSelected(boolean noneSelected)
public java.lang.Boolean getNoneSelected()
public void clearSelection()
clearSelection
in class JmolViewer
public void setSelectionSubset(java.util.BitSet subset)
public java.util.BitSet getSelectionSubset()
public void invertSelection()
public java.util.BitSet getSelectionSet(boolean includeDeleted)
public void setSelectedAtom(int atomIndex, boolean TF)
public boolean isAtomSelected(int atomIndex)
public int getSelectionCount()
getSelectionCount
in class JmolViewer
public 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(ScriptEvaluator eval, java.lang.Object atomExpression)
public java.util.BitSet getAtomBitSet(java.lang.Object atomExpression)
java.util.List getAtomBitSetVector(java.lang.Object atomExpression)
public void setModeMouse(int modeMouse)
setModeMouse
in class JmolViewer
java.awt.Rectangle getRubberBandSelection()
public boolean isBound(int action, int gesture)
public int getCursorX()
public int getCursorY()
java.lang.String getDefaultDirectory()
public java.io.BufferedInputStream getBufferedInputStream(java.lang.String fullPathName)
getBufferedInputStream
in interface AtomDataServer
public java.lang.Object getBufferedReaderOrErrorMessageFromName(java.lang.String name, java.lang.String[] fullPathNameReturn, boolean isBinary)
private java.util.Hashtable setLoadParameters(java.util.Hashtable htParams, boolean isAppend)
public void openFileAsynchronously(java.lang.String fileName)
openFileAsynchronously
in class JmolViewer
fileName
- public java.lang.String openFile(java.lang.String fileName)
openFile
in class JmolSimpleViewer
fileName
-
public java.lang.String openFiles(java.lang.String[] fileNames)
openFiles
in class JmolSimpleViewer
fileNames
-
public java.lang.String openReader(java.lang.String fullPathName, java.lang.String fileName, java.io.Reader reader)
openReader
in class JmolViewer
fullPathName
- fileName
- reader
-
public java.lang.String openDOM(java.lang.Object DOMNode)
openDOM
in class JmolSimpleViewer
DOMNode
-
public java.lang.String loadModelFromFile(java.lang.String fullPathName, java.lang.String fileName, java.lang.String[] fileNames, java.lang.Object reader, boolean isAppend, java.util.Hashtable htParams, java.lang.StringBuffer loadScript, int tokType)
fullPathName
- TODOfileName
- fileNames
- reader
- TODOisAppend
- htParams
- loadScript
- tokType
-
private java.lang.Object getAtomSetCollection(java.lang.String fileName, boolean isAppend, java.util.Hashtable htParams, java.lang.StringBuffer loadScript)
fileName
- isAppend
- htParams
- loadScript
- only necessary for string reading
public java.lang.String openStringInline(java.lang.String strModel)
openStringInline
in class JmolSimpleViewer
public java.lang.String loadInline(java.lang.String strModel)
loadInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String strModel, char newLine)
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[] arrayModels)
loadInline
in class JmolViewer
public java.lang.String loadInline(java.lang.String[] arrayModels, boolean isAppend)
loadInline
in class JmolViewer
arrayModels
- and array of models, each of which is a String
public java.lang.String loadInline(java.util.List arrayData, boolean isAppend)
loadInline
in class JmolViewer
arrayData
- isAppend
-
public java.lang.String loadInline(java.lang.String strModel, char newLine, boolean isAppend, java.util.Hashtable htParams)
public java.lang.String fixInlineString(java.lang.String strModel, char newLine)
private java.lang.String openStringInline(java.lang.String strModel, java.util.Hashtable htParams, boolean isAppend)
private java.lang.String openStringsInline(java.lang.String[] arrayModels, java.util.Hashtable htParams, boolean isAppend)
public char getInlineChar()
java.lang.String getDataSeparator()
private java.lang.String createModelSetAndReturnError(java.lang.Object atomSetCollection, boolean isAppend, java.lang.StringBuffer loadScript)
atomSetCollection
- isAppend
- loadScript
-
private java.lang.String loadAtomDataAndReturnError(java.lang.Object atomSetCollection, int tokType)
atomSetCollection
- tokType
-
public java.lang.String writeCurrentFile(java.io.OutputStream os)
public java.lang.Object getFileAsBytes(java.lang.String pathName, java.io.OutputStream os)
getFileAsBytes
in class JmolViewer
public java.lang.String getCurrentFileAsString()
public java.lang.String getFullPathName()
public java.lang.String getFileName()
