public class Viewer extends JmolViewer implements AtomDataServer, javajs.api.PlatformViewer
Modifier and Type | Class and Description |
---|---|
static class |
Viewer.ACCESS |
Modifier and Type | Field and Description |
---|---|
private Viewer.ACCESS |
access |
ActionManager |
acm |
(package private) javajs.util.Lst<String> |
actionStates |
(package private) javajs.util.Lst<String> |
actionStatesRedo |
boolean |
allowArrayDotNotation |
private boolean |
allowScripting |
AnimationManager |
am |
private JmolAnnotationParser |
annotationParser |
boolean |
antialiased |
JmolAppConsoleInterface |
appConsole |
static String |
appletCodeBase |
static String |
appletDocumentBase |
static String |
appletIdiomaBase |
String |
appletName |
boolean |
async |
boolean |
autoExit |
private boolean |
axesAreTainted |
private BS |
bsRotateBranch |
(package private) BS |
bsUserVdws |
Map<String,Object> |
captureParams |
private boolean |
chainCaseSpecified |
private javajs.util.Lst<String> |
chainList |
Map<Object,Object> |
chainMap |
ColorManager |
cm |
private CommandHistory |
commandHistory |
private String |
commandOptions |
Object |
compiler |
boolean |
creatingImage |
(package private) int |
currentCursor |
private int |
currentShapeID |
private String |
currentShapeState |
private boolean |
dataOnly |
(package private) VDW |
defaultVdw |
Map<String,Object> |
definedAtomSets |
(package private) javajs.awt.Dimension |
dimScreen |
Object |
display |
boolean |
displayLoadErrors |
(package private) JmolDataManager |
dm |
private JmolAnnotationParser |
dssrParser |
private String |
errorMessage |
private String |
errorMessageUntranslated |
JmolScriptEvaluator |
eval |
Object |
executor |
FileManager |
fm |
boolean |
frankOn |
String |
fullName |
GlobalSettings |
g |
GData |
gdata |
private Object |
gRight
A graphics from a "slave" stereo display that has been synchronized with
this this applet.
|
boolean |
haveDisplay |
private boolean |
haveJDX |
boolean |
headless
determined by GraphicsEnvironment.isHeadless() from java
-Djava.awt.headless=true
disables command threading
disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN
|
private Map<String,Object> |
headlessImageParams |
private int |
hoverAtomIndex |
private boolean |
hoverEnabled |
private String |
hoverLabel |
private String |
hoverText |
Object |
html5Applet |
String |
htmlName |
float |
imageFontScaling |
private boolean |
inMotion |
private String |
insertedCommand |
boolean |
isApplet |
boolean |
isJNLP |
boolean |
isJS |
(package private) boolean |
isKiosk |
private boolean |
isParallel |
boolean |
isPreviewOnly |
boolean |
isPrintOnly |
boolean |
isSignedApplet |
private boolean |
isSignedAppletLocal |
private boolean |
isSilent |
boolean |
isSingleThreaded |
private boolean |
isStereoSlave
A flag to indicate that THIS is the right-side panel of a pair of synced
applets running a left-right stereo display (that would be piped into a
dual-image polarized projector system such as GeoWall).
|
boolean |
isSyntaxAndFileCheck |
boolean |
isSyntaxCheck |
(package private) boolean |
isTainted |
boolean |
isWebGL |
(package private) BioResolver |
jbr |
private JmolChimeMessenger |
jcm |
(package private) javajs.api.GenericMenuInterface |
jmolpopup |
(package private) JmolStateCreator |
jsc |
static String |
jsDocumentBase |
private JmolRendererInterface |
jsExporter3D |
private javajs.util.JSJSONParser |
jsonParser |
private Map<String,Object> |
jsParams |
private JmolJSpecView |
jsv |
private javajs.api.GenericZipTools |
jzt |
private Object[] |
lastData |
(package private) Map<String,Object> |
ligandModels |
(package private) Map<String,Boolean> |
ligandModelSet |
boolean |
listCommands |
(package private) Map<String,JmolScriptFunction> |
localFunctions |
(package private) String |
logFileName |
(package private) String |
logFilePath |
private int |
maximumSize |
private Minimizer |
minimizer |
ModelManager |
mm |
private JmolAdapter |
modelAdapter |
private javajs.api.GenericMenuInterface |
modelkitPopup |
private int |
motionEventNumber |
private javajs.api.GenericMouseInterface |
mouse
either org.jmol.awt.Mouse or org.jmol.awtjs2d.Mouse
|
BS |
movableBitSet |
private boolean |
movingSelected |
ModelSet |
ms |
private boolean |
multiTouch |
(package private) boolean |
mustRender |
(package private) JmolNMRInterface |
nmrCalculation |
boolean |
noFrankEcho |
boolean |
noGraphicsAllowed |
static int |
nProcessors |
private OutputManager |
outputManager |
(package private) JmolPropertyManager |
pm |
private int |
prevFrame |
private float |
prevMorphModel |
private double |
privateKey |
private javajs.util.P3 |
ptTemp |
boolean |
queueOnHold |
RadiusData |
rd |
private boolean |
refreshing |
(package private) JmolRepaintManager |
rm |
private int |
rotateBondIndex |
private int |
rotatePrev1 |
private int |
rotatePrev2 |
private JmolScriptManager |
scm |
(package private) JmolScriptEditorInterface |
scriptEditor |
boolean |
scriptEditorVisible |
private boolean |
selectionHalosEnabled |
ShapeManager |
shm |
private boolean |
showSelected |
SelectionManager |
slm |
StatusManager |
sm |
private SmilesMatcherInterface |
smilesMatcher |
int |
stateScriptVersionInt |
(package private) static Map<String,JmolScriptFunction> |
staticFunctions |
StateManager |
stm |
static String |
strJavaVendor |
static String |
strJavaVersion |
static String |
strOSName |
static String |
SYNC_GRAPHICS_MESSAGE |
static String |
SYNC_NO_GRAPHICS_MESSAGE |
(package private) String |
syncId |
private TempArray |
tempArray |
boolean |
testAsync |
Map<String,Object> |
timeouts |
TransformManager |
tm |
private Triangulator |
triangulator |
int |
tryPt |
private boolean |
useCommandThread |
(package private) int[] |
userVdwMars |
(package private) float[] |
userVdws |
private static String |
version_date |
Map<String,Object> |
vwrOptions |
apiPlatform, menuStructure
Constructor and Description |
---|
Viewer(Map<String,Object> info)
new way...
|
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) |
BS |
addHydrogensInline(BS bsAtoms,
javajs.util.Lst<Atom> vConnections,
javajs.util.P3[] pts) |
void |
addSelectionListener(JmolSelectionListener listener) |
StateScript |
addStateScript(String script,
boolean addFrameNumber,
boolean postDefinitions) |
void |
addUnitCellOffset(javajs.util.P3 pt) |
void |
alert(String msg) |
protected static JmolViewer |
allocateViewer(Object display,
JmolAdapter modelAdapter,
String fullName,
URL documentBase,
URL codeBase,
String commandOptions,
JmolStatusListener statusListener,
javajs.api.GenericPlatform implementedPlatform)
old way...
