Package org.jmol.viewer
Class Viewer
- java.lang.Object
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- org.jmol.api.JmolViewer
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- org.jmol.viewer.Viewer
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- All Implemented Interfaces:
PlatformViewer
,AtomDataServer
- Direct Known Subclasses:
NMR_Viewer
public class Viewer extends JmolViewer implements AtomDataServer, PlatformViewer
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Viewer.ACCESS
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Field Summary
Fields Modifier and Type Field Description private Viewer.ACCESS
access
ActionManager
acm
(package private) javajs.util.Lst<java.lang.String>
actionStates
(package private) javajs.util.Lst<java.lang.String>
actionStatesRedo
boolean
allowArrayDotNotation
private boolean
allowScripting
AnimationManager
am
private JmolAnnotationParser
annotationParser
boolean
antialiased
private JmolAppConsoleInterface
appConsole
static java.lang.String
appletCodeBase
static java.lang.String
appletDocumentBase
static java.lang.String
appletIdiomaBase
java.lang.String
appletName
boolean
async
int
atomHighlighted
boolean
autoExit
private boolean
axesAreTainted
(package private) javajs.util.BS
bsUserVdws
java.util.Map<java.lang.String,java.lang.Object>
captureParams
private boolean
chainCaseSpecified
private javajs.util.Lst<java.lang.String>
chainList
java.util.Map<java.lang.Object,java.lang.Object>
chainMap
ColorManager
cm
private CommandHistory
commandHistory
private java.lang.String
commandOptions
java.lang.Object
compiler
boolean
creatingImage
int
currentCursor
private int
currentShapeID
private java.lang.String
currentShapeState
private boolean
dataOnly
(package private) VDW
defaultVdw
java.util.Map<java.lang.String,java.lang.Object>
definedAtomSets
java.lang.Object
display
boolean
displayLoadErrors
(package private) JmolDataManager
dm
private JmolAnnotationParser
dssrParser
private java.lang.String
errorMessage
private java.lang.String
errorMessageUntranslated
JmolScriptEvaluator
eval
java.lang.Object
executor
FileManager
fm
boolean
frankOn
java.lang.String
fullName
GlobalSettings
g
GData
gdata
private java.lang.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, ANIMATION ON turns SPIN into just ROTATE private java.util.Map<java.lang.String,java.lang.Object>
headlessImageParams
private int
hoverAtomIndex
private boolean
hoverEnabled
private java.lang.String
hoverLabel
private java.lang.String
hoverText
JSmolAppletObject
html5Applet
java.lang.String
htmlName
float
imageFontScaling
private boolean
inMotion
private java.lang.String
insertedCommand
boolean
isApplet
boolean
isJNLP
static boolean
isJS
static boolean
isJSNoAWT
(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).static boolean
isSwingJS
boolean
isSyntaxAndFileCheck
boolean
isSyntaxCheck
(package private) boolean
isTainted
static boolean
isWebGL
(package private) BioResolver
jbr
private JmolChimeMessenger
jcm
static JmolToJSmolInterface
jmolObject
private GenericMenuInterface
jmolpopup
(package private) JmolStateCreator
jsc
static java.lang.String
jsDocumentBase
private JmolRendererInterface
jsExporter3D
private javajs.util.JSJSONParser
jsonParser
private java.util.Map<java.lang.String,java.lang.Object>
jsParams
private JmolJSpecView
jsv
private javajs.api.GenericZipTools
jzt
private java.lang.Object[]
lastData
(package private) java.util.Map<java.lang.String,java.lang.Object>
ligandModels
(package private) java.util.Map<java.lang.String,java.lang.Boolean>
ligandModelSet
boolean
listCommands
(package private) java.util.Map<java.lang.String,JmolScriptFunction>
localFunctions
(package private) java.lang.String
logFileName
(package private) java.lang.String
logFilePath
private java.util.Map<java.lang.String,java.lang.Object>
macros
private int
maximumSize
private Minimizer
minimizer
ModelManager
mm
private JmolAdapter
modelAdapter
private ModelKitPopup
modelkit
private int
motionEventNumber
private GenericMouseInterface
mouse
either org.jmol.awt.Mouse or org.jmol.awtjs2d.Mousejavajs.util.BS
movableBitSet
private boolean
movingSelected
ModelSet
ms
private boolean
multiTouch
(package private) boolean
mustRender
private NBOParser
nboParser
(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
static int
REFRESH_REPAINT
static int
REFRESH_REPAINT_NO_MOTION_ONLY
static int
REFRESH_SEND_WEBGL_NEW_ORIENTATION
static int
REFRESH_SYNC
static int
REFRESH_SYNC_MASK
private boolean
refreshing
(package private) JmolRepaintManager
rm
private JmolScriptManager
scm
(package private) int
screenHeight
(package private) int
screenWidth
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 java.util.Map<java.lang.String,JmolScriptFunction>
staticFunctions
StateManager
stm
static java.lang.String
strJavaVendor
static java.lang.String
strJavaVersion
static java.lang.String
strOSName
static java.lang.String
SYNC_GRAPHICS_MESSAGE
static java.lang.String
SYNC_NO_GRAPHICS_MESSAGE
(package private) java.lang.String
syncId
private TempArray
tempArray
boolean
testAsync
java.util.Map<java.lang.String,java.lang.Object>
timeouts
TransformManager
tm
private Triangulator
triangulator
int
tryPt
private boolean
useCommandThread
(package private) int[]
userVdwMars
(package private) float[]
userVdws
private static java.lang.String
version_date
java.util.Map<java.lang.String,java.lang.Object>
vwrOptions
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Fields inherited from class org.jmol.api.JmolViewer
apiPlatform, menuStructure
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Constructor Summary
Constructors Constructor Description Viewer(java.util.Map<java.lang.String,java.lang.Object> info)
new way...
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addCommand(java.lang.String command)
Adds one or more commands to the command historyvoid
addFunction(JmolScriptFunction function)
javajs.util.BS
addHydrogens(javajs.util.BS bsAtoms, boolean is2DLoad, boolean isSilent)
javajs.util.BS
addHydrogensInline(javajs.util.BS bsAtoms, javajs.util.Lst<Atom> vConnections, javajs.util.P3[] pts)
void
addSelectionListener(JmolSelectionListener listener)
StateScript
addStateScript(java.lang.String script, boolean addFrameNumber, boolean postDefinitions)
void
addUnitCellOffset(javajs.util.P3 pt)
void
alert(java.lang.String msg)
protected static JmolViewer
allocateViewer(java.lang.Object display, JmolAdapter modelAdapter, java.lang.String fullName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions, JmolStatusListener statusListener, 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
assignAtom(int atomIndex, java.lang.String element, javajs.util.P3 ptNew)
void
autoCalculate(int tokProperty, java.lang.String dataType)
int
autoHbond(javajs.util.BS bsFrom, javajs.util.BS bsTo, boolean onlyIfHaveCalculated)
private void
beginRendering(boolean isDouble, boolean isImageWrite)
void
bindAction(java.lang.String desc, java.lang.String name)
javajs.util.BS
bsA()
void
cacheClear()
int
cacheFileByName(java.lang.String fileName, boolean isAdd)
void
cachePut(java.lang.String key, java.lang.Object data)
JSInterface -- allows saving files in memory for later retrievalvoid
calcAtomsMinMax(javajs.util.BS bs, BoxInfo boxInfo)
void
calcBoundBoxDimensions(javajs.util.BS bs, float scale)
java.lang.String
calculateChirality(javajs.util.BS bsAtoms)
java.lang.String[]
calculateChiralityForSmiles(java.lang.String smiles)
int
calculateFormalCharges(javajs.util.BS bs)
javajs.util.V3
calculateMolecularDipole(javajs.util.BS bsAtoms)
void
calculatePartialCharges(javajs.util.BS bsSelected)
void
calculateStraightness()
java.lang.String
calculateStructures(javajs.util.BS bsAtoms, boolean asDSSP, boolean setStructure, int version)
int
calculateStruts(javajs.util.BS bs1, javajs.util.BS bs2)
javajs.util.P3[]
calculateSurface(javajs.util.BS bsSelected, float envelopeRadius)
java.lang.String
cd(java.lang.String dir)
void
checkCoordinatesChanged()
private static float
checkFloatRange(float value, float min, float max)
boolean
checkHalt(java.lang.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) java.util.Map<java.lang.String,java.lang.Object>
checkObjectClicked(int x, int y, int modifiers)
(package private) boolean
checkObjectDragged(int prevX, int prevY, int x, int y, int action)
boolean
checkObjectHovered(int x, int y)
private boolean
checkOption2(java.lang.String key1, java.lang.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(java.lang.String name)
boolean
checkSelect(java.util.Map<java.lang.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(java.lang.String name)
void
clearTimeouts()
java.lang.String
clipImageOrPasteText(java.lang.String text)
T[]
compileExpr(java.lang.String expr)
void
connectNBO(java.lang.String type)
private java.lang.String
createModelSetAndReturnError(java.lang.Object atomSetCollection, boolean isAppend, javajs.util.SB loadScript, java.util.Map<java.lang.String,java.lang.Object> htParams)
finally(!) we are ready to create the "model set" from the "atom set collection" - does NOT repaintjava.lang.Object
createZip(java.lang.String fileName, java.lang.String type, java.util.Map<java.lang.String,java.lang.Object> params)
void
defineAtomSets(java.util.Map<java.lang.String,java.lang.Object> info)
int
deleteAtoms(javajs.util.BS bsAtoms, boolean fullModels)
void
deleteBonds(javajs.util.BS bsDeleted)
void
deleteMeasurement(int i)
void
deleteModelAtoms(int modelIndex, int firstAtomIndex, int nAtoms, javajs.util.BS bsModelAtoms)
int
deleteModels(int modelIndex, javajs.util.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)
java.lang.String
dialogAsk(java.lang.String type, java.lang.String fileName, java.util.Map<java.lang.String,java.lang.Object> params)
Ask for new file name when opening a filevoid
displayAtoms(javajs.util.BS bs, boolean isDisplay, boolean isGroup, int addRemove, boolean isQuiet)
void
dispose()
end of life for this viewerprivate boolean
doHaveJDX()
(package private) void
dragMinimizeAtom(int iAtom)
private void
drawImage(java.lang.Object graphic, java.lang.Object img, int x, int y, boolean isDTI)
(package private) void
echoMessage(java.lang.String msg)
java.lang.String
evalFile(java.lang.String strFilename)
float
evalFunctionFloat(java.lang.Object func, java.lang.Object params, float[] values)
boolean
evalParallel(ScriptContext context, ShapeManager shapeManager)
java.lang.String
evalString(java.lang.String strScript)
java.lang.String
evalStringQuiet(java.lang.String strScript)
java.lang.String
evalStringQuietSync(java.lang.String strScript, boolean isQuiet, boolean allowSyncScript)
java.lang.Object
evalStringWaitStatusQueued(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList, boolean isQuiet, boolean isQueued)
java.lang.Object
evaluateExpression(java.lang.Object stringOrTokens)
