org.jmol.viewer
Class Viewer
public
class
Viewer
extends JmolViewer
implements AtomDataServer
Method Summary |
void | addCommand(String command)
Adds one or more commands to the command history |
void | addLoadScript(String script) |
void | addSelectionListener(JmolSelectionListener listener) |
void | addStateScript(String script, boolean addFrameNumber, boolean postDefinitions) |
void | addStateScript(String script1, BitSet bsBonds, BitSet bsAtoms1, BitSet bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions) |
static JmolViewer | allocateViewer(Component display, JmolAdapter modelAdapter)
NOTE: for APPLICATION AND APPLET call
setModeMouse(JmolConstants.MOUSE_NONE);
before setting viewer=null
in order to remove references to display window in listeners and hoverWatcher
This is the main access point for creating an application
or applet viewer. |
byte[] | allocTempBytes(int size) |
Point3f[] | allocTempPoints(int size) |
Point3i[] | allocTempScreens(int size) |
boolean | allowRotateSelected() |
boolean | areAxesTainted() |
void | assignAromaticBonds() |
void | atomPicked(int atomIndex, Point3f ptClicked, int modifiers) |
int | autoHbond(BitSet bsBonds) |
int | autoHbond(BitSet bsFrom, BitSet bsTo, BitSet bsBonds) |
void | calcBoundBoxDimensions(BitSet bs) |
float | calcRotationRadius(Point3f center) |
float | calcRotationRadius(BitSet bs) |
void | calcSelectedGroupsCount() |
void | calcSelectedMoleculesCount() |
void | calcSelectedMonomersCount() |
Vector3f | calculateMolecularDipole() |
String | calculatePointGroup() |
void | calculateStraightness() |
void | calculateStructures(BitSet bsAtoms) |
Point3f[] | calculateSurface(BitSet bsSelected, float envelopeRadius) |
boolean | checkHalt(String strScript) |
Point3f | checkObjectClicked(int x, int y, int modifiers) |
void | checkObjectDragged(int prevX, int prevY, int deltaX, int deltaY, int modifiers) |
boolean | checkObjectHovered(int x, int y) |
boolean | checkResume(String strScript) |
void | clear() |
void | clearAllMeasurements() |
void | clearBfactorRange() |
void | clearClickCount() |
void | clearConsole() |
void | clearMeasurements() |
void | clearMinimization() |
void | clearScriptQueue() |
void | clearSelection() |
void | createImage(String type_name) |
String | createImage(String file, String type, Object text_or_bytes, int quality, int width, int height) |
void | defineMeasurement(Vector monitorExpressions, float[] rangeMinMax, boolean isDelete, boolean isAll, boolean isAllConnected, boolean isOn, boolean isOff, String strFormat) |
int | deleteAtoms(BitSet bs, boolean fullModels) |
void | deleteMeasurement(int i) |
void | deleteMeasurement(int[] atomCountPlusIndices) |
void | depthByPixels(int pixels) |
void | depthToPercent(int percentDepth) |
String | dialogAsk(String type, String fileName) |
void | display(BitSet bs, boolean isQuiet) |
void | echoMessage(String msg) |
String | eval(String strEval) |
String | evalFile(String strFilename) |
String | evalString(String strScript) |
String | evalStringQuiet(String strScript) |
String | evalStringQuiet(String strScript, boolean isQuiet, boolean allowSyncScript) |
Object | evalStringWaitStatus(String returnType, String strScript, String statusList) |
Object | evalStringWaitStatus(String returnType, String strScript, String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued) |
Object | evaluateExpression(Object stringOrTokens) |
void | fillAtomData(AtomData atomData, int mode) |
protected void | finalize() |
void | finalizeTransformParameters() |
int | findNearestAtomIndex(int x, int y) |
String | formatText(String text0) |
boolean | frankClicked(int x, int y) |
void | freeTempBytes(byte[] tempBytes) |
void | freeTempPoints(Point3f[] tempPoints) |
void | freeTempScreens(Point3i[] tempScreens) |
float[][] | functionXY(String functionName, int nX, int nY)
fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full
set of Double[][] in one function call. |
String | generateOutput(String type, String fileName, int width, int height) |
Vector | getAllAtomInfo(Object atomExpression) |
Vector | getAllBondInfo(Object atomExpression) |
Hashtable | getAllChainInfo(Object atomExpression) |
boolean | getAllowEmbeddedScripts() |
Hashtable | getAllPolymerInfo(Object atomExpression) |
String | getAllSettings(String prefix) |
String | getAltLocListInModel(int modelIndex) |
static int | getAmbientPercent() |
int | getAnimationDirection() |
int | getAnimationFps() |
Hashtable | getAnimationInfo() |
int | getAnimationReplayMode() |
boolean | getAppendNew() |
Hashtable | getAppletInfo() |
boolean | getApplySymmetryToBonds() |
int | getAtomArgb(int i) |
BitSet | getAtomBits(int tokType, Object specInfo) |
BitSet | getAtomBitSet(Object atomExpression) |
Vector | getAtomBitSetVector(Object atomExpression) |
String | getAtomChain(int i) |
int | getAtomCount() |
int | getAtomCountInModel(int modelIndex) |
void | getAtomIdentityInfo(int atomIndex, Hashtable info) |
int | getAtomIndexFromAtomNumber(int atomNumber) |
int[] | getAtomIndices(BitSet bs) |
String | getAtomInfo(int atomIndex) |
String | getAtomInfoXYZ(int atomIndex, boolean useChimeFormat) |
int | getAtomModelIndex(int i) |
String | getAtomName(int i) |
int | getAtomNumber(int i) |
boolean | getAtomPicking() |
Point3f | getAtomPoint3f(int i) |
float | getAtomRadius(int i) |
BitSet | getAtomsConnected(float min, float max, int intType, BitSet bs) |
BitSet | getAtomsWithin(float distance, Point3f coord) |
BitSet | getAtomsWithin(float distance, Point4f plane) |
BitSet | getAtomsWithin(float distance, BitSet bs, boolean isWithinModelSet) |
String | getAtomSequenceCode(int i) |
Point3f | getAtomSetCenter(BitSet bs) |
float | getAtomVdwRadius(int i) |
float | getAtomX(int i) |
float | getAtomY(int i) |
float | getAtomZ(int i) |
boolean | getAutoBond() |
boolean | getAutoFps() |
Hashtable | getAuxiliaryInfo(Object atomExpression) |
Point3f | getAverageAtomPoint() |
Component | getAwtComponent() |
int | getAxesMode() |
boolean | getAxesOrientationRasmol() |
float | getAxesScale() |
void | getAxisAngle(AxisAngle4f axisAngle) |
Point3f[] | getAxisPoints() |
int | getBackgroundArgb() |
int | getBackgroundModelIndex() |
BitSet | getBitSetSelection() |
BitSet | getBitSetTrajectories() |
int | getBondArgb1(int i) |
int | getBondArgb2(int i) |
int | getBondCount()
For use in setting a for() construct max value |
int | getBondCountInModel(int modelIndex)
from JmolPopup.udateModelSetComputedMenu
|
int | getBondModelIndex(int i) |
short | getBondOrder(int i) |
boolean | getBondPicking() |
Point3f | getBondPoint3f1(int i) |
Point3f | getBondPoint3f2(int i) |
float | getBondRadius(int i) |
BitSet | getBondsForSelectedAtoms(BitSet bsAtoms) |
boolean | getBondSelectionModeOr() |
float | getBondTolerance() |
boolean | getBooleanProperty(String key) |
boolean | getBooleanProperty(String key, boolean doICare) |
Point3f | getBoundBoxCenter() |
int | getBoundBoxCenterX() |
int | getBoundBoxCenterY() |
String | getBoundBoxCommand(boolean withOptions) |
Vector3f | getBoundBoxCornerVector() |
Hashtable | getBoundBoxInfo() |
BitSet | getBoundBoxModels() |
BoxInfo | getBoxInfo(BitSet bs) |
BitSet | getBranchBitSet(int atomIndex, int atomIndexNot) |
Object | getBufferedReaderForString(String string) |
Object | getBufferedReaderOrErrorMessageFromName(String name, String[] fullPathNameReturn, boolean isBinary) |
boolean | getCartoonRocketFlag() |
boolean | getChainCaseSensitive() |
int | getChainCount() |
int | getChainCountInModel(int modelIndex) |
int | getChainCountInModel(int modelIndex, boolean countWater) |
String | getChimeInfo(int tok) |
BitSet | getClickableSet() |
String | getClientAtomStringProperty(Object clientAtom, String propertyName) |
Object | getClientFile() |
short | getColix(Object object) |
int | getColixArgb(short colix) |
short | getColixAtomPalette(Atom atom, byte pid) |
short | getColixBackgroundContrast() |
short | getColixForPropertyValue(float val) |
short | getColixRubberband() |
Point3f | getColorPointForPropertyValue(float val) |
int[] | getColorSchemeArray(String colorScheme) |
String | getColorSchemeList(String colorScheme, boolean ifDefault) |
Compiler | getCompiler() |
String | getCoordinateState(BitSet bsSelected) |
float[] | getCurrentColorRange() |
Object | getCurrentFileAsBytes() |
String | getCurrentFileAsString() |
int | getCurrentModelIndex() |
float | getCurrentSolventProbeRadius() |
SymmetryInterface | getCurrentUnitCell() |
Point3f | getCurrentUnitCellOffset() |
int | getCursorX() |
int | getCursorY() |
Object[] | getData(String type) |
String | getData(String atomExpression, String type) |
float[] | getDataFloat(String label) |
float | getDataFloat(String label, int atomIndex) |
float[][] | getDataFloat2D(String label) |
String | getDataSeparator() |
boolean | getDebugScript() |
String | getDefaultDirectory() |
float | getDefaultDrawArrowScale() |
Point3f | getDefaultLattice() |
String | getDefaultLoadScript() |
short | getDefaultMadAtom() |
String | getDefaultMeasurementLabel(int nPoints) |
float | getDefaultTranslucent() |
String | getDefaultVdw(int iMode) |
int | getDelayMaximum() |
BitSet | getDeletedAtoms() |
static int | getDiffusePercent() |
float | getDipoleScale() |
boolean | getDisablePopupMenu() |
boolean | getDisplayCellParameters() |
int | getDisplayModelIndex() |
int | getDotDensity() |
boolean | getDotsSelectedOnlyFlag() |
boolean | getDotSurfaceFlag() |
boolean | getDrawHover() |
boolean | getDrawPicking() |
boolean | getDynamicMeasurements() |
boolean | getEchoStateActive() |
int | getElementNumber(int i) |
BitSet | getElementsPresentBitSet(int modelIndex) |
String | getElementSymbol(int i) |
Hashtable | getEvalVariables() |
String | getExportDriverList() |
JmolAdapter | getExportJmolAdapter()
This is the method that should be used to extract the model data from Jmol.