public java.lang.String[] getFullPathNameOrError(java.lang.String filename)
filename
-
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 getFilePath(java.lang.String name, boolean asShortName)
public boolean getFileAsString(java.lang.String[] data, int nBytesMax, boolean doSpecialLoad)
getFileAsString
in class JmolViewer
public java.lang.String[] getFileInfo()
public void setFileInfo(java.lang.String[] fileInfo)
public void autoCalculate(int tokProperty)
public float getVolume(java.util.BitSet bs, java.lang.String type)
int getSurfaceDistanceMax()
public void calculateStraightness()
public javax.vecmath.Point3f[] calculateSurface(java.util.BitSet bsSelected, float envelopeRadius)
public boolean getDefaultStructureDSSP()
public java.lang.String calculateStructures(java.util.BitSet bsAtoms, boolean asDSSP, boolean setStructure)
public AtomIndexIterator getSelectedAtomIterator(java.util.BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)
getSelectedAtomIterator
in interface AtomDataServer
public void setIteratorForAtom(AtomIndexIterator iterator, int atomIndex, float distance)
setIteratorForAtom
in interface AtomDataServer
public void setIteratorForPoint(AtomIndexIterator iterator, int modelIndex, javax.vecmath.Point3f pt, float distance)
setIteratorForPoint
in interface AtomDataServer
public void fillAtomData(AtomData atomData, int mode)
fillAtomData
in interface AtomDataServer
public ModelCollection.StateScript addStateScript(java.lang.String script, boolean addFrameNumber, boolean postDefinitions)
public 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()
public void setEchoStateActive(boolean TF)
public void zap(boolean notify, boolean resetUndo, boolean zapModelKit)
private void zap(java.lang.String msg)
void echoMessage(java.lang.String msg)
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 float getUnitCellInfo(int infoType)
public java.util.Hashtable getSpaceGroupInfo(java.lang.String spaceGroup)
public void getPolymerPointsAndVectors(java.util.BitSet bs, java.util.List 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()
public void clearBfactorRange()
public java.lang.String getHybridizationAndAxes(int atomIndex, javax.vecmath.Vector3f z, javax.vecmath.Vector3f x, java.lang.String lcaoType)
public java.util.BitSet getMoleculeBitSet(int atomIndex)
public java.util.BitSet getModelUndeletedAtomsBitSet(int modelIndex)
public java.util.BitSet getModelUndeletedAtomsBitSet(java.util.BitSet bsModels)
public void excludeAtoms(java.util.BitSet bs, boolean ignoreSubset)
public java.util.BitSet getModelBitSet(java.util.BitSet atomList, boolean allTrajectories)
public ModelSet getModelSet()
public java.lang.String getBoundBoxCommand(boolean withOptions)
public void setBoundBox(javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, boolean byCorner, float scale)
public javax.vecmath.Point3f getBoundBoxCenter()
javax.vecmath.Point3f getAverageAtomPoint()
public void calcBoundBoxDimensions(java.util.BitSet bs, float scale)
public BoxInfo getBoxInfo(java.util.BitSet bs, float scale)
float calcRotationRadius(javax.vecmath.Point3f center)
public float calcRotationRadius(java.util.BitSet bs)
public javax.vecmath.Vector3f getBoundBoxCornerVector()
public javax.vecmath.Point3f[] getBoundBoxVertices()
java.util.Hashtable getBoundBoxInfo()
public java.util.BitSet getBoundBoxModels()
public int getBoundBoxCenterX()
public int getBoundBoxCenterY()
public int getModelCount()
getModelCount
in class JmolViewer
public java.lang.String getModelInfoAsString()
public java.lang.String getSymmetryInfoAsString()
public java.lang.String getSymmetryOperation(java.lang.String spaceGroup, int symop, javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, boolean labelOnly)
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()
public 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
public 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
public java.util.BitSet getBondsForSelectedAtoms(java.util.BitSet bsAtoms)
public boolean frankClicked(int x, int y)
public boolean frankClickedModelKit(int x, int y)
public int findNearestAtomIndex(int x, int y)
findNearestAtomIndex
in class JmolViewer
public int findNearestAtomIndex(int x, int y, boolean mustBeMovable)
java.util.BitSet findAtomsInRectangle(java.awt.Rectangle rect)
public void toCartesian(javax.vecmath.Point3f pt, boolean asAbsolute)
pt
- asAbsolute
- TODOpublic void toFractional(javax.vecmath.Point3f pt, boolean asAbsolute)
