public class Viewer extends JmolViewer implements AtomDataServer, javajs.api.PlatformViewer
Modifier and Type | Class and Description |
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static class |
Viewer.ACCESS |
apiPlatform, menuStructure
Constructor and Description |
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Viewer(Map<String,Object> info)
new way...
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Modifier and Type | Method and Description |
---|---|
(package private) void |
actionRotateBond(int deltaX,
int deltaY,
int x,
int y) |
void |
addCommand(String command)
Adds one or more commands to the command history
|
void |
addFunction(JmolScriptFunction function) |
BS |
addHydrogens(BS bsAtoms,
boolean is2DLoad,
boolean isSilent) |
private BS |
addHydrogensInline(BS bsAtoms,
javajs.util.List<Atom> vConnections,
javajs.util.P3[] pts) |
void |
addSelectionListener(JmolSelectionListener listener) |
StateScript |
addStateScript(String script,
boolean addFrameNumber,
boolean postDefinitions) |
StateScript |
addStateScriptRet(String script1,
BS bsBonds,
BS bsAtoms1,
BS bsAtoms2,
String script2,
boolean addFrameNumber,
boolean postDefinitions) |
void |
addUnitCellOffset(javajs.util.P3 pt) |
protected static JmolViewer |
allocateViewer(Object display,
JmolAdapter modelAdapter,
String fullName,
URL documentBase,
URL codeBase,
String commandOptions,
JmolStatusListener statusListener,
javajs.api.GenericPlatform implementedPlatform)
old way...
|
EnumStructure[] |
allocTempEnum(int size) |
javajs.util.P3[] |
allocTempPoints(int size) |
javajs.util.P3i[] |
allocTempScreens(int size) |
boolean |
allowCapture() |
boolean |
allowEmbeddedScripts() |
boolean |
allowSpecAtom() |
boolean |
areAxesTainted() |
void |
assignAromaticBonds() |
void |
assignAtom(int atomIndex,
javajs.util.P3 pt,
String type) |
void |
assignBond(int bondIndex,
char type) |
void |
assignConnect(int index,
int index2) |
void |
autoCalculate(int tokProperty) |
int |
autoHbond(BS bsFrom,
BS bsTo,
boolean onlyIfHaveCalculated) |
private void |
beginRendering(boolean isDouble,
boolean isImageWrite) |
void |
bindAction(String desc,
String name) |
void |
cacheClear() |
int |
cacheFileByName(String fileName,
boolean isAdd)
used in JSmolApplet.js for drag-drop behavior.
|
Object |
cacheGet(String key) |
Map<String,Integer> |
cacheList() |
boolean |
cachePngFiles() |
void |
cachePut(String key,
Object data)
JmolViewer interface -- allows saving files in memory for later retrieval
|
void |
calcAtomsMinMax(BS bs,
BoxInfo boxInfo) |
void |
calcBoundBoxDimensions(BS bs,
float scale) |
float |
calcRotationRadius(javajs.util.P3 center) |
float |
calcRotationRadiusBs(BS bs) |
void |
calcSelectedGroupsCount() |
void |
calcSelectedMoleculesCount() |
void |
calcSelectedMonomersCount() |
int |
calculateFormalCharges(BS bs) |
javajs.util.V3 |
calculateMolecularDipole() |
void |
calculatePartialCharges(BS bsSelected) |
String |
calculatePointGroup() |
void |
calculateStraightness() |
String |
calculateStructures(BS bsAtoms,
boolean asDSSP,
boolean setStructure) |
int |
calculateStruts(BS bs1,
BS bs2) |
javajs.util.P3[] |
calculateSurface(BS bsSelected,
float envelopeRadius) |
String |
cd(String dir) |
void |
checkCoordinatesChanged() |
private static float |
checkFloatRange(float value,
float min,
float max) |
boolean |
checkHalt(String str,
boolean isInsert) |
void |
checkInheritedShapes() |
void |
checkInMotion(int state) |
private static int |
checkIntRange(int value,
int min,
int max) |
private void |
checkMinimization() |
boolean |
checkMotionRendering(int tok)
check motion for rendering during mouse movement, spin, vibration, and
animation
|
(package private) Map<String,Object> |
checkObjectClicked(int x,
int y,
int modifiers) |
(package private) void |
checkObjectDragged(int prevX,
int prevY,
int x,
int y,
int action) |
boolean |
checkObjectHovered(int x,
int y) |
private boolean |
checkOption2(String key1,
String key2) |
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 |
checkPropertyParameter(String name) |
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 |
clearMouse() |
private void |
clearRepaintManager(int iShape) |
void |
clearScriptQueue() |
void |
clearSelection() |
void |
clearShapeRenderers() |
void |
clearThreads() |
void |
clearTimeout(String name) |
void |
clearTimeouts() |
String |
clipImageOrPasteText(String text) |
void |
connect(float[][] connections) |
void |
createModels(int n) |
private String |
createModelSetAndReturnError(Object atomSetCollection,
boolean isAppend,
javajs.util.SB loadScript,
Map<String,Object> htParams)
finally(!) we are ready to create the "model set" from the
"atom set collection" - does NOT repaint
|
String |
createZip(String fileName,
String type,
String[] scripts) |
void |
defineAtomSets(Map<String,Object> info) |
int |
deleteAtoms(BS bs,
boolean fullModels) |
void |
deleteBonds(BS bsDeleted) |
void |
deleteMeasurement(int i) |
void |
deleteModelAtoms(int firstAtomIndex,
int nAtoms,
BS bsDeleted) |
void |
deleteSavedState(String saveName) |
void |
deleteShapeAtoms(Object[] value,
BS bs) |
(package private) void |
depthByPixels(int pixels) |
void |
depthToPercent(int percentDepth) |
(package private) String |
dialogAsk(String type,
String fileName) |
void |
displayAtoms(BS bs,
boolean isDisplay,
boolean isGroup,
int addRemove,
boolean isQuiet) |
void |
displayBonds(BondSet bs,
boolean isDisplay) |
void |
disposeMouse() |
private boolean |
doHaveJDX() |
(package private) void |
echoMessage(String msg) |
String |
evalFile(String strFilename) |
float |
evalFunctionFloat(Object func,
Object params,
float[] values) |
boolean |
evalParallel(ScriptContext context,
ShapeManager shapeManager) |
String |
evalString(String strScript) |
String |
evalStringQuiet(String strScript) |
String |
evalStringQuietSync(String strScript,
boolean isQuiet,
boolean allowSyncScript) |
Object |
evalStringWaitStatusQueued(String returnType,
String strScript,
String statusList,
boolean isScriptFile,
boolean isQuiet,
boolean isQueued) |
Object |
evaluateExpression(Object stringOrTokens) |
SV |
evaluateExpressionAsVariable(Object stringOrTokens) |
private Object |
evalWait(String returnType,
String strScript,
String statusList) |
void |
excludeAtoms(BS bs,
boolean ignoreSubset) |
void |
exitJmol() |
String |
extractMolData(String what) |
Object |
extractProperty(Object property,
SV[] args,
int pt) |
void |
fillAtomData(AtomData atomData,
int mode) |
protected void |
finalize() |
void |
finalizeTransformParameters() |
(package private) BS |
findAtomsInRectangle(Rectangle rect) |
int |
findNearestAtomIndex(int x,
int y) |
int |
findNearestAtomIndexMovable(int x,
int y,
boolean mustBeMovable) |
static String |
fixInlineString(String strModel,
char newLine) |
String |
formatText(String text0) |
boolean |
frankClicked(int x,
int y) |
boolean |
frankClickedModelKit(int x,
int y) |
void |
freeTempEnum(EnumStructure[] temp) |
void |
freeTempPoints(javajs.util.P3[] tempPoints) |
void |
freeTempScreens(javajs.util.P3i[] 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.
|
float[][][] |
functionXYZ(String functionName,
int nX,
int nY,
int nZ) |
String |
generateOutputForExport(Map<String,Object> params) |
ActionManager |
getActionManager() |
javajs.util.P3[] |
getAdditionalHydrogens(BS bsAtoms,
boolean doAll,
boolean justCarbon,
javajs.util.List<Atom> vConnections) |
BS |
getAllAtoms() |
String |
getAllSettings(String prefix) |
String |
getAltLocListInModel(int modelIndex) |
(package private) int |
getAnimationDirection() |
(package private) Map<String,Object> |
getAnimationInfo() |
EnumAnimationMode |
getAnimationReplayMode() |
Object |
getApplet() |
(package private) Map<String,Object> |
getAppletInfo() |
int |
getArgbMinMax(float val,
float min,
float max) |
int |
getAtomArgb(int i) |
BS |
getAtomBits(int tokType,
Object specInfo) |
BS |
getAtomBitSet(Object atomExpression) |
(package private) BS |
getAtomBitSetEval(JmolScriptEvaluator eval,
Object atomExpression) |
(package private) javajs.util.List<Integer> |
getAtomBitSetVector(Object atomExpression) |
int |
getAtomCount() |
int |
getAtomCountInModel(int modelIndex) |
String |
getAtomDefs(Map<String,Object> names) |
Quaternion[] |
getAtomGroupQuaternions(BS bsAtoms,
int nMax) |
float[] |
getAtomicCharges() |
(package private) void |
getAtomicPropertyState(javajs.util.SB commands,
byte type,
BS bs,
String name,
float[] data) |
void |
getAtomIdentityInfo(int atomIndex,
Map<String,Object> info) |
int |
getAtomIndexFromAtomNumber(int atomNumber) |
int[] |
getAtomIndices(BS bs) |
String |
getAtomInfo(int atomOrPointIndex) |
String |
getAtomInfoXYZ(int atomIndex,
boolean useChimeFormat) |
int |
getAtomModelIndex(int i) |
String |
getAtomName(int i) |
int |
getAtomNumber(int i) |
javajs.util.P3 |
getAtomPoint3f(int i) |
javajs.util.List<javajs.util.P3> |
getAtomPointVector(BS bs) |
Quaternion |
getAtomQuaternion(int i) |
float |
getAtomRadius(int i) |
BS |
getAtomsConnected(float min,
float max,
int intType,
BS bs) |
javajs.util.P3 |
getAtomSetCenter(BS bs) |
String |
getAtomShapeSetState(Shape shape,
AtomShape[] shapes) |
String |
getAtomShapeState(AtomShape shape) |
float |
getAtomShapeValue(int tok,
Group group,
int atomIndex) |
BS |
getAtomsNearPlane(float distance,
javajs.util.P4 plane) |
BS |
getAtomsNearPt(float distance,
javajs.util.P3 coord) |
BS |
getAtomsNearPts(float distance,
javajs.util.P3[] points,
BS bsInclude) |
BS |
getAtomsWithinRadius(float distance,
BS bs,
boolean withinAllModels,
RadiusData rd) |
Map<String,Object> |
getAuxiliaryInfo(Object atomExpression) |
(package private) javajs.util.P3 |
getAverageAtomPoint() |
EnumAxesMode |
getAxesMode() |
void |
getAxisAngle(javajs.util.A4 axisAngle) |
javajs.util.P3[] |
getAxisPoints() |
int |
getBackgroundArgb() |
BS |
getBaseModelBitSet() |
int |
getBfactor100Hi() |
String |
getBindingInfo(String qualifiers) |
BS |
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) |
(package private) boolean |
getBondPicking() |
javajs.util.P3 |
getBondPoint3f1(int i) |
javajs.util.P3 |
getBondPoint3f2(int i) |
float |
getBondRadius(int i) |
BS |
getBondsForSelectedAtoms(BS bsAtoms) |
String |
getBondState(Shape shape,
BS bsOrderSet,
boolean reportAll) |
boolean |
getBoolean(int tok) |
boolean |
getBooleanProperty(String key) |
javajs.util.P3 |
getBoundBoxCenter() |
int |
getBoundBoxCenterX() |
int |
getBoundBoxCenterY() |
String |
getBoundBoxCommand(boolean withOptions) |
javajs.util.V3 |
getBoundBoxCornerVector() |
(package private) Map<String,Object> |
getBoundBoxInfo() |
BS |
getBoundBoxModels() |
javajs.util.P3[] |
getBoundBoxVertices() |
BoxInfo |
getBoxInfo(BS bs,
float scale) |
BS |
getBranchBitSet(int atomIndex,
int atomIndexNot,
boolean allowCyclic) |
BS[] |
getBsBranches(float[] dihedralList) |
BufferedInputStream |
getBufferedInputStream(String fullPathName) |
Object |
getBufferedReaderOrErrorMessageFromName(String name,
String[] fullPathNameReturn,
boolean isBinary) |
javajs.util.P3 |
getCamera() |
float |
getCameraDepth() |
javajs.util.P3[] |
getCameraFactors() |
javajs.util.P3[][] |
getCenterAndPoints(javajs.util.List<Object[]> atomSets,
boolean addCenter) |
int |
getChainCount() |
int |
getChainCountInModel(int modelIndex) |
int |
getChainCountInModelWater(int modelIndex,
boolean countWater) |
int |
getChainID(String id)
Create a unique integer for any chain string.