|
Object | getFileAsImage(String pathName, Hashtable htParams) |
String | getFileAsString(String name) |
boolean | getFileAsString(String[] data) |
String | getFileHeader() |
String[] | getFileInfo() |
String | getFileName() |
Font3D | getFont3D(String fontFace, String fontStyle, float fontSize) |
boolean | getFontScaling() |
boolean | getForceAutoBond() |
FrameRenderer | getFrameRenderer() |
String | getFrameTitle(int modelIndex) |
String | getFrameTitle() |
String | getFullPathName() |
StateManager.GlobalSettings | getGlobalSettings() |
Graphics3D | getGraphics3D() |
boolean | getGreyscaleRendering() |
int | getGroupCount() |
int | getGroupCountInModel(int modelIndex) |
boolean | getHbondsBackbone() |
boolean | getHbondsSolid() |
void | getHelp(String what) |
int | getHermiteLevel() |
Hashtable | getHeteroList(int modelIndex) |
String | getHexColorFromIndex(short colix) |
BitSet | getHiddenSet() |
boolean | getHideNameInPopup() |
boolean | getHighResolution() |
int | getHoverDelay() |
String | getHtmlName() |
String | getHybridizationAndAxes(int atomIndex, Vector3f z, Vector3f x, String lcaoType, boolean hybridizationCompatible) |
Image | getImage(boolean isDouble) |
float | getImageFontScaling() |
char | getInlineChar() |
boolean | getInMotion() |
String | getInterruptScript() |
boolean | getIsosurfacePropertySmoothing() |
String | getJavaVendor() |
String | getJavaVersion() |
int | getJmolDataFrameIndex(int modelIndex, String type) |
int | getJmolDataSourceFrame(int modelIndex) |
String | getJmolFrameType(int modelIndex) |
static String | getJmolVersion() |
static int | getJmolVersionInt() |
Object | getJpeg(int quality, boolean asString) |
boolean | getJustifyMeasurements() |
Object | getListVariable(String name, Object value) |
String | getLoadFormat() |
String | getLoadState() |
static int | getLogLevel() |
short | getMadBond() |
short | getMarBond() |
Matrix3f | getMatrixRotate() |
Matrix4f | getMatrixtransform() |
float | getMaxZoomPercent() |
boolean | getMeasureAllModelsFlag() |
String | getMeasureDistanceUnits() |
int | getMeasurementCount() |
int[] | getMeasurementCountPlusIndices(int i) |
Vector | getMeasurementInfo() |
String | getMeasurementInfoAsString() |
String | getMeasurementStringValue(int i) |
String | getMenu(String type) |
Hashtable | getMessageQueue() |
boolean | getMessageStyleChime() |
float | getMinBondDistance() |
String | getMinimizationInfo() |
MinimizerInterface | getMinimizer() |
BitSet | getModelAtomBitSet(int modelIndex, boolean asCopy) |
Hashtable | getModelAuxiliaryInfo(int modelIndex) |
Object | getModelAuxiliaryInfo(int modelIndex, String keyName) |
BitSet | getModelBitSet(BitSet atomList) |
int | getModelCount() |
Vector3f | getModelDipole() |
String | getModelExtract(Object atomExpression) |
String | getModelFileInfo() |
String | getModelFileInfoAll() |
String | getModelFileName(int modelIndex) |
int | getModelFileNumber(int modelIndex) |
Hashtable | getModelInfo(Object atomExpression) |
String | getModelInfoAsString() |
String | getModelName(int modelIndex) |
int | getModelNumber(int modelIndex) |
String | getModelNumberDotted(int modelIndex) |
int | getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory) |
Properties | getModelProperties(int modelIndex) |
String | getModelProperty(int modelIndex, String propertyName) |
ModelSet | getModelSet() |
Object | getModelSetAuxiliaryInfo(String strKey) |
Hashtable | getModelSetAuxiliaryInfo() |
String | getModelSetFileName() |
String | getModelSetName() |
String | getModelSetPathName() |
Properties | getModelSetProperties() |
String | getModelSetProperty(String strProp) |
String | getModelSetTypeName() |
String | getModelTitle(int modelIndex) |
byte | getModeMultipleBond() |
Vector | getMoleculeInfo(Object atomExpression) |
int | getMotionEventNumber() |
String | getMoveToText(float timespan) |
boolean | getNavigating() |
Point3f | getNavigationCenter() |
boolean | getNavigationCentered() |
float | getNavigationDepthPercent() |
boolean | getNavigationMode() |
Point3f | getNavigationOffset() |
float | getNavigationOffsetPercent(char XorY) |
boolean | getNavigationPeriodic() |
float | getNavigationSpeed() |
Boolean | getNoneSelected() |
int | getObjectArgb(int objId) |
short | getObjectColix(int objId) |
int | getObjectMad(int objId) |
String | getObjectState(String name) |
String | getOpenFileError()
misnamed -- really this opens the file, gets the data, and returns error or null
|
String | getOpenFileError(boolean isAppend)
the opener for Jmol
|
String | getOperatingSystemName() |
Hashtable | getOrientationInfo() |
String | getOrientationText(int type) |
Object | getParameter(String key) |
Object | getParameterEscaped(String key) |
float[] | getPartialCharges() |
String | getPdbData(BitSet bs) |
String | getPdbData(int modelIndex, String type) |
boolean | getPdbLoadInfo(int type) |
String | getPDBHeader() |
MeasurementPending | getPendingMeasurement() |
int | getPercentVdwAtom() |
boolean | getPerspectiveDepth() |
int | getPickingMode() |
int | getPickingSpinRate() |
int | getPickingStyle() |
String | getPointGroupAsString(boolean asDraw, String type, int index, float scale) |
Hashtable | getPointGroupInfo(Object atomExpression) |
float | getPointGroupTolerance(int type) |
int | getPolymerCount() |
int | getPolymerCountInModel(int modelIndex) |
Point3f[] | getPolymerLeadMidPoints(int modelIndex, int polymerIndex) |
void | getPolymerPointsAndVectors(BitSet bs, Vector vList) |
Object | getProperty(String returnType, String infoType, String paramInfo) |
Object | getProperty(String returnType, String infoType, Object paramInfo) |
String | getPropertyColorScheme() |
String | getProteinStructureState() |
char | getQuaternionFrame() |
boolean | getRasmolHeteroSetting() |
boolean | getRasmolHydrogenSetting() |
boolean | getRefreshing() |
int | getRibbonAspectRatio() |
boolean | getRibbonBorder() |
boolean | getRocketBarrelFlag() |
void | getRotation(Matrix3f matrixRotation) |
Point3f | getRotationCenter() |
float | getRotationRadius() |
Rectangle | getRubberBandSelection() |
String | getSavedCoordinates(String saveName) |
String | getSavedState(String saveName) |
String | getSavedStructure(String saveName) |
float | getScalePixelsPerAngstrom() |
int | getScreenDim() |
int | getScreenHeight() |
Image | getScreenImage() |
int | getScreenWidth() |
int | getScriptDelay() |
boolean | getSelectAllModels() |
int | getSelectionCount() |
boolean | getSelectionHaloEnabled() |
BitSet | getSelectionSet() |
BitSet | getSelectionSubset() |
BitSet | getSequenceBits(String specInfo, BitSet bs) |
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;
|
int | getShapeIdFromObjectName(String objectName) |
Hashtable | getShapeInfo() |
Object | getShapeProperty(int shapeType, String propertyName) |
Object | getShapeProperty(int shapeType, String propertyName, int index) |
int | getShapePropertyAsInt(int shapeID, String propertyName) |
float | getSheetSmoothing() |
boolean | getShowAxes() |
boolean | getShowBbcage() |
boolean | getShowFrank() |
boolean | getShowHiddenSelectionHalos() |
boolean | getShowHydrogens() |
boolean | getShowMeasurementLabels() |
boolean | getShowMeasurements() |
boolean | getShowMultipleBonds() |
boolean | getShowNavigationPoint() |
boolean | getShowUnitCell() |
boolean | getSlabEnabled() |
boolean | getSmartAromatic() |
boolean | getSolventOn() |
float | getSolventProbeRadius() |
String | getSpaceGroupInfoText(String spaceGroup) |
boolean | getSpecular() |
static int | getSpecularPercent() |
String | getSpecularState() |
float | getSpinFps() |
boolean | getSpinOn() |
String | getSpinState() |
float | getSpinX() |
float | getSpinY() |
float | getSpinZ() |
boolean | getSsbondsBackbone() |
String | getStandardLabelFormat() |
String | getStateInfo() |
String | getStateInfo(String type) |
Object | getStatusChanged(String statusNameList) |
float | getStereoDegrees() |
Image | getStereoImage(int stereoMode) |
int | getStereoMode() |
int | getStrandCount(int type) |
String | getStructureState() |
int | getSurfaceDistanceMax() |
String | getSymmetryInfoAsString() |
BitSet | getTaintedAtoms(byte type) |
boolean | getTestFlag1() |
boolean | getTestFlag2() |
boolean | getTestFlag3() |
boolean | getTestFlag4() |
boolean | getTraceAlpha() |
String | getTrajectoryInfo() |
String | getTransformText() |
String | getTranslationScript() |
float | getTranslationXPercent() |
float | getTranslationYPercent() |
float | getTranslationZPercent() |
String | getUnitCellInfoText() |
Matrix4f | getUnscaledTransformMatrix() |
boolean | getUseNumberLocalization() |
int | getVanderwaalsMar(int i) |
int | getVanderwaalsMar(int i, int iMode) |
float | getVectorScale() |
float | getVibrationCoord(int atomIndex, char c) |
float | getVibrationPeriod() |
float | getVibrationScale() |
Vector3f | getVibrationVector(int atomIndex) |
BitSet | getVisibleFramesBitSet() |
BitSet | getVisibleSet() |
boolean | getWireframeRotation() |
AtomIndexIterator | getWithinAtomSetIterator(int atomIndex, float distance, BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased) |
AtomIndexIterator | getWithinModelIterator(Atom atom, float distance) |