|
STR[] |
allocTempEnum(int size) |
javajs.util.P3[] |
allocTempPoints(int size) |
javajs.util.P3i[] |
allocTempScreens(int size) |
boolean |
allowCapture() |
boolean |
allowEmbeddedScripts() |
boolean |
areAxesTainted() |
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) |
BS |
bsA() |
void |
cacheClear() |
int |
cacheFileByName(String fileName,
boolean isAdd) |
void |
cachePut(String key,
Object data)
JSInterface -- allows saving files in memory for later retrieval
|
void |
calcAtomsMinMax(BS bs,
BoxInfo boxInfo) |
void |
calcBoundBoxDimensions(BS bs,
float scale) |
int |
calculateFormalCharges(BS bs) |
javajs.util.V3 |
calculateMolecularDipole(BS bsAtoms) |
void |
calculatePartialCharges(BS bsSelected) |
void |
calculateStraightness() |
String |
calculateStructures(BS bsAtoms,
boolean asDSSP,
boolean setStructure,
int version) |
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 |
checkInMotion(int state) |
private static int |
checkIntRange(int value,
int min,
int max) |
void |
checkMenuUpdate() |
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 vwr and not by some manipulation of the applet.
|
boolean |
checkPropertyParameter(String name) |
boolean |
checkSelect(Map<String,SV> h,
T[] value) |
void |
clearAllMeasurements() |
private void |
clearAtomSets() |
(package private) void |
clearClickCount() |
void |
clearFunctions() |
void |
clearMeasurements() |
(package private) void |
clearMinimization() |
void |
clearModelDependentObjects() |
private void |
clearRepaintManager(int iShape) |
void |
clearScriptQueue() |
void |
clearSelection() |
void |
clearShapeRenderers() |
void |
clearThreads() |
void |
clearTimeout(String name) |
void |
clearTimeouts() |
String |
clipImageOrPasteText(String text) |
T[] |
compileExpr(String expr) |
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
|
Object |
createZip(String fileName,
String type,
Map<String,Object> params) |
void |
defineAtomSets(Map<String,Object> info) |
int |
deleteAtoms(BS bsAtoms,
boolean fullModels) |
void |
deleteBonds(BS bsDeleted) |
void |
deleteMeasurement(int i) |
void |
deleteModelAtoms(int modelIndex,
int firstAtomIndex,
int nAtoms,
BS bsModelAtoms) |
int |
deleteModels(int modelIndex,
BS bsAtoms)
called by ZAP {atomExpression} when atoms are present or the command is
specific for a model, such as ZAP 2.1
|
(package private) void |
depthByPixels(int pixels) |
String |
dialogAsk(String type,
String fileName,
Map<String,Object> params)
Ask for new file name when opening a file
|
void |
displayAtoms(BS bs,
boolean isDisplay,
boolean isGroup,
int addRemove,
boolean isQuiet) |
void |
dispose()
end of life for this viewer
|
private boolean |
doHaveJDX() |
(package private) void |
dragMinimizeAtom(int iAtom) |
private void |
drawImage(Object graphic,
Object img,
int x,
int y,
boolean isDTI) |
(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 isQuiet,
boolean isQueued) |
Object |
evaluateExpression(Object stringOrTokens)
synchronized here trapped the eventQueue; see also
evaluateExpressionAsVariable
|
SV |
evaluateExpressionAsVariable(Object stringOrTokens) |
private Object |
evalWait(String returnType,
String strScript,
String statusList) |
void |
exitJmol() |
String |
extractMolData(String what) |
Object |
extractProperty(Object property,
Object args,
int pt) |
void |
fillAtomData(AtomData atomData,
int mode) |
protected void |
finalize() |
void |
finalizeTransformParameters() |
int |
findNearestAtomIndex(int x,
int y) |
int |
findNearestAtomIndexMovable(int x,
int y,
boolean mustBeMovable) |
static String |
fixInlineString(String strModel,
char newLine) |
boolean |
frankClicked(int x,
int y) |
boolean |
frankClickedModelKit(int x,
int y) |
void |
freeTempEnum(STR[] 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)
for POV-Ray
|
javajs.util.P3[] |
getAdditionalHydrogens(BS bsAtoms,
boolean doAll,
boolean justCarbon,
javajs.util.Lst<Atom> vConnections) |
BS |
getAllAtoms() |
String |
getAllSettings(String prefix) |
String |
getAnnotationInfo(SV d,
String match,
int type) |
JmolAnnotationParser |
getAnnotationParser(boolean isDSSR) |
BS |
getAtomBitSet(Object atomExpression) |
(package private) BS |
getAtomBitSetEval(JmolScriptEvaluator eval,
Object atomExpression) |
String |
getAtomDefs(Map<String,Object> names) |
javajs.util.Quat[] |
getAtomGroupQuaternions(BS bsAtoms,
int nMax) |
(package private) void |
getAtomicPropertyState(javajs.util.SB commands,
byte type,
BS bs,
String name,
float[] data) |
String |
getAtomInfo(int atomOrPointIndex) |
private String |
getAtomInfoXYZ(int atomIndex,
boolean useChimeFormat) |
BS |
getAtomsNearPt(float distance,
javajs.util.P3 coord) |
javajs.util.Lst<Float> |
getAtomValidation(String type,
Atom atom) |
Object |
getAuxiliaryInfoForAtoms(Object atomExpression) |
int |
getBackgroundArgb() |
BS |
getBaseModelBitSet() |
String |
getBindingInfo(String qualifiers) |
String |
getBioSmiles(BS bs) |
(package private) boolean |
getBondPicking() |
BS |
getBondsForSelectedAtoms(BS bsAtoms) |
boolean |
getBoolean(int tok) |
boolean |
getBooleanProperty(String key) |
javajs.util.P3 |
getBoundBoxCenter() |
int |
getBoundBoxCenterX() |
int |
getBoundBoxCenterY() |
javajs.util.V3 |
getBoundBoxCornerVector() |
BS |
getBranchBitSet(int atomIndex,
int atomIndexNot,
boolean allowCyclic) |
BufferedInputStream |
getBufferedInputStream(String fullPathName) |
javajs.util.P3[][] |
getCenterAndPoints(javajs.util.Lst<Object[]> atomSets,
boolean addCenter) |
int |
getChainID(String id,
boolean isAssign)
Create a unique integer for any chain string.