|
String |
getChainIDStr(int id) |
String |
getChemicalInfo(String smiles,
char type,
String info) |
String |
getChimeInfo(int tok) |
Map<String,Object> |
getCifData(int modelIndex) |
BS |
getClickableSet() |
String |
getClipboardText() |
(package private) short |
getColix(Object object) |
short |
getColixAtomPalette(Atom atom,
byte pid) |
short |
getColixBackgroundContrast() |
short |
getColixBondPalette(Bond bond,
int pid) |
short |
getColixForPropertyValue(float val) |
short |
getColixRubberband() |
int |
getColorArgbOrGray(short colix) |
ColorEncoder |
getColorEncoder(String colorScheme) |
javajs.util.P3 |
getColorPointForPropertyValue(float val) |
String |
getColorSchemeList(String colorScheme) |
String |
getCommands(Map<String,BS> htDefine,
Map<String,BS> htMore,
String select) |
BS |
getConformation(int iModel,
int conformationIndex,
boolean doSet) |
Map<String,SV> |
getContextVariables() |
String |
getCoordinateState(BS bsSelected) |
int |
getCurrentAtom() |
float[] |
getCurrentColorRange() |
String |
getCurrentFileAsString() |
int |
getCurrentModelIndex() |
float |
getCurrentSolventProbeRadius() |
SymmetryInterface |
getCurrentUnitCell() |
int |
getCursor() |
int |
getCursorX() |
int |
getCursorY() |
Object[] |
getData(String type) |
String |
getData(String atomExpression,
String type) |
float[] |
getDataFloat(String label) |
float[][] |
getDataFloat2D(String label) |
float[][][] |
getDataFloat3D(String label) |
float |
getDataFloatAt(String label,
int atomIndex) |
private JmolDataManager |
getDataManager() |
(package private) String |
getDataSeparator() |
(package private) String |
getDefaultDirectory() |
javajs.util.P3 |
getDefaultLattice() |
String |
getDefaultLoadFilter() |
String |
getDefaultLoadScript() |
String |
getDefaultMeasurementLabel(int nPoints) |
String |
getDefaultPropertyParam(int propertyID) |
RadiusData |
getDefaultRadiusData() |
String |
getDefaultStructure(BS bsAtoms,
BS bsAllAtoms) |
String |
getDefaultVdwNameOrData(int mode,
EnumVdw type,
BS bs) |
BS |
getDefinedAtomSet(String name) |
int |
getDelayMaximumMs() |
BS |
getDeletedAtoms() |
int[][] |
getDihedralMap(int[] atoms) |
Object |
getDisplay() |
int |
getDisplayModelIndex() |
String |
getDistanceUnits(String s) |
(package private) boolean |
getDragSelected() |
boolean |
getDrawHover() |
boolean |
getEchoStateActive() |
String[] |
getElectronDensityLoadInfo() |
(package private) int |
getElementNumber(int i) |
BS |
getElementsPresentBitSet(int modelIndex) |
(package private) String |
getElementSymbol(int i) |
String |
getEmbeddedFileState(String filename) |
String |
getEnergyUnits() |
String |
getErrorMessage() |
String |
getErrorMessageUn() |
ScriptContext |
getEvalContextAndHoldQueue(JmolScriptEvaluator jse) |
Object |
getExecutor() |
String |
getExportDriverList() |
Object |
getFileAsBytes(String pathName,
javajs.util.OC out) |
String |
getFileAsString(String name) |
String |
getFileAsString4(String name,
int nBytesMax,
boolean doSpecialLoad,
boolean allowBinary,
boolean checkProtected) |
boolean |
getFileAsStringBin(String[] data) |
(package private) Object |
getFileData() |
(package private) String |
getFileHeader() |
String[] |
getFileInfo() |
String |
getFileName() |
String |
getFilePath(String name,
boolean asShortName) |
float |
getFloat(int tok) |
javajs.awt.Font |
getFont3D(String fontFace,
String fontStyle,
float fontSize) |
String |
getFontLineShapeState(String s,
String myType,
TickInfo[] tickInfos) |
String |
getFontState(String myType,
javajs.awt.Font font3d) |
int |
getFrameCount() |
long |
getFrameDelayMs(int i) |
BS |
getFrameOffsets() |
String |
getFrameTitle() |
int |
getFrontPlane() |
String |
getFullPathName(boolean orPrevious) |
String[] |
getFullPathNameOrError(String filename) |
JmolScriptFunction |
getFunction(String name) |
String |
getFunctionCalls(String selectedFunction) |
Map<String,JmolScriptFunction> |
getFunctions(boolean isStatic) |
GData |
getGraphicsData() |
int |
getGroupCount() |
int |
getGroupCountInModel(int modelIndex) |
BS |
getGroupsWithin(int nResidues,
BS bs) |
Object |
getHelixData(BS bs,
int tokType) |
void |
getHelp(String what) |
int |
getHermiteLevel() |
Map<String,String> |
getHeteroList(int modelIndex) |
BS |
getHiddenSet() |
int |
getHoverDelay() |
String |
getHtmlName() |
String |
getHybridizationAndAxes(int atomIndex,
javajs.util.V3 z,
javajs.util.V3 x,
String lcaoType) |
private Object |
getImage(boolean isDouble,
boolean isImageWrite) |
byte[] |
getImageAsBytes(String type,
int width,
int height,
int quality,
String[] errMsg) |
float |
getImageFontScaling() |
char |
getInlineChar() |
boolean |
getInMotion(boolean includeAnim) |
String |
getInsertedCommand() |
int |
getInt(int tok) |
int |
getIsosurfacePropertySmoothing(boolean asPower) |
String |
getJavaVendor() |
String |
getJavaVersion() |
int |
getJDXBaseModelIndex(int modelIndex)
get the model designated as "baseModel" in a JCamp-MOL file for example,
the model used for bonding for an XYZVIB file or the model used as the base
model for a mass spec file.
|
int |
getJmolDataFrameIndex(int modelIndex,
String type) |
int |
getJmolDataSourceFrame(int modelIndex) |
(package private) String |
getJmolFrameType(int modelIndex) |
static String |
getJmolVersion() |
Object |
getJspecViewProperties(Object myParam) |
private JmolJSpecView |
getJSV() |
String |
getLanguage() |
Object |
getLigandModel(String id,
String prefix,
String suffix,
String terminator)
obtain CIF data for a ligand for purposes of adding hydrogens
|
(package private) String |
getLoadState(Map<String,Object> htParams) |
String |
getLocalUrl(String fileName) |
String |
getLogFileName() |
(package private) String |
getLogFilePath() |
short |
getMadBond() |
short |
getMarBond() |
(package private) javajs.util.M3 |
getMatrixRotate() |
javajs.util.M4 |
getMatrixtransform() |
float |
getMaxZoomPercent() |
String |
getMeasureDistanceUnits() |
int |
getMeasurementCount() |
int[] |
getMeasurementCountPlusIndices(int i) |
(package private) javajs.util.List<Map<String,Object>> |
getMeasurementInfo() |
String |
getMeasurementInfoAsString() |
String |
getMeasurementState(Measures measures,
javajs.util.List<Measurement> mList,
int measurementCount,
javajs.awt.Font font3d,
TickInfo ti) |
String |
getMeasurementStringValue(int i) |
String |
getMenu(String type) |
Map<String,javajs.util.List<javajs.util.List<Object>>> |
getMessageQueue() |
String |
getMinimizationInfo() |
MinimizerInterface |
getMinimizer(boolean createNew) |
JmolAdapter |
getModelAdapter() |
String |
getModelAtomProperty(Atom atom,
String text) |
Map<String,Object> |
getModelAuxiliaryInfo(int modelIndex) |
Object |
getModelAuxiliaryInfoValue(int modelIndex,
String keyName) |
BS |
getModelBitSet(BS atomList,
boolean allTrajectories) |
String |
getModelCml(BS bs,
int nAtomsMax,
boolean addBonds) |
int |
getModelCount() |
javajs.util.V3 |
getModelDipole() |
String |
getModelExtract(Object atomExpression,
boolean doTransform,
boolean isModelKit,
String type) |
String |
getModelFileInfo() |
String |
getModelFileInfoAll() |
String |
getModelFileName(int modelIndex) |
int |
getModelFileNumber(int modelIndex) |
int |
getModelIndexFromId(String id) |
String |
getModelInfoAsString() |
(package private) BS |
getModelKitStateBitSet(BS bs,
BS bsDeleted) |
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() |
Map<String,Object> |
getModelSetAuxiliaryInfo() |
Object |
getModelSetAuxiliaryInfoValue(String strKey) |
String |
getModelSetFileName() |
String |
getModelSetName() |
String |
getModelSetPathName() |
Properties |
getModelSetProperties() |
String |
getModelSetProperty(String strProp) |
String |
getModelSetTypeName() |
private String |
getModelTitle(int modelIndex) |
BS |
getModelUndeletedAtomsBitSet(int modelIndex) |
BS |
getModelUndeletedAtomsBitSetBs(BS bsModels) |
SymmetryInterface |
getModelUnitCell(int modelIndex) |
byte |
getModeMultipleBond() |
javajs.util.List<Object> |
getModulationList(BS bs,
String type,
javajs.util.P3 t456) |
String |
getMoInfo(int modelIndex) |
BS |
getMoleculeBitSet(int atomIndex) |
int |
getMotionEventNumber() |
BS |
getMotionFixedAtoms() |
boolean |
getMouseEnabled() |
Object |
getMouseInfo() |
String |
getMoveToText(float timespan) |
MeasurementPending |
getMP() |
javajs.util.P3 |
getNavigationCenter() |
float |
getNavigationDepthPercent() |
javajs.util.P3 |
getNavigationOffset() |
float |
getNavigationOffsetPercent(char XorY) |
boolean |
getNavOn() |
JmolNMRInterface |
getNMRCalculation() |
String |
getNMRPredict(boolean openURL) |
Boolean |
getNoneSelected() |
(package private) int |
getObjectArgb(int objId) |
short |
getObjectColix(int objId) |
int |
getObjectMad(int objId) |
void |
getObjectMap(Map<String,?> map,
char c)
used in autocompletion in console using TAB
|
String |
getOperatingSystemName() |
Orientation |
getOrientation() |
(package private) Map<String,Object> |
getOrientationInfo() |
String |
getOrientationText(int type,
String name) |
SV |
getOrSetNewVariable(String key,
boolean doSet) |
javajs.util.OC |
getOutputChannel(String localName,
String[] fullPath) |
private OutputManager |
getOutputManager() |
Object |
getParameter(String key) |
Object |
getParameterEscaped(String key) |
float[] |
getPartialCharges() |
String |
getPathForAllFiles() |
String |
getPdbAtomData(BS bs,
javajs.util.OC sb) |
String[][] |
getPdbBondInfo(String group3) |
String |
getPdbData(int modelIndex,
String type,
Object[] parameters) |
String |
getPDBHeader() |
(package private) MeasurementPending |
getPendingMeasurement() |
boolean |
getPerspectiveDepth() |
int |
getPickingMode() |
javajs.util.List<Object> |
getPlaneIntersection(int type,
javajs.util.P4 plane,
float scale,
int flags) |
String |
getPointGroupAsString(boolean asDraw,
String type,
int index,
float scale) |
Map<String,Object> |
getPointGroupInfo(Object atomExpression) |
int |
getPolymerCount() |
int |
getPolymerCountInModel(int modelIndex) |
javajs.util.P3[] |
getPolymerLeadMidPoints(int modelIndex,
int polymerIndex) |
void |
getPolymerPointsAndVectors(BS bs,
javajs.util.List<javajs.util.P3[]> vList) |
private Object |
getPopupMenu() |
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.