boolean | getZeroBasedXyzRasmol() |
boolean | getZoomEnabled() |
boolean | getZoomLarge() |
int | getZoomPercent() |
float | getZoomPercentFloat() |
float | getZoomSetting() |
boolean | getZShade() |
void | haltScriptExecution() |
boolean | handleOldJvm10Event(Event e) |
boolean | hasCalculatedHBonds(BitSet bsAtoms) |
boolean | haveFileSet() |
boolean | haveFrame() |
boolean | haveModelSet() |
boolean | havePartialCharges() |
void | hide(BitSet bs, boolean isQuiet) |
void | hideMeasurements(boolean isOFF) |
void | homePosition() |
void | hoverOff() |
void | hoverOn(int atomIndex) |
void | hoverOn(int x, int y, String text) |
void | initialize() |
void | initializeModel() |
void | invertSelected(Point3f pt, BitSet bs) |
void | invertSelected(Point3f pt, Point4f plane) |
void | invertSelection() |
boolean | isAnimationOn() |
boolean | isApplet() |
boolean | isInPosition(Point3f pt, float degrees) |
boolean | isInSelectionSubset(int atomIndex) |
boolean | isJmolDataFrame(int modelIndex) |
boolean | isJmolDataFrame() |
boolean | isJmolVariable(String key) |
boolean | isJvm12orGreater() |
boolean | isPreviewOnly() |
boolean | isRangeSelected() |
boolean | isScriptExecuting() |
boolean | isSelected(int atomIndex) |
boolean | isSignedApplet() |
boolean | isTrajectory(int modelIndex) |
boolean | isVibrationOn() |
boolean | isWindowCentered() |
String | listSavedStates() |
void | loadData(int type, String name, String coordinateData) |
void | loadInline(String strModel) |
void | loadInline(String strModel, boolean isAppend) |
void | loadInline(String strModel, char newLine) |
boolean | loadInline(String strModel, char newLine, boolean isAppend) |
void | loadInline(String[] arrayModels) |
void | loadInline(String[] arrayModels, boolean isAppend) |
void | loadShape(int shapeID) |
int[] | makeConnections(float minDistance, float maxDistance, short order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds) |
boolean | modelHasVibrationVectors(int modelIndex) |
boolean | modelSetHasVibrationVectors() |
void | move(Vector3f dRot, float dZoom, Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps) |
void | moveTo(float floatSecondsTotal, Point3f center, Point3f pt, float degrees, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth) |
void | moveTo(float floatSecondsTotal, Matrix3f rotationMatrix, Point3f center, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth) |
void | moveUpdate(float floatSecondsTotal) |
boolean | mustRenderFlag() |
void | navigate(int keyWhere, int modifiers) |
void | navigate(float timeSeconds, Point3f[] path, float[] theta, int indexStart, int indexEnd) |
void | navigate(float timeSeconds, Point3f center) |
void | navigate(float timeSeconds, Point3f[][] pathGuide) |
void | navigate(float timeSeconds, Vector3f rotAxis, float degrees) |
void | navTranslate(float timeSeconds, Point3f center) |
void | navTranslatePercent(float timeSeconds, float x, float y) |
void | notifyMinimizationStatus() |
void | openClientFile(String fullPathName, String fileName, Object clientFile) |
void | openDOM(Object DOMNode) |
void | openFile(String name) |
void | openFile(String name, Hashtable htParams, String loadScript, boolean isAppend) |
void | openFiles(String modelName, String[] names) |
void | openFiles(String modelName, String[] names, String loadScript, boolean isAppend) |
void | openReader(String fullPathName, String name, Reader reader)
Opens the file, given the reader.
name is a text name of the file ... to be displayed in the window no need
to pass a BufferedReader ... |
void | openStringInline(String strModel) |
boolean | openStringInline(String strModel, Hashtable htParams, boolean isAppend) |
void | openStringsInline(String[] arrayModels, Hashtable htParams, boolean isAppend) |
void | pauseAnimation() |
void | pauseScriptExecution() |
void | popHoldRepaint() |
void | popupMenu(int x, int y) |
void | pushHoldRepaint() |
void | rebond() |
void | refresh(int mode, String strWhy)
initiate a repaint/update sequence if it has not already been requested.
invoked whenever any operation causes changes that require new rendering.
|
void | refreshMeasures() |
void | releaseScreenImage() |
String | removeCommand()
Removes one command from the command history |
void | removeSelectionListener(JmolSelectionListener listener) |
void | removeUserVariable(String key) |
void | render() |
void | render1(Graphics g, Image img, int x, int y) |
void | renderScreenImage(Graphics g, Dimension size, Rectangle clip) |
void | repaint() |
void | repaintView() |
void | reportSelection(String msg) |
void | requestRepaintAndWait() |
void | reset() |
void | resetAromatic() |
void | resizeImage(int width, int height, boolean isImageWrite, boolean isGenerator, boolean isReset) |
boolean | restoreBonds(String saveName) |
void | restoreModelOrientation(int modelIndex) |
void | restoreModelRotation(int modelIndex) |
boolean | restoreOrientation(String saveName, float timeSeconds) |
void | restoreRotation(String saveName, float timeSeconds) |
boolean | restoreSelection(String saveName) |
void | resumeAnimation() |
void | resumeScriptExecution() |
void | reverseAnimation() |
void | rewindAnimation() |
void | rotateAboutPointsInternal(Point3f point1, Point3f point2, float nDegrees, float endDegrees, boolean isSpin, BitSet bsSelected) |
void | rotateAtoms(Matrix3f mNew, Matrix3f matrixRotate, boolean fullMolecule, Point3f center, boolean isInternal, BitSet bsAtoms) |
void | rotateAxisAngleAtCenter(Point3f rotCenter, Vector3f rotAxis, float degrees, float endDegrees, boolean isSpin, BitSet bsSelected) |
void | rotateFront() |
void | rotateMolecule(int deltaX, int deltaY) |
void | rotatePoint(Point3f pt, Point3f ptRot) |
void | rotateX(float angleRadians) |
void | rotateX(int angleDegrees) |
void | rotateXYBy(int xDelta, int yDelta) |
void | rotateY(float angleRadians) |
void | rotateY(int angleDegrees) |
void | rotateZ(float angleRadians) |
void | rotateZBy(int zDelta) |
void | saveBonds(String saveName) |
void | saveCoordinates(String saveName, BitSet bsSelected) |
void | saveModelOrientation() |
void | saveOrientation(String saveName) |
void | saveSelection(String saveName) |
void | saveState(String saveName) |
void | saveStructure(String saveName) |
float | scaleToPerspective(int z, float sizeAngstroms) |
short | scaleToScreen(int z, int milliAngstroms) |
String | script(String strScript) |
String | scriptCheck(String strScript) |
void | scriptEcho(String strEcho) |
void | scriptError(String msg) |
void | scriptStatus(String strStatus) |
String | scriptWait(String strScript) |
Object | scriptWaitStatus(String strScript, String statusList) |
void | select(BitSet bs, boolean isQuiet) |
void | selectAll() |
void | selectBonds(BitSet bs) |
void | selectRectangle(Rectangle rect, int modifiers) |
void | setAllowRotateSelected(boolean TF) |
static void | setAmbientPercent(int ambientPercent) |
void | setAnimationDirection(int direction) |
void | setAnimationFps(int fps) |
void | setAnimationLast() |
void | setAnimationNext() |
void | setAnimationOn(boolean animationOn) |
void | setAnimationPrevious() |
void | setAnimationRange(int modelIndex1, int modelIndex2) |
void | setAnimationReplayMode(int replay, float firstFrameDelay, float lastFrameDelay) |
void | setAntialias(int mode, boolean TF) |
void | setAppendNew(boolean value) |
void | setAppletContext(String fullName, URL documentBase, URL codeBase, String commandOptions) |
void | setApplySymmetryToBonds(boolean TF) |
void | setAtomCoord(int atomIndex, float x, float y, float z) |
void | setAtomCoord(BitSet bs, int tokType, Object xyzValues) |
void | setAtomCoordRelative(int atomIndex, float x, float y, float z) |
void | setAtomCoordRelative(Point3f offset) |
void | setAtomProperty(BitSet bs, int tok, int iValue, float fValue, float[] values) |
void | setAutoBond(boolean TF) |
void | setAxesModeMolecular(boolean TF) |
void | setAxesModeUnitCell(boolean TF) |
void | setAxesOrientationRasmol(boolean TF) |
void | setAxesScale(float scale) |
void | setBackgroundImage(String fileName, Image image) |
void | setBackgroundModelIndex(int modelIndex) |
void | setBondTolerance(float bondTolerance) |
void | setBooleanProperty(String key, boolean value) |
boolean | setBooleanProperty(String key, boolean value, boolean defineNew) |
void | setBoundBox(Point3f pt1, Point3f pt2, boolean byCorner) |
void | setCenterAt(String relativeTo, Point3f pt) |
void | setCenterBitSet(BitSet bsCenter, boolean doScale) |
void | setCenterSelected() |
void | setColorBackground(String colorName) |
BitSet | setConformation() |
BitSet | setConformation(int conformationIndex) |
void | setCurrentColorRange(String label) |
void | setCurrentColorRange(float[] data, BitSet bs) |
void | setCurrentColorRange(float min, float max) |
void | setCurrentModelIndex(int modelIndex) |
void | setCurrentModelIndex(int modelIndex, boolean clearBackground) |
void | setCurrentUnitCellOffset(int offset) |
void | setCurrentUnitCellOffset(Point3f pt) |
void | setCursor(int cursor) |
void | setData(String type, Object[] data, int atomCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount) |