synchronized here trapped the eventQueue; see also evaluateExpressionAsVariableSV
evaluateExpressionAsVariable(java.lang.Object stringOrTokens)
private java.lang.Object
evalWait(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList)
void
exitJmol()
java.lang.String
extractMolData(java.lang.String what)
java.lang.Object
extractProperty(java.lang.Object property, java.lang.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 java.lang.String
fixInlineString(java.lang.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(java.lang.String functionName, int nX, int nY)
fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call.float[][][]
functionXYZ(java.lang.String functionName, int nX, int nY, int nZ)
java.lang.String
generateOutputForExport(java.util.Map<java.lang.String,java.lang.Object> params)
for POV-Rayjavajs.util.P3[]
getAdditionalHydrogens(javajs.util.BS bsAtoms, boolean doAll, boolean justCarbon, javajs.util.Lst<Atom> vConnections)
javajs.util.BS
getAllAtoms()
java.lang.String
getAllSettings(java.lang.String prefix)
java.lang.String
getAnnotationInfo(SV d, java.lang.String match, int type)
JmolAnnotationParser
getAnnotationParser(boolean isDSSR)
java.lang.String
getAsciiFileOrNull(java.lang.String name)
javajs.util.BS
getAtomBitSet(java.lang.Object atomExpression)
(package private) javajs.util.BS
getAtomBitSetEval(JmolScriptEvaluator eval, java.lang.Object atomExpression)
java.lang.String
getAtomDefs(java.util.Map<java.lang.String,java.lang.Object> names)
javajs.util.Quat[]
getAtomGroupQuaternions(javajs.util.BS bsAtoms, int nMax)
(package private) void
getAtomicPropertyState(javajs.util.SB commands, byte type, javajs.util.BS bs, java.lang.String name, float[] data)
java.lang.String
getAtomInfo(int atomOrPointIndex)
private java.lang.String
getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
javajs.util.BS
getAtomsNearPt(float distance, javajs.util.P3 coord)
javajs.util.Lst<java.lang.Float>
getAtomValidation(java.lang.String type, Atom atom)
java.lang.Object
getAuxiliaryInfoForAtoms(java.lang.Object atomExpression)
int
getBackgroundArgb()
javajs.util.BS
getBaseModelBitSet()
java.lang.String
getBindingInfo(java.lang.String qualifiers)
java.lang.String
getBioSmiles(javajs.util.BS bs)
javajs.util.BS
getBondsForSelectedAtoms(javajs.util.BS bsAtoms)
(package private) boolean
getBondsPickable()
boolean
getBoolean(int tok)
boolean
getBooleanProperty(java.lang.String key)
javajs.util.P3
getBoundBoxCenter()
int
getBoundBoxCenterX()
int
getBoundBoxCenterY()
javajs.util.V3
getBoundBoxCornerVector()
javajs.util.BS
getBranchBitSet(int atomIndex, int atomIndexNot, boolean allowCyclic)
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself,deliver the set of atoms constituting this branch.java.io.BufferedInputStream
getBufferedInputStream(java.lang.String fullPathName)
javajs.util.P3[][]
getCenterAndPoints(javajs.util.Lst<java.lang.Object[]> atomSets, boolean addCenter)
int
getChainID(java.lang.String id, boolean isAssign)
Create a unique integer for any chain string.java.lang.String
getChainIDStr(int id)
java.lang.String
getChemicalInfo(java.lang.String smiles, java.lang.String info, javajs.util.BS bsAtoms)
java.lang.String
getChimeInfo(int tok)
JmolChimeMessenger
getChimeMessenger()
java.util.Map<java.lang.String,java.lang.Object>
getCifData(int modelIndex)
java.lang.String
getClipboardText()
javajs.util.P3
getColorPointForPropertyValue(float val)
java.lang.String
getCommands(java.util.Map<java.lang.String,javajs.util.BS> htDefine, java.util.Map<java.lang.String,javajs.util.BS> htMore, java.lang.String select)
JmolAppConsoleInterface
getConsole()
java.lang.String
getCoordinateState(javajs.util.BS bsSelected)
float[]
getCurrentColorRange()
java.lang.String
getCurrentFileAsString(java.lang.String state)
java.util.Map<java.lang.String,java.lang.Object>
getCurrentModelAuxInfo()
float
getCurrentSolventProbeRadius()
SymmetryInterface
getCurrentUnitCell()
int
getCursorX()
int
getCursorY()
java.lang.String
getData(java.lang.String atomExpression, java.lang.String type)
private JmolDataManager
getDataManager()
java.lang.Object
getDataObj(java.lang.String key, javajs.util.BS bsSelected, int dataType)
Retrieve a data object(package private) java.lang.String
getDataSeparator()
java.lang.String
getDefaultDirectory()
javajs.util.P3
getDefaultLattice()
java.lang.String
getDefaultMeasurementLabel(int nPoints)
java.lang.String
getDefaultPropertyParam(int propertyID)
java.lang.String
getDefaultVdwNameOrData(int mode, VDW type, javajs.util.BS bs)
javajs.util.BS
getDefinedAtomSet(java.lang.String name)
int
getDelayMaximumMs()
java.lang.String
getDistanceUnits(java.lang.String s)
(package private) boolean
getDragSelected()
boolean
getDrawHover()
javajs.util.BS
getElementsPresentBitSet(int modelIndex)
java.lang.String
getErrorMessage()
java.lang.String
getErrorMessageUn()
ScriptContext
getEvalContextAndHoldQueue(JmolScriptEvaluator eval)
java.lang.String
getExportDriverList()
java.lang.String
getFileAsString(java.lang.String fileName)
java.lang.String
getFileAsString3(java.lang.String name, boolean checkProtected, java.lang.String state)
java.lang.String
getFileAsString4(java.lang.String name, int nBytesMax, boolean doSpecialLoad, boolean allowBinary, boolean checkProtected, java.lang.String state)
(package private) java.lang.Object
getFileData()
(package private) java.lang.String
getFileHeader()
float
getFloat(int tok)
Font
getFont3D(java.lang.String fontFace, java.lang.String fontStyle, float fontSize)
javajs.util.BS
getFrameAtoms()
java.lang.String
getFrameTitle()
java.lang.String[]
getFullPathNameOrError(java.lang.String filename)
JmolScriptFunction
getFunction(java.lang.String name)
java.lang.String
getFunctionCalls(java.lang.String selectedFunction)
java.util.Map<java.lang.String,JmolScriptFunction>
getFunctions(boolean isStatic)
java.lang.Object
getGLmolView()
This method is only called by JmolGLmol applet._refresh();javajs.util.BS
getGroupsWithin(int nResidues, javajs.util.BS bs)
void
getHelp(java.lang.String what)
int
getHermiteLevel()
int
getHoverDelay()
java.lang.String
getHybridizationAndAxes(int atomIndex, javajs.util.V3 z, javajs.util.V3 x, java.lang.String lcaoType)
private java.lang.Object
getImage(boolean isDouble, boolean isImageWrite)
byte[]
getImageAsBytes(java.lang.String type, int width, int height, int quality, java.lang.String[] errMsg)
char
getInlineChar()
boolean
getInMotion(boolean includeAnim)
java.lang.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 java.lang.String
getJmolVersion()
private javajs.util.JSJSONParser
getJSJSONParser()
java.lang.Object
getJspecViewProperties(java.lang.Object myParam)
(package private) JmolJSpecView
getJSV()
javajs.api.GenericZipTools
getJzt()
java.lang.Object
getLigandModel(java.lang.String id, java.lang.String prefix, java.lang.String suffix, java.lang.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 statejava.lang.String
getLightingState()
java.lang.String
getLocalUrl(java.lang.String fileName)
java.lang.String
getLogFileName()
java.lang.String
getMacro(java.lang.String key)
retrieve macros.json from the directoryshort
getMadBond()
int
getMeasurementCount()
int[]
getMeasurementCountPlusIndices(int i)
java.lang.String
getMeasurementInfoAsString()
java.lang.String
getMeasurementStringValue(int i)
java.lang.String
getMenu(java.lang.String type)
java.lang.String
getMinimizationInfo()
Minimizer
getMinimizer(boolean createNew)
JmolAdapter
getModelAdapter()
java.lang.String
getModelCml(javajs.util.BS bs, int nAtomsMax, boolean addBonds, boolean doTransform)
javajs.util.V3
getModelDipole()
java.lang.String
getModelExtract(java.lang.Object atomExpression, boolean doTransform, boolean isModelKit, java.lang.String type)
V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQRjava.lang.String
getModelFileData(java.lang.String atomExpression, java.lang.String type, boolean allTrajectories)
java.lang.String
getModelFileInfo()
java.lang.String
getModelFileInfoAll()
int
getModelFileNumber(int modelIndex)
Model
getModelForAtomIndex(int iatom)
int
getModelIndexFromId(java.lang.String id)
java.lang.Object
getModelInfo(java.lang.String key)
get a value from the current model's Model.auxiliaryInfoModelKitPopup
getModelkit(boolean andShow)
java.lang.Object
getModelkitProperty(java.lang.Object nameOrData)
java.lang.String
getModelName(int modelIndex)
int
getModelNumber(int modelIndex)
java.lang.String
getModelNumberDotted(int modelIndex)
java.util.Properties
getModelProperties(int modelIndex)
java.util.Map<java.lang.String,java.lang.Object>
getModelSetAuxiliaryInfo()
java.lang.String
getModelSetFileName()
java.lang.String
getModelSetPathName()
java.util.Properties
getModelSetProperties()
javajs.util.BS
getModelUndeletedAtomsBitSet(int modelIndex)
javajs.util.BS
getModelUndeletedAtomsBitSetBs(javajs.util.BS bsModels)
int
getMotionEventNumber()
javajs.util.BS
getMotionFixedAtoms()
boolean
getMouseEnabled()
java.lang.String
getNBOAtomLabel(Atom atom)
private NBOParser
getNBOParser()
JmolNMRInterface
getNMRCalculation()
java.lang.String
getNMRPredict(java.lang.String type)
short
getObjectColix(int objId)
int
getObjectMad10(int objId)
void
getObjectMap(java.util.Map<java.lang.String,?> map, char c)
used in autocompletion in console using TABjava.lang.String
getOpenSmiles(javajs.util.BS bs)
float[]
getOrCalcPartialCharges(javajs.util.BS bsSelected, javajs.util.BS bsIgnore)
java.lang.Object
getOrientationText(int type, java.lang.String name, javajs.util.BS bs)
javajs.util.OC
getOutputChannel(java.lang.String localName, java.lang.String[] fullPath)
private OutputManager
getOutputManager()
java.lang.Object
getP(java.lang.String key)
java.lang.Object
getParameter(java.lang.String key)
java.lang.String
getPdbAtomData(javajs.util.BS bs, javajs.util.OC out, boolean asPQR, boolean doTransform)
java.lang.String
getPdbData(int modelIndex, java.lang.String type, javajs.util.BS bsAtoms, java.lang.Object[] parameters, javajs.util.OC oc, boolean getStructure)
java.lang.String
getPdbID()
MeasurementPending
getPendingMeasurement()
int
getPickingMode()
void
getPolymerPointsAndVectors(javajs.util.BS bs, javajs.util.Lst<javajs.util.P3[]> vList)
private java.lang.Object
getPopupMenu()
java.lang.Object
getPOrNull(java.lang.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.java.lang.Object
getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
private JmolPropertyManager
getPropertyManager()
int
getPropertyNumber(java.lang.String name)
char
getQuaternionFrame()
boolean
getRefreshing()
Rectangle
getRubberBandSelection()
float
getScalePixelsPerAngstrom(boolean asAntialiased)
int
getScreenDim()
int
getScreenHeight()
java.lang.Object
getScreenImage()
java.lang.Object
getScreenImageBuffer(java.lang.Object graphic, boolean isImageWrite)
Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereoint
getScreenWidth()
ScriptContext
getScriptContext(java.lang.String why)
private JmolScriptManager
getScriptManager()
java.lang.Boolean
getScriptQueueInfo()
AtomIndexIterator
getSelectedAtomIterator(javajs.util.BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel)
boolean
getSelectionHalosEnabled()
java.lang.String
getSetHistory(int howFarBack)
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;java.lang.String
getShapeErrorState()
java.lang.Object
getShapeProperty(int shapeType, java.lang.String propertyName)
private int
getShapePropertyAsInt(int shapeID, java.lang.String propertyName)
boolean
getShowAxes()
boolean
getShowBbcage()
boolean
getShowFrank()
boolean
getShowNavigationPoint()
boolean
getShowSelectedOnce()
boolean
getShowUnitCell()
int[][]
getSmartsMap(java.lang.String smilesOrSmarts, javajs.util.BS bsSelected, int flags)
javajs.util.BS
getSmartsMatch(java.lang.String smarts, javajs.util.BS bsSelected)
javajs.util.BS
getSmartsMatchForNodes(java.lang.String smarts, Node[] atoms)
java.lang.String
getSmiles(javajs.util.BS bs)
Node[]
getSmilesAtoms(java.lang.String smiles)
SmilesMatcherInterface
getSmilesMatcher()
java.lang.String
getSmilesOpt(javajs.util.BS bsSelected, int index1, int index2, int flags, java.lang.String options)
returns the SMILES string for a sequence or atom set does not include attached protons on groupsjava.lang.String
getSpinState()
java.lang.String
getStandardLabelFormat(int type)
JmolStateCreator
getStateCreator()
java.lang.String
getStateInfo()
java.lang.String
getStateInfo3(java.lang.String type, int width, int height)
javajs.util.Lst<javajs.util.Lst<javajs.util.Lst<java.lang.Object>>>
getStatusChanged(java.lang.String statusNameList)
int
getStrandCount(int type)
java.util.Map<STR,float[]>
getStructureList()
java.lang.String
getStructureState()
javajs.util.BS[]
getSubstructureSetArray(java.lang.String pattern, javajs.util.BS bsSelected, int flags)
javajs.util.BS[]
getSubstructureSetArrayForNodes(java.lang.String pattern, Node[] nodes, int flags)
java.lang.Object
getSymmetryInfo(int iatom, java.lang.String xyz, int iOp, javajs.util.P3 pt1, javajs.util.P3 pt2, int type, java.lang.String desc, float scaleFactor, int nth, int options)
A general method for retrieving symmetry information with full capability of the symop() scripting function.SymmetryInterface
getSymTemp()
Retrieve a Symmetry object, possibly re-using an old one.java.lang.String
getTrajectoryState()
Triangulator
getTriangulator()
private javajs.util.BS
getUndeletedGroupAtomBits(javajs.util.BS bs)
float
getUnitCellInfo(int infoType)
java.lang.String
getUnitCellInfoText()
javajs.util.T3[]
getV0abc(java.lang.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)
javajs.util.BS
getVisibleFramesBitSet()
java.lang.String
getWrappedStateScript()
java.lang.String
getZapName()
void
haltScriptExecution()
void
handleError(java.lang.Error er, boolean doClear)
static boolean
hasDatabasePrefix(java.lang.String fileName)
boolean
hasFocus()
boolean
haveAccess(Viewer.ACCESS a)
boolean
haveFileSet()
void
highlight(javajs.util.BS bs)
void
highlightBond(int index, int closestAtomIndex, int x, int y)
from Sticksjava.lang.String
historyFind(java.lang.String cmd, int dir)
void
homePosition()
(package private) void
hoverOff()
(package private) void
hoverOn(int atomIndex, boolean isLabel)
void
hoverOnPt(int x, int y, java.lang.String text, java.lang.String id, javajs.util.T3 pt)
Hover over an arbitrary point.void
initialize(boolean clearUserVariables, boolean isPyMOL)
JmolRendererInterface
initializeExporter(java.util.Map<java.lang.String,java.lang.Object> params)
private void
initializeModel(boolean isAppend)
void
invertAtomCoordPlane(javajs.util.P4 plane, javajs.util.BS bs)
void
invertAtomCoordPt(javajs.util.P3 pt, javajs.util.BS bs)
void
invertRingAt(int atomIndex, boolean isClick)
void
invertSelected(javajs.util.P3 pt, javajs.util.P4 plane, int iAtom, javajs.util.BS bsAtoms)
boolean
isBound(int mouseAction, int jmolAction)
static boolean
isDatabaseCode(char ch)
boolean
isFunction(java.lang.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(java.lang.String name)
private void
jmolTest()
java.lang.String
jsEval(java.lang.String strEval)
SV
jsEvalSV(java.lang.String strEval)
private java.lang.String
loadAtomDataAndReturnError(java.lang.Object atomSetCollection, int tokType)
or just apply the data to the current model setboolean
loadImageData(java.lang.Object image, java.lang.String nameOrError, java.lang.String echoName, ScriptContext sc)
NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java as well as from FileManager.loadImagejava.lang.String
loadInline(java.lang.String strModel)
from Applet and external applications onlyjava.lang.String
loadInline(java.lang.String[] arrayModels)
external apps onlyjava.lang.String
loadInline(java.lang.String[] arrayModels, boolean isAppend)
external apps and applet onlyjava.lang.String
loadInline(java.lang.String strModel, char newLine)
external apps onlyjava.lang.String
loadInline(java.util.List<java.lang.Object> arrayData, boolean isAppend)
External applications only; does not preserve state -- intentionally!java.lang.String
loadInlineAppend(java.lang.String strModel, boolean isAppend)
used by applet and consoleprivate java.lang.String
loadInlineScript(java.lang.String strModel, char newLine, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams)
used by loadInline and openFileFullprivate java.lang.String
loadInlineScriptRepaint(java.lang.String strModel, char newLine, boolean isAppend)
java.lang.String
loadModelFromFile(java.lang.String fullPathName, java.lang.String fileName, java.lang.String[] fileNames, java.lang.Object reader, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams, javajs.util.SB loadScript, javajs.util.SB sOptions, int tokType, java.lang.String filecat)
Used by the ScriptEvaluator LOAD command to open one or more files.private java.lang.String
loadModelFromFileRepaint(java.lang.String fullPathName, java.lang.String fileName, java.lang.String[] fileNames, java.lang.Object reader)
for JmolSimpleViewer -- external applications only (and no-script JavaScript)void
log(java.lang.String data)
int[]
makeConnections(float minDistance, float maxDistance, int order, int connectOperation, javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.BS bsBonds, boolean isBonds, boolean addGroup, float energy)
boolean
menuEnabled()
void
minimize(JmolScriptEvaluator eval, int steps, float crit, javajs.util.BS bsSelected, javajs.util.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, javajs.util.BS bsAtoms, boolean translationOnly)
protected void
moveAtomWithHydrogens(int atomIndex, int deltaX, int deltaY, int deltaZ, javajs.util.BS bsAtoms)
void
moveSelected(int deltaX, int deltaY, int deltaZ, int x, int y, javajs.util.BS bsSelected, boolean isTranslation, boolean asAtoms, int modifiers)
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(java.lang.String id, javajs.util.Lst<java.lang.Object> points)
void
notifyError(java.lang.String errType, java.lang.String errMsg, java.lang.String errMsgUntranslated)
void
notifyMinimizationStatus()
int
notifyMouseClicked(int x, int y, int action, int mode)
void
notifyScriptEditor(int msWalltime, java.lang.Object[] data)
void
notifyStatusReady(boolean isReady)
void
notifyViewerRepaintDone()
java.lang.String
openDOM(java.lang.Object DOMNode)
applet DOM method -- does not preserve statejavajs.util.OC
openExportChannel(double privateKey, java.lang.String fileName, boolean asWriter)
java.lang.String
openFile(java.lang.String fileName)
for JmolSimpleViewer -- external applications only (and no-script JavaScript)void
openFileAsyncSpecial(java.lang.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 java.lang.Object
openFileFull(java.lang.String fileName, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams, javajs.util.SB loadScript)
does NOT repaintjava.lang.String
openFiles(java.lang.String[] fileNames)
for JmolSimpleViewer -- external applications onlyjava.lang.String
openReader(java.lang.String fullPathName, java.lang.String fileName, java.lang.Object reader)
Opens the file, given an already-created reader.java.lang.String
openStringInline(java.lang.String strModel)
only used by file dropper.java.lang.String
openStringInlineParamsAppend(java.lang.String strModel, java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)
Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.private java.lang.String
openStringsInlineParamsAppend(java.lang.String[] arrayModels, java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)
opens multiple files inline; does NOT repaintjava.lang.String
outputToFile(java.util.Map<java.lang.String,java.lang.Object> params)
java.lang.Object
parseJSON(java.lang.String str)
javajs.util.Lst<java.lang.Object>
parseJSONArray(java.lang.String jsonArray)
java.util.Map<java.lang.String,java.lang.Object>
parseJSONMap(java.lang.String jsonMap)
void
pauseScriptExecution()
void
popHoldRepaint(java.lang.String why)
void
popState()
(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)
java.lang.String
processWriteOrCapture(java.util.Map<java.lang.String,java.lang.Object> params)
from eval write command only includes option to write set of filesjava.lang.String
prompt(java.lang.String label, java.lang.String data, java.lang.String[] list, boolean asButtons)
void
pushHoldRepaint()
void
pushHoldRepaintWhy(java.lang.String why)
void
pushState()
java.util.Map<java.lang.String,java.lang.Object>
readCifData(java.lang.String fileName, java.lang.Object rdrOrStringData, java.lang.String type)
java.util.Map<java.lang.String,java.lang.Object>
readCifData(java.lang.String fileName, java.lang.String type)
void
rebond()
void
rebondState(boolean isStateScript)
void
refresh(int mode, java.lang.String strWhy)
initiate a repaint/update sequence if it has not already been requested.void
refreshMeasures(boolean andStopMinimization)
void
releaseScreenImage()
java.lang.String
removeCommand()
Removes one command from the command historyvoid
removeFunction(java.lang.String name)
void
removeSelectionListener(JmolSelectionListener listener)
void
removeUserVariable(java.lang.String key)
private void
render()
void
renderScreenImage(java.lang.Object g, int width, int height)
JmolViewer interface uses this, but that is allvoid
renderScreenImageStereo(java.lang.Object gLeft, boolean checkStereoSlave, int width, int height)
(package private) void
reportSelection(java.lang.String msg)
void
requestRepaintAndWait(java.lang.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) java.lang.String
resolveDatabaseFormat(java.lang.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, javajs.util.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, javajs.util.BS bsSelected)
void