pt
- asAbsolute
- TODOpublic void toUnitCell(javax.vecmath.Point3f pt, javax.vecmath.Point3f offset)
pt
- offset
- public void setCurrentUnitCellOffset(int ijk)
public void setCurrentUnitCellOffset(javax.vecmath.Point3f pt)
public boolean getFractionalRelative()
public void addUnitCellOffset(javax.vecmath.Point3f pt)
public void setAtomData(int type, java.lang.String name, java.lang.String coordinateData, boolean isDefault)
public void setCenterSelected()
setCenterSelected
in class JmolViewer
public boolean getApplySymmetryToBonds()
void setApplySymmetryToBonds(boolean TF)
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
public int[] getAtomIndices(java.util.BitSet bs)
public java.util.BitSet getAtomBits(int tokType, java.lang.Object specInfo)
public java.util.BitSet getSequenceBits(java.lang.String specInfo, java.util.BitSet bs)
public java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point3f coord)
public java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point4f plane)
public java.util.BitSet getAtomsWithin(float distance, java.util.BitSet bs, boolean withinAllModels)
public java.util.BitSet getAtomsConnected(float min, float max, int intType, java.util.BitSet bs)
public java.util.BitSet getBranchBitSet(int atomIndex, int atomIndexNot)
public 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
public java.util.BitSet getVisibleSet()
public java.util.BitSet getClickableSet()
public void calcSelectedGroupsCount()
public void calcSelectedMonomersCount()
public void calcSelectedMoleculesCount()
java.lang.String getFileHeader()
java.lang.Object getFileData()
public java.util.Hashtable getCifData(int modelIndex)
public java.lang.String getPDBHeader()
public java.util.Hashtable getModelInfo(java.lang.Object atomExpression)
public java.util.Hashtable getAuxiliaryInfo(java.lang.Object atomExpression)
java.util.List getAllAtomInfo(java.lang.Object atomExpression)
java.util.List getAllBondInfo(java.lang.Object atomExpression)
java.util.List 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 getWrappedState(boolean isImage)
public java.lang.String getStateInfo()
getStateInfo
in class JmolViewer
public java.lang.String getStateInfo(java.lang.String type)
public java.lang.String getStructureState()
public java.lang.String getProteinStructureState()
public java.lang.String getCoordinateState(java.util.BitSet bsSelected)
public void setCurrentColorRange(java.lang.String label)
public void setCurrentColorRange(float[] data, java.util.BitSet bs)
public void setCurrentColorRange(float min, float max)
public void setData(java.lang.String type, java.lang.Object[] data, int atomCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)
public java.lang.Object[] getData(java.lang.String type)
public float[] getDataFloat(java.lang.String label)
public 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 getConformation(int iModel, int conformationIndex, boolean doSet)
public int autoHbond(java.util.BitSet bsFrom, java.util.BitSet bsTo)
public float getHbondsAngleMin()
public float getHbondsDistanceMax()
public boolean getHbondsRasmol()
public boolean hasCalculatedHBonds(java.util.BitSet bsAtoms)
public boolean havePartialCharges()
havePartialCharges
in class JmolViewer
public SymmetryInterface getCurrentUnitCell()
public SymmetryInterface getModelUnitCell(int modelIndex)
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.List getMeasurementInfo()
public java.lang.String getMeasurementInfoAsString()
public int[] getMeasurementCountPlusIndices(int i)
getMeasurementCountPlusIndices
in class JmolViewer
void setPendingMeasurement(MeasurementPending measurementPending)
MeasurementPending getPendingMeasurement()
public void clearAllMeasurements()
public void clearMeasurements()
clearMeasurements
in class JmolViewer
public boolean getJustifyMeasurements()
public void setAnimation(int tok)
public void setAnimationDirection(int direction)
int getAnimationDirection()
java.util.Hashtable getAnimationInfo()
public void setAnimationFps(int fps)
setAnimationFps
in class JmolViewer
public int getAnimationFps()
getAnimationFps
in class JmolViewer
public void setAnimationReplayMode(int replay, float firstFrameDelay, float lastFrameDelay)
int getAnimationReplayMode()
public void setAnimationOn(boolean animationOn)
public void setAnimationRange(int modelIndex1, int modelIndex2)
public java.util.BitSet getVisibleFramesBitSet()
getVisibleFramesBitSet