void | setDebugScript(boolean debugScript) |
void | setDefaultColors(String colorScheme) |
void | setDefaultDrawArrowScale(float scale) |
void | setDefaultLattice(Point3f ptLattice) |
void | setDefaults(String type) |
void | setDefaultVdw(String mode) |
static void | setDiffusePercent(int diffusePercent) |
void | setDynamicMeasurements(boolean TF) |
void | setEchoStateActive(boolean TF) |
void | setElementArgb(int elementNumber, int argb) |
void | setFileInfo(String[] fileInfo) |
void | setFloatProperty(String key, float value) |
boolean | setFloatProperty(String key, float value, boolean isInt) |
void | setFormalCharges(int formalCharge) |
void | setFrameTitle(int modelIndex, String title) |
void | setFrameTitle(String title) |
void | setFrameVariables(int firstModelIndex, int lastModelIndex) |
void | setFrankOn(boolean TF) |
void | setImageFontScaling(int width, int height) |
void | setInMotion(boolean inMotion) |
void | setIntProperty(String key, int value) |
void | setIntProperty(String key, int value, boolean defineNew) |
void | setJmolDataFrame(String type, int modelIndex, int dataIndex) |
void | setJmolDefaults() |
void | setJmolStatusListener(JmolStatusListener jmolStatusListener) |
void | setLabel(String strLabel) |
void | setListVariable(String name, Token value) |
void | setMarBond(short marBond) |
void | setMaximumSize(int x) |
void | setMeasureDistanceUnits(String units) |
void | setMeasurementFormats(String strFormat) |
void | setMenu(String fileOrText, boolean isFile) |
void | setMinBondDistance(float minBondDistance) |
void | setMinimizer(MinimizerInterface minimizer) |
void | setModelVisibility() |
void | setModeMouse(int modeMouse) |
void | setNavigationDepthPercent(float timeSec, float percent) |
void | setNavigationMode(boolean TF) |
void | setNewRotationCenter(Point3f center) |
void | setNoneSelected(boolean noneSelected) |
void | setObjectArgb(String name, int argb) |
void | setObjectColor(String name, String colorName) |
void | setObjectMad(int iShape, String name, int mad) |
void | setPdbConectBonding(boolean isAuto) |
void | setPendingMeasurement(MeasurementPending measurementPending) |
void | setPercentVdwAtom(int percentVdwAtom) |
void | setPerspectiveDepth(boolean perspectiveDepth) |
void | setPerspectiveModel(int mode) |
void | setPickingMode(String mode) |
void | setPickingStyle(String style) |
void | setPropertyColorScheme(String scheme, boolean isOverloaded) |
void | setProteinType(byte iType, BitSet bs) |
void | setRasmolDefaults() |
void | setRefreshing(boolean TF) |
void | setRotationRadius(float angstroms, boolean doAll) |
void | setRubberbandArgb(int argb) |
void | setScreenDimension(Dimension dim) |
void | setSelectionHalos(boolean TF) |
void | setSelectionSet(BitSet set) |
void | setSelectionSubset(BitSet subset) |
void | setShapeProperty(int shapeID, String propertyName, Object value) |
void | setShapeProperty(int shapeID, String propertyName, Object value, BitSet bs) |
void | setShapePropertyArgb(int shapeID, String propertyName, int argb) |
void | setShapeSize(int shapeID, int size) |
void | setShapeSize(int shapeID, int size, 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) |
static void | setSpecular(boolean specular) |
static void | setSpecularExponent(int specularExponent) |
static void | setSpecularPercent(int specularPercent) |
static void | setSpecularPower(int specularPower) |
void | setSpin(String key, int value) |
void | setSpinOn(boolean spinOn) |
void | setStatusAtomHovered(int atomIndex, String info) |
void | setStatusAtomPicked(int atomIndex, String info) |
void | setStatusFileLoaded(int ptLoad, String fullPathName, String fileName, String modelName, String strError) |
void | setStatusFileNotLoaded(String fullPathName, String errorMsg) |
void | setStatusFrameChanged(int frameNo) |
void | setStatusMeasurePicked(int iatom, String strMeasure) |
void | setStatusMeasuring(String status, int count, String strMeasure) |
void | setStatusResized(int width, int height) |
void | setStatusScriptStarted(int iscript, String script) |
void | setStereoMode(int[] twoColors, int stereoMode, float degrees) |
void | setStrandCount(int type, int value) |
void | setStringProperty(String key, String value) |
void | setSync() |
void | setSyncDriver(int mode) |
void | setSyncTarget(int mode, boolean TF) |
void | setTainted(boolean TF) |
void | setTaintedAtoms(BitSet bs, byte type) |
void | setTrajectory(int modelIndex) |
void | setTrajectory(BitSet bsModels) |
void | setTransformManagerDefaults() |
static void | setUserScale(int[] scale) |
void | setVectorScale(float scale) |
void | setVibrationOff() |
void | setVibrationPeriod(float period) |
void | setVibrationScale(float scale) |
void | setVisualRange(float angstroms) |
void | showConsole(boolean showConsole) |
void | showMeasurement(int[] atomCountPlusIndices, boolean isON) |
boolean | showModelSetDownload() |
void | showParameter(String key, boolean ifNotSet, int nMax) |
void | showString(String str) |
void | showUrl(String urlString) |
void | slabByPixels(int pixels) |
void | slabDepthByPixels(int pixels) |
void | slabInternal(Point4f plane, boolean isDepth) |
void | slabReset() |
void | slabToPercent(int percentSlab) |
void | startSpinningAxis(int atomIndex1, int atomIndex2, boolean isClockwise) |
void | startSpinningAxis(Point3f pt1, Point3f pt2, boolean isClockwise) |
void | syncScript(String script, String applet) |
void | toCartesian(Point3f pt) |
void | toFractional(Point3f pt) |
void | toggleMeasurement(int[] atomCountPlusIndices, String strFormat) |
void | togglePickingLabel(BitSet bs) |
void | toUnitCell(Point3f pt, Point3f offset) |
Point3i | transformPoint(Point3f pointAngstroms) |
Point3i | transformPoint(Point3f pointAngstroms, Vector3f vibrationVector) |
void | transformPoint(Point3f pointAngstroms, Point3i pointScreen) |
void | transformPoint(Point3f pointAngstroms, Point3f pointScreen) |
void | transformPointNoClip(Point3f pointAngstroms, Point3f pt) |
void | transformPoints(Point3f[] pointsAngstroms, Point3i[] pointsScreens) |
void | transformVector(Vector3f vectorAngstroms, Vector3f vectorTransformed) |
void | translateToXPercent(float percent) |
void | translateToYPercent(float percent) |
void | translateToZPercent(float percent) |
void | translateXYBy(int xDelta, int yDelta) |
void | unsetProperty(String name) |
void | unTransformPoint(Point3f pointScreen, Point3f pointAngstroms) |
boolean | useMinimizationThread() |
boolean | usingScriptQueue() |
void | writeTextFile(String file, String data) |
void | zap(boolean notify, boolean resetUndo) |
void | zap(String msg) |
void | zoomBy(int pixels) |
void | zoomByFactor(float factor) |
int | zValueFromPercent(int zPercent) |
private boolean antialiasDisplay
private String appletCodeBase
private String appletDocumentBase
private boolean autoExit
private boolean axesAreTainted
boolean checking
private boolean checkScriptOnly
private boolean creatingImage
private int currentCursor
public static final int CURSOR_CROSSHAIR
public static final int CURSOR_DEFAULT
public static final int CURSOR_HAND
public static final int CURSOR_MOVE
public static final int CURSOR_WAIT
final Dimension dimScreen
private Component display
private Hashtable evalVariables
private boolean fileOpenCheck
boolean frankOn
private String fullName
private boolean haveDisplay
int hoverAtomIndex
String hoverText
private String htmlName
private float imageFontScaling
String interruptScript
private boolean isApplet
private boolean isPreviewOnly
boolean isScriptQueued
private boolean isSignedApplet
private boolean isSilent
boolean isTainted
private boolean jvm11orGreater
private boolean jvm12orGreater
private boolean jvm14orGreater
private boolean listCommands
private int maximumSize
int motionEventNumber
private boolean mustRender
private boolean noneSelected
int prevFrame
private boolean refreshing
int scriptIndex
private String strJavaVendor
private String strJavaVersion
private String strOSName
private String syncId
static final String STATE_VERSION_STAMP
public static Object testData
public static Object testData2
private boolean useCommandThread
boolean wasInMotion
private String writeInfo
public Viewer(Component display,
JmolAdapter modelAdapter)
void addCommand(String command)
Adds one or more commands to the command history
Parameters: command the command to add
void addLoadScript(String script)
void addStateScript(String script, boolean addFrameNumber, boolean postDefinitions)
void addStateScript(String script1, BitSet bsBonds, BitSet bsAtoms1, BitSet bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)
NOTE: for APPLICATION AND APPLET call
setModeMouse(JmolConstants.MOUSE_NONE);
before setting viewer=null
in order to remove references to display window in listeners and hoverWatcher
This is the main access point for creating an application
or applet viewer. After allocation it is MANDATORY that one of
the next commands is either
viewer.evalString("ZAP");
or at least:
viewer.setAppletContext("",null,null,"")
One or the other of these is necessary to establish the
first modelset, which might be required by one or more
later evaluated commands or file loadings.