|
String |
getChainIDStr(int id) |
String |
getChemicalInfo(String smiles,
String info) |
String |
getChimeInfo(int tok) |
JmolChimeMessenger |
getChimeMessenger() |
Map<String,Object> |
getCifData(int modelIndex) |
String |
getClipboardText() |
javajs.util.P3 |
getColorPointForPropertyValue(float val) |
String |
getCommands(Map<String,BS> htDefine,
Map<String,BS> htMore,
String select) |
JmolAppConsoleInterface |
getConsole() |
String |
getCoordinateState(BS bsSelected) |
float[] |
getCurrentColorRange() |
String |
getCurrentFileAsString(String state) |
float |
getCurrentSolventProbeRadius() |
SymmetryInterface |
getCurrentUnitCell() |
int |
getCursorX() |
int |
getCursorY() |
String |
getData(String atomExpression,
String type) |
private JmolDataManager |
getDataManager() |
Object |
getDataObj(String key,
BS bsSelected,
int dataType)
Retrieve a data object
|
(package private) String |
getDataSeparator() |
String |
getDefaultDirectory() |
javajs.util.P3 |
getDefaultLattice() |
String |
getDefaultMeasurementLabel(int nPoints) |
String |
getDefaultPropertyParam(int propertyID) |
String |
getDefaultVdwNameOrData(int mode,
VDW type,
BS bs) |
BS |
getDefinedAtomSet(String name) |
int |
getDelayMaximumMs() |
String |
getDistanceUnits(String s) |
(package private) boolean |
getDragSelected() |
boolean |
getDrawHover() |
BS |
getElementsPresentBitSet(int modelIndex) |
String |
getErrorMessage() |
String |
getErrorMessageUn() |
ScriptContext |
getEvalContextAndHoldQueue(JmolScriptEvaluator eval) |
String |
getExportDriverList() |
String |
getFileAsString3(String name,
boolean checkProtected,
String state) |
String |
getFileAsString4(String name,
int nBytesMax,
boolean doSpecialLoad,
boolean allowBinary,
boolean checkProtected,
String state) |
(package private) Object |
getFileData() |
(package private) String |
getFileHeader() |
float |
getFloat(int tok) |
javajs.awt.Font |
getFont3D(String fontFace,
String fontStyle,
float fontSize) |
BS |
getFrameAtoms() |
String |
getFrameTitle() |
String[] |
getFullPathNameOrError(String filename) |
JmolScriptFunction |
getFunction(String name) |
String |
getFunctionCalls(String selectedFunction) |
Map<String,JmolScriptFunction> |
getFunctions(boolean isStatic) |
Object |
getGLmolView()
This method is only called by JmolGLmol applet._refresh();
|
BS |
getGroupsWithin(int nResidues,
BS bs) |
void |
getHelp(String what) |
int |
getHermiteLevel() |
int |
getHoverDelay() |
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) |
char |
getInlineChar() |
boolean |
getInMotion(boolean includeAnim) |
String |
getInsertedCommand() |
int |
getInt(int tok) |
int |
getIsosurfacePropertySmoothing(boolean asPower) |
BioResolver |
getJBR() |
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.
|
static String |
getJmolVersion() |
Object |
getJspecViewProperties(Object myParam) |
(package private) JmolJSpecView |
getJSV() |
javajs.api.GenericZipTools |
getJzt() |
Object |
getLigandModel(String id,
String prefix,
String suffix,
String terminator)
obtain CIF data for a ligand for purposes of adding hydrogens
or for any other purpose in terms of saving a data set for a file
in a state
|
String |
getLightingState() |
String |
getLocalUrl(String fileName) |
String |
getLogFileName() |
short |
getMadBond() |
int |
getMeasurementCount() |
int[] |
getMeasurementCountPlusIndices(int i) |
String |
getMeasurementInfoAsString() |
String |
getMeasurementStringValue(int i) |
String |
getMenu(String type) |
String |
getMinimizationInfo() |
Minimizer |
getMinimizer(boolean createNew) |
JmolAdapter |
getModelAdapter() |
String |
getModelCml(BS bs,
int nAtomsMax,
boolean addBonds,
boolean doTransform) |
javajs.util.V3 |
getModelDipole() |
String |
getModelExtract(Object atomExpression,
boolean doTransform,
boolean isModelKit,
String type)
V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
|
String |
getModelFileData(String atomExpression,
String type,
boolean allTrajectories) |
String |
getModelFileInfo() |
String |
getModelFileInfoAll() |
int |
getModelFileNumber(int modelIndex) |
int |
getModelIndexFromId(String id) |
String |
getModelName(int modelIndex) |
int |
getModelNumber(int modelIndex) |
String |
getModelNumberDotted(int modelIndex) |
Properties |
getModelProperties(int modelIndex) |
Map<String,Object> |
getModelSetAuxiliaryInfo() |
String |
getModelSetFileName() |
String |
getModelSetPathName() |
Properties |
getModelSetProperties() |
BS |
getModelUndeletedAtomsBitSet(int modelIndex) |
BS |
getModelUndeletedAtomsBitSetBs(BS bsModels) |
int |
getMotionEventNumber() |
BS |
getMotionFixedAtoms() |
boolean |
getMouseEnabled() |
JmolNMRInterface |
getNMRCalculation() |
String |
getNMRPredict(String type) |
short |
getObjectColix(int objId) |
int |
getObjectMad10(int objId) |
void |
getObjectMap(Map<String,?> map,
char c)
used in autocompletion in console using TAB
|
String |
getOpenSmiles(BS bs) |
float[] |
getOrCalcPartialCharges(BS bsSelected,
BS bsIgnore) |
String |
getOrientationText(int type,
String name) |
javajs.util.OC |
getOutputChannel(String localName,
String[] fullPath) |
private OutputManager |
getOutputManager() |
Object |
getP(String key) |
Object |
getParameter(String key) |
String |
getPdbAtomData(BS bs,
javajs.util.OC out,
boolean asPQR,
boolean doTransform) |
String |
getPdbData(int modelIndex,
String type,
BS bsAtoms,
Object[] parameters,
javajs.util.OC oc,
boolean getStructure) |
(package private) MeasurementPending |
getPendingMeasurement() |
int |
getPickingMode() |
void |
getPolymerPointsAndVectors(BS bs,
javajs.util.Lst<javajs.util.P3[]> vList) |
private Object |
getPopupMenu() |
Object |
getPOrNull(String key) |
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) |
private JmolPropertyManager |
getPropertyManager() |
int |
getPropertyNumber(String name) |
char |
getQuaternionFrame() |
boolean |
getRefreshing() |
(package private) int |
getRotateBondIndex() |
Rectangle |
getRubberBandSelection() |
float |
getScalePixelsPerAngstrom(boolean asAntialiased) |
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) |
boolean |
getSelectionHalosEnabled() |
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() |
Object |
getShapeProperty(int shapeType,
String propertyName) |
private int |
getShapePropertyAsInt(int shapeID,
String propertyName) |
boolean |
getShowAxes() |
boolean |
getShowBbcage() |
boolean |
getShowFrank() |
boolean |
getShowNavigationPoint() |
boolean |
getShowSelectedOnce() |
boolean |
getShowUnitCell() |
BS |
getSmartsMatch(String smarts,
BS bsSelected) |
String |
getSmiles(BS bs) |
SmilesMatcherInterface |
getSmilesMatcher() |
String |
getSmilesOpt(BS bsSelected,
int index1,
int index2,
int flags,
String options)
returns the SMILES string for a sequence or atom set does not include
attached protons on groups
|
String |
getSpinState() |
String |
getStandardLabelFormat(int type) |
JmolStateCreator |
getStateCreator() |
String |
getStateInfo() |
String |
getStateInfo3(String type,
int width,
int height) |
javajs.util.Lst<javajs.util.Lst<javajs.util.Lst<Object>>> |
getStatusChanged(String statusNameList) |
int |
getStrandCount(int type) |
Map<STR,float[]> |
getStructureList() |
String |
getStructureState() |
SymmetryInterface |
getSymTemp()
Retrieve a Symmetry object, possibly re-using an old one.
|
String |
getTrajectoryState() |
Triangulator |
getTriangulator() |
private BS |
getUndeletedGroupAtomBits(BS bs) |
float |
getUnitCellInfo(int infoType) |
String |
getUnitCellInfoText() |
javajs.util.T3[] |
getV0abc(Object def)
convert string abc;offset or M3 or M4 to origin and three vectors -- a, b,
c.