in class JmolViewer
boolean isAnimationOn()
public void setCurrentModelIndex(int modelIndex)
void setTrajectory(int modelIndex)
public void setTrajectory(java.util.BitSet bsModels)
public boolean isTrajectory(int modelIndex)
public java.util.BitSet getBitSetTrajectories()
public 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
public boolean haveFileSet()
public void setBackgroundModelIndex(int modelIndex)
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
public void pushHoldRepaint(java.lang.String why)
public void popHoldRepaint()
popHoldRepaint
in class JmolViewer
public void popHoldRepaint(java.lang.String why)
private void setRefreshing(boolean TF)
public boolean getRefreshing()
public void refresh(int mode, java.lang.String strWhy)
refresh
in class JmolViewer
mode
- strWhy
- public void requestRepaintAndWait()
void setSync()
public void notifyViewerRepaintDone()
notifyViewerRepaintDone
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 isExport, 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(java.awt.Graphics g)
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"
java.lang.Object getImageAs(java.lang.String type, int quality, int width, int height, java.lang.String fileName, java.io.OutputStream os, java.lang.String comment)
type
- "PNG", "JPG", "JPEG", "JPG64", "PPM", "GIF"quality
- width
- height
- fileName
- os
- comment
-
public void releaseScreenImage()
releaseScreenImage
in class JmolViewer
public boolean getAllowEmbeddedScripts()
public java.lang.String evalFile(java.lang.String strFilename)
evalFile
in class JmolSimpleViewer
public java.lang.String getInterruptScript()
public java.lang.String script(java.lang.String strScript)
script
in class JmolViewer
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 isInterrupt)
private boolean checkUndo(java.lang.String str)
public boolean usingScriptQueue()
public void clearScriptQueue()
private void setScriptQueue(boolean TF)
public boolean checkResume(java.lang.String str)
public boolean checkStepping(java.lang.String str)
public boolean checkHalt(java.lang.String str, boolean isInterrupt)
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)
public 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()
public java.lang.String getDefaultLoadFilter()
public java.lang.String getDefaultLoadScript()
public java.lang.Object setLoadFormat(java.lang.String name, char type, boolean withPrefix)
public java.lang.String[] getElectronDensityLoadInfo()
public java.lang.String getStandardLabelFormat()
public int getRibbonAspectRatio()
public float getSheetSmoothing()
public boolean getSsbondsBackbone()
public boolean getHbondsBackbone()
public boolean getHbondsSolid()
public javax.vecmath.Point3f[] getAdditionalHydrogens(java.util.BitSet bsAtoms, boolean doAll, boolean justCarbon, java.util.List vConnections)
public java.util.BitSet addHydrogens(java.util.BitSet bsAtoms, boolean asScript, boolean isSilent)
public java.util.BitSet addHydrogensInline(java.util.BitSet bsAtoms, java.util.List vConnections, javax.vecmath.Point3f[] pts) throws java.lang.Exception
java.lang.Exception
public void setMarBond(short marBond)
setMarBond
in class JmolViewer
public boolean isHoverEnabled()
public void setHoverLabel(java.lang.String strLabel)
void hoverOn(int atomIndex, int action)
int getHoverDelay()
public void hoverOn(int x, int y, java.lang.String text)
void hoverOff()
public void clearShapeRenderers()
public int getBfactor100Hi()
short getColix(java.lang.Object object)
public boolean getRasmolSetting(int tok)
public boolean getDebugScript()
public void setDebugScript(boolean debugScript)
setDebugScript
in class JmolViewer
void clearClickCount()
public int getCursor()
public void setCursor(int cursor)
void setPickingMode(java.lang.String strMode, int pickingMode)
public int getPickingMode()
public boolean getDrawPicking()
public boolean isModelKitMode()
public boolean getBondPicking()
private boolean getAtomPicking()
void setPickingStyle(java.lang.String style, int pickingStyle)
public boolean getDrawHover()
public java.lang.String getAtomInfo(int atomOrPointIndex)
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.util.List getStatusChanged(java.lang.String statusNameList)
public boolean menuEnabled()
void popupMenu(int x, int y, char type)
public java.lang.String getMenu(java.lang.String type)
public void setMenu(java.lang.String fileOrText, boolean isFile)
void setStatusFrameChanged(int frameNo)