Parameters: display either DisplayPanel or WrappedApplet modelAdapter the model reader
Returns: a viewer instance
public byte[] allocTempBytes(int size)
public Point3f[] allocTempPoints(int size)
public Point3i[] allocTempScreens(int size)
boolean allowRotateSelected()
public boolean areAxesTainted()
void assignAromaticBonds()
void atomPicked(int atomIndex, Point3f ptClicked, int modifiers)
int autoHbond(BitSet bsBonds)
int autoHbond(BitSet bsFrom, BitSet bsTo, BitSet bsBonds)
void calcBoundBoxDimensions(BitSet bs)
float calcRotationRadius(Point3f center)
public float calcRotationRadius(BitSet bs)
void calcSelectedGroupsCount()
void calcSelectedMoleculesCount()
void calcSelectedMonomersCount()
public Vector3f calculateMolecularDipole()
String calculatePointGroup()
public void calculateStraightness()
void calculateStructures(BitSet bsAtoms)
public Point3f[] calculateSurface(BitSet bsSelected, float envelopeRadius)
public boolean checkHalt(String strScript)
Point3f checkObjectClicked(int x, int y, int modifiers)
void checkObjectDragged(int prevX, int prevY, int deltaX, int deltaY, int modifiers)
boolean checkObjectHovered(int x, int y)
public boolean checkResume(String strScript)
private void clear()
void clearAllMeasurements()
void clearBfactorRange()
void clearClickCount()
void clearConsole()
public void clearMeasurements()
private void clearMinimization()
public void clearScriptQueue()
public void clearSelection()
private void createImage(String type_name)
Parameters: type_name TYPE:filename\twidth\theight\tquality
public String createImage(String file, String type, Object text_or_bytes, int quality, int width, int height)
void defineMeasurement(Vector monitorExpressions, float[] rangeMinMax, boolean isDelete, boolean isAll, boolean isAllConnected, boolean isOn, boolean isOff, String strFormat)
public int deleteAtoms(BitSet bs, boolean fullModels)
public void deleteMeasurement(int i)
void deleteMeasurement(int[] atomCountPlusIndices)
void depthByPixels(int pixels)
void depthToPercent(int percentDepth)
public String dialogAsk(String type, String fileName)
void display(BitSet bs, boolean isQuiet)
void echoMessage(String msg)
String eval(String strEval)
public String evalFile(String strFilename)
public String evalString(String strScript)
public String evalStringQuiet(String strScript)
private String evalStringQuiet(String strScript, boolean isQuiet, boolean allowSyncScript)
public Object evalStringWaitStatus(String returnType, String strScript, String statusList)
Object evalStringWaitStatus(String returnType, String strScript, String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)
public Object evaluateExpression(Object stringOrTokens)
public void fillAtomData(
AtomData atomData, int mode)
protected void finalize()
void finalizeTransformParameters()
int findNearestAtomIndex(int x, int y)
public String formatText(String text0)
boolean frankClicked(int x, int y)
public void freeTempBytes(byte[] tempBytes)
public void freeTempPoints(Point3f[] tempPoints)
public void freeTempScreens(Point3i[] tempScreens)
public float[][] functionXY(String functionName, int nX, int nY)
fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full
set of Double[][] in one function call. Otherwise it reads the values using
individual function calls, which each return Double.
If the functionName begins with "file:" then data are read from
a file specified after the colon. The sign of nX is not relevant in that case.
The file may contain mixed numeric and non-numeric values;
the non-numeric values will be skipped by Parser.parseFloatArray
Parameters: functionName nX nY
Returns: nX by nY array of floating values
public String generateOutput(String type, String fileName, int width, int height)
Vector getAllAtomInfo(Object atomExpression)
Vector getAllBondInfo(Object atomExpression)
public Hashtable getAllChainInfo(Object atomExpression)
boolean getAllowEmbeddedScripts()
public Hashtable getAllPolymerInfo(Object atomExpression)
String getAllSettings(String prefix)
public String getAltLocListInModel(int modelIndex)
static int getAmbientPercent()
int getAnimationDirection()
public int getAnimationFps()
Hashtable getAnimationInfo()
int getAnimationReplayMode()
public boolean getAppendNew()
Hashtable getAppletInfo()
public boolean getApplySymmetryToBonds()
public int getAtomArgb(int i)
public BitSet getAtomBits(int tokType, Object specInfo)
BitSet getAtomBitSet(Object atomExpression)
Vector getAtomBitSetVector(Object atomExpression)
String getAtomChain(int i)
public int getAtomCount()
public int getAtomCountInModel(int modelIndex)
public void getAtomIdentityInfo(int atomIndex, Hashtable info)
int getAtomIndexFromAtomNumber(int atomNumber)
int[] getAtomIndices(BitSet bs)
public String getAtomInfo(int atomIndex)
public String getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
public int getAtomModelIndex(int i)
public String getAtomName(int i)
public int getAtomNumber(int i)
private boolean getAtomPicking()
public Point3f getAtomPoint3f(int i)
public float getAtomRadius(int i)
BitSet getAtomsConnected(float min, float max, int intType, BitSet bs)
BitSet getAtomsWithin(float distance, Point3f coord)
BitSet getAtomsWithin(float distance, Point4f plane)
BitSet getAtomsWithin(float distance, BitSet bs, boolean isWithinModelSet)
String getAtomSequenceCode(int i)
public Point3f getAtomSetCenter(BitSet bs)
public float getAtomVdwRadius(int i)
float getAtomX(int i)
float getAtomY(int i)
float getAtomZ(int i)
public boolean getAutoBond()
boolean getAutoFps()
public Hashtable getAuxiliaryInfo(Object atomExpression)
Point3f getAverageAtomPoint()
public Component getAwtComponent()
public int getAxesMode()
public boolean getAxesOrientationRasmol()
public float getAxesScale()
void getAxisAngle(AxisAngle4f axisAngle)
public Point3f[] getAxisPoints()
public int getBackgroundArgb()
public int getBackgroundModelIndex()
BitSet getBitSetSelection()
public BitSet getBitSetTrajectories()
public int getBondArgb1(int i)
public int getBondArgb2(int i)
public int getBondCount()
For use in setting a for() construct max value
Returns: used size of the bonds array;
public int getBondCountInModel(int modelIndex)
from JmolPopup.udateModelSetComputedMenu
Parameters: modelIndex the model of interest or -1 for all
Returns: the actual number of connections
public int getBondModelIndex(int i)
public short getBondOrder(int i)
public boolean getBondPicking()
public Point3f getBondPoint3f1(int i)
public Point3f getBondPoint3f2(int i)
public float getBondRadius(int i)
BitSet getBondsForSelectedAtoms(BitSet bsAtoms)
public boolean getBondSelectionModeOr()
public float getBondTolerance()
public boolean getBooleanProperty(String key)
public boolean getBooleanProperty(String key, boolean doICare)
Parameters: key doICare true if you want an error message if it doesn't exist
Returns: the boolean property mth 2005 06 24 and/or these property names
should be interned strings so that we can just do == comparisions
between strings
public Point3f getBoundBoxCenter()
public int getBoundBoxCenterX()
public int getBoundBoxCenterY()
public String getBoundBoxCommand(boolean withOptions)
public Vector3f getBoundBoxCornerVector()
Hashtable getBoundBoxInfo()
public BitSet getBoundBoxModels()
BitSet getBranchBitSet(int atomIndex, int atomIndexNot)
Object getBufferedReaderForString(String string)
Object getBufferedReaderOrErrorMessageFromName(String name, String[] fullPathNameReturn, boolean isBinary)
public boolean getCartoonRocketFlag()
public boolean getChainCaseSensitive()
public int getChainCount()
public int getChainCountInModel(int modelIndex)
public int getChainCountInModel(int modelIndex, boolean countWater)
public String getChimeInfo(int tok)
BitSet getClickableSet()
public String getClientAtomStringProperty(Object clientAtom, String propertyName)
Object getClientFile()
short getColix(Object object)
public int getColixArgb(short colix)
public short getColixAtomPalette(
Atom atom, byte pid)
public short getColixBackgroundContrast()
public short getColixForPropertyValue(float val)
public short getColixRubberband()
Point3f getColorPointForPropertyValue(float val)
public int[] getColorSchemeArray(String colorScheme)
public String getColorSchemeList(String colorScheme, boolean ifDefault)
public String getCoordinateState(BitSet bsSelected)
public float[] getCurrentColorRange()
public Object getCurrentFileAsBytes()
public String getCurrentFileAsString()
public int getCurrentModelIndex()
public float getCurrentSolventProbeRadius()
Point3f getCurrentUnitCellOffset()
public int getCursorX()
public int getCursorY()
Object[] getData(String type)
public String getData(String atomExpression, String type)
float[] getDataFloat(String label)
public float getDataFloat(String label, int atomIndex)
float[][] getDataFloat2D(String label)
String getDataSeparator()
boolean getDebugScript()
String getDefaultDirectory()
public float getDefaultDrawArrowScale()
Point3f getDefaultLattice()
String getDefaultLoadScript()
public short getDefaultMadAtom()
public String getDefaultMeasurementLabel(int nPoints)
float getDefaultTranslucent()
String getDefaultVdw(int iMode)
int getDelayMaximum()
public BitSet getDeletedAtoms()
static int getDiffusePercent()
public float getDipoleScale()
boolean getDisablePopupMenu()
public boolean getDisplayCellParameters()
public int getDisplayModelIndex()
public int getDotDensity()
public boolean getDotsSelectedOnlyFlag()
public boolean getDotSurfaceFlag()
public boolean getDrawHover()
public boolean getDrawPicking()
public boolean getDynamicMeasurements()
public boolean getEchoStateActive()
int getElementNumber(int i)
public BitSet getElementsPresentBitSet(int modelIndex)
String getElementSymbol(int i)
Hashtable getEvalVariables()
public String getExportDriverList()
This is the method that should be used to extract the model data from Jmol.