rotateFront()
(package private) void
rotateSelected(float deltaX, float deltaY, javajs.util.BS bsSelected)
(package private) void
rotateXYBy(float degX, float degY)
void
rotateZBy(int zDelta, int x, int y)
java.lang.String
runScript(java.lang.String script)
Run a script using the script function script("xxxxxx") using direct script tokens for script ( "xxxxxxx" )java.lang.String
runScriptCautiously(java.lang.String script)
formerly runScript(), this method really can ONLY be called by the viewer being run from an already-running script.(package private) void
saveModelOrientation()
java.lang.String
script(java.lang.String strScript)
java.lang.Object
scriptCheck(java.lang.String strScript)
private java.lang.Object
scriptCheckRet(java.lang.String strScript, boolean returnContext)
void
scriptEcho(java.lang.String strEcho)
void
scriptStatus(java.lang.String strStatus)
void
scriptStatusMsg(java.lang.String strStatus, java.lang.String statusMessage)
java.lang.String
scriptWait(java.lang.String strScript)
java.lang.Object
scriptWaitStatus(java.lang.String strScript, java.lang.String statusList)
void
select(javajs.util.BS bs, boolean isGroup, int addRemove, boolean isQuiet)
void
selectAll()
void
selectBonds(javajs.util.BS bs)
void
sendConsoleMessage(java.lang.String msg)
void
setAnimation(int tok)
void
setAnimationFps(int fps)
private void
setAnimationMode(java.lang.String mode)
void
setAnimationOn(boolean animationOn)
void
setAnimationRange(int modelIndex1, int modelIndex2)
void
setAnimDisplay(javajs.util.BS bs)
private void
setAntialias(int tok, boolean TF)
(package private) void
setApplySymmetryToBonds(boolean TF)
void
setAtomCoords(javajs.util.BS bs, int tokType, java.lang.Object xyzValues)
void
setAtomCoordsRelative(javajs.util.T3 offset, javajs.util.BS bs)
void
setAtomData(int type, java.lang.String name, java.lang.String coordinateData, boolean isDefault)
void
setAtomProperty(javajs.util.BS bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.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(java.lang.String fileName, java.lang.Object image)
void
setBackgroundModelIndex(int modelIndex)
void
setBondTolerance(float bondTolerance)
void
setBooleanProperty(java.lang.String key, boolean value)
private void
setBooleanPropertyTok(java.lang.String key, int tok, boolean value)
void
setCenterBitSet(javajs.util.BS bsCenter, boolean doScale)
void
setCenterSelected()
void
setCGO(javajs.util.Lst<java.lang.Object> info)
void
setColorBackground(java.lang.String colorName)
void
setCurrentCage(java.lang.String isosurfaceId)
void
setCurrentColorRange(java.lang.String label)
void
setCurrentModelID(java.lang.String id)
void
setCurrentModelIndex(int modelIndex)
void
setCurrentModelIndexClear(int modelIndex, boolean clearBackground)
void
setCursor(int cursor)
void
setData(java.lang.String key, java.lang.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(java.lang.String type)
void
setDihedrals(float[] dihedralList, javajs.util.BS[] bsBranches, float rate)
void
setDisplay(java.lang.Object canvas)
void
setElementArgb(int elementNumber, int argb)
java.lang.String
setErrorMessage(java.lang.String errMsg, java.lang.String errMsgUntranslated)
private void
setFileLoadStatus(FIL ptLoad, java.lang.String fullPathName, java.lang.String fileName, java.lang.String modelName, java.lang.String strError, java.lang.Boolean isAsync)
void
setFloatProperty(java.lang.String key, float value)
private void
setFloatPropertyTok(java.lang.String key, int tok, float value)
void
setFocus()
void
setFrameDelayMs(long millis)
void
setFrameOffsets(javajs.util.BS bsAtoms, boolean isFull)
void
setFrameTitle(int modelIndex, java.lang.String title)
void
setFrameTitleObj(java.lang.Object title)
(package private) void
setFrameVariables()
void
setFrankOn(boolean TF)
void
setHistory(java.lang.String fileName)
private void
setHoverEnabled(boolean tf)
void
setHoverLabel(java.lang.String strLabel)
void
setInMotion(boolean inMotion)
void
setInsertedCommand(java.lang.String strScript)
void
setIntProperty(java.lang.String key, int value)
private void
setIntPropertyTok(java.lang.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(java.lang.String key, java.lang.String data)
java.lang.Object
setLoadFormat(java.lang.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.java.util.Map<java.lang.String,java.lang.Object>
setLoadParameters(java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)
void
setMarBond(short marBond)
private void
setMaximumSize(int x)
void
setMenu(java.lang.String fileOrText, boolean isFile)
void
setMeshCreator(java.lang.Object meshCreator)
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer 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)
java.lang.Object
setModelkitProperty(java.lang.String key, java.lang.Object value)
void
setModelKitRotateBondIndex(int i)
void
setModelSet(ModelSet modelSet)
void
setModelVisibility()
void
setModulation(javajs.util.BS bs, boolean isOn, javajs.util.P3 t1, boolean isQ)
void
setMotionFixedAtoms(javajs.util.BS bs)
private javajs.util.BS
setMovableBitSet(javajs.util.BS bsSelected, boolean checkMolecule)
void
setNavigationDepthPercent(float percent)
void
setNavigationMode(boolean TF)
void
setNewRotationCenter(javajs.util.P3 center)
void
setObjectArgb(java.lang.String name, int argb)
(package private) void
setObjectColor(java.lang.String name, java.lang.String colorName)
void
setObjectMad10(int iShape, java.lang.String name, int mad10)
input here is a JC.SHAPE_xxxx identifierjava.lang.String
setObjectProp(java.lang.String id, int tokCommand)
void
setObjectVisibility(java.lang.String name, boolean b)
void
setOptions(java.util.Map<java.lang.String,java.lang.Object> info)
boolean
setParallel(boolean TF)
(package private) void
setPendingMeasurement(MeasurementPending mp)
void
setPercentVdwAtom(int value)
void
setPerspectiveDepth(boolean perspectiveDepth)
void
setPicked(int atomIndex, boolean andReset)
(package private) void
setPickingMode(java.lang.String strMode, int pickingMode)
(package private) void
setPickingStyle(java.lang.String style, int pickingStyle)
void
setPropertyColorScheme(java.lang.String scheme, boolean isTranslucent, boolean isOverloaded)
void
setProteinType(STR type, javajs.util.BS bs)
void
setRasmolDefaults()
private void
setRefreshing(boolean TF)
void
setRotateBondIndex(int i)
void
setRotationRadius(float angstroms, boolean doAll)
void
setScreenDimension(int width, int height)
private void
setScriptQueue(boolean TF)
void
setScriptStatus(java.lang.String strStatus, java.lang.String statusMessage, int msWalltime, java.lang.String strErrorMessageUntranslated)
void
setSelectionHalosEnabled(boolean TF)
void
setSelectionSet(javajs.util.BS set)
void
setShapeErrorState(int shapeID, java.lang.String state)
void
setShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object value)
void
setShapeSize(int shapeID, int madOrMad10, javajs.util.BS bsSelected)
void
setShowAxes(boolean value)
void
setShowBbcage(boolean value)
void
setShowHydrogens(boolean TF)
void
setShowMeasurements(boolean TF)
void
setShowUnitCell(boolean value)
void
setSmilesString(java.lang.String s)
void
setSpin(java.lang.String key, int value)
private void
setStartupBooleans()
void
setStatusAtomPicked(int atomIndex, java.lang.String info, java.util.Map<java.lang.String,java.lang.Object> map, boolean andSelect)
boolean
setStatusDragDropped(int mode, int x, int y, java.lang.String fileName)
(package private) void
setStatusFrameChanged(boolean isVib, boolean doNotify)
void
setStatusMeasuring(java.lang.String status, int intInfo, java.lang.String strMeasure, float value)
void
setStatusResized(int width, int height)
void
setStereo(boolean isStereoSlave, java.lang.Object gRight)
void
setStereoMode(int[] twoColors, STER stereoMode, float degrees)
private void
setStrandCount(int type, int value)
void
setStringProperty(java.lang.String key, java.lang.String value)
private void
setStringPropertyTok(java.lang.String key, int tok, java.lang.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(java.lang.String name, int mSec, java.lang.String script)
void
setUnits(java.lang.String units, boolean isDistance)
(package private) void
setUserVdw(VDW mode)
(package private) void
setVdwStr(java.lang.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(java.lang.String[] file_text)
void
showParameter(java.lang.String key, boolean ifNotSet, int nMax)
void
showString(java.lang.String str, boolean isPrint)
java.lang.String
showTimeout(java.lang.String name)
void
showUrl(java.lang.String urlString)
(package private) void
slabByPixels(int pixels)
(package private) void
slabDepthByPixels(int pixels)
void
spinXYBy(int xDelta, int yDelta, float speed)
void
startHoverWatcher(boolean tf)
void
startNBO(java.lang.String options)
void
startPlugin(java.lang.String plugin)
startup -U nbo optionvoid
startSpinningAxis(javajs.util.T3 pt1, javajs.util.T3 pt2, boolean isClockwise)
(package private) void
stopMinimization()
void
syncScript(java.lang.String script, java.lang.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 ignoreOffset)
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, javajs.util.BS bsAtoms)
void
translateXYBy(int xDelta, int yDelta)
void
triggerTimeout(java.lang.String name)
void
unBindAction(java.lang.String desc, java.lang.String name)
(package private) void
undoClear()
void
undoMoveAction(int action, int n)
void
undoMoveActionClear(int taintedAtom, int type, boolean clearRedo)
void
unsetProperty(java.lang.String key)
void
updateJS()
for JavaScript onlyprivate 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()
java.lang.String
writeFileData(java.lang.String fileName, java.lang.String type, int modelIndex, java.lang.Object[] parameters)
java.lang.String
writeTextFile(java.lang.String fileName, java.lang.String data)
void
zap(boolean notify, boolean resetUndo, boolean zapModelKit)
private void
zapMsg(java.lang.String msg)
(package private) void
zoomBy(int pixels)
(package private) void
zoomByFactor(float factor, int x, int y)
-
Methods inherited from class org.jmol.api.JmolViewer
allocateViewer, allocateViewer, openFileAsync, openReader, renderScreenImage, setConsole
-
-
-
-
Field Detail
-
testAsync
public boolean testAsync
-
autoExit
public boolean autoExit
-
haveDisplay
public boolean haveDisplay
-
isJS
public static boolean isJS
-
isJSNoAWT
public static boolean isJSNoAWT
-
isSwingJS
public static boolean isSwingJS
-
isWebGL
public static boolean isWebGL
-
isSingleThreaded
public boolean isSingleThreaded
-
queueOnHold
public boolean queueOnHold
-
fullName
public java.lang.String fullName
-
appletDocumentBase
public static java.lang.String appletDocumentBase
-
appletCodeBase
public static java.lang.String appletCodeBase
-
appletIdiomaBase
public static java.lang.String appletIdiomaBase
-
jsDocumentBase