|
Object |
getProperty(String returnType,
String infoType,
Object paramInfo) |
String |
getPropertyColorScheme() |
private JmolPropertyManager |
getPropertyManager() |
int |
getPropertyNumber(String name) |
String |
getProteinStructureState() |
char |
getQuaternionFrame() |
boolean |
getRefreshing() |
BS |
getRenderableBitSet() |
(package private) int |
getRotateBondIndex() |
void |
getRotation(javajs.util.M3 matrixRotation) |
javajs.util.P3 |
getRotationCenter() |
Quaternion |
getRotationQuaternion() |
Rectangle |
getRubberBandSelection() |
String |
getSavedCoordinates(String saveName) |
String |
getSavedState(String saveName) |
String |
getSavedStructure(String saveName) |
float |
getScalePixelsPerAngstrom(boolean asAntialiased) |
String[] |
getSceneList() |
int |
getScreenDim() |
int |
getScreenHeight() |
Object |
getScreenImageBuffer(Object graphic,
boolean isImageWrite)
Image.getJpgImage, ImageCreator.clipImage, getImageBytes,
Viewer.renderScreenImageStereo
|
int |
getScreenWidth() |
ScriptContext |
getScriptContext(String why) |
private JmolScriptManager |
getScriptManager() |
Boolean |
getScriptQueueInfo() |
AtomIndexIterator |
getSelectedAtomIterator(BS bsSelected,
boolean isGreaterOnly,
boolean modelZeroBased,
boolean isMultiModel) |
int |
getSelectionCount() |
boolean |
getSelectionHaloEnabled(boolean isRenderer) |
BS |
getSelectionSet(boolean includeDeleted) |
BS |
getSelectionSubset() |
BS |
getSequenceBits(String specInfo,
BS 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;
|
String |
getShapeErrorState() |
Map<String,Object> |
getShapeInfo() |
ShapeManager |
getShapeManager() |
Object |
getShapeProperty(int shapeType,
String propertyName) |
private int |
getShapePropertyAsInt(int shapeID,
String propertyName) |
boolean |
getShapePropertyData(int shapeType,
String propertyName,
Object[] data) |
Object |
getShapePropertyIndex(int shapeType,
String propertyName,
int index) |
void |
getShapeSetState(AtomShape atomShape,
Shape shape,
int monomerCount,
Group[] monomers,
BS bsSizeDefault,
Map<String,BS> temp,
Map<String,BS> temp2) |
String |
getShapeState(Shape shape) |
boolean |
getShowAxes() |
boolean |
getShowBbcage() |
boolean |
getShowFrank() |
boolean |
getShowNavigationPoint() |
boolean |
getShowUnitCell() |
boolean |
getSlabEnabled() |
BS |
getSmartsMatch(String smarts,
BS bsSelected) |
String |
getSmiles(int index1,
int index2,
BS bsSelected,
boolean isBioSmiles,
boolean allowUnmatchedRings,
boolean addCrossLinks,
boolean addComment)
returns the SMILES string for a sequence or atom set does not include
attached protons on groups
|
SmilesMatcherInterface |
getSmilesMatcher() |
Map<String,Object> |
getSpaceGroupInfo(String spaceGroup) |
String |
getSpecularState() |
boolean |
getSpinOn() |
String |
getSpinState() |
String |
getStandardLabelFormat(int type) |
JmolStateCreator |
getStateCreator() |
String |
getStateInfo() |
String |
getStateInfo3(String type,
int width,
int height) |
javajs.util.List<javajs.util.List<javajs.util.List<Object>>> |
getStatusChanged(String statusNameList) |
(package private) StatusManager |
getStatusManager() |
int |
getStrandCount(int type) |
Map<EnumStructure,float[]> |
getStructureList() |
String |
getStructureState() |
(package private) int |
getSurfaceDistanceMax() |
SymmetryInterface |
getSymmetry() |
Object |
getSymmetryInfo(BS bsAtoms,
String xyz,
int op,
javajs.util.P3 pt,
javajs.util.P3 pt2,
String id,
int type) |
String |
getSymmetryInfoAsString() |
String |
getSymmetryOperation(String spaceGroup,
int symop,
javajs.util.P3 pt1,
javajs.util.P3 pt2,
boolean labelOnly) |
BS |
getTaintedAtoms(byte type) |
boolean |
getTestFlag(int i) |
Map<String,Object> |
getTimeouts() |
String |
getTrajectoryState() |
String |
getTransformText() |
String |
getTranslationScript() |
float |
getTranslationXPercent() |
float |
getTranslationYPercent() |
(package private) float |
getTranslationZPercent() |
private BS |
getUndeletedGroupAtomBits(BS bs) |
float |
getUnitCellInfo(int infoType) |
String |
getUnitCellInfoText() |
javajs.util.M4 |
getUnscaledTransformMatrix() |
int |
getVanderwaalsMar(int i) |
int |
getVanderwaalsMarType(int atomicAndIsotopeNumber,
EnumVdw type) |
Object |
getVariableList() |
Vibration |
getVibration(int atomIndex) |
Point3fi |
getVibrationPoint(Vibration vibration,
Point3fi pt) |
Map<String,Object> |
getViewerOptions() |
BS |
getVisibleFramesBitSet() |
BS |
getVisibleSet() |
String |
getWrappedStateScript() |
String |
getZapName() |
boolean |
getZoomEnabled() |
int |
getZoomPercent() |
float |
getZoomPercentFloat() |
float |
getZoomSetting() |
int |
getZShadeStart() |
void |
haltScriptExecution() |
void |
handleError(Error er,
boolean doClear) |
static boolean |
hasDatabasePrefix(String fileName) |
boolean |
hasDisplay() |
boolean |
hasFocus() |
boolean |
haveAccess(Viewer.ACCESS a) |
boolean |
haveFileSet() |
boolean |
haveFrame() |
(package private) boolean |
haveModelKit() |
(package private) boolean |
haveModelSet() |
boolean |
havePartialCharges() |
void |
highlight(BS bs) |
void |
highlightBond(int index,
boolean isHover) |
void |
homePosition() |
(package private) void |
hoverOff() |
(package private) void |
hoverOn(int atomIndex,
boolean isLabel) |
void |
hoverOnPt(int x,
int y,
String text,
String id,
javajs.util.P3 pt) |
void |
initialize(boolean clearUserVariables) |
JmolRendererInterface |
initializeExporter(Map<String,Object> params) |
private void |
initializeModel(boolean isAppend) |
void |
invertAtomCoordPlane(javajs.util.P4 plane,
BS bs) |
void |
invertAtomCoordPt(javajs.util.P3 pt,
BS bs) |
void |
invertSelected(javajs.util.P3 pt,
javajs.util.P4 plane,
int iAtom,
BS invAtoms) |
void |
invertSelection() |
(package private) boolean |
isAnimationOn() |
boolean |
isAntialiased() |
boolean |
isApplet() |
(package private) boolean |
isAtomAssignable(int i) |
boolean |
isAtomPDB(int i) |
boolean |
isAtomSelected(int atomIndex) |
boolean |
isBound(int action,
int gesture) |
static boolean |
isDatabaseCode(char ch) |
boolean |
isFunction(String name) |
boolean |
isHeadless() |
boolean |
isInPosition(javajs.util.V3 axis,
float degrees) |
(package private) boolean |
isInSelectionSubset(int atomIndex) |
boolean |
isJmolDataFrame() |
boolean |
isJmolDataFrameForModel(int modelIndex) |
boolean |
isJmolVariable(String key) |
(package private) boolean |
isKiosk() |
boolean |
isModelPDB(int i) |
boolean |
isMovie() |
boolean |
isNavigating() |
boolean |
isParallel() |
boolean |
isPreviewOnly() |
boolean |
isRepaintPending() |
boolean |
isScriptExecuting() |
private boolean |
isScriptQueued() |
boolean |
isSelected(int atomIndex) |
boolean |
isSignedApplet() |
private static boolean |
isStaticFunction(String name) |
(package private) boolean |
isStereoDouble() |
boolean |
isTrajectory(int modelIndex) |
boolean |
isVibrationOn() |
boolean |
isWindowCentered() |
private void |
jmolTest() |
String |
jsEval(String strEval) |
String |
listSavedStates() |
private String |
loadAtomDataAndReturnError(Object atomSetCollection,
int tokType)
or just apply the data to the current model set
|
void |
loadImage(String pathName,
String echoName) |
(package private) void |
loadImageData(Object image,
String nameOrError,
String echoName,
ScriptContext sc) |
String |
loadInline(List<Object> arrayData,
boolean isAppend)
External applications only; does not preserver state -- intentionally!
|
String |
loadInline(String strModel)
from Applet and external applications only
|
String |
loadInline(String[] arrayModels)
external apps only
|
String |
loadInline(String[] arrayModels,
boolean isAppend)
external apps and applet only
|
String |
loadInline(String strModel,
char newLine)
external apps only
|
String |
loadInlineAppend(String strModel,
boolean isAppend)
used by applet and console
|
private String |
loadInlineScript(String strModel,
char newLine,
boolean isAppend,
Map<String,Object> htParams)
used by loadInline and openFileFull
|
private String |
loadInlineScriptRepaint(String strModel,
char newLine,
boolean isAppend) |
String |
loadModelFromFile(String fullPathName,
String fileName,
String[] fileNames,
Object reader,
boolean isAppend,
Map<String,Object> htParams,
javajs.util.SB loadScript,
int tokType)
Used by the ScriptEvaluator LOAD command to open one or more files.
|
private String |
loadModelFromFileRepaint(String fullPathName,
String fileName,
String[] fileNames,
Object reader) |
void |
loadShape(int shapeID) |
void |
log(String data) |
int[] |
makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
BS bsA,
BS bsB,
BS bsBonds,
boolean isBonds,
boolean addGroup,
float energy) |
boolean |
menuEnabled() |
void |
mergeShapes(Shape[] newShapes) |
void |
minimize(int steps,
float crit,
BS bsSelected,
BS bsFixed,
float rangeFixed,
boolean addHydrogen,
boolean isOnly,
boolean isSilent,
boolean isLoad2D) |
int |
modelGetLastVibrationIndex(int modelIndex,
int tok) |
boolean |
modelHasVibrationVectors(int modelIndex) |
(package private) boolean |
modelSetHasVibrationVectors() |
void |
morph(float frame) |
void |
move(JmolScriptEvaluator eval,
javajs.util.V3 dRot,
float dZoom,
javajs.util.V3 dTrans,
float dSlab,
float floatSecondsTotal,
int fps) |
void |
moveAtoms(javajs.util.M3 mNew,
javajs.util.M3 matrixRotate,
javajs.util.V3 translation,
javajs.util.P3 center,
boolean isInternal,
BS bsAtoms,
boolean translationOnly) |
protected void |
moveAtomWithHydrogens(int atomIndex,
int deltaX,
int deltaY,
int deltaZ,
BS bsAtoms) |
boolean |
movePyMOL(JmolScriptEvaluator eval,
float floatSecondsTotal,
float[] pymolView) |
void |
moveSelected(int deltaX,
int deltaY,
int deltaZ,
int x,
int y,
BS bsSelected,
boolean isTranslation,
boolean asAtoms) |
void |
moveTo(JmolScriptEvaluator eval,
float floatSecondsTotal,
javajs.util.P3 center,
javajs.util.V3 rotAxis,
float degrees,
javajs.util.M3 rotationMatrix,
float zoom,
float xTrans,
float yTrans,
float rotationRadius,
javajs.util.P3 navCenter,
float xNav,
float yNav,
float navDepth,
float cameraDepth,
float cameraX,
float cameraY) |
void |
moveUpdate(float floatSecondsTotal) |
(package private) void |
navigate(int keyWhere,
int modifiers) |
void |
navigateAxis(javajs.util.V3 rotAxis,
float degrees) |
void |
navigateList(JmolScriptEvaluator eval,
javajs.util.List<Object[]> list) |
void |
navigatePt(javajs.util.P3 center) |
void |
navTranslatePercent(float x,
float y) |
boolean |
noGraphicsAllowed() |
void |
notifyError(String errType,
String errMsg,
String errMsgUntranslated) |
void |
notifyMinimizationStatus() |
int |
notifyMouseClicked(int x,
int y,
int action,
int mode) |
void |
notifyStatusReady(boolean isReady) |
void |
notifyViewerRepaintDone() |
String |
openDOM(Object DOMNode)
applet DOM method -- does not preserve state
|
javajs.util.OC |
openExportChannel(double privateKey,
String fileName,
boolean asWriter) |
String |
openFile(String fileName)
for JmolSimpleViewer -- external applications only (and no-script
JavaScript)
|
void |
openFileAsyncSpecial(String fileName,
int flags)
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
|
private Object |
openFileFull(String fileName,
boolean isAppend,
Map<String,Object> htParams,
javajs.util.SB loadScript)
does NOT repaint
|
String |
openFiles(String[] fileNames)
for JmolSimpleViewer -- external applications only
|
String |
openReader(String fullPathName,
String fileName,
Reader reader)
Opens the file, given an already-created reader.
|
String |
openStringInline(String strModel)
only used by file dropper.
|
String |
openStringInlineParamsAppend(String strModel,
Map<String,Object> htParams,
boolean isAppend)
Only used for adding hydrogen atoms and adding the model kit methane model;
not part of the public interface.
|
private String |
openStringsInlineParamsAppend(String[] arrayModels,
Map<String,Object> htParams,
boolean isAppend)
opens multiple files inline; does NOT repaint
|
String |
outputToFile(Map<String,Object> params) |
void |
pauseScriptExecution() |
void |
popHoldRepaint(String why) |
(package private) void |
popupMenu(int x,
int y,
char type) |
boolean |
processMouseEvent(int id,
int x,
int y,
int modifiers,
long time) |
void |
processMultitouchEvent(int groupID,
int eventType,
int touchID,
int iData,
javajs.util.P3 pt,
long time) |
void |
processTwoPointGesture(float[][][] touches) |
String |
processWriteOrCapture(Map<String,Object> params)
from eval write command only includes option to write set of files
|
String |
prompt(String label,
String data,
String[] list,
boolean asButtons) |
void |
pushHoldRepaint() |
void |
pushHoldRepaintWhy(String why) |
void |
rebond() |
void |
rebondState(boolean isStateScript) |
void |
refresh(int mode,
String strWhy)
initiate a repaint/update sequence if it has not already been requested.