|
int |
getVanderwaalsMar(int i) |
int |
getVanderwaalsMarType(int atomicAndIsotopeNumber,
VDW type) |
BS |
getVisibleFramesBitSet() |
String |
getWrappedStateScript() |
String |
getZapName() |
void |
haltScriptExecution() |
void |
handleError(Error er,
boolean doClear) |
static boolean |
hasDatabasePrefix(String fileName) |
boolean |
hasFocus() |
boolean |
haveAccess(Viewer.ACCESS a) |
boolean |
haveFileSet() |
void |
highlight(BS bs) |
void |
highlightBond(int index,
boolean isHover) |
String |
historyFind(String cmd,
int dir) |
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.T3 pt) |
void |
initialize(boolean clearUserVariables,
boolean isPyMOL) |
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 |
invertRingAt(int atomIndex,
boolean isClick) |
void |
invertSelected(javajs.util.P3 pt,
javajs.util.P4 plane,
int iAtom,
BS invAtoms) |
boolean |
isBound(int mouseAction,
int jmolAction) |
static boolean |
isDatabaseCode(char ch) |
boolean |
isFunction(String name) |
boolean |
isJmolDataFrame() |
(package private) boolean |
isKiosk() |
boolean |
isModelPDB(int i) |
boolean |
isParallel() |
boolean |
isRepaintPending() |
boolean |
isScriptExecuting() |
private boolean |
isScriptQueued() |
private static boolean |
isStaticFunction(String name) |
private void |
jmolTest() |
String |
jsEval(String strEval) |
SV |
jsEvalSV(String strEval) |
private String |
loadAtomDataAndReturnError(Object atomSetCollection,
int tokType)
or just apply the data to the current model set
|
boolean |
loadImageData(Object image,
String nameOrError,
String echoName,
ScriptContext sc)
NOTE: This method is called from within a j2sNative block in
awtjs2d.Platform.java as well as from FileManager.loadImage
|
String |
loadInline(List<Object> arrayData,
boolean isAppend)
External applications only; does not preserve 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,
javajs.util.SB sOptions,
int tokType,
boolean isConcat)
Used by the ScriptEvaluator LOAD command to open one or more files.
|
private String |
loadModelFromFileRepaint(String fullPathName,
String fileName,
String[] fileNames,
Object reader)
for JmolSimpleViewer -- external applications only (and no-script
JavaScript)
|
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 |
minimize(JmolScriptEvaluator eval,
int steps,
float crit,
BS bsSelected,
BS bsFixed,
float rangeFixed,
boolean addHydrogen,
boolean isOnly,
boolean isSilent,
boolean isLoad2D) |
boolean |
modelHasVibrationVectors(int modelIndex) |
void |
move(JmolScriptEvaluator eval,
javajs.util.V3 dRot,
float dZoom,
javajs.util.V3 dTrans,
float dSlab,
float floatSecondsTotal,
int fps) |
void |
moveAtoms(javajs.util.M4 m4,
javajs.util.M3 mNew,
javajs.util.M3 rotation,
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) |
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 |
navigatePt(javajs.util.P3 center) |
void |
navTranslatePercent(float x,
float y) |
MeasurementData |
newMeasurementData(String id,
javajs.util.Lst<Object> points) |
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,
Object 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) |
Map<String,Object> |
parseJSON(String ann) |
void |
pauseScriptExecution() |
void |
playAudio(String fileNameOrDataURI) |
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 |
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() |
void |
renderScreenImage(Object g,
int width,
int height)
JmolViewer interface uses this, but that is all
|
void |
renderScreenImageStereo(Object gLeft,
boolean checkStereoSlave,
int width,
int height) |
(package private) void |
reportSelection(String msg) |
void |
requestRepaintAndWait(String why) |
void |
reset(boolean includingSpin) |
void |
resetShapes(boolean andCreateNew) |
(package private) void |
resizeImage(int width,
int height,
boolean isImageWrite,
boolean isExport,
boolean isReset) |
int[] |
resizeInnerPanel(int width,
int height) |
(package private) String |
resolveDatabaseFormat(String fileName) |
(package private) void |
restoreModelOrientation(int modelIndex) |
(package private) void |
restoreModelRotation(int modelIndex) |
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.Lst<javajs.util.P3> finalPoints,
float[] dihedralList,
javajs.util.M4 m4) |
boolean |
rotateAxisAngleAtCenter(JmolScriptEvaluator eval,
javajs.util.P3 rotCenter,
javajs.util.V3 rotAxis,
float degreesPerSecond,
float endDegrees,
boolean isSpin,
BS bsSelected) |
void |
rotateFront() |
(package private) void |
rotateSelected(float deltaX,
float deltaY,
BS bsSelected) |
(package private) void |
rotateXYBy(float degX,
float degY) |
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
|
(package private) void |
saveModelOrientation() |
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 |
setAnimationFps(int fps) |
private void |
setAnimationMode(String mode) |
void |
setAnimationOn(boolean animationOn) |
void |
setAnimationRange(int modelIndex1,
int modelIndex2) |
void |
setAnimDisplay(BS bs) |
private void |
setAntialias(int tok,
boolean TF) |
(package private) void |
setApplySymmetryToBonds(boolean TF) |
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) |
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) |
(package private) void |
setAxesMode(int mode) |
void |
setAxesOrientationRasmol(boolean TF) |
private void |
setAxesScale(int tok,
float val) |
void |
setBackgroundImage(String fileName,
Object image) |
void |
setBackgroundModelIndex(int modelIndex) |
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 |
setCenterBitSet(BS bsCenter,
boolean doScale) |
void |
setCenterSelected() |
void |
setCGO(javajs.util.Lst<Object> info) |
void |
setColorBackground(String colorName) |
void |
setCurrentCage(String isosurfaceId) |
void |
setCurrentColorRange(String label) |
void |
setCurrentModelID(String id) |
void |
setCurrentModelIndex(int modelIndex) |
void |
setCurrentModelIndexClear(int modelIndex,
boolean clearBackground) |
void |
setCursor(int cursor) |
void |
setData(String key,
Object[] data,
int dataType,
int matchField,
int matchFieldColumnCount,
int dataField,
int dataFieldColumnCount)
A general-purpose data storage method.
|
void |
setDebugScript(boolean debugScript) |
private void |
setDefaultColors(boolean isRasmol) |
void |
setDefaultLattice(javajs.util.P3 p) |
private void |
setDefaultsType(String type) |
void |
setDihedrals(float[] dihedralList,
BS[] bsBranches,
float rate) |
void |
setDisplay(Object canvas) |
void |
setElementArgb(int elementNumber,
int argb) |
String |
setErrorMessage(String errMsg,
String errMsgUntranslated) |
private void |
setFileLoadStatus(FIL 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 |
setFrameDelayMs(long millis) |
void |
setFrameOffsets(BS bsAtoms,
boolean isFull) |
void |
setFrameTitle(int modelIndex,
String title) |
void |
setFrameTitleObj(Object title) |
(package private) void |
setFrameVariables() |
void |
setFrankOn(boolean TF) |
void |
setHistory(String fileName) |
private void |
setHoverEnabled(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.T3 pt,
float distance) |
void |
setJmolCallbackListener(JmolCallbackListener listener) |
void |
setJmolDefaults() |
void |
setJmolStatusListener(JmolStatusListener listener) |
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.