Note that the API provided by JmolAdapter is used to import data into Jmol
and to export data out of Jmol.
When exporting, a few of the methods in JmolAdapter do not make sense.
openBufferedReader(...) Others may be implemented in the future, but are
not currently all pdb specific things Just pass in null for the methods
that want a clientFile. The main methods to use are getFrameCount(null) ->
currently always returns 1 getAtomCount(null, 0) getAtomIterator(null, 0)
getBondIterator(null, 0)
The AtomIterator and BondIterator return Objects as unique IDs to identify
the atoms. atomIterator.getAtomUid() bondIterator.getAtomUid1() &
bondIterator.getAtomUid2() The ExportJmolAdapter will return the 0-based
atom index as a boxed Integer. That means that you can cast the results to
get a zero-based atom index int atomIndex =
((Integer)atomIterator.getAtomUid()).intValue(); ... int bondedAtom1 =
((Integer)bondIterator.getAtomUid1()).intValue(); int bondedAtom2 =
((Integer)bondIterator.getAtomUid2()).intValue();
post questions to jmol-developers@lists.sf.net
Returns: A JmolAdapter
Object getFileAsImage(String pathName, Hashtable htParams)
public String getFileAsString(String name)
boolean getFileAsString(String[] data)
String getFileHeader()
String[] getFileInfo()
public String getFileName()
Font3D getFont3D(String fontFace, String fontStyle, float fontSize)
public boolean getFontScaling()
public boolean getForceAutoBond()
String getFrameTitle(int modelIndex)
public String getFrameTitle()
public String getFullPathName()
boolean getGreyscaleRendering()
public int getGroupCount()
public int getGroupCountInModel(int modelIndex)
public boolean getHbondsBackbone()
public boolean getHbondsSolid()
void getHelp(String what)
public int getHermiteLevel()
public Hashtable getHeteroList(int modelIndex)
public String getHexColorFromIndex(short colix)
BitSet getHiddenSet()
boolean getHideNameInPopup()
public boolean getHighResolution()
int getHoverDelay()
String getHtmlName()
public String getHybridizationAndAxes(int atomIndex, Vector3f z, Vector3f x, String lcaoType, boolean hybridizationCompatible)
private Image getImage(boolean isDouble)
public float getImageFontScaling()
public char getInlineChar()
public boolean getInMotion()
String getInterruptScript()
boolean getIsosurfacePropertySmoothing()
public String getJavaVendor()
public String getJavaVersion()
int getJmolDataFrameIndex(int modelIndex, String type)
public int getJmolDataSourceFrame(int modelIndex)
String getJmolFrameType(int modelIndex)
public static String getJmolVersion()
private static int getJmolVersionInt()
public Object getJpeg(int quality, boolean asString)
Parameters: quality asString
Returns: base64-encoded or binary version of the image
public boolean getJustifyMeasurements()
Object getListVariable(String name, Object value)
String getLoadFormat()
String getLoadState()
static int getLogLevel()
public short getMadBond()
public short getMarBond()
Matrix3f getMatrixRotate()
public Matrix4f getMatrixtransform()
float getMaxZoomPercent()
public boolean getMeasureAllModelsFlag()
public String getMeasureDistanceUnits()
public int getMeasurementCount()
public int[] getMeasurementCountPlusIndices(int i)
Vector getMeasurementInfo()
public String getMeasurementInfoAsString()
public String getMeasurementStringValue(int i)
String getMenu(String type)
public Hashtable getMessageQueue()
boolean getMessageStyleChime()
public float getMinBondDistance()
public String getMinimizationInfo()
public BitSet getModelAtomBitSet(int modelIndex, boolean asCopy)
public Hashtable getModelAuxiliaryInfo(int modelIndex)
public Object getModelAuxiliaryInfo(int modelIndex, String keyName)
public BitSet getModelBitSet(BitSet atomList)
public int getModelCount()
public Vector3f getModelDipole()
String getModelExtract(Object atomExpression)
public String getModelFileInfo()
String getModelFileInfoAll()
private String getModelFileName(int modelIndex)
public int getModelFileNumber(int modelIndex)
public Hashtable getModelInfo(Object atomExpression)
String getModelInfoAsString()
public String getModelName(int modelIndex)
public int getModelNumber(int modelIndex)
public String getModelNumberDotted(int modelIndex)
int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
public Properties getModelProperties(int modelIndex)
public String getModelProperty(int modelIndex, String propertyName)
public Object getModelSetAuxiliaryInfo(String strKey)
public Hashtable getModelSetAuxiliaryInfo()
public String getModelSetFileName()
public String getModelSetName()
public String getModelSetPathName()
public Properties getModelSetProperties()
public String getModelSetProperty(String strProp)
public String getModelSetTypeName()
private String getModelTitle(int modelIndex)
public byte getModeMultipleBond()
Vector getMoleculeInfo(Object atomExpression)
public int getMotionEventNumber()
String getMoveToText(float timespan)
public boolean getNavigating()
Point3f getNavigationCenter()
public boolean getNavigationCentered()
float getNavigationDepthPercent()
boolean getNavigationMode()
public Point3f getNavigationOffset()
float getNavigationOffsetPercent(char XorY)
boolean getNavigationPeriodic()
float getNavigationSpeed()
Boolean getNoneSelected()
int getObjectArgb(int objId)
public short getObjectColix(int objId)
public int getObjectMad(int objId)
public String getObjectState(String name)
public String getOpenFileError()
misnamed -- really this opens the file, gets the data, and returns error or null
Returns: errorMsg
String getOpenFileError(boolean isAppend)
the opener for Jmol
Parameters: isAppend
Returns: errorMsg
public String getOperatingSystemName()
Hashtable getOrientationInfo()
String getOrientationText(int type)
public Object getParameter(String key)
Object getParameterEscaped(String key)
public float[] getPartialCharges()
public String getPdbData(BitSet bs)
String getPdbData(int modelIndex, String type)
public boolean getPdbLoadInfo(int type)
String getPDBHeader()
public int getPercentVdwAtom()
public boolean getPerspectiveDepth()
public int getPickingMode()
int getPickingSpinRate()
int getPickingStyle()
public String getPointGroupAsString(boolean asDraw, String type, int index, float scale)
public Hashtable getPointGroupInfo(Object atomExpression)
public float getPointGroupTolerance(int type)
public int getPolymerCount()
public int getPolymerCountInModel(int modelIndex)
public Point3f[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
void getPolymerPointsAndVectors(BitSet bs, Vector vList)
public Object getProperty(String returnType, String infoType, String paramInfo)
public Object getProperty(String returnType, String infoType, Object paramInfo)
public String getPropertyColorScheme()
String getProteinStructureState()
public char getQuaternionFrame()
boolean getRasmolHeteroSetting()
boolean getRasmolHydrogenSetting()
boolean getRefreshing()
public int getRibbonAspectRatio()
public boolean getRibbonBorder()
public boolean getRocketBarrelFlag()
void getRotation(Matrix3f matrixRotation)
public Point3f getRotationCenter()
public float getRotationRadius()
Rectangle getRubberBandSelection()
String getSavedCoordinates(String saveName)
public String getSavedState(String saveName)
String getSavedStructure(String saveName)
public float getScalePixelsPerAngstrom()
public int getScreenDim()
public int getScreenHeight()
public Image getScreenImage()
public int getScreenWidth()
int getScriptDelay()
boolean getSelectAllModels()
public int getSelectionCount()
public boolean getSelectionHaloEnabled()
public BitSet getSelectionSet()
public BitSet getSelectionSubset()
BitSet getSequenceBits(String specInfo, BitSet bs)
public String getSetHistory(int howFarBack)
Options include:
; all n == Integer.MAX_VALUE
; n prev n >= 1
; next n == -1
; set max to -2 - n n <= -3
; just clear n == -2
; clear and turn off; return "" n == 0
; clear and turn on; return "" n == Integer.MIN_VALUE;