public void scriptEcho(java.lang.String strEcho)
public void notifyError(java.lang.String errType, java.lang.String errMsg, java.lang.String errMsgUntranslated)
public 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 java.lang.String getZapName()
public void setStatusMeasuring(java.lang.String status, int intInfo, java.lang.String strMeasure, float value)
public void notifyMinimizationStatus()
public void setStatusAtomPicked(int atomIndex, java.lang.String info)
public void setStatusResized(int width, int height)
public void scriptStatus(java.lang.String strStatus)
public void scriptStatus(java.lang.String strStatus, java.lang.String statusMessage)
public void scriptStatus(java.lang.String strStatus, java.lang.String statusMessage, int msWalltime, java.lang.String strErrorMessageUntranslated)
private java.lang.String getModelTitle(int modelIndex)
public java.lang.String getModelFileName(int modelIndex)
getModelFileName
in class JmolViewer
public java.lang.String dialogAsk(java.lang.String type, java.lang.String fileName)
public int getScriptDelay()
public void showUrl(java.lang.String urlString)
showUrl
in class JmolViewer
public void setMeshCreator(java.lang.Object meshCreator)
meshCreator
- public void showConsole(boolean showConsole)
public void clearConsole()
public java.lang.Object getParameterEscaped(java.lang.String key)
public java.lang.Object getParameter(java.lang.String key)
getParameter
in class JmolViewer
public ScriptVariable getOrSetNewVariable(java.lang.String key, boolean doSet)
public ScriptVariable setUserVariable(java.lang.String name, ScriptVariable value)
public void unsetProperty(java.lang.String name)
public java.lang.String getVariableList()
public boolean getBooleanProperty(java.lang.String key)
getBooleanProperty
in class JmolViewer
public void setStringProperty(java.lang.String key, java.lang.String value)
setStringProperty
in class JmolViewer
public void setStringProperty(java.lang.String key, int tok, java.lang.String value)
public void setFloatProperty(java.lang.String key, float value)
setFloatProperty
in class JmolViewer
public boolean setFloatProperty(java.lang.String key, int tok, float value, boolean isInt)
public void setIntProperty(java.lang.String key, int value)
setIntProperty
in class JmolViewer
public void setIntProperty(java.lang.String key, int tok, int value)
public void setBooleanProperty(java.lang.String key, boolean value)
setBooleanProperty
in class JmolViewer
private boolean setBooleanProperty(java.lang.String key, int tok, boolean value, boolean defineNew)
private void setModelKitMode(boolean value)
public boolean getModelkitMode()
public java.lang.String getLanguage()
public void setSmilesString(java.lang.String s)
public void removeUserVariable(java.lang.String key)
public boolean isJmolVariable(java.lang.String key)
private void jmolTest()
public boolean isPdbSequential()
boolean getSelectAllModels()
public boolean getMessageStyleChime()
public boolean getFontCaching()
public boolean getFontScaling()
public void showParameter(java.lang.String key, boolean ifNotSet, int nMax)
public void showString(java.lang.String str, boolean isPrint)
public java.lang.String getAllSettings(java.lang.String prefix)
public java.lang.String getBindingInfo(java.lang.String qualifiers)
public int getDelayMaximum()
public boolean getDotSurfaceFlag()
public boolean getDotsSelectedOnlyFlag()
public int getDotDensity()
public int getDotScale()
public boolean isRangeSelected()
public boolean getIsosurfacePropertySmoothing()
public boolean getWireframeRotation()
public boolean isWindowCentered()
public void setNavigationDepthPercent(float timeSec, float percent)
float getNavigationSpeed()
public boolean getShowNavigationPoint()
public 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()
public void resetError()
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()
public boolean getCartoonBaseEdgesFlag()
private void setStrandCount(int type, int value)
public int getStrandCount(int type)
boolean getHideNameInPopup()
boolean getNavigationPeriodic()
private void stopAnimationThreads(java.lang.String fromWhere)
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 javax.vecmath.Point3f[] getCameraFactors()
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
public int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsBonds, boolean isBonds, float energy)
public void rebond()
rebond
in class JmolViewer