|
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 vwr = applet.getViewer(); vwr.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 |
setModulation(BS bs,
boolean isOn,
javajs.util.P3 t1,
boolean isQ) |
void |
setMotionFixedAtoms(BS bs) |
private BS |
setMovableBitSet(BS bsSelected,
boolean checkMolecule) |
void |
setNavigationDepthPercent(float percent) |
void |
setNavigationMode(boolean TF) |
void |
setNewRotationCenter(javajs.util.P3 center) |
void |
setObjectArgb(String name,
int argb) |
(package private) void |
setObjectColor(String name,
String colorName) |
void |
setObjectMad10(int iShape,
String name,
int mad10)
input here is a JC.SHAPE_xxxx identifier
|
String |
setObjectProp(String id,
int tokCommand) |
void |
setObjectVisibility(String name,
boolean b) |
void |
setOptions(Map<String,Object> info) |
boolean |
setParallel(boolean TF) |
(package private) void |
setPendingMeasurement(MeasurementPending mp) |
void |
setPercentVdwAtom(int value) |
void |
setPerspectiveDepth(boolean perspectiveDepth) |
void |
setPicked(int atomIndex) |
(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(STR type,
BS bs) |
void |
setRasmolDefaults() |
private void |
setRefreshing(boolean TF) |
void |
setRotateBondIndex(int index) |
void |
setRotationRadius(float angstroms,
boolean doAll) |
void |
setScreenDimension(int width,
int height) |
private void |
setScriptQueue(boolean TF) |
void |
setScriptStatus(String strStatus,
String statusMessage,
int msWalltime,
String strErrorMessageUntranslated) |
void |
setSelectionHalosEnabled(boolean TF) |
void |
setSelectionSet(BS set) |
void |
setShapeErrorState(int shapeID,
String state) |
void |
setShapeProperty(int shapeID,
String propertyName,
Object value) |
void |
setShapeSize(int shapeID,
int madOrMad10,
BS bsSelected) |
void |
setShowAxes(boolean value) |
void |
setShowBbcage(boolean value) |
void |
setShowHydrogens(boolean TF) |
void |
setShowMeasurements(boolean TF) |
void |
setShowUnitCell(boolean value) |
void |
setSmilesString(String s) |
void |
setSpin(String key,
int value) |
private void |
setStartupBooleans() |
void |
setStatusAtomPicked(int atomIndex,
String info,
Map<String,Object> map) |
boolean |
setStatusDragDropped(int mode,
int x,
int y,
String fileName) |
(package private) void |
setStatusFrameChanged(boolean isVib,
boolean doNotify) |
void |
setStatusMeasuring(String status,
int intInfo,
String strMeasure,
float value) |
void |
setStatusResized(int width,
int height) |
void |
setStereo(boolean isStereoSlave,
Object gRight) |
void |
setStereoMode(int[] twoColors,
STER 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,
STR type) |
private void |
setSync() |
void |
setSyncDriver(int mode) |
private void |
setSyncTarget(int mode,
boolean TF) |
void |
setTainted(boolean TF) |
void |
setTimeout(String name,
int mSec,
String script) |
void |
setUnits(String units,
boolean isDistance) |
(package private) void |
setUserVdw(VDW mode) |
(package private) void |
setVdwStr(String name) |
void |
setVectorScale(float scale) |
void |
setVibrationPeriod(float period) |
void |
setVibrationScale(float scale) |
void |
setWidthHeightVar() |
void |
setWindowDimensions(float[] dims) |
void |
showConsole(boolean showConsole) |
void |
showEditor(String[] file_text) |
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 |
spinXYBy(int xDelta,
int yDelta,
float speed) |
void |
startHoverWatcher(boolean tf) |
void |
startSpinningAxis(javajs.util.T3 pt1,
javajs.util.T3 pt2,
boolean isClockwise) |
(package private) void |
stopMinimization() |
void |
syncScript(String script,
String applet,
int port) |
void |
toCartesian(javajs.util.T3 pt,
boolean ignoreOffset)
absolute or relative to origin of UNITCELL {x y z}
|
void |
toFractional(javajs.util.T3 pt,
boolean asAbsolute)
absolute or relative to origin of UNITCELL {x y z}
|
void |
toUnitCell(javajs.util.P3 pt,
javajs.util.P3 offset)
relative to origin without regard to UNITCELL {x y z}
|
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) |
void |
unsetProperty(String key) |
void |
updateJS()
for JavaScript only
|
private void |
updateJSView(int imodel,
int iatom)
File has been loaded or model has been changed or atom picked.
|
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) |
allocateViewer, allocateViewer, openFileAsync, openReader, renderScreenImage, setConsole
public boolean testAsync
public boolean autoExit
public boolean haveDisplay
public boolean isJS
public boolean isWebGL
public boolean isSingleThreaded
public boolean queueOnHold
public String fullName
public static String appletDocumentBase
public static String appletCodeBase
public static String appletIdiomaBase
public static String jsDocumentBase
public Object compiler
public ModelSet ms
public FileManager fm
public boolean isApplet
public boolean isJNLP
public boolean isSyntaxAndFileCheck
public boolean isSyntaxCheck
public boolean listCommands
boolean mustRender
public String htmlName
public String appletName
public int tryPt
private String insertedCommand
public GData gdata
public Object html5Applet
public ActionManager acm
public AnimationManager am
public ColorManager cm
JmolDataManager dm
public ShapeManager shm
public SelectionManager slm
JmolRepaintManager rm
public GlobalSettings g
public StatusManager sm
public TransformManager tm
public static String strJavaVendor
public static String strOSName
public static String strJavaVersion
String syncId
String logFilePath
private boolean allowScripting
public boolean isPrintOnly
public boolean isSignedApplet
private boolean isSignedAppletLocal
private boolean isSilent
private boolean multiTouch
public boolean noGraphicsAllowed
private boolean useCommandThread
private String commandOptions
public Object display
private JmolAdapter modelAdapter
private Viewer.ACCESS access
private CommandHistory commandHistory
public ModelManager mm
public StateManager stm
private JmolScriptManager scm
public JmolScriptEvaluator eval
private TempArray tempArray
public boolean allowArrayDotNotation
public boolean async
public Object executor
private static String version_date
final javajs.awt.Dimension dimScreen
final javajs.util.Lst<String> actionStates
final javajs.util.Lst<String> actionStatesRedo
VDW defaultVdw
public RadiusData rd
private javajs.util.Lst<String> chainList
private String errorMessage
private String errorMessageUntranslated
private double privateKey
private boolean dataOnly
public boolean isPreviewOnly
public boolean headless
public BS movableBitSet
private javajs.api.GenericMouseInterface mouse
private JmolAnnotationParser annotationParser
private JmolAnnotationParser dssrParser
private Minimizer minimizer
private SmilesMatcherInterface smilesMatcher
JmolStateCreator jsc
private Object[] lastData
private int motionEventNumber
private boolean inMotion
private boolean refreshing
private boolean axesAreTainted
private int maximumSize
private Object gRight
private boolean isStereoSlave
public float imageFontScaling
public boolean antialiased
private int hoverAtomIndex
private String hoverText
private String hoverLabel
private boolean hoverEnabled
int currentCursor
private javajs.util.P3 ptTemp
private int prevFrame
private float prevMorphModel
private boolean haveJDX
private JmolJSpecView jsv
private boolean selectionHalosEnabled
public boolean frankOn
public boolean noFrankEcho
public boolean scriptEditorVisible
public 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
private int currentShapeID
private String currentShapeState
static final Map<String,JmolScriptFunction> staticFunctions
Map<String,JmolScriptFunction> localFunctions
boolean isKiosk
public static int nProcessors
public boolean displayLoadErrors
private boolean isParallel
public int stateScriptVersionInt
private JmolRendererInterface jsExporter3D