|
void |
refreshMeasures(boolean andStopMinimization) |
void |
releaseScreenImage() |
String |
removeCommand()
Removes one command from the command history
|
void |
removeFunction(String name) |
void |
removeSelectionListener(JmolSelectionListener listener) |
void |
removeUserVariable(String key) |
private void |
render() |
private void |
render1(Object graphic,
Object img,
int x,
int y) |
void |
renderScreenImage(Object g,
int width,
int height) |
void |
renderScreenImageStereo(Object gLeft,
Object gRight,
int width,
int height)
an added class for rendering stereo in two independent applets
|
(package private) void |
reportSelection(String msg) |
void |
requestRepaintAndWait(String why) |
void |
reset(boolean includingSpin) |
void |
resetAromatic() |
void |
resetBioshapes(BS bsAllAtoms) |
void |
resetError() |
void |
resetShapes(boolean andCreateNew) |
(package private) void |
resizeImage(int width,
int height,
boolean isImageWrite,
boolean isExport,
boolean isReset) |
javajs.awt.Dimension |
resizeInnerPanel(int width,
int height) |
(package private) String |
resolveDatabaseFormat(String fileName) |
boolean |
restoreBonds(String saveName) |
(package private) void |
restoreModelOrientation(int modelIndex) |
(package private) void |
restoreModelRotation(int modelIndex) |
boolean |
restoreOrientation(String saveName,
float timeSeconds) |
void |
restoreRotation(String saveName,
float timeSeconds) |
void |
restoreScene(String saveName,
float timeSeconds) |
boolean |
restoreSelection(String saveName) |
boolean |
rotateAboutPointsInternal(JmolScriptEvaluator eval,
javajs.util.P3 point1,
javajs.util.P3 point2,
float degreesPerSecond,
float endDegrees,
boolean isSpin,
BS bsSelected,
javajs.util.V3 translation,
javajs.util.List<javajs.util.P3> finalPoints,
float[] dihedralList) |
(package private) void |
rotateArcBall(int x,
int y,
float factor) |
boolean |
rotateAxisAngleAtCenter(JmolScriptEvaluator eval,
javajs.util.P3 rotCenter,
javajs.util.V3 rotAxis,
float degreesPerSecond,
float endDegrees,
boolean isSpin,
BS bsSelected) |
void |
rotateFront() |
void |
rotatePoint(javajs.util.P3 pt,
javajs.util.P3 ptRot) |
(package private) void |
rotateSelected(float deltaX,
float deltaY,
BS bsSelected) |
void |
rotateX(float angleRadians) |
void |
rotateXDeg(int angleDegrees) |
(package private) void |
rotateXYBy(float xDelta,
float yDelta) |
void |
rotateY(float angleRadians) |
void |
rotateYDeg(int angleDegrees) |
void |
rotateZ(float angleRadians) |
void |
rotateZBy(int zDelta,
int x,
int y) |
String |
runScript(String script)
run a script immediately and return output buffer string
Jmol 13.1.15
|
void |
saveBonds(String saveName) |
void |
saveCoordinates(String saveName,
BS bsSelected) |
(package private) void |
saveModelOrientation() |
void |
saveOrientation(String saveName,
float[] pymolView) |
void |
saveScene(String saveName,
Map<String,Object> scene) |
void |
saveSelection(String saveName) |
void |
saveState(String saveName) |
void |
saveStructure(String saveName) |
float |
scaleToPerspective(int z,
float sizeAngstroms) |
float |
scaleToScreen(int z,
int milliAngstroms) |
String |
script(String strScript) |
Object |
scriptCheck(String strScript) |
private Object |
scriptCheckRet(String strScript,
boolean returnContext) |
void |
scriptEcho(String strEcho) |
void |
scriptStatus(String strStatus) |
void |
scriptStatusMsg(String strStatus,
String statusMessage) |
String |
scriptWait(String strScript) |
Object |
scriptWaitStatus(String strScript,
String statusList) |
void |
select(BS bs,
boolean isGroup,
int addRemove,
boolean isQuiet) |
void |
selectAll() |
void |
selectBonds(BS bs) |
void |
setAnimation(int tok) |
void |
setAnimationDirection(int direction) |
void |
setAnimationFps(int fps) |
private void |
setAnimationMode(String mode) |
void |
setAnimationOn(boolean animationOn) |
void |
setAnimationRange(int modelIndex1,
int modelIndex2) |
void |
setAnimationReplayMode(EnumAnimationMode replayMode,
float firstFrameDelay,
float lastFrameDelay) |
void |
setAnimDisplay(BS bs) |
void |
setAnimMorphCount(int n) |
private void |
setAntialias(int tok,
boolean TF) |
void |
setAppendNew(boolean value) |
(package private) void |
setApplySymmetryToBonds(boolean TF) |
void |
setAtomCoord(int atomIndex,
float x,
float y,
float z) |
void |
setAtomCoordRelative(int atomIndex,
float x,
float y,
float z) |
void |
setAtomCoords(BS bs,
int tokType,
Object xyzValues) |
void |
setAtomCoordsRelative(javajs.util.T3 offset,
BS bs) |
void |
setAtomData(int type,
String name,
String coordinateData,
boolean isDefault) |
void |
setAtomLabel(String value,
int i) |
private void |
setAtomPickingOption(String option) |
void |
setAtomProperty(BS bs,
int tok,
int iValue,
float fValue,
String sValue,
float[] values,
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(String fileName,
Object image) |
void |
setBackgroundModelIndex(int modelIndex) |
void |
setBondParameters(int modelIndex,
int i,
BS bsBonds,
float rad,
float pymolValence,
int argb,
float trans) |
private void |
setBondPickingOption(String option) |
void |
setBondTolerance(float bondTolerance) |
void |
setBooleanProperty(String key,
boolean value) |
private void |
setBooleanPropertyTok(String key,
int tok,
boolean value) |
void |
setBoundBox(javajs.util.P3 pt1,
javajs.util.P3 pt2,
boolean byCorner,
float scale) |
void |
setCenterAt(String relativeTo,
javajs.util.P3 pt) |
void |
setCenterBitSet(BS bsCenter,
boolean doScale) |
void |
setCenterSelected() |
void |
setCentroid(BS bs,
int[] minmax) |
void |
setCGO(javajs.util.List<Object> info) |
void |
setColorBackground(String colorName) |
BS |
setConformation() |
void |
setCurrentAtom(int iAtom) |
void |
setCurrentCage(String isosurfaceId) |
void |
setCurrentCagePts(javajs.util.P3[] points) |
void |
setCurrentColorRange(float min,
float max) |
void |
setCurrentColorRange(String label) |
void |
setCurrentColorRangeData(float[] data,
BS bs) |
void |
setCurrentModelID(String id) |
void |
setCurrentModelIndex(int modelIndex) |
void |
setCurrentModelIndexClear(int modelIndex,
boolean clearBackground) |
void |
setCurrentUnitCellOffset(javajs.util.P3 pt,
int ijk) |
void |
setCursor(int cursor) |
void |
setData(String type,
Object[] data,
int arrayCount,
int matchField,
int matchFieldColumnCount,
int field,
int fieldColumnCount) |
void |
setDebugScript(boolean debugScript) |
private void |
setDefaultColors(boolean isRasmol) |
void |
setDefaultLattice(javajs.util.P3 ptLattice) |
private void |
setDefaults() |
private void |
setDefaultsType(String type) |
void |
setDihedrals(float[] dihedralList,
BS[] bsBranches,
float rate) |
void |
setDisplay(Object canvas) |
void |
setEchoStateActive(boolean TF) |
void |
setElementArgb(int elementNumber,
int argb) |
String |
setErrorMessage(String errMsg,
String errMsgUntranslated) |
void |
setFileInfo(String[] fileInfo) |
private void |
setFileLoadStatus(EnumFileStatus ptLoad,
String fullPathName,
String fileName,
String modelName,
String strError,
Boolean isAsync) |
void |
setFloatProperty(String key,
float value) |
private void |
setFloatPropertyTok(String key,
int tok,
float value) |
void |
setFocus() |
void |
setFormalCharges(int formalCharge) |
void |
setFrame(int i) |
void |
setFrameDelayMs(long millis) |
(package private) void |
setFrameOffset(int modelIndex) |
void |
setFrameOffsets(BS bsAtoms) |
void |
setFrameTitle(int modelIndex,
String title) |
void |
setFrameTitleObj(Object title) |
(package private) void |
setFrameVariables() |
void |
setFrankOn(boolean TF) |
void |
setHoverLabel(String strLabel) |
void |
setInMotion(boolean inMotion) |
void |
setInsertedCommand(String strScript) |
void |
setIntProperty(String key,
int value) |
private void |
setIntPropertyTok(String key,
int tok,
int value) |
void |
setIteratorForAtom(AtomIndexIterator iterator,
int atomIndex,
float distance) |
void |
setIteratorForPoint(AtomIndexIterator iterator,
int modelIndex,
javajs.util.P3 pt,
float distance) |
void |
setJmolCallbackListener(JmolCallbackListener jmolCallbackListener) |
void |
setJmolDataFrame(String type,
int modelIndex,
int dataIndex) |
void |
setJmolDefaults() |
void |
setJmolStatusListener(JmolStatusListener jmolStatusListener) |
void |
setLigandModel(String key,
String data) |
Object |
setLoadFormat(String name,
char type,
boolean withPrefix)
Jmol will either specify a type or look for it in the first character,
making sure it is found using isDatabaseCode() first.
|
private Map<String,Object> |
setLoadParameters(Map<String,Object> htParams,
boolean isAppend) |
void |
setMarBond(short marBond) |
private void |
setMaximumSize(int x) |
void |
setMenu(String fileOrText,
boolean isFile) |
void |
setMeshCreator(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 |
setModelSet(ModelSet modelSet) |
void |
setModelVisibility() |
void |
setModeMouse(int modeMouse) |
void |
setModulation(BS bs,
boolean isOn,
javajs.util.P3 t1,
boolean isQ) |
void |
setMotionFixedAtoms(BS bs) |
void |
setMouseEnabled(boolean TF) |
private BS |
setMovableBitSet(BS bsSelected,
boolean checkMolecule) |
void |
setMovie(Map<String,Object> info) |
void |
setNavigationDepthPercent(float percent) |
void |
setNavigationMode(boolean TF) |
void |
setNavOn(boolean navOn) |
void |
setNavXYZ(float x,
float y,
float z) |
void |
setNewRotationCenter(javajs.util.P3 center) |
void |
setNoneSelected(boolean noneSelected) |
void |
setObjectArgb(String name,
int argb) |
(package private) void |
setObjectColor(String name,
String colorName) |
void |
setObjectMad(int iShape,
String name,
int mad) |
String |
setObjectProp(String id,
int tokCommand) |
void |
setObjectVisibility(String name,
boolean b) |
private void |
setOptions(Map<String,Object> info) |
boolean |
setParallel(boolean TF) |
void |
setPdbConectBonding(boolean isAuto,
boolean isStateScript) |
(package private) void |
setPendingMeasurement(MeasurementPending measurementPending) |
void |
setPercentVdwAtom(int value) |
void |
setPerspectiveDepth(boolean perspectiveDepth) |
void |
setPicked(int iAtom) |
(package private) void |
setPickingMode(String strMode,
int pickingMode) |
(package private) void |
setPickingStyle(String style,
int pickingStyle) |
void |
setPropertyColorScheme(String scheme,
boolean isTranslucent,
boolean isOverloaded) |
void |
setProteinType(EnumStructure type,
BS bs) |
void |
setRasmolDefaults() |
private void |
setRefreshing(boolean TF) |
(package private) void |
setRotateBondIndex(int index) |
void |
setRotationMatrix(javajs.util.M3 rotationMatrix) |
void |
setRotationRadius(float angstroms,
boolean doAll) |
void |
setRubberbandArgb(int argb) |
void |
setScreenDimension(int width,
int height) |
private void |
setScriptQueue(boolean TF) |
void |
setScriptStatus(String strStatus,
String statusMessage,
int msWalltime,
String strErrorMessageUntranslated) |
void |
setSelectedAtom(int atomIndex,
boolean TF) |
void |
setSelectionHalos(boolean TF) |
void |
setSelectionSet(BS set) |
void |
setSelectionSubset(BS subset) |
void |
setShapeErrorState(int shapeID,
String state) |
void |
setShapeProperty(int shapeID,
String propertyName,
Object value) |
void |
setShapeSize(int shapeID,
int mad,
BS bsSelected) |
void |
setShapeSizeRD(int shapeID,
RadiusData rd,
BS 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(String s) |
void |
setSpin(String key,
int value) |
void |
setSpinOn(boolean spinOn) |
private void |
setStartupBooleans() |
void |
setStateScriptVersion(String version) |
void |
setStatusAtomHovered(int atomIndex,
String info) |
void |
setStatusAtomPicked(int atomIndex,
String info) |
(package private) void |
setStatusFrameChanged(boolean isVib,
boolean doNotify) |
void |
setStatusMeasuring(String status,
int intInfo,
String strMeasure,
float value) |
void |
setStatusObjectHovered(String id,
String info,
javajs.util.P3 pt) |
void |
setStatusResized(int width,
int height) |
void |
setStereoMode(int[] twoColors,
EnumStereoMode stereoMode,
float degrees) |
private void |
setStrandCount(int type,
int value) |
void |
setStringProperty(String key,
String value) |
private void |
setStringPropertyTok(String key,
int tok,
String value) |
void |
setStructureList(float[] list,
EnumStructure type) |
private void |
setSync() |
void |
setSyncDriver(int mode) |
private void |
setSyncTarget(int mode,
boolean TF) |
void |
setTainted(boolean TF) |
void |
setTaintedAtoms(BS bs,
byte type) |
void |
setTimeout(String name,
int mSec,
String script) |
(package private) void |
setTrajectory(int modelIndex) |
void |
setTrajectoryBs(BS bsModels) |
private void |
setTransformManagerDefaults() |
void |
setUnits(String units,
boolean isDistance) |
void |
setUserScale(int[] scale) |
SV |
setUserVariable(String name,
SV value) |
(package private) void |
setUserVdw(EnumVdw mode) |
(package private) void |
setVdwStr(String name) |
void |
setVectorScale(float scale) |
void |
setVibrationOff() |
void |
setVibrationPeriod(float period) |
void |
setVibrationScale(float scale) |
void |
setZslabPoint(javajs.util.P3 pt) |
void |
show2D(String smiles) |
void |
showConsole(boolean showConsole) |
void |
showEditor(String[] file_text) |
void |
showMessage(String s) |
void |
showParameter(String key,
boolean ifNotSet,
int nMax) |
void |
showString(String str,
boolean isPrint) |
String |
showTimeout(String name) |
void |
showUrl(String urlString) |
(package private) void |
slabByPixels(int pixels) |
(package private) void |
slabDepthByPixels(int pixels) |
void |
slabInternal(javajs.util.P4 plane,
boolean isDepth) |
void |
slabReset() |
void |
slabToPercent(int percentSlab) |
void |
spinXYBy(int xDelta,
int yDelta,
float speed) |
void |
startHoverWatcher(boolean tf) |
void |
startSpinningAxis(javajs.util.P3 pt1,
javajs.util.P3 pt2,
boolean isClockwise) |
(package private) void |
stopMinimization() |
void |
stopMotion() |
void |