public static java.lang.String jsDocumentBase
-
compiler
public java.lang.Object compiler
-
definedAtomSets
public java.util.Map<java.lang.String,java.lang.Object> definedAtomSets
-
ms
public ModelSet ms
-
fm
public FileManager fm
-
isApplet
public boolean isApplet
-
isJNLP
public boolean isJNLP
-
isSyntaxAndFileCheck
public boolean isSyntaxAndFileCheck
-
isSyntaxCheck
public boolean isSyntaxCheck
-
listCommands
public boolean listCommands
-
mustRender
boolean mustRender
-
htmlName
public java.lang.String htmlName
-
appletName
public java.lang.String appletName
-
tryPt
public int tryPt
-
insertedCommand
private java.lang.String insertedCommand
-
gdata
public GData gdata
-
html5Applet
public JSmolAppletObject html5Applet
-
jmolObject
public static JmolToJSmolInterface jmolObject
-
acm
public ActionManager acm
-
am
public AnimationManager am
-
cm
public ColorManager cm
-
dm
JmolDataManager dm
-
shm
public ShapeManager shm
-
slm
public SelectionManager slm
-
rm
JmolRepaintManager rm
-
g
public GlobalSettings g
-
sm
public StatusManager sm
-
tm
public TransformManager tm
-
strJavaVendor
public static java.lang.String strJavaVendor
-
strOSName
public static java.lang.String strOSName
-
strJavaVersion
public static java.lang.String strJavaVersion
-
syncId
java.lang.String syncId
-
logFilePath
java.lang.String logFilePath
-
allowScripting
private boolean allowScripting
-
isPrintOnly
public boolean isPrintOnly
-
isSignedApplet
public boolean isSignedApplet
-
isSignedAppletLocal
private boolean isSignedAppletLocal
-
isSilent
private boolean isSilent
-
multiTouch
private boolean multiTouch
-
noGraphicsAllowed
public boolean noGraphicsAllowed
-
useCommandThread
private boolean useCommandThread
-
commandOptions
private java.lang.String commandOptions
-
vwrOptions
public java.util.Map<java.lang.String,java.lang.Object> vwrOptions
-
display
public java.lang.Object display
-
modelAdapter
private JmolAdapter modelAdapter
-
access
private Viewer.ACCESS access
-
commandHistory
private CommandHistory commandHistory
-
mm
public ModelManager mm
-
stm
public StateManager stm
-
scm
private JmolScriptManager scm
-
eval
public JmolScriptEvaluator eval
-
tempArray
private TempArray tempArray
-
allowArrayDotNotation
public boolean allowArrayDotNotation
-
async
public boolean async
-
executor
public java.lang.Object executor
-
version_date
private static java.lang.String version_date
-
screenWidth
int screenWidth
-
screenHeight
int screenHeight
-
actionStates
final javajs.util.Lst<java.lang.String> actionStates
-
actionStatesRedo
final javajs.util.Lst<java.lang.String> actionStatesRedo
-
defaultVdw
VDW defaultVdw
-
rd
public RadiusData rd
-
chainMap
public java.util.Map<java.lang.Object,java.lang.Object> chainMap
-
chainList
private javajs.util.Lst<java.lang.String> chainList
-
errorMessage
private java.lang.String errorMessage
-
errorMessageUntranslated
private java.lang.String errorMessageUntranslated
-
privateKey
private double privateKey
-
dataOnly
private boolean dataOnly
-
isPreviewOnly
public boolean isPreviewOnly
-
headless
public boolean headless
determined by GraphicsEnvironment.isHeadless() from java -Djava.awt.headless=true disables command threading disables DELAY, TIMEOUT, PAUSE, LOOP, GOTO, SPIN, ANIMATION ON turns SPIN into just ROTATE
-
movableBitSet
public javajs.util.BS movableBitSet
-
mouse
private GenericMouseInterface mouse
either org.jmol.awt.Mouse or org.jmol.awtjs2d.Mouse
-
ligandModels
java.util.Map<java.lang.String,java.lang.Object> ligandModels
-
ligandModelSet
java.util.Map<java.lang.String,java.lang.Boolean> ligandModelSet
-
annotationParser
private JmolAnnotationParser annotationParser
-
dssrParser
private JmolAnnotationParser dssrParser
-
minimizer
private Minimizer minimizer
-
smilesMatcher
private SmilesMatcherInterface smilesMatcher
-
jsc
JmolStateCreator jsc
-
lastData
private java.lang.Object[] lastData
-
motionEventNumber
private int motionEventNumber
-
inMotion
private boolean inMotion
-
refreshing
private boolean refreshing
-
REFRESH_REPAINT
public static final int REFRESH_REPAINT
- See Also:
- Constant Field Values
-
REFRESH_SYNC
public static final int REFRESH_SYNC
- See Also:
- Constant Field Values
-
REFRESH_SYNC_MASK
public static final int REFRESH_SYNC_MASK
- See Also:
- Constant Field Values
-
REFRESH_REPAINT_NO_MOTION_ONLY
public static final int REFRESH_REPAINT_NO_MOTION_ONLY
- See Also:
- Constant Field Values
-
REFRESH_SEND_WEBGL_NEW_ORIENTATION
public static final int REFRESH_SEND_WEBGL_NEW_ORIENTATION
- See Also:
- Constant Field Values
-
axesAreTainted
private boolean axesAreTainted
-
maximumSize
private int maximumSize
-
gRight
private java.lang.Object gRight
A graphics from a "slave" stereo display that has been synchronized with this this applet.
-
isStereoSlave
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).
-
imageFontScaling
public float imageFontScaling
-
captureParams
public java.util.Map<java.lang.String,java.lang.Object> captureParams
-
jsParams
private java.util.Map<java.lang.String,java.lang.Object> jsParams
-
antialiased
public boolean antialiased
-
hoverAtomIndex
private int hoverAtomIndex
-
hoverText
private java.lang.String hoverText
-
hoverLabel
private java.lang.String hoverLabel
-
hoverEnabled
private boolean hoverEnabled
-
currentCursor
public int currentCursor
-
ptTemp
private javajs.util.P3 ptTemp
-
prevFrame
private int prevFrame
-
prevMorphModel
private float prevMorphModel
-
haveJDX
private boolean haveJDX
-
jsv
private JmolJSpecView jsv
-
selectionHalosEnabled
private boolean selectionHalosEnabled
-
frankOn
public boolean frankOn
-
noFrankEcho
public boolean noFrankEcho
-
scriptEditorVisible
public boolean scriptEditorVisible
-
appConsole
private JmolAppConsoleInterface appConsole
-
scriptEditor
private JmolScriptEditorInterface scriptEditor
-
jmolpopup
private GenericMenuInterface jmolpopup
-
modelkit
private ModelKitPopup modelkit
-
headlessImageParams
private java.util.Map<java.lang.String,java.lang.Object> headlessImageParams
-
pm
JmolPropertyManager pm
-
isTainted
boolean isTainted
-
movingSelected
private boolean movingSelected
-
showSelected
private boolean showSelected
-
atomHighlighted
public int atomHighlighted
-
creatingImage
public boolean creatingImage
-
outputManager
private OutputManager outputManager
-
SYNC_GRAPHICS_MESSAGE
public static final java.lang.String SYNC_GRAPHICS_MESSAGE
- See Also:
- Constant Field Values
-
SYNC_NO_GRAPHICS_MESSAGE
public static final java.lang.String SYNC_NO_GRAPHICS_MESSAGE
- See Also:
- Constant Field Values
-
bsUserVdws
javajs.util.BS bsUserVdws
-
userVdws
float[] userVdws
-
userVdwMars
int[] userVdwMars
-
currentShapeID
private int currentShapeID
-
currentShapeState
private java.lang.String currentShapeState
-
staticFunctions
static final java.util.Map<java.lang.String,JmolScriptFunction> staticFunctions
-
localFunctions
java.util.Map<java.lang.String,JmolScriptFunction> localFunctions
-
isKiosk
boolean isKiosk
-
nProcessors
public static int nProcessors
-
displayLoadErrors
public boolean displayLoadErrors
-
isParallel
private boolean isParallel
-
stateScriptVersionInt
public int stateScriptVersionInt
-
jsExporter3D
private JmolRendererInterface jsExporter3D
-
timeouts
public java.util.Map<java.lang.String,java.lang.Object> timeouts
-
chainCaseSpecified
private boolean chainCaseSpecified
-
nmrCalculation
JmolNMRInterface nmrCalculation
-
logFileName
java.lang.String logFileName
-
jzt
private javajs.api.GenericZipTools jzt
-
jbr
BioResolver jbr
-
jcm
private JmolChimeMessenger jcm
-
jsonParser
private javajs.util.JSJSONParser jsonParser
-
triangulator
private Triangulator triangulator
-
nboParser
private NBOParser nboParser
-
macros
private java.util.Map<java.lang.String,java.lang.Object> macros
-
-
Constructor Detail
-
Viewer
public Viewer(java.util.Map<java.lang.String,java.lang.Object> info)
new way...- Parameters:
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"
-
-
Method Detail
-
finalize
protected void finalize() throws java.lang.Throwable
- Overrides:
finalize
in classjava.lang.Object
- Throws:
java.lang.Throwable
-
setInsertedCommand
public void setInsertedCommand(java.lang.String strScript)
-
getJmolVersion
public static java.lang.String getJmolVersion()
-
allocateViewer
protected static JmolViewer allocateViewer(java.lang.Object display, JmolAdapter modelAdapter, java.lang.String fullName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions, JmolStatusListener statusListener, GenericPlatform implementedPlatform)
old way...- Parameters:
display
-modelAdapter
-fullName
-documentBase
-codeBase
-commandOptions
-statusListener
-implementedPlatform
-- Returns:
- JmolViewer object
-
haveAccess
public boolean haveAccess(Viewer.ACCESS a)
-
getModelAdapter
public JmolAdapter getModelAdapter()
- Specified by:
getModelAdapter
in classJmolViewer
-
getSmartsMatch
public javajs.util.BS getSmartsMatch(java.lang.String smarts, javajs.util.BS bsSelected) throws java.lang.Exception
- Specified by:
getSmartsMatch
in classJmolViewer
- Throws:
java.lang.Exception
-
getSmartsMatchForNodes
public javajs.util.BS getSmartsMatchForNodes(java.lang.String smarts, Node[] atoms) throws java.lang.Exception
- Throws:
java.lang.Exception
-
getSmartsMap
public int[][] getSmartsMap(java.lang.String smilesOrSmarts, javajs.util.BS bsSelected, int flags) throws java.lang.Exception
- Parameters:
smilesOrSmarts
-bsSelected
-flags
- can be bitwise OR of JC.SMILES_* options, in particular, JC.SMILES_TYPE_SMARTS, JC.SMILES_TYPE_SMILES, and JC.SMILES_MAP_UNIQUE- Returns:
- map
- Throws:
java.lang.Exception
-
setOptions
public void setOptions(java.util.Map<java.lang.String,java.lang.Object> info)
-
setDisplay
public void setDisplay(java.lang.Object canvas)
-
newMeasurementData
public MeasurementData newMeasurementData(java.lang.String id, javajs.util.Lst<java.lang.Object> points)
-
getDataManager
private JmolDataManager getDataManager()
-
getScriptManager
private JmolScriptManager getScriptManager()
-
checkOption2
private boolean checkOption2(java.lang.String key1, java.lang.String key2)
-
setStartupBooleans
private void setStartupBooleans()
-
getExportDriverList
public java.lang.String getExportDriverList()
-
dispose
public void dispose()
end of life for this viewer- Overrides:
dispose
in classJmolViewer
-
reset
public void reset(boolean includingSpin)
-
homePosition
public void homePosition()
- Specified by:
homePosition
in classJmolViewer
-
initialize
public void initialize(boolean clearUserVariables, boolean isPyMOL)
-
setWidthHeightVar
public void setWidthHeightVar()
-
saveModelOrientation
void saveModelOrientation()
-
restoreModelOrientation
void restoreModelOrientation(int modelIndex)
-
restoreModelRotation
void restoreModelRotation(int modelIndex)
-
getGLmolView
public java.lang.Object getGLmolView()