private boolean chainCaseSpecified
JmolNMRInterface nmrCalculation
String logFileName
private javajs.api.GenericZipTools jzt
BioResolver jbr
private JmolChimeMessenger jcm
private javajs.util.JSJSONParser jsonParser
private Triangulator triangulator
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" "async"protected void finalize() throws Throwable
public void setInsertedCommand(String strScript)
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
- public boolean haveAccess(Viewer.ACCESS a)
public JmolAdapter getModelAdapter()
getModelAdapter
in class JmolViewer
public BS getSmartsMatch(String smarts, BS bsSelected) throws Exception
getSmartsMatch
in class JmolViewer
Exception
public void setDisplay(Object canvas)
public MeasurementData newMeasurementData(String id, javajs.util.Lst<Object> points)
private JmolDataManager getDataManager()
private JmolScriptManager getScriptManager()
private void setStartupBooleans()
public String getExportDriverList()
public void dispose()
dispose
in class JmolViewer
public void reset(boolean includingSpin)
public void homePosition()
homePosition
in class JmolViewer
public void initialize(boolean clearUserVariables, boolean isPyMOL)
public void setWidthHeightVar()
void saveModelOrientation()
void restoreModelOrientation(int modelIndex)
void restoreModelRotation(int modelIndex)
public Object getGLmolView()
public void setRotationRadius(float angstroms, boolean doAll)
public void setCenterBitSet(BS bsCenter, boolean doScale)
public void setNewRotationCenter(javajs.util.P3 center)
void navigate(int keyWhere, int modifiers)
public void move(JmolScriptEvaluator eval, javajs.util.V3 dRot, float dZoom, javajs.util.V3 dTrans, float dSlab, float floatSecondsTotal, int fps)
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 void navigatePt(javajs.util.P3 center)
public void navigateAxis(javajs.util.V3 rotAxis, float degrees)
public void navTranslatePercent(float x, float y)
void zoomBy(int pixels)
void zoomByFactor(float factor, int x, int y)
void rotateXYBy(float degX, float degY)
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 translate(char xyz, float x, char type, BS bsAtoms)
void slabByPixels(int pixels)
void depthByPixels(int pixels)
void slabDepthByPixels(int pixels)
public void finalizeTransformParameters()
public float getScalePixelsPerAngstrom(boolean asAntialiased)
public void setSpin(String key, int value)
public String getSpinState()
public float[] getCurrentColorRange()
private void setDefaultColors(boolean isRasmol)
public void setElementArgb(int elementNumber, int argb)
public void setVectorScale(float scale)
setVectorScale
in class JmolViewer
public void setVibrationScale(float scale)
setVibrationScale
in class JmolViewer
public void setVibrationPeriod(float period)
setVibrationPeriod
in class JmolViewer
public void setObjectVisibility(String name, boolean b)
public void setObjectArgb(String name, int argb)
public short getObjectColix(int objId)
public void setColorBackground(String colorName)
setColorBackground
in class JmolViewer
public int getBackgroundArgb()
getBackgroundArgb
in class JmolViewer
public void setObjectMad10(int iShape, String name, int mad10)
iShape
- name
- mad10
- public int getObjectMad10(int objId)
objId
- public void setPropertyColorScheme(String scheme, boolean isTranslucent, boolean isOverloaded)
public String getLightingState()
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)
void reportSelection(String msg)
private void clearAtomSets()
public void selectAll()
selectAll
in class JmolViewer
public void clearSelection()
clearSelection
in class JmolViewer
public BS bsA()
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 processTwoPointGesture(float[][][] touches)
public boolean processMouseEvent(int id, int x, int y, int modifiers, long time)
public Rectangle getRubberBandSelection()
public boolean isBound(int mouseAction, int jmolAction)
public int getCursorX()
public int getCursorY()
public String getDefaultDirectory()
public BufferedInputStream getBufferedInputStream(String fullPathName)
getBufferedInputStream
in interface AtomDataServer
public Map<String,Object> setLoadParameters(Map<String,Object> htParams, boolean isAppend)
public void openFileAsyncSpecial(String fileName, int flags)
openFileAsyncSpecial
in class JmolViewer
fileName
- flags
- 1=pdbCartoons, 2=no scripting, 4=append, 8=fileOpenpublic 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, Object reader)
openReader
in class JmolViewer
fullPathName
- fileName
- name without path or can just be nullreader
- could be Reader, BufferedInputStream, or byte[]public String openDOM(Object DOMNode)
openDOM
in class JmolViewer
DOMNode
- private String loadModelFromFileRepaint(String fullPathName, String fileName, String[] fileNames, Object reader)
fullPathName
- fileName
- fileNames
- reader
- public String loadModelFromFile(String fullPathName, String fileName, String[] fileNames, Object reader, boolean isAppend, Map<String,Object> htParams, javajs.util.SB loadScript, javajs.util.SB sOptions, int tokType, boolean isConcat)
fullPathName
- may be null; used only when reader != nullfileName
- must not be nullfileNames
- when present, reader is ignoredreader
- may be a Reader, BufferedReader, byte[], or BufferedInputStreamisAppend
- htParams
- loadScript
- sOptions
- tokType
- isConcat
- public Object getLigandModel(String id, String prefix, String suffix, String terminator)
id
- unique key; if null, clear "bad" entries from the set.prefix
- suffix
- or fileNameterminator
- 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[] getFullPathNameOrError(String filename)
filename
- public String getFileAsString4(String name, int nBytesMax, boolean doSpecialLoad, boolean allowBinary, boolean checkProtected, String state)
public void autoCalculate(int tokProperty)
public void calculateStraightness()
public javajs.util.P3[] calculateSurface(BS bsSelected, float envelopeRadius)
public void setStructureList(float[] list, STR type)
public String calculateStructures(BS bsAtoms, boolean asDSSP, boolean setStructure, int version)
bsAtoms
- asDSSP
- setStructure
- to actually change structuresversion
- public JmolAnnotationParser getAnnotationParser(boolean isDSSR)
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.T3 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 Minimizer getMinimizer(boolean createNew)
public SmilesMatcherInterface getSmilesMatcher()
public 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)
public String getModelSetPathName()
getModelSetPathName
in class JmolViewer
public String getModelSetFileName()
getModelSetFileName
in class JmolViewer
public String getUnitCellInfoText()
public float getUnitCellInfo(int infoType)
public javajs.util.T3[] getV0abc(Object def)
def
- a string or an M3 or M4public void getPolymerPointsAndVectors(BS bs, javajs.util.Lst<javajs.util.P3[]> vList)
public String getHybridizationAndAxes(int atomIndex, javajs.util.V3 z, javajs.util.V3 x, String lcaoType)
public BS getAllAtoms()
public BS getModelUndeletedAtomsBitSet(int modelIndex)
public javajs.util.P3 getBoundBoxCenter()
getBoundBoxCenter
in class JmolViewer
public void calcBoundBoxDimensions(BS bs, float scale)
public javajs.util.V3 getBoundBoxCornerVector()
getBoundBoxCornerVector
in class JmolViewer
public int getBoundBoxCenterX()
public int getBoundBoxCenterY()
public Properties getModelSetProperties()
getModelSetProperties
in class JmolViewer
public Properties getModelProperties(int modelIndex)
getModelProperties
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 boolean modelHasVibrationVectors(int modelIndex)
public boolean frankClicked(int x, int y)
public boolean frankClickedModelKit(int x, int y)
public int findNearestAtomIndex(int x, int y)