syncScript(String script,
String applet,
int port) |
void |
toCartesian(javajs.util.P3 pt,
boolean asAbsolute)
absolute or relative to origin of UNITCELL {x y z}
|
void |
toFractional(javajs.util.P3 pt,
boolean asAbsolute)
absolute or relative to origin of UNITCELL {x y z}
|
void |
togglePickingLabel(BS bs) |
void |
toUnitCell(javajs.util.P3 pt,
javajs.util.P3 offset)
relative to origin without regard to UNITCELL {x y z}
|
void |
transformPoints(javajs.util.P3[] pointsAngstroms,
javajs.util.P3i[] pointsScreens) |
javajs.util.P3i |
transformPt(javajs.util.P3 pointAngstroms) |
void |
transformPt3f(javajs.util.P3 pointAngstroms,
javajs.util.P3 pointScreen) |
void |
transformPtNoClip(javajs.util.P3 pointAngstroms,
javajs.util.P3 pt) |
void |
transformPtScr(javajs.util.P3 pointAngstroms,
javajs.util.P3i pointScreen) |
javajs.util.P3i |
transformPtVib(javajs.util.P3 pointAngstroms,
Vibration vibrationVector) |
void |
transformVector(javajs.util.V3 vectorAngstroms,
javajs.util.V3 vectorTransformed) |
void |
translate(char xyz,
float x,
char type,
BS bsAtoms) |
void |
translateXYBy(int xDelta,
int yDelta) |
void |
triggerTimeout(String name) |
void |
unBindAction(String desc,
String name) |
(package private) void |
undoClear() |
void |
undoMoveAction(int action,
int n) |
(package private) void |
undoMoveActionClear(int taintedAtom,
int type,
boolean clearRedo) |
float |
unscaleToScreen(float z,
float screenDistance) |
void |
unsetProperty(String key) |
void |
unTransformPoint(javajs.util.P3 pointScreen,
javajs.util.P3 pointAngstroms) |
void |
updateJS(int width,
int height)
for JavaScript only
|
private boolean |
updateWindow(int width,
int height) |
boolean |
useMinimizationThread() |
String |
writeFileData(String fileName,
String type,
int modelIndex,
Object[] parameters) |
void |
writeTextFile(String fileName,
String data) |
void |
zap(boolean notify,
boolean resetUndo,
boolean zapModelKit) |
private void |
zapMsg(String msg) |
(package private) void |
zoomBy(int pixels) |
(package private) void |
zoomByFactor(float factor,
int x,
int y) |
int |
zValueFromPercent(int zPercent) |
allocateViewer, allocateViewer, checkOption, getJmolValueAsString, getJsObjectInfo, mouseEvent, openFileAsync, renderScreenImage, setConsole
public boolean autoExit
public boolean haveDisplay
public boolean isJS
public boolean isWebGL
public boolean isSingleThreaded
public boolean queueOnHold
public String fullName
public String appletDocumentBase
public String appletCodeBase
public String appletIdiomaBase
public static String jsDocumentBase
public Object compiler
public ModelSet modelSet
public FileManager fileManager
private boolean isApplet
private boolean isJNLP
public boolean isSyntaxAndFileCheck
public boolean isSyntaxCheck
public boolean listCommands
boolean mustRender
String htmlName
private String insertedCommand
GData gdata
Object applet
ActionManager actionManager
AnimationManager animationManager
ColorManager colorManager
JmolDataManager dataManager
ShapeManager shapeManager
SelectionManager selectionManager
JmolRepaintManager repaintManager
public GlobalSettings global
public StatusManager statusManager
TransformManager transformManager
private static final String strJavaVendor
private static final String strOSName
private static final String strJavaVersion
private String syncId
private String logFilePath
private boolean allowScripting
private boolean isPrintOnly
private boolean isSignedApplet
private boolean isSignedAppletLocal
private boolean isSilent
private boolean multiTouch
private boolean noGraphicsAllowed
private boolean useCommandThread
private String commandOptions
private Object display
private JmolAdapter modelAdapter
private Viewer.ACCESS access
private CommandHistory commandHistory
private SymmetryInterface symmetry
private SmilesMatcherInterface smilesMatcher
private ModelManager modelManager
private StateManager stateManager
private JmolScriptManager scriptManager
public JmolScriptEvaluator eval
private TempArray tempArray
private static String version_date
private boolean isPreviewOnly
private javajs.api.GenericMouseInterface mouse
private boolean mouseEnabled
private boolean noneSelected
JmolStateCreator sc
BS bsFrameOffsets
javajs.util.P3[] frameOffsets
private int motionEventNumber
private boolean inMotion
private boolean refreshing
private boolean axesAreTainted
final javajs.awt.Dimension dimScreen
private int maximumSize
private float imageFontScaling
private boolean antialiasDisplay
int hoverAtomIndex
String hoverText
public boolean hoverEnabled
private int currentCursor
int prevFrame
private boolean haveJDX
private JmolJSpecView jsv
private String language
private RadiusData rd
private boolean frankOn
public boolean scriptEditorVisible
JmolAppConsoleInterface appConsole
JmolScriptEditorInterface scriptEditor
javajs.api.GenericMenuInterface jmolpopup
private javajs.api.GenericMenuInterface modelkitPopup
JmolPropertyManager pm
boolean isTainted
private boolean movingSelected
private boolean showSelected
private int rotateBondIndex
private int rotatePrev1
private int rotatePrev2
private BS bsRotateBranch
public boolean creatingImage
private OutputManager outputManager
public static final String SYNC_GRAPHICS_MESSAGE
public static final String SYNC_NO_GRAPHICS_MESSAGE
BS bsUserVdws
float[] userVdws
int[] userVdwMars
EnumVdw defaultVdw
private String errorMessage
private String errorMessageUntranslated
private int currentShapeID
private String currentShapeState
static final Map<String,JmolScriptFunction> staticFunctions
Map<String,JmolScriptFunction> localFunctions
private double privateKey
boolean isKiosk
private MinimizerInterface minimizer
private Object executor
public static int nProcessors
public boolean displayLoadErrors
boolean isParallel
final javajs.util.List<String> actionStates
final javajs.util.List<String> actionStatesRedo
private int stateScriptVersionInt
private JmolRendererInterface jsExporter3D
public javajs.util.List<String> chainList
JmolNMRInterface nmrCalculation
String logFileName
public Viewer(Map<String,Object> info)
info
- "display" "adapter" "statusListener" "platform" "options" "fullName"
"documentBase" "codeBase" "multiTouch" [options] "noGraphics"
"printOnly" "previewOnly" "debug" "applet" "signedApplet"
"appletProxy" "useCommandThread" "platform" [option]
"backgroundTransparent" "exit" "listCommands" "check" "checkLoad"
"silent" "access:READSPT" "access:NONE" "menuFile"
"headlessMaxTimeMs" "headlessImage" "isDataOnly"protected void finalize() throws Throwable
public boolean hasDisplay()
public boolean isApplet()
isApplet
in class JmolViewer
public void setInsertedCommand(String strScript)
public ActionManager getActionManager()
String getLogFilePath()
public boolean isSignedApplet()
public static String getJmolVersion()
protected static JmolViewer allocateViewer(Object display, JmolAdapter modelAdapter, String fullName, URL documentBase, URL codeBase, String commandOptions, JmolStatusListener statusListener, javajs.api.GenericPlatform implementedPlatform)
display
- modelAdapter
- fullName
- documentBase
- codeBase
- commandOptions
- statusListener
- implementedPlatform
- StatusManager getStatusManager()
public boolean haveAccess(Viewer.ACCESS a)
public JmolAdapter getModelAdapter()
getModelAdapter
in class JmolViewer
public SymmetryInterface getSymmetry()
public Object getSymmetryInfo(BS bsAtoms, String xyz, int op, javajs.util.P3 pt, javajs.util.P3 pt2, String id, int type)
public SmilesMatcherInterface getSmilesMatcher()
public BS getSmartsMatch(String smarts, BS bsSelected)
getSmartsMatch
in class JmolViewer
public void setDisplay(Object canvas)
private JmolDataManager getDataManager()
private JmolScriptManager getScriptManager()
public boolean isPreviewOnly()
public boolean isHeadless()
private void setStartupBooleans()
public boolean noGraphicsAllowed()
public String getExportDriverList()
public String getHtmlName()
public Object getDisplay()
getDisplay
in class JmolViewer
public void clearMouse()
public void disposeMouse()
public void processTwoPointGesture(float[][][] touches)
processTwoPointGesture
in interface javajs.api.JSInterface
public boolean processMouseEvent(int id, int x, int y, int modifiers, long time)
processMouseEvent
in interface javajs.api.JSInterface
processMouseEvent
in class JmolViewer
public void reset(boolean includingSpin)
public void homePosition()
homePosition
in class JmolViewer
public void initialize(boolean clearUserVariables)
public String listSavedStates()
public void saveOrientation(String saveName, float[] pymolView)
public void restoreScene(String saveName, float timeSeconds)
public boolean restoreOrientation(String saveName, float timeSeconds)
public void restoreRotation(String saveName, float timeSeconds)
void saveModelOrientation()
public Orientation getOrientation()
void restoreModelOrientation(int modelIndex)
void restoreModelRotation(int modelIndex)
public void saveBonds(String saveName)
public boolean restoreBonds(String saveName)
public void saveState(String saveName)
public void deleteSavedState(String saveName)
public void saveStructure(String saveName)
public void saveSelection(String saveName)
public boolean restoreSelection(String saveName)
public javajs.util.M4 getMatrixtransform()
public Quaternion getRotationQuaternion()
public void setRotationRadius(float angstroms, boolean doAll)
public javajs.util.P3 getRotationCenter()
public void setCenterAt(String relativeTo, javajs.util.P3 pt)
public void setCenterBitSet(BS bsCenter, boolean doScale)
public void setNewRotationCenter(javajs.util.P3 center)
public javajs.util.P3 getNavigationCenter()
public float getNavigationDepthPercent()
void navigate(int keyWhere, int modifiers)
public javajs.util.P3 getNavigationOffset()
public float getNavigationOffsetPercent(char XorY)
public boolean isNavigating()
public boolean isInPosition(javajs.util.V3 axis, float degrees)
public void move(JmolScriptEvaluator eval, javajs.util.V3 dRot, float dZoom, javajs.util.V3 dTrans, float dSlab, float floatSecondsTotal, int fps)
public void stopMotion()
public void setRotationMatrix(javajs.util.M3 rotationMatrix)
public void moveTo(JmolScriptEvaluator eval, float floatSecondsTotal, javajs.util.P3 center, javajs.util.V3 rotAxis, float degrees, javajs.util.M3 rotationMatrix, float zoom, float xTrans, float yTrans, float rotationRadius, javajs.util.P3 navCenter, float xNav, float yNav, float navDepth, float cameraDepth, float cameraX, float cameraY)
public void moveUpdate(float floatSecondsTotal)
public String getMoveToText(float timespan)
public void navigateList(JmolScriptEvaluator eval, javajs.util.List<Object[]> list)
public void navigatePt(javajs.util.P3 center)
public void navigateAxis(javajs.util.V3 rotAxis, float degrees)
public void navTranslatePercent(float x, float y)
public void setMouseEnabled(boolean TF)
public void processMultitouchEvent(int groupID, int eventType, int touchID, int iData, javajs.util.P3 pt, long time)
processMultitouchEvent
in class JmolViewer
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 rotateSelected(float deltaX, float deltaY, BS bsSelected)
public void translateXYBy(int xDelta, int yDelta)
public void rotateFront()
rotateFront
in class JmolViewer
public void rotateX(float angleRadians)
rotateX
in class JmolViewer
public void rotateY(float angleRadians)
rotateY
in class JmolViewer
public void rotateZ(float angleRadians)
rotateZ
in class JmolViewer
public void rotateXDeg(int angleDegrees)
rotateXDeg
in class JmolViewer
public void rotateYDeg(int angleDegrees)
rotateYDeg
in class JmolViewer
public void translate(char xyz, float x, char type, BS bsAtoms)
public float getTranslationXPercent()
public float getTranslationYPercent()
float getTranslationZPercent()
public String getTranslationScript()
public int getZShadeStart()
public boolean isWindowCentered()
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()
void slabByPixels(int pixels)
void depthByPixels(int pixels)
void slabDepthByPixels(int pixels)
public void slabInternal(javajs.util.P4 plane, boolean isDepth)
public void slabToPercent(int percentSlab)
public void depthToPercent(int percentDepth)
public void setSlabDepthInternal(boolean isDepth)
public int zValueFromPercent(int zPercent)
public javajs.util.M4 getUnscaledTransformMatrix()
getUnscaledTransformMatrix
in class JmolViewer
public void finalizeTransformParameters()
public void rotatePoint(javajs.util.P3 pt, javajs.util.P3 ptRot)
public javajs.util.P3i transformPt(javajs.util.P3 pointAngstroms)
public javajs.util.P3i transformPtVib(javajs.util.P3 pointAngstroms, Vibration vibrationVector)
public void transformPtScr(javajs.util.P3 pointAngstroms, javajs.util.P3i pointScreen)
public void transformPtNoClip(javajs.util.P3 pointAngstroms, javajs.util.P3 pt)
public void transformPt3f(javajs.util.P3 pointAngstroms, javajs.util.P3 pointScreen)
public void transformPoints(javajs.util.P3[] pointsAngstroms, javajs.util.P3i[] pointsScreens)
public void transformVector(javajs.util.V3 vectorAngstroms, javajs.util.V3 vectorTransformed)
public void unTransformPoint(javajs.util.P3 pointScreen, javajs.util.P3 pointAngstroms)
public float getScalePixelsPerAngstrom(boolean asAntialiased)
public float scaleToScreen(int z, int milliAngstroms)
public float unscaleToScreen(float z, float screenDistance)
public float scaleToPerspective(int z, float sizeAngstroms)
public void setSpin(String key, int value)
public String getSpinState()
public void setSpinOn(boolean spinOn)
public boolean getSpinOn()
public void setNavOn(boolean navOn)
public boolean getNavOn()
public void setNavXYZ(float x, float y, float z)
javajs.util.M3 getMatrixRotate()
public void getAxisAngle(javajs.util.A4 axisAngle)
public String getTransformText()
public void getRotation(javajs.util.M3 matrixRotation)
public float[] getCurrentColorRange()