Parameters: howFarBack number of lines (-1 for next line)
Returns: one or more lines of command history
int getShapeIdFromObjectName(String objectName)
public Hashtable getShapeInfo()
public Object getShapeProperty(int shapeType, String propertyName)
Object getShapeProperty(int shapeType, String propertyName, int index)
int getShapePropertyAsInt(int shapeID, String propertyName)
public float getSheetSmoothing()
public boolean getShowAxes()
public boolean getShowBbcage()
public boolean getShowFrank()
public boolean getShowHiddenSelectionHalos()
public boolean getShowHydrogens()
public boolean getShowMeasurementLabels()
public boolean getShowMeasurements()
public boolean getShowMultipleBonds()
public boolean getShowNavigationPoint()
public boolean getShowUnitCell()
public boolean getSlabEnabled()
public boolean getSmartAromatic()
boolean getSolventOn()
float getSolventProbeRadius()
public String getSpaceGroupInfoText(String spaceGroup)
boolean getSpecular()
static int getSpecularPercent()
String getSpecularState()
float getSpinFps()
boolean getSpinOn()
String getSpinState()
float getSpinX()
float getSpinY()
float getSpinZ()
public boolean getSsbondsBackbone()
public String getStandardLabelFormat()
public String getStateInfo()
public String getStateInfo(String type)
Object getStatusChanged(String statusNameList)
float getStereoDegrees()
private Image getStereoImage(int stereoMode)
int getStereoMode()
public int getStrandCount(int type)
public String getStructureState()
int getSurfaceDistanceMax()
String getSymmetryInfoAsString()
BitSet getTaintedAtoms(byte type)
public boolean getTestFlag1()
public boolean getTestFlag2()
public boolean getTestFlag3()
public boolean getTestFlag4()
public boolean getTraceAlpha()
String getTrajectoryInfo()
String getTransformText()
String getTranslationScript()
float getTranslationXPercent()
float getTranslationYPercent()
float getTranslationZPercent()
public String getUnitCellInfoText()
public Matrix4f getUnscaledTransformMatrix()
public boolean getUseNumberLocalization()
public int getVanderwaalsMar(int i)
public int getVanderwaalsMar(int i, int iMode)
public float getVectorScale()
float getVibrationCoord(int atomIndex, char c)
float getVibrationPeriod()
float getVibrationScale()
public Vector3f getVibrationVector(int atomIndex)
public BitSet getVisibleFramesBitSet()
BitSet getVisibleSet()
public boolean getWireframeRotation()
public
AtomIndexIterator getWithinAtomSetIterator(int atomIndex, float distance, BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased)
public boolean getZeroBasedXyzRasmol()
boolean getZoomEnabled()
boolean getZoomLarge()
public int getZoomPercent()
public float getZoomPercentFloat()
float getZoomSetting()
boolean getZShade()
public void haltScriptExecution()
public boolean handleOldJvm10Event(Event e)
public boolean hasCalculatedHBonds(BitSet bsAtoms)
boolean haveFileSet()
public boolean haveFrame()
boolean haveModelSet()
public boolean havePartialCharges()
void hide(BitSet bs, boolean isQuiet)
void hideMeasurements(boolean isOFF)
public void homePosition()
void hoverOff()
public void hoverOn(int atomIndex)
public void hoverOn(int x, int y, String text)
void initialize()
private void initializeModel()
void invertSelected(Point3f pt, BitSet bs)
void invertSelected(Point3f pt, Point4f plane)
void invertSelection()
boolean isAnimationOn()
public boolean isApplet()
boolean isInPosition(Point3f pt, float degrees)
boolean isInSelectionSubset(int atomIndex)
public boolean isJmolDataFrame(int modelIndex)
public boolean isJmolDataFrame()
boolean isJmolVariable(String key)
public boolean isJvm12orGreater()
boolean isPreviewOnly()
public boolean isRangeSelected()
public boolean isScriptExecuting()
public boolean isSelected(int atomIndex)
public boolean isSignedApplet()
boolean isTrajectory(int modelIndex)
public boolean isVibrationOn()
boolean isWindowCentered()
String listSavedStates()
void loadData(int type, String name, String coordinateData)
public void loadInline(String strModel)
public void loadInline(String strModel, boolean isAppend)
public void loadInline(String strModel, char newLine)
boolean loadInline(String strModel, char newLine, boolean isAppend)
public void loadInline(String[] arrayModels)
public void loadInline(String[] arrayModels, boolean isAppend)
public void loadShape(int shapeID)
int[] makeConnections(float minDistance, float maxDistance, short order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds)
public boolean modelHasVibrationVectors(int modelIndex)
boolean modelSetHasVibrationVectors()
void move(Vector3f dRot, float dZoom, Vector3f dTrans, float dSlab, float floatSecondsTotal, int fps)
void moveTo(float floatSecondsTotal, Point3f center, Point3f pt, float degrees, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth)
void moveTo(float floatSecondsTotal, Matrix3f rotationMatrix, Point3f center, float zoom, float xTrans, float yTrans, float rotationRadius, Point3f navCenter, float xNav, float yNav, float navDepth)
private void moveUpdate(float floatSecondsTotal)
boolean mustRenderFlag()
void navigate(int keyWhere, int modifiers)
void navigate(float timeSeconds, Point3f[] path, float[] theta, int indexStart, int indexEnd)
void navigate(float timeSeconds, Point3f center)
void navigate(float timeSeconds, Point3f[][] pathGuide)
void navigate(float timeSeconds, Vector3f rotAxis, float degrees)
void navTranslate(float timeSeconds, Point3f center)
void navTranslatePercent(float timeSeconds, float x, float y)
public void notifyMinimizationStatus()
public void openClientFile(String fullPathName, String fileName, Object clientFile)
public void openDOM(Object DOMNode)
public void openFile(String name)
void openFile(String name, Hashtable htParams, String loadScript, boolean isAppend)
public void openFiles(String modelName, String[] names)
void openFiles(String modelName, String[] names, String loadScript, boolean isAppend)
public void openReader(String fullPathName, String name, Reader reader)
Opens the file, given the reader.
name is a text name of the file ... to be displayed in the window no need
to pass a BufferedReader ... ... the FileManager will wrap a buffer around
it
DO NOT USE IN JMOL -- THIS METHOD IS ONLY HERE BECAUSE IT IS
PART OF THE LEGACY INTERFACE
IF USED BY ANOTHER APPLICATION, YOU ARE RESPONSIBLE FOR CLOSING THE READER
Parameters: fullPathName name reader
public void openStringInline(String strModel)
private boolean openStringInline(String strModel, Hashtable htParams, boolean isAppend)
private void openStringsInline(String[] arrayModels, Hashtable htParams, boolean isAppend)
void pauseAnimation()
public void pauseScriptExecution()
public void popHoldRepaint()
void popupMenu(int x, int y)
public void pushHoldRepaint()
public void rebond()
public void refresh(int mode, String strWhy)
initiate a repaint/update sequence if it has not already been requested.
invoked whenever any operation causes changes that require new rendering.
The repaint/update sequence will only be invoked if (a) no repaint is already
pending and (b) there is no hold flag set in repaintManager.
Sequence is as follows:
1) RepaintManager.refresh() checks flags and then calls Viewer.repaint()
2) Viewer.repaint() invokes display.repaint(), provided display is not null (headless)
3) The system responds with an invocation of Jmol.update(Graphics g), which we are
routing through Jmol.paint(Graphics g).
4) Jmol.update invokes Viewer.setScreenDimension(size), which makes the
necessary changes in parameters for any new window size.
5) Jmol.update invokes Viewer.renderScreenImage(g, size, rectClip)
6) Viewer.renderScreenImage checks object visibility, invokes render1 to
do the actual creation of the image pixel map and send it to the screen,
and then invokes repaintView()
7) Viewer.repaintView() invokes RepaintManager.repaintDone(), to clear the flags and
then use notify() to release any threads holding on wait().