public void setPdbConectBonding(boolean isAuto)
boolean getGreyscaleRendering()
boolean getDisablePopupMenu()
public boolean getForceAutoBond()
public void setPercentVdwAtom(int value)
setPercentVdwAtom
in class JmolViewer
public int getPercentVdwAtom()
getPercentVdwAtom
in class JmolViewer
public RadiusData getDefaultRadiusData()
public short getMadBond()
getMadBond
in class JmolViewer
public short getMarBond()
public byte getModeMultipleBond()
public boolean getShowMultipleBonds()
public float getMultipleBondSpacing()
public float getMultipleBondRadiusFactor()
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()
public void setMeasureDistanceUnits(java.lang.String units)
public java.lang.String getMeasureDistanceUnits()
public boolean getUseNumberLocalization()
public 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)
public 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
public Quaternion[] getAtomGroupQuaternions(java.util.BitSet bsAtoms, int nMax)
public Quaternion getAtomQuaternion(int i)
public javax.vecmath.Point3f getAtomPoint3f(int i)
getAtomPoint3f
in class JmolViewer
public java.util.List getAtomPointVector(java.util.BitSet bs)
public float getAtomRadius(int i)
getAtomRadius
in class JmolViewer
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 int getBondOrder(int i)
getBondOrder
in class JmolViewer
public void assignAromaticBonds()
public boolean getSmartAromatic()
public 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
public void setStereoMode(int[] twoColors, int stereoMode, float degrees)
boolean isStereoDouble()
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)
public 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)
public java.lang.String getModelExtract(java.lang.Object atomExpression, boolean doTransform, boolean asSDF, boolean asV3000)
public void setTainted(boolean TF)
public int notifyMouseClicked(int x, int y, int action, int mode)
Token checkObjectClicked(int x, int y, int modifiers)
boolean checkObjectHovered(int x, int y)
void checkObjectDragged(int prevX, int prevY, int x, int y, int action)
public void rotateAxisAngleAtCenter(javax.vecmath.Point3f rotCenter, javax.vecmath.Vector3f rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, java.util.BitSet bsSelected)
public void rotateAboutPointsInternal(javax.vecmath.Point3f point1, javax.vecmath.Point3f point2, float degreesPerSecond, float endDegrees, boolean isSpin, java.util.BitSet bsSelected, javax.vecmath.Vector3f translation, java.util.List finalPoints)
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)
public void setDefaultLattice(javax.vecmath.Point3f ptLattice)
public javax.vecmath.Point3f getDefaultLattice()
public 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.String getModelCml(java.util.BitSet bs, int nAtomsMax, boolean addBonds)
public java.lang.Object evaluateExpression(java.lang.Object stringOrTokens)
public java.lang.Object getHelixData(java.util.BitSet bs, int tokType)
public java.lang.String getPdbData(java.util.BitSet bs, OutputStringBuffer sb)
public boolean isJmolDataFrame(int modelIndex)
public boolean isJmolDataFrame()
public int getJmolDataFrameIndex(int modelIndex, java.lang.String type)
public void setJmolDataFrame(java.lang.String type, int modelIndex, int dataIndex)
public void setFrameTitle(int modelIndex, java.lang.String title)
public void setFrameTitle(java.lang.String title)
public java.lang.String getFrameTitle()
java.lang.String getJmolFrameType(int modelIndex)
public int getJmolDataSourceFrame(int modelIndex)
public void setAtomProperty(java.util.BitSet bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
public void checkCoordinatesChanged()
public void setAtomCoord(int atomIndex, float x, float y, float z)
public void setAtomCoord(java.util.BitSet bs, int tokType, java.lang.Object xyzValues)
public void setAtomCoordRelative(int atomIndex, float x, float y, float z)
public void setAtomCoordRelative(javax.vecmath.Tuple3f offset, java.util.BitSet bs)
void setAllowRotateSelected(boolean TF)
boolean allowRotateSelected()
public void invertAtomCoord(javax.vecmath.Point3f pt, java.util.BitSet bs)
public void invertAtomCoord(javax.vecmath.Point4f plane, java.util.BitSet bs)
public void invertSelected(javax.vecmath.Point3f pt, javax.vecmath.Point4f plane, int iAtom, java.util.BitSet invAtoms)
public void moveSelected(int deltaX, int deltaY, int x, int y, java.util.BitSet bsSelected, boolean isTranslation)