private void setDefaultColors(boolean isRasmol)
public int getColorArgbOrGray(short colix)
public void setRubberbandArgb(int argb)
public short getColixRubberband()
public void setElementArgb(int elementNumber, int argb)
public void setVectorScale(float scale)
setVectorScale
in class JmolViewer
public boolean isVibrationOn()
public void setVibrationScale(float scale)
setVibrationScale
in class JmolViewer
public void setVibrationOff()
public void setVibrationPeriod(float period)
setVibrationPeriod
in class JmolViewer
public void setObjectVisibility(String name, boolean b)
public void setObjectArgb(String name, int argb)
int getObjectArgb(int objId)
public short getObjectColix(int objId)
public void setColorBackground(String colorName)
setColorBackground
in class JmolViewer
public int getBackgroundArgb()
getBackgroundArgb
in class JmolViewer
public void setObjectMad(int iShape, String name, int mad)
public int getObjectMad(int objId)
public void setPropertyColorScheme(String scheme, boolean isTranslucent, boolean isOverloaded)
public String getPropertyColorScheme()
public short getColixBackgroundContrast()
public String getSpecularState()
public short getColixAtomPalette(Atom atom, byte pid)
public short getColixBondPalette(Bond bond, int pid)
public void setUserScale(int[] scale)
public short getColixForPropertyValue(float val)
public javajs.util.P3 getColorPointForPropertyValue(float val)
public void select(BS bs, boolean isGroup, int addRemove, boolean isQuiet)
public void setSelectionSet(BS set)
setSelectionSet
in class JmolViewer
public void selectBonds(BS bs)
public void displayAtoms(BS bs, boolean isDisplay, boolean isGroup, int addRemove, boolean isQuiet)
public BS getHiddenSet()
public boolean isSelected(int atomIndex)
boolean isInSelectionSubset(int atomIndex)
void reportSelection(String msg)
public javajs.util.P3 getAtomSetCenter(BS bs)
private void clearAtomSets()
public void selectAll()
selectAll
in class JmolViewer
public void setNoneSelected(boolean noneSelected)
public Boolean getNoneSelected()
public void clearSelection()
clearSelection
in class JmolViewer
public void setSelectionSubset(BS subset)
public BS getSelectionSubset()
public void invertSelection()
public BS 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
BS getAtomBitSetEval(JmolScriptEvaluator eval, Object atomExpression)
public void setModeMouse(int modeMouse)
setModeMouse
in class JmolViewer
public Rectangle getRubberBandSelection()
public boolean isBound(int action, int gesture)
public int getCursorX()
public int getCursorY()
String getDefaultDirectory()
public BufferedInputStream getBufferedInputStream(String fullPathName)
getBufferedInputStream
in interface AtomDataServer
public Object getBufferedReaderOrErrorMessageFromName(String name, String[] fullPathNameReturn, boolean isBinary)
private Map<String,Object> setLoadParameters(Map<String,Object> htParams, boolean isAppend)
public void openFileAsyncSpecial(String fileName, int flags)
openFileAsyncSpecial
in interface javajs.api.JSInterface
openFileAsyncSpecial
in class JmolViewer
fileName
- flags
- 1 = check PDBcartoonspublic String openFile(String fileName)
openFile
in class JmolViewer
fileName
- public String openFiles(String[] fileNames)
openFiles
in class JmolViewer
fileNames
- public String openReader(String fullPathName, String fileName, Reader reader)
openReader
in class JmolViewer
fullPathName
- fileName
- reader
- public String openDOM(Object DOMNode)
openDOM
in class JmolViewer
DOMNode
- private String loadModelFromFileRepaint(String fullPathName, String fileName, String[] fileNames, Object reader)
public String loadModelFromFile(String fullPathName, String fileName, String[] fileNames, Object reader, boolean isAppend, Map<String,Object> htParams, javajs.util.SB loadScript, int tokType)
fullPathName
- TODOfileName
- fileNames
- reader
- TODOisAppend
- htParams
- loadScript
- tokType
- public Object getLigandModel(String id, String prefix, String suffix, String terminator)
id
- if null, clear "bad" entries from the set.prefix
- suffix
- terminator
- Only save to this if not nullprivate Object openFileFull(String fileName, boolean isAppend, Map<String,Object> htParams, javajs.util.SB loadScript)
fileName
- isAppend
- htParams
- loadScript
- only necessary for string readingpublic String openStringInline(String strModel)
openStringInline
in class JmolViewer
public String loadInline(String strModel)
loadInline
in class JmolViewer
public String loadInline(String strModel, char newLine)
loadInline
in class JmolViewer
public String loadInlineAppend(String strModel, boolean isAppend)
loadInlineAppend
in class JmolViewer
private String loadInlineScriptRepaint(String strModel, char newLine, boolean isAppend)
public String loadInline(String[] arrayModels)
loadInline
in class JmolViewer
public String loadInline(String[] arrayModels, boolean isAppend)
loadInline
in class JmolViewer
arrayModels
- and array of models, each of which is a Stringpublic String loadInline(List<Object> arrayData, boolean isAppend)
loadInline
in class JmolViewer
arrayData
- isAppend
- private String loadInlineScript(String strModel, char newLine, boolean isAppend, Map<String,Object> htParams)
strModel
- newLine
- isAppend
- htParams
- public String openStringInlineParamsAppend(String strModel, Map<String,Object> htParams, boolean isAppend)
strModel
- htParams
- isAppend
- private String openStringsInlineParamsAppend(String[] arrayModels, Map<String,Object> htParams, boolean isAppend)
arrayModels
- htParams
- isAppend
- public char getInlineChar()
String getDataSeparator()
private String createModelSetAndReturnError(Object atomSetCollection, boolean isAppend, javajs.util.SB loadScript, Map<String,Object> htParams)
atomSetCollection
- isAppend
- loadScript
- if null, then some special method like DOM; turn of preserveStatehtParams
- private String loadAtomDataAndReturnError(Object atomSetCollection, int tokType)
atomSetCollection
- tokType
- public String getEmbeddedFileState(String filename)
getEmbeddedFileState
in class JmolViewer
public Object getFileAsBytes(String pathName, javajs.util.OC out)
getFileAsBytes
in class JmolViewer
public String getCurrentFileAsString()
public String getFullPathName(boolean orPrevious)
public String getFileName()
public String[] getFullPathNameOrError(String filename)
filename
- public String getFileAsString(String name)
getFileAsString
in class JmolViewer
public String getFileAsString4(String name, int nBytesMax, boolean doSpecialLoad, boolean allowBinary, boolean checkProtected)
public boolean getFileAsStringBin(String[] data)
public String[] getFileInfo()
public void setFileInfo(String[] fileInfo)
public void autoCalculate(int tokProperty)
int getSurfaceDistanceMax()
public void calculateStraightness()
public javajs.util.P3[] calculateSurface(BS bsSelected, float envelopeRadius)
public Map<EnumStructure,float[]> getStructureList()
public void setStructureList(float[] list, EnumStructure type)
public String calculateStructures(BS bsAtoms, boolean asDSSP, boolean setStructure)
public AtomIndexIterator getSelectedAtomIterator(BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel)
getSelectedAtomIterator
in interface AtomDataServer
public void setIteratorForAtom(AtomIndexIterator iterator, int atomIndex, float distance)
setIteratorForAtom
in interface AtomDataServer
public void setIteratorForPoint(AtomIndexIterator iterator, int modelIndex, javajs.util.P3 pt, float distance)
setIteratorForPoint
in interface AtomDataServer
public void fillAtomData(AtomData atomData, int mode)
fillAtomData
in interface AtomDataServer
public StateScript addStateScript(String script, boolean addFrameNumber, boolean postDefinitions)
public StateScript addStateScriptRet(String script1, BS bsBonds, BS bsAtoms1, BS bsAtoms2, String script2, boolean addFrameNumber, boolean postDefinitions)
public boolean getEchoStateActive()
public void setEchoStateActive(boolean TF)
private void clearModelDependentObjects()
public void zap(boolean notify, boolean resetUndo, boolean zapModelKit)
private void zapMsg(String msg)
void echoMessage(String msg)
private void initializeModel(boolean isAppend)
public void startHoverWatcher(boolean tf)
startHoverWatcher
in interface javajs.api.JSInterface
public String getModelSetName()
getModelSetName
in class JmolViewer
public String getModelSetFileName()
getModelSetFileName
in class JmolViewer
public String getUnitCellInfoText()
public float getUnitCellInfo(int infoType)
public void getPolymerPointsAndVectors(BS bs, javajs.util.List<javajs.util.P3[]> vList)
public String getModelSetPathName()
getModelSetPathName
in class JmolViewer
public String getModelSetTypeName()
public boolean haveFrame()
haveFrame
in class JmolViewer
boolean haveModelSet()
public void clearBfactorRange()
public String getHybridizationAndAxes(int atomIndex, javajs.util.V3 z, javajs.util.V3 x, String lcaoType)
public BS getMoleculeBitSet(int atomIndex)
public BS getAllAtoms()
public BS getModelUndeletedAtomsBitSet(int modelIndex)
public void excludeAtoms(BS bs, boolean ignoreSubset)
public ModelSet getModelSet()
public String getBoundBoxCommand(boolean withOptions)
public void setBoundBox(javajs.util.P3 pt1, javajs.util.P3 pt2, boolean byCorner, float scale)
public javajs.util.P3 getBoundBoxCenter()
getBoundBoxCenter
in class JmolViewer
javajs.util.P3 getAverageAtomPoint()
public void calcBoundBoxDimensions(BS bs, float scale)
public float calcRotationRadius(javajs.util.P3 center)
public float calcRotationRadiusBs(BS bs)
public javajs.util.V3 getBoundBoxCornerVector()
getBoundBoxCornerVector
in class JmolViewer
public javajs.util.P3[] getBoundBoxVertices()
public BS getBoundBoxModels()
public int getBoundBoxCenterX()
public int getBoundBoxCenterY()
public int getModelCount()
getModelCount
in class JmolViewer
public String getModelInfoAsString()
public String getSymmetryInfoAsString()
public String getSymmetryOperation(String spaceGroup, int symop, javajs.util.P3 pt1, javajs.util.P3 pt2, boolean labelOnly)
public Properties getModelSetProperties()
getModelSetProperties
in class JmolViewer
public Map<String,Object> getModelSetAuxiliaryInfo()
getModelSetAuxiliaryInfo
in class JmolViewer
public int getModelNumber(int modelIndex)
getModelNumber
in class JmolViewer
public int getModelFileNumber(int modelIndex)
public String getModelNumberDotted(int modelIndex)
getModelNumberDotted
in class JmolViewer
public String getModelName(int modelIndex)
getModelName
in class JmolViewer
public Properties getModelProperties(int modelIndex)
getModelProperties
in class JmolViewer
public String getModelProperty(int modelIndex, String propertyName)
getModelProperty
in class JmolViewer
public String getModelFileInfo()
public String getModelFileInfoAll()
public Map<String,Object> getModelAuxiliaryInfo(int modelIndex)
getModelAuxiliaryInfo
in class JmolViewer
public Object getModelAuxiliaryInfoValue(int modelIndex, String keyName)
getModelAuxiliaryInfoValue
in class JmolViewer
public int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
boolean modelSetHasVibrationVectors()
public int modelGetLastVibrationIndex(int modelIndex, int tok)
modelGetLastVibrationIndex
in class JmolViewer
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 getChainCountInModelWater(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 allpublic 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 findNearestAtomIndexMovable(int x, int y, boolean mustBeMovable)
public void toCartesian(javajs.util.P3 pt, boolean asAbsolute)
pt
- asAbsolute
- TODOpublic void toFractional(javajs.util.P3 pt, boolean asAbsolute)
pt
- asAbsolute
- TODOpublic void toUnitCell(javajs.util.P3 pt, javajs.util.P3 offset)
pt
- offset
- public void setCurrentCage(String isosurfaceId)
public void setCurrentCagePts(javajs.util.P3[] points)
public void setCurrentUnitCellOffset(javajs.util.P3 pt, int ijk)
public void addUnitCellOffset(javajs.util.P3 pt)
public void setAtomData(int type, String name, String coordinateData, boolean isDefault)
public void setCenterSelected()
setCenterSelected
in class JmolViewer
void setApplySymmetryToBonds(boolean TF)
public void setBondTolerance(float bondTolerance)
setBondTolerance
in class JmolViewer
public void setMinBondDistance(float minBondDistance)
setMinBondDistance
in class JmolViewer
public int[] getAtomIndices(BS bs)
public BS getAtomsNearPt(float distance, javajs.util.P3 coord)
public BS getAtomsNearPlane(float distance, javajs.util.P4 plane)
public BS getAtomsWithinRadius(float distance, BS bs, boolean withinAllModels, RadiusData rd)
public BS getBranchBitSet(int atomIndex, int atomIndexNot, boolean allowCyclic)
public int getAtomIndexFromAtomNumber(int atomNumber)
public BS getElementsPresentBitSet(int modelIndex)
getElementsPresentBitSet
in class JmolViewer
public Map<String,String> getHeteroList(int modelIndex)
getHeteroList
in class JmolViewer
public BS getVisibleSet()
public BS getClickableSet()
public void calcSelectedGroupsCount()
public void calcSelectedMonomersCount()
public void calcSelectedMoleculesCount()
String getFileHeader()
Object getFileData()
public String getPDBHeader()
public String getChimeInfo(int tok)
public JmolStateCreator getStateCreator()
public String getWrappedStateScript()
public String getStateInfo()
getStateInfo
in class JmolViewer
public String getStructureState()
public String getProteinStructureState()
public void setCurrentColorRange(String label)
public void setCurrentColorRangeData(float[] data, BS bs)
public void setCurrentColorRange(float min, float max)
public int getArgbMinMax(float val, float min, float max)
public void setData(String type, Object[] data, int arrayCount, int matchField, int matchFieldColumnCount, int field, int fieldColumnCount)
public float[] getDataFloat(String label)