Parameters: mode strWhy
public void refreshMeasures()
public void releaseScreenImage()
String removeCommand()
Removes one command from the command history
Returns: command removed
void removeUserVariable(String key)
private void render()
private void render1(Graphics g, Image img, int x, int y)
public void renderScreenImage(Graphics g, Dimension size, Rectangle clip)
void repaint()
public void repaintView()
void reportSelection(String msg)
void requestRepaintAndWait()
void reset()
void resetAromatic()
private void resizeImage(int width, int height, boolean isImageWrite, boolean isGenerator, boolean isReset)
boolean restoreBonds(String saveName)
void restoreModelOrientation(int modelIndex)
void restoreModelRotation(int modelIndex)
boolean restoreOrientation(String saveName, float timeSeconds)
public void restoreRotation(String saveName, float timeSeconds)
boolean restoreSelection(String saveName)
void resumeAnimation()
public void resumeScriptExecution()
void reverseAnimation()
void rewindAnimation()
void rotateAboutPointsInternal(Point3f point1, Point3f point2, float nDegrees, float endDegrees, boolean isSpin, BitSet bsSelected)
void rotateAtoms(Matrix3f mNew, Matrix3f matrixRotate, boolean fullMolecule, Point3f center, boolean isInternal, BitSet bsAtoms)
void rotateAxisAngleAtCenter(Point3f rotCenter, Vector3f rotAxis, float degrees, float endDegrees, boolean isSpin, BitSet bsSelected)
public void rotateFront()
void rotateMolecule(int deltaX, int deltaY)
public void rotatePoint(Point3f pt, Point3f ptRot)
public void rotateX(float angleRadians)
public void rotateX(int angleDegrees)
void rotateXYBy(int xDelta, int yDelta)
public void rotateY(float angleRadians)
public void rotateY(int angleDegrees)
public void rotateZ(float angleRadians)
void rotateZBy(int zDelta)
void saveBonds(String saveName)
public void saveCoordinates(String saveName, BitSet bsSelected)
void saveModelOrientation()
void saveOrientation(String saveName)
void saveSelection(String saveName)
void saveState(String saveName)
void saveStructure(String saveName)
public float scaleToPerspective(int z, float sizeAngstroms)
public short scaleToScreen(int z, int milliAngstroms)
public String script(String strScript)
public String scriptCheck(String strScript)
public void scriptEcho(String strEcho)
private void scriptError(String msg)
void scriptStatus(String strStatus)
public String scriptWait(String strScript)
public Object scriptWaitStatus(String strScript, String statusList)
void select(BitSet bs, boolean isQuiet)
public void selectAll()
void selectBonds(BitSet bs)
void selectRectangle(Rectangle rect, int modifiers)
void setAllowRotateSelected(boolean TF)
private static void setAmbientPercent(int ambientPercent)
void setAnimationDirection(int direction)
public void setAnimationFps(int fps)
void setAnimationLast()
void setAnimationNext()
void setAnimationOn(boolean animationOn)
void setAnimationPrevious()
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)
public void setAppletContext(String fullName, URL documentBase, URL codeBase, String commandOptions)
void setApplySymmetryToBonds(boolean TF)
public void setAtomCoord(int atomIndex, float x, float y, float z)
void setAtomCoord(BitSet bs, int tokType, Object xyzValues)
public void setAtomCoordRelative(int atomIndex, float x, float y, float z)
void setAtomCoordRelative(Point3f offset)
void setAtomProperty(BitSet bs, int tok, int iValue, float fValue, float[] values)
public void setAutoBond(boolean TF)
private void setAxesModeMolecular(boolean TF)
void setAxesModeUnitCell(boolean TF)
public void setAxesOrientationRasmol(boolean TF)
void setAxesScale(float scale)
void setBackgroundImage(String fileName, Image image)
void setBackgroundModelIndex(int modelIndex)
public void setBondTolerance(float bondTolerance)
public void setBooleanProperty(String key, boolean value)
boolean setBooleanProperty(String key, boolean value, boolean defineNew)
void setBoundBox(Point3f pt1, Point3f pt2, boolean byCorner)
void setCenterAt(String relativeTo, Point3f pt)
void setCenterBitSet(BitSet bsCenter, boolean doScale)
public void setCenterSelected()
public void setColorBackground(String colorName)
public BitSet setConformation()
public BitSet setConformation(int conformationIndex)
void setCurrentColorRange(String label)
void setCurrentColorRange(float[] data, BitSet bs)
public void setCurrentColorRange(float min, float max)
void setCurrentModelIndex(int modelIndex)
public void setCurrentModelIndex(int modelIndex, boolean clearBackground)
void setCurrentUnitCellOffset(int offset)
void setCurrentUnitCellOffset(Point3f pt)
public void setCursor(int cursor)
public void setData(String type, Object[] data, int atomCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)
public void setDebugScript(boolean debugScript)
private void setDefaultColors(String colorScheme)
public void setDefaultDrawArrowScale(float scale)
void setDefaultLattice(Point3f ptLattice)
private void setDefaults(String type)
void setDefaultVdw(String mode)
private static void setDiffusePercent(int diffusePercent)
void setDynamicMeasurements(boolean TF)
void setEchoStateActive(boolean TF)
void setElementArgb(int elementNumber, int argb)
void setFileInfo(String[] fileInfo)
public void setFloatProperty(String key, float value)
private boolean setFloatProperty(String key, float value, boolean isInt)
void setFormalCharges(int formalCharge)
void setFrameTitle(int modelIndex, String title)
void setFrameTitle(String title)
void setFrameVariables(int firstModelIndex, int lastModelIndex)
public void setFrankOn(boolean TF)
private void setImageFontScaling(int width, int height)
void setInMotion(boolean inMotion)
public void setIntProperty(String key, int value)
private void setIntProperty(String key, int value, boolean defineNew)
void setJmolDataFrame(String type, int modelIndex, int dataIndex)
public void setJmolDefaults()
void setLabel(String strLabel)
void setListVariable(String name,
Token value)
public void setMarBond(short marBond)
private void setMaximumSize(int x)
void setMeasureDistanceUnits(String units)
void setMeasurementFormats(String strFormat)
void setMenu(String fileOrText, boolean isFile)
public void setMinBondDistance(float minBondDistance)
void setModelVisibility()
public void setModeMouse(int modeMouse)
void setNavigationDepthPercent(float timeSec, float percent)
private void setNavigationMode(boolean TF)
void setNewRotationCenter(Point3f center)
void setNoneSelected(boolean noneSelected)
void setObjectArgb(String name, int argb)
void setObjectColor(String name, String colorName)
void setObjectMad(int iShape, String name, int mad)
void setPdbConectBonding(boolean isAuto)
public void setPercentVdwAtom(int percentVdwAtom)
public void setPerspectiveDepth(boolean perspectiveDepth)
private void setPerspectiveModel(int mode)
private void setPickingMode(String mode)
private void setPickingStyle(String style)
public void setPropertyColorScheme(String scheme, boolean isOverloaded)
void setProteinType(byte iType, BitSet bs)
public void setRasmolDefaults()
void setRefreshing(boolean TF)
void setRotationRadius(float angstroms, boolean doAll)
void setRubberbandArgb(int argb)
public void setScreenDimension(Dimension dim)
public void setSelectionHalos(boolean TF)
public void setSelectionSet(BitSet set)
void setSelectionSubset(BitSet subset)
public void setShapeProperty(int shapeID, String propertyName, Object value)
void setShapeProperty(int shapeID, String propertyName, Object value, BitSet bs)
void setShapePropertyArgb(int shapeID, String propertyName, int argb)
void setShapeSize(int shapeID, int size)
public void setShapeSize(int shapeID, int size, BitSet bsAtoms)
public void setShowAxes(boolean value)
public void setShowBbcage(boolean value)
public void setShowHydrogens(boolean TF)
public void setShowMeasurements(boolean TF)
public void setShowUnitCell(boolean value)
void setSlabDepthInternal(boolean isDepth)
private static void setSpecular(boolean specular)
private static void setSpecularExponent(int specularExponent)
private static void setSpecularPercent(int specularPercent)
private static void setSpecularPower(int specularPower)
void setSpin(String key, int value)
void setSpinOn(boolean spinOn)
public void setStatusAtomHovered(int atomIndex, String info)
public void setStatusAtomPicked(int atomIndex, String info)
void setStatusFileLoaded(int ptLoad, String fullPathName, String fileName, String modelName, String strError)
private void setStatusFileNotLoaded(String fullPathName, String errorMsg)
void setStatusFrameChanged(int frameNo)
public void setStatusMeasurePicked(int iatom, String strMeasure)
public void setStatusMeasuring(String status, int count, String strMeasure)
public void setStatusResized(int width, int height)
void setStatusScriptStarted(int iscript, String script)
void setStereoMode(int[] twoColors, int stereoMode, float degrees)
private void setStrandCount(int type, int value)
public void setStringProperty(String key, String value)
void setSync()
void setSyncDriver(int mode)
private void setSyncTarget(int mode, boolean TF)
void setTainted(boolean TF)
public void setTaintedAtoms(BitSet bs, byte type)
void setTrajectory(int modelIndex)
public void setTrajectory(BitSet bsModels)
private void setTransformManagerDefaults()
public static void setUserScale(int[] scale)
public void setVectorScale(float scale)
void setVibrationOff()
public void setVibrationPeriod(float period)
public void setVibrationScale(float scale)
public void setVisualRange(float angstroms)
void showConsole(boolean showConsole)
public void showMeasurement(int[] atomCountPlusIndices, boolean isON)
public boolean showModelSetDownload()
void showParameter(String key, boolean ifNotSet, int nMax)
public void showString(String str)
public void showUrl(String urlString)
void slabByPixels(int pixels)
void slabDepthByPixels(int pixels)
void slabInternal(Point4f plane, boolean isDepth)
void slabReset()
void slabToPercent(int percentSlab)
public void startSpinningAxis(int atomIndex1, int atomIndex2, boolean isClockwise)
public void startSpinningAxis(Point3f pt1, Point3f pt2, boolean isClockwise)
public void syncScript(String script, String applet)
void toCartesian(Point3f pt)
void toFractional(Point3f pt)
void toggleMeasurement(int[] atomCountPlusIndices, String strFormat)
void togglePickingLabel(BitSet bs)
void toUnitCell(Point3f pt, Point3f offset)
public Point3i transformPoint(Point3f pointAngstroms)
public Point3i transformPoint(Point3f pointAngstroms, Vector3f vibrationVector)
public void transformPoint(Point3f pointAngstroms, Point3i pointScreen)
public void transformPoint(Point3f pointAngstroms, Point3f pointScreen)
public void transformPointNoClip(Point3f pointAngstroms, Point3f pt)
public void transformPoints(Point3f[] pointsAngstroms, Point3i[] pointsScreens)
public void transformVector(Vector3f vectorAngstroms, Vector3f vectorTransformed)
void translateToXPercent(float percent)
void translateToYPercent(float percent)
void translateToZPercent(float percent)
void translateXYBy(int xDelta, int yDelta)
void unsetProperty(String name)
public void unTransformPoint(Point3f pointScreen, Point3f pointAngstroms)
public boolean useMinimizationThread()
boolean usingScriptQueue()
public void writeTextFile(String file, String data)
public void zap(boolean notify, boolean resetUndo)
private void zap(String msg)
void zoomBy(int pixels)
void zoomByFactor(float factor)
public int zValueFromPercent(int zPercent)