This method is only called by JmolGLmol applet._refresh();- Returns:
- enough data to update a WebGL view
-
setRotationRadius
public void setRotationRadius(float angstroms, boolean doAll)
-
setCenterBitSet
public void setCenterBitSet(javajs.util.BS bsCenter, boolean doScale)
-
setNewRotationCenter
public void setNewRotationCenter(javajs.util.P3 center)
-
navigate
void navigate(int keyWhere, int modifiers)
-
move
public void move(JmolScriptEvaluator eval, javajs.util.V3 dRot, float dZoom, javajs.util.V3 dTrans, float dSlab, float floatSecondsTotal, int fps)
-
moveTo
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)
-
moveUpdate
public void moveUpdate(float floatSecondsTotal)
-
navigatePt
public void navigatePt(javajs.util.P3 center)
-
navigateAxis
public void navigateAxis(javajs.util.V3 rotAxis, float degrees)
-
navTranslatePercent
public void navTranslatePercent(float x, float y)
-
zoomBy
void zoomBy(int pixels)
-
zoomByFactor
void zoomByFactor(float factor, int x, int y)
-
rotateXYBy
void rotateXYBy(float degX, float degY)
-
spinXYBy
public void spinXYBy(int xDelta, int yDelta, float speed)
-
rotateZBy
public void rotateZBy(int zDelta, int x, int y)
-
rotateSelected
void rotateSelected(float deltaX, float deltaY, javajs.util.BS bsSelected)
-
setMovableBitSet
private javajs.util.BS setMovableBitSet(javajs.util.BS bsSelected, boolean checkMolecule)
-
translateXYBy
public void translateXYBy(int xDelta, int yDelta)
-
rotateFront
public void rotateFront()
- Specified by:
rotateFront
in classJmolViewer
-
translate
public void translate(char xyz, float x, char type, javajs.util.BS bsAtoms)
-
slabByPixels
void slabByPixels(int pixels)
-
depthByPixels
void depthByPixels(int pixels)
-
slabDepthByPixels
void slabDepthByPixels(int pixels)
-
finalizeTransformParameters
public void finalizeTransformParameters()
-
getScalePixelsPerAngstrom
public float getScalePixelsPerAngstrom(boolean asAntialiased)
-
setSpin
public void setSpin(java.lang.String key, int value)
-
getSpinState
public java.lang.String getSpinState()
-
getOrientationText
public java.lang.Object getOrientationText(int type, java.lang.String name, javajs.util.BS bs)
- Parameters:
type
-name
-bs
-- Returns:
- String or Quat or P3[]
-
getCurrentColorRange
public float[] getCurrentColorRange()
-
setDefaultColors
private void setDefaultColors(boolean isRasmol)
-
setElementArgb
public void setElementArgb(int elementNumber, int argb)
-
setVectorScale
public void setVectorScale(float scale)
- Specified by:
setVectorScale
in classJmolViewer
-
setVibrationScale
public void setVibrationScale(float scale)
- Specified by:
setVibrationScale
in classJmolViewer
-
setVibrationPeriod
public void setVibrationPeriod(float period)
- Specified by:
setVibrationPeriod
in classJmolViewer
-
setObjectColor
void setObjectColor(java.lang.String name, java.lang.String colorName)
-
setObjectVisibility
public void setObjectVisibility(java.lang.String name, boolean b)
-
setObjectArgb
public void setObjectArgb(java.lang.String name, int argb)
-
setBackgroundImage
public void setBackgroundImage(java.lang.String fileName, java.lang.Object image)
-
getObjectColix
public short getObjectColix(int objId)
-
setColorBackground
public void setColorBackground(java.lang.String colorName)
- Specified by:
setColorBackground
in classJmolViewer
-
getBackgroundArgb
public int getBackgroundArgb()
- Specified by:
getBackgroundArgb
in classJmolViewer
-
setObjectMad10
public void setObjectMad10(int iShape, java.lang.String name, int mad10)
input here is a JC.SHAPE_xxxx identifier- Parameters:
iShape
-name
-mad10
-
-
getObjectMad10
public int getObjectMad10(int objId)
- Parameters:
objId
-- Returns:
- mad10
-
setPropertyColorScheme
public void setPropertyColorScheme(java.lang.String scheme, boolean isTranslucent, boolean isOverloaded)
-
getLightingState
public java.lang.String getLightingState()
-
getColorPointForPropertyValue
public javajs.util.P3 getColorPointForPropertyValue(float val)
-
select
public void select(javajs.util.BS bs, boolean isGroup, int addRemove, boolean isQuiet)
-
setSelectionSet
public void setSelectionSet(javajs.util.BS set)
- Specified by:
setSelectionSet
in classJmolViewer
-
selectBonds
public void selectBonds(javajs.util.BS bs)
-
displayAtoms
public void displayAtoms(javajs.util.BS bs, boolean isDisplay, boolean isGroup, int addRemove, boolean isQuiet)
-
getUndeletedGroupAtomBits
private javajs.util.BS getUndeletedGroupAtomBits(javajs.util.BS bs)
-
reportSelection
void reportSelection(java.lang.String msg)
-
clearAtomSets
private void clearAtomSets()
-
getDefinedAtomSet
public javajs.util.BS getDefinedAtomSet(java.lang.String name)
-
selectAll
public void selectAll()
- Specified by:
selectAll
in classJmolViewer
-
clearSelection
public void clearSelection()
- Specified by:
clearSelection
in classJmolViewer
-
bsA
public javajs.util.BS bsA()
-
addSelectionListener
public void addSelectionListener(JmolSelectionListener listener)
- Specified by:
addSelectionListener
in classJmolViewer
-
removeSelectionListener
public void removeSelectionListener(JmolSelectionListener listener)
- Specified by:
removeSelectionListener
in classJmolViewer
-
getAtomBitSetEval
javajs.util.BS getAtomBitSetEval(JmolScriptEvaluator eval, java.lang.Object atomExpression)
-
processTwoPointGesture
public void processTwoPointGesture(float[][][] touches)
-
processMouseEvent
public boolean processMouseEvent(int id, int x, int y, int modifiers, long time)
-
getRubberBandSelection
public Rectangle getRubberBandSelection()
-
isBound
public boolean isBound(int mouseAction, int jmolAction)
-
getCursorX
public int getCursorX()
-
getCursorY
public int getCursorY()
-
getDefaultDirectory
public java.lang.String getDefaultDirectory()
-
getLocalUrl
public java.lang.String getLocalUrl(java.lang.String fileName)
-
getFileAsString
public java.lang.String getFileAsString(java.lang.String fileName)
-
getBufferedInputStream
public java.io.BufferedInputStream getBufferedInputStream(java.lang.String fullPathName)
- Specified by:
getBufferedInputStream
in interfaceAtomDataServer
-
setLoadParameters
public java.util.Map<java.lang.String,java.lang.Object> setLoadParameters(java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)
-
openFileAsyncSpecial
public void openFileAsyncSpecial(java.lang.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. Called from (JSmolCore.js)Jmol.$appEvent(,,"drop").reader.onloadend()- Specified by:
openFileAsyncSpecial
in classJmolViewer
- Parameters:
fileName
-flags
- 1=pdbCartoons, 2=no scripting, 4=append, 8=fileOpen
-
openFile
public java.lang.String openFile(java.lang.String fileName)
for JmolSimpleViewer -- external applications only (and no-script JavaScript)- Specified by:
openFile
in classJmolViewer
- Parameters:
fileName
-- Returns:
- null or error
-
openFiles
public java.lang.String openFiles(java.lang.String[] fileNames)
for JmolSimpleViewer -- external applications only- Specified by:
openFiles
in classJmolViewer
- Parameters:
fileNames
-- Returns:
- null or error
-
openReader
public java.lang.String openReader(java.lang.String fullPathName, java.lang.String fileName, java.lang.Object reader)
Opens the file, given an already-created reader.- Specified by:
openReader
in classJmolViewer
- Parameters:
fullPathName
-fileName
- name without path or can just be nullreader
- could be Reader, BufferedInputStream, or byte[]- Returns:
- null or error message
-
openDOM
public java.lang.String openDOM(java.lang.Object DOMNode)
applet DOM method -- does not preserve state- Specified by:
openDOM
in classJmolViewer
- Parameters:
DOMNode
-- Returns:
- null or error
-
loadModelFromFileRepaint
private java.lang.String loadModelFromFileRepaint(java.lang.String fullPathName, java.lang.String fileName, java.lang.String[] fileNames, java.lang.Object reader)
for JmolSimpleViewer -- external applications only (and no-script JavaScript)- Parameters:
fullPathName
-fileName
-fileNames
-reader
-- Returns:
- error message or null
-
loadModelFromFile
public java.lang.String loadModelFromFile(java.lang.String fullPathName, java.lang.String fileName, java.lang.String[] fileNames, java.lang.Object reader, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams, javajs.util.SB loadScript, javajs.util.SB sOptions, int tokType, java.lang.String filecat)
Used by the ScriptEvaluator LOAD command to open one or more files. Now necessary for EVERY load of a file, as loadScript must be passed to the ModelLoader.- Parameters:
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
-filecat
- + or null, -, or space- Returns:
- null or error
-
setLigandModel
public void setLigandModel(java.lang.String key, java.lang.String data)
-
getLigandModel
public java.lang.Object getLigandModel(java.lang.String id, java.lang.String prefix, java.lang.String suffix, java.lang.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- Parameters:
id
- unique key; if null, clear "bad" entries from the set.prefix
-suffix
- or fileNameterminator
- Only save to this if not null- Returns:
- a ligand model or a string if just file data or null
-
openFileFull
private java.lang.Object openFileFull(java.lang.String fileName, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams, javajs.util.SB loadScript)
does NOT repaint- Parameters:
fileName
-isAppend
-htParams
-loadScript
- only necessary for string reading- Returns:
- an AtomSetCollection or a String (error)
-
openStringInline
public java.lang.String openStringInline(java.lang.String strModel)
only used by file dropper.- Specified by:
openStringInline
in classJmolViewer
-
loadInline
public java.lang.String loadInline(java.lang.String strModel)
from Applet and external applications only- Specified by:
loadInline
in classJmolViewer
-
loadInline
public java.lang.String loadInline(java.lang.String strModel, char newLine)
external apps only- Specified by:
loadInline
in classJmolViewer
-
loadInlineAppend
public java.lang.String loadInlineAppend(java.lang.String strModel, boolean isAppend)
used by applet and console- Specified by:
loadInlineAppend
in classJmolViewer
-
loadInlineScriptRepaint
private java.lang.String loadInlineScriptRepaint(java.lang.String strModel, char newLine, boolean isAppend)
-
loadInline
public java.lang.String loadInline(java.lang.String[] arrayModels)
external apps only- Specified by:
loadInline
in classJmolViewer
-
loadInline
public java.lang.String loadInline(java.lang.String[] arrayModels, boolean isAppend)
external apps and applet only- Specified by:
loadInline
in classJmolViewer
- Parameters:
arrayModels
- and array of models, each of which is a String- Returns:
- null or error message
-
loadInline
public java.lang.String loadInline(java.util.List<java.lang.Object> arrayData, boolean isAppend)