findNearestAtomIndex
in class JmolViewer
public int findNearestAtomIndexMovable(int x, int y, boolean mustBeMovable)
public void toCartesian(javajs.util.T3 pt, boolean ignoreOffset)
pt
- ignoreOffset
- TODOpublic void toFractional(javajs.util.T3 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 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 BS getAtomsNearPt(float distance, javajs.util.P3 coord)
public BS getBranchBitSet(int atomIndex, int atomIndexNot, boolean allowCyclic)
public BS getElementsPresentBitSet(int modelIndex)
getElementsPresentBitSet
in class JmolViewer
String getFileHeader()
Object getFileData()
public JmolStateCreator getStateCreator()
public String getWrappedStateScript()
public String getStateInfo()
getStateInfo
in class JmolViewer
public String getStructureState()
public void setCurrentColorRange(String label)
public void setData(String key, Object[] data, int dataType, int matchField, int matchFieldColumnCount, int dataField, int dataFieldColumnCount)
key
- a simple key name for the data, starting with "property_" if user-defineddata
- data[0] -- label
data[1] -- string or float[] or float[][] or float[][][]
data[2] -- selection bitset or int[] atomMap when field > 0
data[3] -- arrayDepth 0(String),1(float[]),2(float[][]),3(float[][][]) or -1
to indidate that it is set by data type
data[4] -- Boolean.TRUE == saveInStatedataType
- see JmolDataManager interfacematchField
- if positive, data must match atomNo in this column
if 0, no match columnmatchFieldColumnCount
- if positive, this number of characters in match column if 0,
reference is to tokens, not charactersdataField
- if positive, column containing the data
if 0, values are a simple list; clear the data
if Integer.MAX_VALUE, values are a simple list; don't clear the data
if Integer.MIN_VALUE, have one SINGLE data value for all selected
atomsdataFieldColumnCount
- if positive, this number of characters in data column
if 0, reference is to tokens, not characterspublic Object getDataObj(String key, BS bsSelected, int dataType)
key
- bsSelected
- selected atoms; for DATA_AF onlydataType
- see JmolDataManager interfacepublic SymmetryInterface getCurrentUnitCell()
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 mp)
MeasurementPending getPendingMeasurement()
public void clearAllMeasurements()
public void clearMeasurements()
clearMeasurements
in class JmolViewer
public void setAnimation(int tok)
public void setAnimationFps(int fps)
setAnimationFps
in class JmolViewer
private void setAnimationMode(String mode)
public void setAnimationOn(boolean animationOn)
public void setAnimationRange(int modelIndex1, int modelIndex2)
public BS getVisibleFramesBitSet()
getVisibleFramesBitSet
in class JmolViewer
public BS getFrameAtoms()
public void setAnimDisplay(BS bs)
public void setCurrentModelIndex(int modelIndex)
public String getTrajectoryState()
public void setFrameOffsets(BS bsAtoms, boolean isFull)
public void setCurrentModelIndexClear(int modelIndex, boolean clearBackground)
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 class JmolViewer
public void setStereo(boolean isStereoSlave, Object gRight)
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)
JmolViewer
generateOutputForExport
in class JmolViewer
private void clearRepaintManager(int iShape)
public void renderScreenImageStereo(Object gLeft, boolean checkStereoSlave, int width, int height)
public void updateJS()
private void updateJSView(int imodel, int iatom)
imodel
- iatom
- 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)
private void render()
private void drawImage(Object graphic, Object img, int x, int y, boolean isDTI)
graphic
- In JavaScript/HTML5, a Canvas.Context2dimg
- x
- y
- isDTI
- DTI format -- scrunch width by factor of twopublic 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 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 static boolean hasDatabasePrefix(String fileName)
public static boolean isDatabaseCode(char ch)
public Object setLoadFormat(String name, char type, boolean withPrefix)
name
- type
- withPrefix
- public String getStandardLabelFormat(int type)
public javajs.util.P3[] getAdditionalHydrogens(BS bsAtoms, boolean doAll, boolean justCarbon, javajs.util.Lst<Atom> vConnections)
public void setMarBond(short marBond)
setMarBond
in class JmolViewer
public void setHoverLabel(String strLabel)
private void setHoverEnabled(boolean tf)
void hoverOn(int atomIndex, boolean isLabel)
void hoverOff()
public void setDebugScript(boolean debugScript)
setDebugScript
in class JmolViewer
void clearClickCount()
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)
private String getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
private void setSync()
public void setJmolCallbackListener(JmolCallbackListener listener)
setJmolCallbackListener
in class JmolViewer
public void setJmolStatusListener(JmolStatusListener listener)
setJmolStatusListener
in class JmolViewer
public javajs.util.Lst<javajs.util.Lst<javajs.util.Lst<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)
setMenu
in class JmolViewer
void setStatusFrameChanged(boolean isVib, boolean doNotify)
isVib
- doNotify
- ignored; not implementedprivate boolean doHaveJDX()
JmolJSpecView getJSV()
public int getJDXBaseModelIndex(int modelIndex)
modelIndex
- public void scriptEcho(String strEcho)
private boolean isScriptQueued()
private void setFileLoadStatus(FIL 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, Map<String,Object> map)
public boolean setStatusDragDropped(int mode, int x, int y, String fileName)
public void setStatusResized(int width, int height)
public void scriptStatus(String strStatus)
public void setScriptStatus(String strStatus, String statusMessage, int msWalltime, String strErrorMessageUntranslated)
public void showUrl(String urlString)
showUrl
in class JmolViewer
public void setMeshCreator(Object meshCreator)
meshCreator
- public void showConsole(boolean showConsole)
public JmolAppConsoleInterface getConsole()
public Object getParameter(String key)
getParameter
in class JmolViewer
public void unsetProperty(String key)
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 void setSmilesString(String s)
public void removeUserVariable(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 void setPerspectiveDepth(boolean perspectiveDepth)
setPerspectiveDepth
in class JmolViewer
public void setAxesOrientationRasmol(boolean TF)
setAxesOrientationRasmol
in class JmolViewer
private void setAxesScale(int tok, float val)
void setAxesMode(int mode)
public boolean getSelectionHalosEnabled()
public void setSelectionHalosEnabled(boolean TF)
public boolean getShowSelectedOnce()
private void setStrandCount(int type, int value)
public int getStrandCount(int type)
public void setNavigationMode(boolean TF)
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 setPercentVdwAtom(int value)
setPercentVdwAtom
in class JmolViewer
public short getMadBond()
getMadBond
in class JmolViewer
public void setShowHydrogens(boolean TF)
setShowHydrogens
in class JmolViewer
public void setShowBbcage(boolean value)
public boolean getShowBbcage()
public void setShowUnitCell(boolean value)
public boolean getShowUnitCell()
public void setShowAxes(boolean value)
public boolean getShowAxes()
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 void setRasmolDefaults()
setRasmolDefaults
in class JmolViewer
public void setJmolDefaults()
setJmolDefaults
in class JmolViewer
private void setDefaultsType(String type)
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 STR[] allocTempEnum(int size)
public void freeTempEnum(STR[] temp)
public javajs.util.Quat[] getAtomGroupQuaternions(BS bsAtoms, int nMax)
public void setStereoMode(int[] twoColors, STER stereoMode, float degrees)