public float[][] getDataFloat2D(String label)
public float[][][] getDataFloat3D(String label)
public float getDataFloatAt(String label, int atomIndex)
public String getAltLocListInModel(int modelIndex)
getAltLocListInModel
in class JmolViewer
public BS setConformation()
public BS getConformation(int iModel, int conformationIndex, boolean doSet)
public boolean havePartialCharges()
havePartialCharges
in class JmolViewer
public SymmetryInterface getCurrentUnitCell()
public SymmetryInterface getModelUnitCell(int modelIndex)
public String getDefaultMeasurementLabel(int nPoints)
public int getMeasurementCount()
getMeasurementCount
in class JmolViewer
public String getMeasurementStringValue(int i)
getMeasurementStringValue
in class JmolViewer
public 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 void setAnimation(int tok)
public void setAnimationDirection(int direction)
int getAnimationDirection()
public void setAnimationFps(int fps)
setAnimationFps
in class JmolViewer
private void setAnimationMode(String mode)
public void setAnimationReplayMode(EnumAnimationMode replayMode, float firstFrameDelay, float lastFrameDelay)
public EnumAnimationMode getAnimationReplayMode()
public void setAnimationOn(boolean animationOn)
public void setAnimationRange(int modelIndex1, int modelIndex2)
public BS getVisibleFramesBitSet()
getVisibleFramesBitSet
in class JmolViewer
boolean isAnimationOn()
public void setAnimMorphCount(int n)
public boolean isMovie()
public int getFrameCount()
public void morph(float frame)
public void setAnimDisplay(BS bs)
public void setCurrentModelIndex(int modelIndex)
void setTrajectory(int modelIndex)
public void setTrajectoryBs(BS bsModels)
public boolean isTrajectory(int modelIndex)
public BS getBitSetTrajectories()
public String getTrajectoryState()
void setFrameOffset(int modelIndex)
public void setFrameOffsets(BS bsAtoms)
public BS getFrameOffsets()
public void setCurrentModelIndexClear(int modelIndex, boolean clearBackground)
public int getCurrentModelIndex()
public int getDisplayModelIndex()
getDisplayModelIndex
in class JmolViewer
public boolean haveFileSet()
public void setBackgroundModelIndex(int modelIndex)
void setFrameVariables()
public boolean getInMotion(boolean includeAnim)
public int getMotionEventNumber()
getMotionEventNumber
in class JmolViewer
public void setInMotion(boolean inMotion)
setInMotion
in class JmolViewer
private void setRefreshing(boolean TF)
public boolean getRefreshing()
public void pushHoldRepaint()
pushHoldRepaint
in class JmolViewer
public void pushHoldRepaintWhy(String why)
why
- public void popHoldRepaint(String why)
popHoldRepaint
in class JmolViewer
public void refresh(int mode, String strWhy)
refresh
in class JmolViewer
mode
- strWhy
- public void requestRepaintAndWait(String why)
public void clearShapeRenderers()
public boolean isRepaintPending()
public void notifyViewerRepaintDone()
notifyViewerRepaintDone
in class JmolViewer
public boolean areAxesTainted()
private void setMaximumSize(int x)
public void setScreenDimension(int width, int height)
setScreenDimension
in interface javajs.api.JSInterface
setScreenDimension
in class JmolViewer
public float getImageFontScaling()
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 String generateOutputForExport(Map<String,Object> params)
generateOutputForExport
in class JmolViewer
private void clearRepaintManager(int iShape)
public void renderScreenImageStereo(Object gLeft, Object gRight, int width, int height)
JmolViewer
renderScreenImageStereo
in class JmolViewer
public void updateJS(int width, int height)
updateJS
in interface javajs.api.JSInterface
width
- height
- private boolean updateWindow(int width, int height)
public void renderScreenImage(Object g, int width, int height)
renderScreenImage
in class JmolViewer
private Object getImage(boolean isDouble, boolean isImageWrite)
isDouble
- isImageWrite
- TODOprivate void beginRendering(boolean isDouble, boolean isImageWrite)
public boolean isAntialiased()
private void render()
public Object getScreenImageBuffer(Object graphic, boolean isImageWrite)
getScreenImageBuffer
in class JmolViewer
public byte[] getImageAsBytes(String type, int width, int height, int quality, String[] errMsg)
getImageAsBytes
in class JmolViewer
errMsg
- TODOpublic void releaseScreenImage()
releaseScreenImage
in class JmolViewer
public String evalFile(String strFilename)
evalFile
in class JmolViewer
public String getInsertedCommand()
public String script(String strScript)
script
in class JmolViewer
public String evalString(String strScript)
evalString
in class JmolViewer
public String evalStringQuiet(String strScript)
evalStringQuiet
in class JmolViewer
public String evalStringQuietSync(String strScript, boolean isQuiet, boolean allowSyncScript)
public void clearScriptQueue()
private void setScriptQueue(boolean TF)
public boolean checkHalt(String str, boolean isInsert)
checkHalt
in class JmolViewer
public String scriptWait(String strScript)
scriptWait
in class JmolViewer
public Object scriptWaitStatus(String strScript, String statusList)
scriptWaitStatus
in class JmolViewer
public Object evalStringWaitStatusQueued(String returnType, String strScript, String statusList, boolean isScriptFile, boolean isQuiet, boolean isQueued)
public void exitJmol()
public Object scriptCheck(String strScript)
scriptCheck
in class JmolViewer
public boolean isScriptExecuting()
isScriptExecuting
in class JmolViewer
public void haltScriptExecution()
haltScriptExecution
in class JmolViewer
public void pauseScriptExecution()
public String getDefaultLoadFilter()
public String getDefaultLoadScript()
public static boolean isDatabaseCode(char ch)
public static boolean hasDatabasePrefix(String fileName)
public Object setLoadFormat(String name, char type, boolean withPrefix)
name
- type
- withPrefix
- public String[] getElectronDensityLoadInfo()
public String getStandardLabelFormat(int type)
public javajs.util.P3[] getAdditionalHydrogens(BS bsAtoms, boolean doAll, boolean justCarbon, javajs.util.List<Atom> vConnections)
public void setMarBond(short marBond)
setMarBond
in class JmolViewer
public void setHoverLabel(String strLabel)
void hoverOn(int atomIndex, boolean isLabel)
void hoverOff()
public int getBfactor100Hi()
short getColix(Object object)
public void setDebugScript(boolean debugScript)
setDebugScript
in class JmolViewer
void clearClickCount()
public int getCursor()
public void setCursor(int cursor)
void setPickingMode(String strMode, int pickingMode)
public int getPickingMode()
void setPickingStyle(String style, int pickingStyle)
public boolean getDrawHover()
public String getAtomInfo(int atomOrPointIndex)
getAtomInfo
in class JmolViewer
public String getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
private void setSync()
public void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
setJmolCallbackListener
in class JmolViewer
public void setJmolStatusListener(JmolStatusListener jmolStatusListener)
setJmolStatusListener
in class JmolViewer
public javajs.util.List<javajs.util.List<javajs.util.List<Object>>> getStatusChanged(String statusNameList)
public boolean menuEnabled()
void popupMenu(int x, int y, char type)
private Object getPopupMenu()
public void setMenu(String fileOrText, boolean isFile)
void setStatusFrameChanged(boolean isVib, boolean doNotify)
private boolean doHaveJDX()
private JmolJSpecView getJSV()
public int getJDXBaseModelIndex(int modelIndex)
modelIndex
- public void scriptEcho(String strEcho)
private boolean isScriptQueued()
public void setStatusAtomHovered(int atomIndex, String info)
public void setStatusObjectHovered(String id, String info, javajs.util.P3 pt)
private void setFileLoadStatus(EnumFileStatus ptLoad, String fullPathName, String fileName, String modelName, String strError, Boolean isAsync)
public String getZapName()
public void setStatusMeasuring(String status, int intInfo, String strMeasure, float value)
public void notifyMinimizationStatus()
public void setStatusAtomPicked(int atomIndex, String info)
public void setStatusResized(int width, int height)
public void scriptStatus(String strStatus)
public void setScriptStatus(String strStatus, String statusMessage, int msWalltime, String strErrorMessageUntranslated)
private String getModelTitle(int modelIndex)
public String getModelFileName(int modelIndex)
getModelFileName
in class JmolViewer
public void showUrl(String urlString)
showUrl
in class JmolViewer
public void setMeshCreator(Object meshCreator)
meshCreator
- public void showConsole(boolean showConsole)
public void clearConsole()
public Object getParameter(String key)
getParameter
in class JmolViewer
public void unsetProperty(String key)
public Object getVariableList()
public void notifyStatusReady(boolean isReady)
notifyStatusReady
in class JmolViewer
public boolean getBooleanProperty(String key)
getBooleanProperty
in class JmolViewer
public int getInt(int tok)
getInt
in class JmolViewer
public int getDelayMaximumMs()
public int getHermiteLevel()
public int getHoverDelay()
public boolean getBoolean(int tok)
getBoolean
in class JmolViewer
public boolean allowEmbeddedScripts()
boolean getDragSelected()
boolean getBondPicking()
public boolean useMinimizationThread()
public float getFloat(int tok)
getFloat
in class JmolViewer
public void setStringProperty(String key, String value)
setStringProperty
in class JmolViewer
public void setFloatProperty(String key, float value)
setFloatProperty
in class JmolViewer
private void setFloatPropertyTok(String key, int tok, float value)
public void setIntProperty(String key, int value)
setIntProperty
in class JmolViewer
private void setIntPropertyTok(String key, int tok, int value)
private static int checkIntRange(int value, int min, int max)
private static float checkFloatRange(float value, float min, float max)
public void setBooleanProperty(String key, boolean value)
setBooleanProperty
in class JmolViewer
private void setBooleanPropertyTok(String key, int tok, boolean value)
private void setModelKitMode(boolean value)
public String getLanguage()
public void setSmilesString(String s)
public void removeUserVariable(String key)
public boolean isJmolVariable(String key)
private void jmolTest()
public void showParameter(String key, boolean ifNotSet, int nMax)
public void showString(String str, boolean isPrint)
public int getIsosurfacePropertySmoothing(boolean asPower)
public void setNavigationDepthPercent(float percent)
public boolean getShowNavigationPoint()
public float getCurrentSolventProbeRadius()
public boolean getTestFlag(int i)
public void setPerspectiveDepth(boolean perspectiveDepth)
setPerspectiveDepth
in class JmolViewer
public void setAxesOrientationRasmol(boolean TF)
setAxesOrientationRasmol
in class JmolViewer
void setAxesScale(float scale)
public javajs.util.P3[] getAxisPoints()
public void resetError()
private void setAxesModeMolecular(boolean TF)
void setAxesModeUnitCell(boolean TF)
public EnumAxesMode getAxesMode()
public boolean getPerspectiveDepth()
getPerspectiveDepth
in class JmolViewer
public void setSelectionHalos(boolean TF)
setSelectionHalos
in class JmolViewer
public boolean getSelectionHaloEnabled(boolean isRenderer)
private void setStrandCount(int type, int value)
public int getStrandCount(int type)
public void setNavigationMode(boolean TF)
private void setTransformManagerDefaults()
public javajs.util.P3[] getCameraFactors()
public float getCameraDepth()
public void setAutoBond(boolean TF)
setAutoBond
in class JmolViewer
public int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy)
public void rebond()
rebond
in class JmolViewer
public void rebondState(boolean isStateScript)
public void setPdbConectBonding(boolean isAuto, boolean isStateScript)
public void setPercentVdwAtom(int value)
setPercentVdwAtom
in class JmolViewer
public RadiusData getDefaultRadiusData()
public short getMadBond()
getMadBond
in class JmolViewer
public short getMarBond()
public byte getModeMultipleBond()
public void setShowHydrogens(boolean TF)
setShowHydrogens
in class JmolViewer
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 void setShowMeasurements(boolean TF)
setShowMeasurements
in class JmolViewer
public void setUnits(String units, boolean isDistance)
public String getMeasureDistanceUnits()
public String getEnergyUnits()
public void setAppendNew(boolean value)
public void setRasmolDefaults()
setRasmolDefaults
in class JmolViewer
public void setJmolDefaults()
setJmolDefaults
in class JmolViewer
private void setDefaultsType(String type)
private void setDefaults()
private void setAntialias(int tok, boolean TF)
public javajs.util.P3[] allocTempPoints(int size)
public void freeTempPoints(javajs.util.P3[] tempPoints)
public javajs.util.P3i[] allocTempScreens(int size)
public void freeTempScreens(javajs.util.P3i[] tempScreens)
public EnumStructure[] allocTempEnum(int size)
public void freeTempEnum(EnumStructure[] temp)
String getElementSymbol(int i)
int getElementNumber(int i)
public String getAtomName(int i)
getAtomName
in class JmolViewer
public int getAtomNumber(int i)
getAtomNumber
in class JmolViewer
public Quaternion[] getAtomGroupQuaternions(BS bsAtoms, int nMax)
public Quaternion getAtomQuaternion(int i)
public javajs.util.P3 getAtomPoint3f(int i)
getAtomPoint3f
in class JmolViewer
public javajs.util.List<javajs.util.P3> getAtomPointVector(BS bs)
public float getAtomRadius(int i)
getAtomRadius
in class JmolViewer
public int getAtomArgb(int i)
getAtomArgb
in class JmolViewer
public int getAtomModelIndex(int i)
getAtomModelIndex
in class JmolViewer
public float getBondRadius(int i)
getBondRadius
in class JmolViewer
public int getBondOrder(int i)
getBondOrder
in class JmolViewer
public void assignAromaticBonds()
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 javajs.util.P3[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
getPolymerLeadMidPoints