External applications only; does not preserve state -- intentionally!- Specified by:
loadInline
in classJmolViewer
- Parameters:
arrayData
-isAppend
-- Returns:
- null or error string
-
loadInlineScript
private java.lang.String loadInlineScript(java.lang.String strModel, char newLine, boolean isAppend, java.util.Map<java.lang.String,java.lang.Object> htParams)
used by loadInline and openFileFull- Parameters:
strModel
-newLine
-isAppend
-htParams
-- Returns:
- null or error message
-
fixInlineString
public static java.lang.String fixInlineString(java.lang.String strModel, char newLine)
-
openStringInlineParamsAppend
public java.lang.String openStringInlineParamsAppend(java.lang.String strModel, java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)
Only used for adding hydrogen atoms and adding the model kit methane model; not part of the public interface.- Parameters:
strModel
-htParams
-isAppend
-- Returns:
- null or error string
-
openStringsInlineParamsAppend
private java.lang.String openStringsInlineParamsAppend(java.lang.String[] arrayModels, java.util.Map<java.lang.String,java.lang.Object> htParams, boolean isAppend)
opens multiple files inline; does NOT repaint- Parameters:
arrayModels
-htParams
-isAppend
-- Returns:
- null or error message
-
getInlineChar
public char getInlineChar()
-
getDataSeparator
java.lang.String getDataSeparator()
-
createModelSetAndReturnError
private java.lang.String createModelSetAndReturnError(java.lang.Object atomSetCollection, boolean isAppend, javajs.util.SB loadScript, java.util.Map<java.lang.String,java.lang.Object> htParams)
finally(!) we are ready to create the "model set" from the "atom set collection" - does NOT repaint- Parameters:
atomSetCollection
-isAppend
-loadScript
- if null, then some special method like DOM; turn of preserveStatehtParams
-- Returns:
- errMsg
-
loadAtomDataAndReturnError
private java.lang.String loadAtomDataAndReturnError(java.lang.Object atomSetCollection, int tokType)
or just apply the data to the current model set- Parameters:
atomSetCollection
-tokType
-- Returns:
- error or null
-
getCurrentFileAsString
public java.lang.String getCurrentFileAsString(java.lang.String state)
-
getFullPathNameOrError
public java.lang.String[] getFullPathNameOrError(java.lang.String filename)
- Parameters:
filename
-- Returns:
- String[2] where [0] is fullpathname and [1] is error message or null
-
getFileAsString3
public java.lang.String getFileAsString3(java.lang.String name, boolean checkProtected, java.lang.String state)
-
getFileAsString4
public java.lang.String getFileAsString4(java.lang.String name, int nBytesMax, boolean doSpecialLoad, boolean allowBinary, boolean checkProtected, java.lang.String state)
-
getAsciiFileOrNull
public java.lang.String getAsciiFileOrNull(java.lang.String name)
-
autoCalculate
public void autoCalculate(int tokProperty, java.lang.String dataType)
-
calculateStraightness
public void calculateStraightness()
-
calculateSurface
public javajs.util.P3[] calculateSurface(javajs.util.BS bsSelected, float envelopeRadius)
-
getStructureList
public java.util.Map<STR,float[]> getStructureList()
-
setStructureList
public void setStructureList(float[] list, STR type)
-
calculateStructures
public java.lang.String calculateStructures(javajs.util.BS bsAtoms, boolean asDSSP, boolean setStructure, int version)
- Parameters:
bsAtoms
-asDSSP
-setStructure
- to actually change structuresversion
-- Returns:
- structure string from DSSP
-
getAnnotationParser
public JmolAnnotationParser getAnnotationParser(boolean isDSSR)
-
getSelectedAtomIterator
public AtomIndexIterator getSelectedAtomIterator(javajs.util.BS bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean isMultiModel)
- Specified by:
getSelectedAtomIterator
in interfaceAtomDataServer
-
setIteratorForAtom
public void setIteratorForAtom(AtomIndexIterator iterator, int atomIndex, float distance)
- Specified by:
setIteratorForAtom
in interfaceAtomDataServer
-
setIteratorForPoint
public void setIteratorForPoint(AtomIndexIterator iterator, int modelIndex, javajs.util.T3 pt, float distance)
- Specified by:
setIteratorForPoint
in interfaceAtomDataServer
-
fillAtomData
public void fillAtomData(AtomData atomData, int mode)
- Specified by:
fillAtomData
in interfaceAtomDataServer
-
addStateScript
public StateScript addStateScript(java.lang.String script, boolean addFrameNumber, boolean postDefinitions)
-
getMinimizer
public Minimizer getMinimizer(boolean createNew)
-
getSmilesMatcher
public SmilesMatcherInterface getSmilesMatcher()
-
clearModelDependentObjects
public void clearModelDependentObjects()
-
zap
public void zap(boolean notify, boolean resetUndo, boolean zapModelKit)
-
zapMsg
private void zapMsg(java.lang.String msg)
-
echoMessage
void echoMessage(java.lang.String msg)
-
initializeModel
private void initializeModel(boolean isAppend)
-
startHoverWatcher
public void startHoverWatcher(boolean tf)
-
getModelSetPathName
public java.lang.String getModelSetPathName()
- Specified by:
getModelSetPathName
in classJmolViewer
-
getModelSetFileName
public java.lang.String getModelSetFileName()
- Specified by:
getModelSetFileName
in classJmolViewer
-
getUnitCellInfoText
public java.lang.String getUnitCellInfoText()
-
getUnitCellInfo
public float getUnitCellInfo(int infoType)
-
getV0abc
public javajs.util.T3[] getV0abc(java.lang.Object def)
convert string abc;offset or M3 or M4 to origin and three vectors -- a, b, c. The string can be preceded by ! for "reverse of". For example, "!a-b,-5a-5b,-c;7/8,0,1/8" offset is optional, but it still needs a semicolon: "a/2,b/2,c;"- Parameters:
def
- a string or an M3 or M4- Returns:
- vectors [origin a b c]
-
getPolymerPointsAndVectors
public void getPolymerPointsAndVectors(javajs.util.BS bs, javajs.util.Lst<javajs.util.P3[]> vList)
-
getHybridizationAndAxes
public java.lang.String getHybridizationAndAxes(int atomIndex, javajs.util.V3 z, javajs.util.V3 x, java.lang.String lcaoType)
-
getAllAtoms
public javajs.util.BS getAllAtoms()
-
getModelUndeletedAtomsBitSet
public javajs.util.BS getModelUndeletedAtomsBitSet(int modelIndex)
-
getModelUndeletedAtomsBitSetBs
public javajs.util.BS getModelUndeletedAtomsBitSetBs(javajs.util.BS bsModels)
-
getBoundBoxCenter
public javajs.util.P3 getBoundBoxCenter()
- Specified by:
getBoundBoxCenter
in classJmolViewer
-
calcBoundBoxDimensions
public void calcBoundBoxDimensions(javajs.util.BS bs, float scale)
-
getBoundBoxCornerVector
public javajs.util.V3 getBoundBoxCornerVector()
- Specified by:
getBoundBoxCornerVector
in classJmolViewer
-
getBoundBoxCenterX
public int getBoundBoxCenterX()
-
getBoundBoxCenterY
public int getBoundBoxCenterY()
-
getModelSetProperties
public java.util.Properties getModelSetProperties()
- Specified by:
getModelSetProperties
in classJmolViewer
-
getModelProperties
public java.util.Properties getModelProperties(int modelIndex)
- Specified by:
getModelProperties
in classJmolViewer
-
getModelSetAuxiliaryInfo
public java.util.Map<java.lang.String,java.lang.Object> getModelSetAuxiliaryInfo()
- Specified by:
getModelSetAuxiliaryInfo
in classJmolViewer
-
getModelNumber
public int getModelNumber(int modelIndex)
- Specified by:
getModelNumber
in classJmolViewer
-
getModelFileNumber
public int getModelFileNumber(int modelIndex)
-
getModelNumberDotted
public java.lang.String getModelNumberDotted(int modelIndex)
- Specified by:
getModelNumberDotted
in classJmolViewer
-
getModelName
public java.lang.String getModelName(int modelIndex)
- Specified by:
getModelName
in classJmolViewer
-
modelHasVibrationVectors
public boolean modelHasVibrationVectors(int modelIndex)
-
getBondsForSelectedAtoms
public javajs.util.BS getBondsForSelectedAtoms(javajs.util.BS bsAtoms)
-
frankClicked
public boolean frankClicked(int x, int y)
-
frankClickedModelKit
public boolean frankClickedModelKit(int x, int y)
-
findNearestAtomIndex
public int findNearestAtomIndex(int x, int y)
- Specified by:
findNearestAtomIndex
in classJmolViewer
-
findNearestAtomIndexMovable
public int findNearestAtomIndexMovable(int x, int y, boolean mustBeMovable)
-
toCartesian
public void toCartesian(javajs.util.T3 pt, boolean ignoreOffset)
absolute or relative to origin of UNITCELL {x y z}- Parameters:
pt
-ignoreOffset
- TODO
-
toFractional
public void toFractional(javajs.util.T3 pt, boolean ignoreOffset)
- Parameters:
pt
-ignoreOffset
- set true for relative to {0 0 0}; otherwise relative to origin of UNITCELL {x y z}
-
toUnitCell
public void toUnitCell(javajs.util.P3 pt, javajs.util.P3 offset)
relative to origin without regard to UNITCELL {x y z}- Parameters:
pt
-offset
-
-
setCurrentCage
public void setCurrentCage(java.lang.String isosurfaceId)
-
addUnitCellOffset
public void addUnitCellOffset(javajs.util.P3 pt)
-
setAtomData
public void setAtomData(int type, java.lang.String name, java.lang.String coordinateData, boolean isDefault)
-
setCenterSelected
public void setCenterSelected()
- Specified by:
setCenterSelected
in classJmolViewer
-
setApplySymmetryToBonds
void setApplySymmetryToBonds(boolean TF)
-
setBondTolerance
public void setBondTolerance(float bondTolerance)
- Specified by:
setBondTolerance
in classJmolViewer
-
setMinBondDistance
public void setMinBondDistance(float minBondDistance)
- Specified by:
setMinBondDistance
in classJmolViewer
-
getAtomsNearPt
public javajs.util.BS getAtomsNearPt(float distance, javajs.util.P3 coord)
-
getBranchBitSet
public javajs.util.BS getBranchBitSet(int atomIndex, int atomIndexNot, boolean allowCyclic)
given a set of atoms, a subset of atoms to test, two atoms that start the branch, and whether or not to allow the branch to cycle back on itself,deliver the set of atoms constituting this branch.- Parameters:
atomIndex
-atomIndexNot
-allowCyclic
-- Returns:
-
getElementsPresentBitSet
public javajs.util.BS getElementsPresentBitSet(int modelIndex)
- Specified by:
getElementsPresentBitSet
in classJmolViewer
-
getFileHeader
java.lang.String getFileHeader()
-
getFileData
java.lang.Object getFileData()
-
getCifData
public java.util.Map<java.lang.String,java.lang.Object> getCifData(int modelIndex)
-
readCifData
public java.util.Map<java.lang.String,java.lang.Object> readCifData(java.lang.String fileName, java.lang.String type)
-
readCifData
public java.util.Map<java.lang.String,java.lang.Object> readCifData(java.lang.String fileName, java.lang.Object rdrOrStringData, java.lang.String type)
- Specified by:
readCifData
in interfaceAtomDataServer
-
getStateCreator
public JmolStateCreator getStateCreator()
-
getWrappedStateScript
public java.lang.String getWrappedStateScript()
-
getStateInfo
public java.lang.String getStateInfo()
- Specified by:
getStateInfo
in classJmolViewer
-
getStateInfo3
public java.lang.String getStateInfo3(java.lang.String type, int width, int height)
-
getStructureState
public java.lang.String getStructureState()