public void highlightBond(int index, boolean isHover)
public void highlight(java.util.BitSet bs)
void setRotateBondIndex(int index)
int getRotateBondIndex()
void actionRotateBond(int deltaX, int deltaY, int x, int y)
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(boolean andStopMinimization)
void setDynamicMeasurements(boolean TF)
public boolean getDynamicMeasurements()
public float[][] functionXY(java.lang.String functionName, int nX, int nY)
functionName
- nX
- nY
-
public float[][][] functionXYZ(java.lang.String functionName, int nX, int nY, int nZ)
public void getHelp(java.lang.String what)
public void addCommand(java.lang.String command)
command
- the command to addpublic java.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
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, java.util.BitSet bsFrames, java.lang.String[] fullPath)
fileName
- type
- text_or_bytes
- quality
- width
- height
- bsFrames
- fullPath
-
public java.lang.Object 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
public java.lang.Object createImage(java.lang.String fileName, java.lang.String type, java.lang.Object text_or_bytes, int quality, int width, int height, java.lang.String[] fullPath)
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 heightfullPath
-
private java.lang.Object createImage(java.lang.String fileName, java.lang.String type, java.lang.Object text_or_bytes, int quality, int width, int height, java.lang.String[] fullPath, boolean doCheck)
private java.lang.String getFileNameFromDialog(java.lang.String fileName, int quality)
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()
public float[] getAtomicPotentials(boolean isMep, java.util.BitSet bsSelected, java.util.BitSet bsIgnore, java.lang.String fileName)
public 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 iType)
void setDefaultVdw(java.lang.String type)
public java.lang.String getDefaultVdwTypeNameOrData(int iMode)
public int deleteAtoms(java.util.BitSet bs, boolean fullModels)
public void deleteBonds(java.util.BitSet bsDeleted)
public void deleteModelAtoms(int firstAtomIndex, int nAtoms, java.util.BitSet bsDeleted)
public java.util.BitSet getDeletedAtoms()
public char getQuaternionFrame()
public int getHelixStep()
public 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)
public java.lang.Object getFileAsImage(java.lang.String pathName, java.util.Hashtable htParams)
public 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 void setShapeErrorState(int shapeID, java.lang.String state)
public java.lang.String getShapeErrorState()
public void handleError(java.lang.Error er, boolean doClear)
public float[] getAtomicCharges()
public ScriptFunction getFunction(java.lang.String name)
public void addFunction(ScriptFunction f)
public void clearFunctions()
public boolean isFunction(java.lang.String name)
public java.lang.String getFunctionCalls(java.lang.String selectedFunction)
public void showMessage(java.lang.String s)
public java.lang.String getMoInfo(int modelIndex)
boolean isRepaintPending()
public java.util.Hashtable getContextVariables()
public boolean checkPrivateKey(double privateKey)
checkPrivateKey
in class JmolViewer
privateKey
-
public void bindAction(java.lang.String desc, java.lang.String name, javax.vecmath.Point3f range1, javax.vecmath.Point3f range2)
public void unBindAction(java.lang.String desc, java.lang.String name)
public java.lang.Object getMouseInfo()
public void clearTimeout(java.lang.String name)
public void setTimeout(java.lang.String name, int mSec, java.lang.String script)
public java.lang.String showTimeout(java.lang.String name)
public int getFrontPlane()
public java.util.List getPlaneIntersection(int type, javax.vecmath.Point4f plane, float scale, int flags)
void repaint()
public java.io.OutputStream getOutputStream(java.lang.String localName, java.lang.String[] fullPath)
public int calculateStruts(java.util.BitSet bs1, java.util.BitSet bs2)
public boolean getStrutsMultiple()
public int getStrutSpacingMinimum()
public float getStrutLengthMaximum()
public float getStrutDefaultRadius()
public boolean getPreserveState()
public boolean getDragSelected()
public float getLoadAtomDataTolerance()
public boolean getAllowGestures()
public boolean getLogGestures()
public boolean allowMultiTouch()
public boolean logCommands()
public java.lang.String getLogFile()
private java.lang.String setLogFile(java.lang.String value)
public void log(java.lang.String data)