public String getChimeInfo(int tok)
public String getModelFileInfo()
public String getModelFileInfoAll()
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 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.Lst<javajs.util.P3> finalPoints, float[] dihedralList, javajs.util.M4 m4)
public void startSpinningAxis(javajs.util.T3 pt1, javajs.util.T3 pt2, boolean isClockwise)
public javajs.util.V3 getModelDipole()
public javajs.util.V3 calculateMolecularDipole(BS bsAtoms) throws Exception
Exception
public void setDefaultLattice(javajs.util.P3 p)
public javajs.util.P3 getDefaultLattice()
public String getModelExtract(Object atomExpression, boolean doTransform, boolean isModelKit, String type)
atomExpression
- doTransform
- isModelKit
- type
- public String getData(String atomExpression, String type)
getData
in class JmolViewer
public String getModelFileData(String atomExpression, String type, boolean allTrajectories)
atomExpression
- -- will be wrapped in { } and evaluatedtype
- -- lower case means "atom data only; UPPERCASE returns full file dataallTrajectories
- public String getPdbAtomData(BS bs, javajs.util.OC out, boolean asPQR, boolean doTransform)
public boolean isJmolDataFrame()
public void setFrameTitle(int modelIndex, String title)
public void setFrameTitleObj(Object title)
public String getFrameTitle()
public void setAtomProperty(BS bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)
public void checkCoordinatesChanged()
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 invertRingAt(int atomIndex, boolean isClick)
public void invertSelected(javajs.util.P3 pt, javajs.util.P4 plane, int iAtom, BS invAtoms)
public void moveAtoms(javajs.util.M4 m4, javajs.util.M3 mNew, javajs.util.M3 rotation, 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)
public 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 void getHelp(String what)
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 setHistory(String fileName)
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)
getModelIndexFromId
in class JmolViewer
id
- some_id,
filename#id, or
~fileNo.modelNo
added ".basemodel" indicates to get the first model in a
series from a JDX-MOL file.public void setSyncDriver(int mode)
public int getVanderwaalsMar(int i)
public int getVanderwaalsMarType(int atomicAndIsotopeNumber, VDW type)
void setVdwStr(String name)
void setUserVdw(VDW mode)
public int deleteAtoms(BS bsAtoms, boolean fullModels)
public int deleteModels(int modelIndex, BS bsAtoms)
modelIndex
- bsAtoms
- public void deleteBonds(BS bsDeleted)
public void deleteModelAtoms(int modelIndex, int firstAtomIndex, int nAtoms, BS bsModelAtoms)
public char getQuaternionFrame()
public boolean loadImageData(Object image, String nameOrError, String echoName, ScriptContext sc)
image
- could be a byte arraynameOrError
- echoName
- if this is an echo rather than the backgroundsc
- delivered in JavaScript from Platform.javapublic 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 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 boolean checkPrivateKey(double privateKey)
privateKey
- public boolean getPreserveState()
boolean isKiosk()
public boolean hasFocus()
public void setFocus()
void stopMinimization()
void clearMinimization()
public String getMinimizationInfo()
private void checkMinimization()
public void minimize(JmolScriptEvaluator eval, int steps, float crit, BS bsSelected, BS bsFixed, float rangeFixed, boolean addHydrogen, boolean isOnly, boolean isSilent, boolean isLoad2D) throws Exception
eval
- steps
- Integer.MAX_VALUE --> use defaultscrit
- -1 --> use defaultsbsSelected
- bsFixed
- rangeFixed
- addHydrogen
- isOnly
- isSilent
- isLoad2D
- Exception
public void setMotionFixedAtoms(BS bs)
public BS getMotionFixedAtoms()
void getAtomicPropertyState(javajs.util.SB commands, byte type, BS bs, String name, float[] data)
public javajs.util.P3[][] getCenterAndPoints(javajs.util.Lst<Object[]> atomSets, boolean addCenter)
public String writeFileData(String fileName, String type, int modelIndex, Object[] parameters)
public String getPdbData(int modelIndex, String type, BS bsAtoms, Object[] parameters, javajs.util.OC oc, boolean getStructure)
public void setShapeSize(int shapeID, int madOrMad10, BS bsSelected)
shapeID
- madOrMad10
- for axes, unitcell, and boundbox 10*mad; otherwise milliangstrom
diameterbsSelected
- private int getShapePropertyAsInt(int shapeID, String propertyName)
public void setModelVisibility()
public void resetShapes(boolean andCreateNew)
public boolean setParallel(boolean TF)
public boolean isParallel()
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)
protected void moveAtomWithHydrogens(int atomIndex, int deltaX, int deltaY, int deltaZ, BS bsAtoms)
public boolean isModelPDB(int i)
public void deleteMeasurement(int i)
deleteMeasurement
in class JmolViewer
public String getSmiles(BS bs) throws Exception
getSmiles
in class JmolViewer
Exception
public String getOpenSmiles(BS bs) throws Exception
getOpenSmiles
in class JmolViewer
Exception
public String getSmilesOpt(BS bsSelected, int index1, int index2, int flags, String options) throws Exception
bsSelected
- selected atom set or null for current or specified rangeindex1
- when bsSeleced == null, first atomIndex or -1 for currentindex2
- when bsSeleced == null, end atomIndex or -1 for currentflags
- see JC.SMILES_xxxxoptions
- e.g. /strict,open/Exception
public void alert(String msg)
public String dialogAsk(String type, String fileName, Map<String,Object> params)
type
- fileName
- params
- public JmolRendererInterface initializeExporter(Map<String,Object> params)
public boolean getMouseEnabled()
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 atomIndex)
public String runScript(String script)
JmolViewer
runScript
in class JmolViewer
public void setFrameDelayMs(long millis)
public BS getBaseModelBitSet()
public void clearTimeouts()
public void triggerTimeout(String name)
public void clearTimeout(String name)
public float[] getOrCalcPartialCharges(BS bsSelected, BS bsIgnore) throws JmolAsyncException
JmolAsyncException
public void calculatePartialCharges(BS bsSelected) throws JmolAsyncException
JmolAsyncException
public void setCurrentModelID(String id)
public void cacheClear()
public void cachePut(String key, Object data)
key
- data
- public int cacheFileByName(String fileName, boolean isAdd)
public void clearThreads()
public ScriptContext getEvalContextAndHoldQueue(JmolScriptEvaluator eval)
public int[] resizeInnerPanel(int width, int height)
resizeInnerPanel
in class JmolViewer
public String getDefaultPropertyParam(int propertyID)
public int getPropertyNumber(String name)
public boolean checkPropertyParameter(String name)
public BS addHydrogensInline(BS bsAtoms, javajs.util.Lst<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 void setCGO(javajs.util.Lst<Object> info)
public void setModelSet(ModelSet modelSet)
public void setDihedrals(float[] dihedralList, BS[] bsBranches, float rate)
public int getChainID(String id, boolean isAssign)
id
- < 256 is just the character of a single-character upper-case chain
id, upper or lower case query;
>= 256 < 300 is lower case found in structureisAssign
- from a file reader, not a select querypublic String getChainIDStr(int id)
public Boolean getScriptQueueInfo()
public JmolNMRInterface getNMRCalculation()
public int calculateFormalCharges(BS bs)
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 javajs.api.GenericZipTools getJzt()
void dragMinimizeAtom(int iAtom)
public BioResolver getJBR()
public void checkMenuUpdate()
public JmolChimeMessenger getChimeMessenger()
public SymmetryInterface getSymTemp()
public void setWindowDimensions(float[] dims)
public Triangulator getTriangulator()
public void playAudio(String fileNameOrDataURI)