in class JmolViewer
public void setStereoMode(int[] twoColors, EnumStereoMode stereoMode, float degrees)
boolean isStereoDouble()
public String getOperatingSystemName()
getOperatingSystemName
in class JmolViewer
public String getJavaVendor()
getJavaVendor
in class JmolViewer
public String getJavaVersion()
getJavaVersion
in class JmolViewer
public GData getGraphicsData()
public Object getProperty(String returnType, String infoType, Object paramInfo)
getProperty
in class JmolViewer
returnType
- "JSON", "string", "readable", and anything else returns the Java object.public void showEditor(String[] file_text)
private JmolPropertyManager getPropertyManager()
public String getModelExtract(Object atomExpression, boolean doTransform, boolean isModelKit, String type)
public void setTainted(boolean TF)
public int notifyMouseClicked(int x, int y, int action, int mode)
public boolean checkObjectHovered(int x, int y)
void checkObjectDragged(int prevX, int prevY, int x, int y, int action)
public boolean rotateAxisAngleAtCenter(JmolScriptEvaluator eval, javajs.util.P3 rotCenter, javajs.util.V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected)
public boolean rotateAboutPointsInternal(JmolScriptEvaluator eval, javajs.util.P3 point1, javajs.util.P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, BS bsSelected, javajs.util.V3 translation, javajs.util.List<javajs.util.P3> finalPoints, float[] dihedralList)
public void startSpinningAxis(javajs.util.P3 pt1, javajs.util.P3 pt2, boolean isClockwise)
public javajs.util.V3 getModelDipole()
public javajs.util.V3 calculateMolecularDipole()
public void setDefaultLattice(javajs.util.P3 ptLattice)
public javajs.util.P3 getDefaultLattice()
public BS getTaintedAtoms(byte type)
public void setTaintedAtoms(BS bs, byte type)
public String getData(String atomExpression, String type)
getData
in class JmolViewer
public boolean isJmolDataFrameForModel(int modelIndex)
public boolean isJmolDataFrame()
public int getJmolDataFrameIndex(int modelIndex, String type)
public void setJmolDataFrame(String type, int modelIndex, int dataIndex)
public void setFrameTitle(int modelIndex, String title)
public void setFrameTitleObj(Object title)
public String getFrameTitle()
String getJmolFrameType(int modelIndex)
public int getJmolDataSourceFrame(int modelIndex)
public void setAtomProperty(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)
public void checkCoordinatesChanged()
public void setAtomCoord(int atomIndex, float x, float y, float z)
public void setAtomCoordRelative(int atomIndex, float x, float y, float z)
public void setAtomCoordsRelative(javajs.util.T3 offset, BS bs)
public void invertAtomCoordPt(javajs.util.P3 pt, BS bs)
public void invertAtomCoordPlane(javajs.util.P4 plane, BS bs)
public void invertSelected(javajs.util.P3 pt, javajs.util.P4 plane, int iAtom, BS invAtoms)
public void moveAtoms(javajs.util.M3 mNew, javajs.util.M3 matrixRotate, javajs.util.V3 translation, javajs.util.P3 center, boolean isInternal, BS bsAtoms, boolean translationOnly)
public void moveSelected(int deltaX, int deltaY, int deltaZ, int x, int y, BS bsSelected, boolean isTranslation, boolean asAtoms)
public void highlightBond(int index, boolean isHover)
public void highlight(BS bs)
void setRotateBondIndex(int index)
int getRotateBondIndex()
void actionRotateBond(int deltaX, int deltaY, int x, int y)
public void refreshMeasures(boolean andStopMinimization)
public float[][] functionXY(String functionName, int nX, int nY)
functionName
- nX
- nY
- public float[][][] functionXYZ(String functionName, int nX, int nY, int nZ)
public String extractMolData(String what)
extractMolData
in class JmolViewer
public String getNMRPredict(boolean openURL)
public void getHelp(String what)
public void show2D(String smiles)
public void addCommand(String command)
command
- the command to addpublic String removeCommand()
public String getSetHistory(int howFarBack)
getSetHistory
in class JmolViewer
howFarBack
- number of lines (-1 for next line)public void writeTextFile(String fileName, String data)
writeTextFile
in class JmolViewer
public String clipImageOrPasteText(String text)
clipImageOrPasteText
in class JmolViewer
text
- null here clips image; String pastes textpublic String getClipboardText()
getClipboardText
in class JmolViewer
public String processWriteOrCapture(Map<String,Object> params)
params
- public String outputToFile(Map<String,Object> params)
outputToFile
in class JmolViewer
params
- include type, fileName, text, bytes, quality, width, heightprivate OutputManager getOutputManager()
private void setSyncTarget(int mode, boolean TF)
public void syncScript(String script, String applet, int port)
syncScript
in class JmolViewer
public int getModelIndexFromId(String id)
public void setSyncDriver(int mode)
public float[] getPartialCharges()
public void setProteinType(EnumStructure type, BS bs)
public javajs.util.P3 getBondPoint3f1(int i)
getBondPoint3f1
in class JmolViewer
public javajs.util.P3 getBondPoint3f2(int i)
getBondPoint3f2
in class JmolViewer
public Vibration getVibration(int atomIndex)
public int getVanderwaalsMar(int i)
public int getVanderwaalsMarType(int atomicAndIsotopeNumber, EnumVdw type)
void setVdwStr(String name)
void setUserVdw(EnumVdw mode)
public int deleteAtoms(BS bs, boolean fullModels)
public void deleteBonds(BS bsDeleted)
public void deleteModelAtoms(int firstAtomIndex, int nAtoms, BS bsDeleted)
public BS getDeletedAtoms()
public char getQuaternionFrame()
public String calculatePointGroup()
public String getPointGroupAsString(boolean asDraw, String type, int index, float scale)
void loadImageData(Object image, String nameOrError, String echoName, ScriptContext sc)
public String getErrorMessage()
getErrorMessage
in class JmolViewer
public String getErrorMessageUn()
getErrorMessageUn
in class JmolViewer
public void setShapeErrorState(int shapeID, String state)
public String getShapeErrorState()
public void handleError(Error er, boolean doClear)
public float[] getAtomicCharges()
public Map<String,JmolScriptFunction> getFunctions(boolean isStatic)
public void removeFunction(String name)
public JmolScriptFunction getFunction(String name)
private static boolean isStaticFunction(String name)
public boolean isFunction(String name)
public void clearFunctions()
public void addFunction(JmolScriptFunction function)
public void showMessage(String s)
public String getMoInfo(int modelIndex)
public boolean checkPrivateKey(double privateKey)
privateKey
- public Object getMouseInfo()
public int getFrontPlane()
public javajs.util.List<Object> getPlaneIntersection(int type, javajs.util.P4 plane, float scale, int flags)
public boolean getPreserveState()
boolean isKiosk()
public boolean hasFocus()
public void setFocus()
public MinimizerInterface getMinimizer(boolean createNew)
void stopMinimization()
void clearMinimization()
public String getMinimizationInfo()
private void checkMinimization()
public void minimize(int steps, float crit, BS bsSelected, BS bsFixed, float rangeFixed, boolean addHydrogen, boolean isOnly, boolean isSilent, boolean isLoad2D)
steps
- Integer.MAX_VALUE --> use defaultscrit
- -1 --> use defaultsbsSelected
- bsFixed
- rangeFixed
- addHydrogen
- isOnly
- isSilent
- isLoad2D
- public void setMotionFixedAtoms(BS bs)
public BS getMotionFixedAtoms()
void rotateArcBall(int x, int y, float factor)
void getAtomicPropertyState(javajs.util.SB commands, byte type, BS bs, String name, float[] data)
public javajs.util.P3[][] getCenterAndPoints(javajs.util.List<Object[]> atomSets, boolean addCenter)
public String writeFileData(String fileName, String type, int modelIndex, Object[] parameters)
public Object getExecutor()
public void togglePickingLabel(BS bs)
public void loadShape(int shapeID)
public void setShapeSize(int shapeID, int mad, BS bsSelected)
public void setShapeSizeRD(int shapeID, RadiusData rd, BS bsAtoms)
public boolean getShapePropertyData(int shapeType, String propertyName, Object[] data)
public Object getShapePropertyIndex(int shapeType, String propertyName, int index)
private int getShapePropertyAsInt(int shapeID, String propertyName)
public void setModelVisibility()
public void resetShapes(boolean andCreateNew)
public void setAtomLabel(String value, int i)
public void resetBioshapes(BS 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 BS getRenderableBitSet()
private void setAtomPickingOption(String option)
private void setBondPickingOption(String option)
void undoClear()
public void undoMoveAction(int action, int n)
action
- Token.undo or Token.redon
- number of steps to go back/forward; 0 for all; -1 for clear; -2 for
clear BOTHvoid undoMoveActionClear(int taintedAtom, int type, boolean clearRedo)
public void assignBond(int bondIndex, char type)
public void assignAtom(int atomIndex, javajs.util.P3 pt, String type)
public void assignConnect(int index, int index2)
protected void moveAtomWithHydrogens(int atomIndex, int deltaX, int deltaY, int deltaZ, BS bsAtoms)
public boolean isAtomPDB(int i)
public boolean isModelPDB(int i)
boolean isAtomAssignable(int i)
public void deleteMeasurement(int i)
deleteMeasurement
in class JmolViewer
boolean haveModelKit()
public String getSmiles(int index1, int index2, BS bsSelected, boolean isBioSmiles, boolean allowUnmatchedRings, boolean addCrossLinks, boolean addComment)
index1
- index2
- bsSelected
- isBioSmiles
- allowUnmatchedRings
- TODOaddCrossLinks
- TODOaddComment
- public void connect(float[][] connections)
public ColorEncoder getColorEncoder(String colorScheme)
public void displayBonds(BondSet bs, boolean isDisplay)
public void setStateScriptVersion(String version)
public JmolRendererInterface initializeExporter(Map<String,Object> params)
public boolean getMouseEnabled()
public void setZslabPoint(javajs.util.P3 pt)
public void calcAtomsMinMax(BS bs, BoxInfo boxInfo)
calcAtomsMinMax
in class JmolViewer
public void getObjectMap(Map<String,?> map, char c)
map
- c
- public void setPicked(int iAtom)
public String runScript(String script)
JmolViewer
runScript
in class JmolViewer
public boolean allowSpecAtom()
public void setFrameDelayMs(long millis)
public long getFrameDelayMs(int i)
public BS getBaseModelBitSet()
public void clearTimeouts()
public void triggerTimeout(String name)
public void clearTimeout(String name)
public void calculatePartialCharges(BS bsSelected)
public void setCurrentModelID(String id)
public void setCentroid(BS bs, int[] minmax)
public String getPathForAllFiles()
public void cacheClear()
public void cachePut(String key, Object data)
cachePut
in interface javajs.api.JSInterface
cachePut
in class JmolViewer
key
- data
- public int cacheFileByName(String fileName, boolean isAdd)
JmolViewer
cacheFileByName
in interface javajs.api.JSInterface
cacheFileByName
in class JmolViewer
public void clearThreads()
public ScriptContext getEvalContextAndHoldQueue(JmolScriptEvaluator jse)
public void checkInheritedShapes()
public javajs.awt.Dimension resizeInnerPanel(int width, int height)
resizeInnerPanel
in class JmolViewer
public String getFontLineShapeState(String s, String myType, TickInfo[] tickInfos)
public void getShapeSetState(AtomShape atomShape, Shape shape, int monomerCount, Group[] monomers, BS bsSizeDefault, Map<String,BS> temp, Map<String,BS> temp2)
public String getMeasurementState(Measures measures, javajs.util.List<Measurement> mList, int measurementCount, javajs.awt.Font font3d, TickInfo ti)
public String getDefaultPropertyParam(int propertyID)
public int getPropertyNumber(String name)
public boolean checkPropertyParameter(String name)
private BS addHydrogensInline(BS bsAtoms, javajs.util.List<Atom> vConnections, javajs.util.P3[] pts) throws Exception
Exception
public float evalFunctionFloat(Object func, Object params, float[] values)
evalFunctionFloat
in interface AtomDataServer
public boolean evalParallel(ScriptContext context, ShapeManager shapeManager)
public Object evaluateExpression(Object stringOrTokens)
evaluateExpression
in class JmolViewer
public ScriptContext getScriptContext(String why)
public String getAtomDefs(Map<String,Object> names)
getAtomDefs
in class JmolViewer
public void createModels(int n)
public void setCGO(javajs.util.List<Object> info)
public void setFrame(int i)
public boolean movePyMOL(JmolScriptEvaluator eval, float floatSecondsTotal, float[] pymolView)
public javajs.util.P3 getCamera()
public void setModelSet(ModelSet modelSet)
public String[] getSceneList()
public void setBondParameters(int modelIndex, int i, BS bsBonds, float rad, float pymolValence, int argb, float trans)
public int[][] getDihedralMap(int[] atoms)
public void setDihedrals(float[] dihedralList, BS[] bsBranches, float rate)
public BS[] getBsBranches(float[] dihedralList)
public int getChainID(String id)
id
- < 256 is just the character of a single-character chain id; >= 256
indicates a list pointer into chainList.public String getChainIDStr(int id)
public Boolean getScriptQueueInfo()
public JmolNMRInterface getNMRCalculation()
public int calculateFormalCharges(BS bs)
public boolean cachePngFiles()
public void setModulation(BS bs, boolean isOn, javajs.util.P3 t1, boolean isQ)
public void checkInMotion(int state)
public boolean checkMotionRendering(int tok)
tok
- public javajs.util.OC openExportChannel(double privateKey, String fileName, boolean asWriter) throws IOException
IOException
public void log(String data)
log
in interface AtomDataServer
public String getLogFileName()
public String getCommands(Map<String,BS> htDefine, Map<String,BS> htMore, String select)
public boolean allowCapture()
public MeasurementPending getMP()
public Object getApplet()
getApplet
in interface javajs.api.JSInterface
public javajs.util.List<Object> getModulationList(BS bs, String type, javajs.util.P3 t456)
public void setCurrentAtom(int iAtom)
public int getCurrentAtom()