boolean isKiosk()
public boolean hasFocus()
public void setFocus()
public MinimizerInterface getMinimizer(boolean createNew)
void stopMinimization()
void clearMinimization()
public java.lang.String getMinimizationInfo()
public boolean useMinimizationThread()
private void checkMinimization()
public void minimize(int steps, float crit, java.util.BitSet bsSelected, java.util.BitSet bsFixed, float rangeFixed, boolean addHydrogen, boolean isSilent, boolean asScript)
steps
- Integer.MAX_VALUE --> use defaultscrit
- -1 --> use defaultsbsSelected
- bsFixed
- TODOrangeFixed
- addHydrogen
- isSilent
- asScript
- public void setMotionFixedAtoms(java.util.BitSet bs)
public java.util.BitSet getMotionFixedAtoms()
boolean useArcBall()
void rotateArcBall(int x, int y, float factor)
void getAtomicPropertyState(java.lang.StringBuffer commands, byte type, java.util.BitSet bs, java.lang.String name, float[] data)
public javax.vecmath.Point3f[][] getCenterAndPoints(java.util.List atomSets, boolean addCenter)
public int getSmallMoleculeMaxAtoms()
public java.lang.String streamFileData(java.lang.String fileName, java.lang.String type, java.lang.String type2, int modelIndex, java.lang.Object[] parameters)
public java.lang.String getPdbData(int modelIndex, java.lang.String type, java.lang.Object[] parameters)
public int getRepaintWait()
public java.util.BitSet getGroupsWithin(int nResidues, java.util.BitSet bs)
public java.lang.Object getExecutor()
public boolean eval(ScriptContext context, ShapeManager shapeManager)
public java.util.Hashtable getShapeInfo()
public void togglePickingLabel(java.util.BitSet bs)
public void loadShape(int shapeID)
public void setShapeSize(int shapeID, int mad, java.util.BitSet bsSelected)
public void setShapeSize(int shapeID, RadiusData rd, java.util.BitSet bsAtoms)
public void setShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object value)
public java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName)
public boolean getShapeProperty(int shapeType, java.lang.String propertyName, java.lang.Object[] data)
public java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName, int index)
private int getShapePropertyAsInt(int shapeID, java.lang.String propertyName)
public void setModelVisibility()
public void resetShapes()
public void setAtomLabel(java.lang.String value, int i)
public void deleteShapeAtoms(java.lang.Object[] value, java.util.BitSet bs)
public void getShapeState(java.lang.StringBuffer commands, boolean isAll)
public void resetBioshapes(java.util.BitSet bsAllAtoms)
public float getAtomShapeValue(int tok, Group group, int atomIndex)
public void mergeShapes(Shape[] newShapes)
public ShapeManager getShapeManager()
public boolean setParallel(boolean TF)
public boolean isParallel()
public java.util.BitSet transformAtoms(boolean firstPass)
private void setAtomPickingOption(java.lang.String option)
private void setBondPickingOption(java.lang.String option)
void undoAction(boolean isSave, int taintedAtom, int type)
public void assignBond(int bondIndex, char type)
public void assignAtom(int atomIndex, javax.vecmath.Point3f pt, java.lang.String type)
public void assignConnect(int index, int index2)
void moveAtomWithHydrogens(int atomIndex, int deltaX, int deltaY, java.util.BitSet bsAtoms)
void appendLoadStates(java.lang.StringBuffer commands)
public static void getInlineData(java.lang.StringBuffer loadScript, java.lang.String strModel, boolean isAppend)
boolean isAtomPDB(int i)
boolean isAtomAssignable(int i)
public void deleteMeasurement(int i)
deleteMeasurement
in class JmolViewer
boolean haveModelKit()
java.util.BitSet getModelKitStateBitSet(java.util.BitSet bs, java.util.BitSet bsDeleted)
public java.lang.String getSmiles(int index1, int index2, java.util.BitSet bsSelected, boolean isBioSmiles, boolean allowUnmatchedRings, boolean addCrossLinks, boolean addComment)
index1
- index2
- bsSelected
- isBioSmiles
- allowUnmatchedRings
- TODOaddCrossLinks
- TODOaddComment
-
public void connect(float[][] connections)
public java.lang.String prompt(java.lang.String label, java.lang.String data, java.lang.String[] list, boolean asButtons)
java.lang.String getMenuName(int i)
public void setStateScriptVersion(java.lang.String version)
public boolean checkAutoBondLegacy()
public ColorEncoder getColorEncoder(java.lang.String colorScheme)
public boolean getMouseEnabled()
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