-
getCoordinateState
public java.lang.String getCoordinateState(javajs.util.BS bsSelected)
-
setCurrentColorRange
public void setCurrentColorRange(java.lang.String label)
-
setData
public void setData(java.lang.String key, java.lang.Object[] data, int dataType, int matchField, int matchFieldColumnCount, int dataField, int dataFieldColumnCount)
A general-purpose data storage method. Note that matchFieldCount and dataFieldCount should both be positive or both be negative.- Parameters:
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 characters
-
getDataObj
public java.lang.Object getDataObj(java.lang.String key, javajs.util.BS bsSelected, int dataType)
Retrieve a data object- Parameters:
key
-bsSelected
- selected atoms; for DATA_AF onlydataType
- see JmolDataManager interface- Returns:
- data object data[0] -- label (same as key) 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 indicate that it is set by data type data[4] -- Boolean.TRUE == saveInState
-
autoHbond
public int autoHbond(javajs.util.BS bsFrom, javajs.util.BS bsTo, boolean onlyIfHaveCalculated)
-
getCurrentUnitCell
public SymmetryInterface getCurrentUnitCell()
-
getDefaultMeasurementLabel
public java.lang.String getDefaultMeasurementLabel(int nPoints)
-
getMeasurementCount
public int getMeasurementCount()
- Specified by:
getMeasurementCount
in classJmolViewer
-
getMeasurementStringValue
public java.lang.String getMeasurementStringValue(int i)
- Specified by:
getMeasurementStringValue
in classJmolViewer
-
getMeasurementInfoAsString
public java.lang.String getMeasurementInfoAsString()
-
getMeasurementCountPlusIndices
public int[] getMeasurementCountPlusIndices(int i)
- Specified by:
getMeasurementCountPlusIndices
in classJmolViewer
-
setPendingMeasurement
void setPendingMeasurement(MeasurementPending mp)
-
getPendingMeasurement
public MeasurementPending getPendingMeasurement()
-
clearAllMeasurements
public void clearAllMeasurements()
-
clearMeasurements
public void clearMeasurements()
- Specified by:
clearMeasurements
in classJmolViewer
-
setAnimation
public void setAnimation(int tok)
-
setAnimationFps
public void setAnimationFps(int fps)
- Specified by:
setAnimationFps
in classJmolViewer
-
setAnimationMode
private void setAnimationMode(java.lang.String mode)
-
setAnimationOn
public void setAnimationOn(boolean animationOn)
-
setAnimationRange
public void setAnimationRange(int modelIndex1, int modelIndex2)
-
getVisibleFramesBitSet
public javajs.util.BS getVisibleFramesBitSet()
- Specified by:
getVisibleFramesBitSet
in classJmolViewer
-
getFrameAtoms
public javajs.util.BS getFrameAtoms()
-
defineAtomSets
public void defineAtomSets(java.util.Map<java.lang.String,java.lang.Object> info)
-
setAnimDisplay
public void setAnimDisplay(javajs.util.BS bs)
-
setCurrentModelIndex
public void setCurrentModelIndex(int modelIndex)
-
getTrajectoryState
public java.lang.String getTrajectoryState()
-
setFrameOffsets
public void setFrameOffsets(javajs.util.BS bsAtoms, boolean isFull)
-
setCurrentModelIndexClear
public void setCurrentModelIndexClear(int modelIndex, boolean clearBackground)
-
haveFileSet
public boolean haveFileSet()
-
setBackgroundModelIndex
public void setBackgroundModelIndex(int modelIndex)
-
setFrameVariables
void setFrameVariables()
-
getInMotion
public boolean getInMotion(boolean includeAnim)
-
getMotionEventNumber
public int getMotionEventNumber()
- Specified by:
getMotionEventNumber
in classJmolViewer
-
setInMotion
public void setInMotion(boolean inMotion)
- Specified by:
setInMotion
in classJmolViewer
-
setRefreshing
private void setRefreshing(boolean TF)
-
getRefreshing
public boolean getRefreshing()
-
pushHoldRepaint
public void pushHoldRepaint()
- Specified by:
pushHoldRepaint
in classJmolViewer
-
pushHoldRepaintWhy
public void pushHoldRepaintWhy(java.lang.String why)
- Parameters:
why
-
-
popHoldRepaint
public void popHoldRepaint(java.lang.String why)
- Specified by:
popHoldRepaint
in classJmolViewer
-
refresh
public void refresh(int mode, java.lang.String strWhy)
initiate a repaint/update sequence if it has not already been requested. invoked whenever any operation causes changes that require new rendering. The repaint/update sequence will only be invoked if (a) no repaint is already pending and (b) there is no hold flag set in repaintManager. Sequence is as follows: 1) RepaintManager.refresh() checks flags and then calls Viewer.repaint() 2) Viewer.repaint() invokes display.repaint(), provided display is not null (headless) 3) The system responds with an invocation of Jmol.update(Graphics g), which we are routing through Jmol.paint(Graphics g). 4) Jmol.update invokes Viewer.setScreenDimensions(size), which makes the necessary changes in parameters for any new window size. 5) Jmol.update invokes Viewer.renderScreenImage(g, size, rectClip) 6) Viewer.renderScreenImage checks object visibility, invokes render1 to do the actual creation of the image pixel map and send it to the screen, and then invokes repaintView() 7) Viewer.repaintView() invokes RepaintManager.repaintDone(), to clear the flags and then use notify() to release any threads holding on wait().- Specified by:
refresh
in classJmolViewer
- Parameters:
mode
- REFRESH_REPAINT: ONLY do a repaint -- no syncing REFRESH_SYNC: mouse motion requiring synchronization -- not going through Eval so we bypass Eval and mainline on the other vwr! Also called from j2sApplet.js REFRESH_REPAINT_SYNC_MASK: same as REFRESH_REPAINT, but not WebGL REFRESH_NO_MOTION_ONLY: refresh only if not in motion REFRESH_SEND_WEBGL_NEW_ORIENTATION: send WebGL a "new orientation" command at the end of a script using html5applet._refresh()strWhy
- debugging or for passing mouse command when using REFRESH_SYNC
-
requestRepaintAndWait
public void requestRepaintAndWait(java.lang.String why)
-
clearShapeRenderers
public void clearShapeRenderers()
-
isRepaintPending
public boolean isRepaintPending()
-
notifyViewerRepaintDone
public void notifyViewerRepaintDone()
- Specified by:
notifyViewerRepaintDone
in classJmolViewer
-
areAxesTainted
public boolean areAxesTainted()
-
setMaximumSize
private void setMaximumSize(int x)
-
setScreenDimension
public void setScreenDimension(int width, int height)
- Specified by:
setScreenDimension
in classJmolViewer
-
setStereo
public void setStereo(boolean isStereoSlave, java.lang.Object gRight)
-
resizeImage
void resizeImage(int width, int height, boolean isImageWrite, boolean isExport, boolean isReset)
-
getScreenWidth
public int getScreenWidth()
- Specified by:
getScreenWidth
in classJmolViewer
-
getScreenHeight
public int getScreenHeight()
- Specified by:
getScreenHeight
in classJmolViewer
-
getScreenDim
public int getScreenDim()
-
generateOutputForExport
public java.lang.String generateOutputForExport(java.util.Map<java.lang.String,java.lang.Object> params)
Description copied from class:JmolViewer
for POV-Ray- Specified by:
generateOutputForExport
in classJmolViewer
- Returns:
- INI file
-
clearRepaintManager
private void clearRepaintManager(int iShape)
-
renderScreenImageStereo
public void renderScreenImageStereo(java.lang.Object gLeft, boolean checkStereoSlave, int width, int height)
-
updateJS
public void updateJS()
for JavaScript only
-
updateJSView
private void updateJSView(int imodel, int iatom)
File has been loaded or model has been changed or atom picked. This is a call to Jmol.View for view sets (new in Jmol 14.1.8)- Parameters:
imodel
-iatom
-
-
updateWindow
private boolean updateWindow(int width, int height)
-
renderScreenImage
public void renderScreenImage(java.lang.Object g, int width, int height)
JmolViewer interface uses this, but that is all- Specified by:
renderScreenImage
in classJmolViewer
-
getImage
private java.lang.Object getImage(boolean isDouble, boolean isImageWrite)
- Parameters:
isDouble
-isImageWrite
- TODO- Returns:
- a java.awt.Image in the case of standard Jmol; an int[] in the case of Jmol-Android a canvas in the case of JSmol
-
beginRendering
private void beginRendering(boolean isDouble, boolean isImageWrite)
-
render
private void render()
-
drawImage
private void drawImage(java.lang.Object graphic, java.lang.Object img, int x, int y, boolean isDTI)
- Parameters:
graphic
- In JavaScript/HTML5, a Canvas.Context2dimg
-x
-y
-isDTI
- DTI format -- scrunch width by factor of two
-
getScreenImage
public java.lang.Object getScreenImage()
-
getScreenImageBuffer
public java.lang.Object getScreenImageBuffer(java.lang.Object graphic, boolean isImageWrite)
Image.getJpgImage, ImageCreator.clipImage, getImageBytes, Viewer.renderScreenImageStereo- Specified by:
getScreenImageBuffer
in classJmolViewer
-
getImageAsBytes
public byte[] getImageAsBytes(java.lang.String type, int width, int height, int quality, java.lang.String[] errMsg)
- Specified by:
getImageAsBytes
in classJmolViewer
errMsg
- TODO- Returns:
- byte[] image, or null and an error message
-
releaseScreenImage
public void releaseScreenImage()
- Specified by:
releaseScreenImage
in classJmolViewer
-
evalFile
public java.lang.String evalFile(java.lang.String strFilename)
- Specified by:
evalFile
in classJmolViewer
-
getInsertedCommand
public java.lang.String getInsertedCommand()
-
script
public java.lang.String script(java.lang.String strScript)
- Specified by:
script
in classJmolViewer
-
evalString
public java.lang.String evalString(java.lang.String strScript)
- Specified by:
evalString
in classJmolViewer
-
evalStringQuiet
public java.lang.String evalStringQuiet(java.lang.String strScript)
- Specified by:
evalStringQuiet
in classJmolViewer
-
evalStringQuietSync
public java.lang.String evalStringQuietSync(java.lang.String strScript, boolean isQuiet, boolean allowSyncScript)
-
clearScriptQueue
public void clearScriptQueue()
-
setScriptQueue
private void setScriptQueue(boolean TF)
-
checkHalt
public boolean checkHalt(java.lang.String str, boolean isInsert)
- Specified by:
checkHalt
in classJmolViewer
-
scriptWait
public java.lang.String scriptWait(java.lang.String strScript)
- Specified by:
scriptWait
in classJmolViewer
-
scriptWaitStatus
public java.lang.Object scriptWaitStatus(java.lang.String strScript, java.lang.String statusList)
- Specified by:
scriptWaitStatus
in classJmolViewer
-
evalWait
private java.lang.Object evalWait(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList)
-
evalStringWaitStatusQueued
public java.lang.Object evalStringWaitStatusQueued(java.lang.String returnType, java.lang.String strScript, java.lang.String statusList, boolean isQuiet, boolean isQueued)
-
exitJmol
public void exitJmol()
-
scriptCheckRet
private java.lang.Object scriptCheckRet(java.lang.String strScript, boolean returnContext)
-
scriptCheck
public java.lang.Object scriptCheck(java.lang.String strScript)
- Specified by:
scriptCheck
in classJmolViewer
-
isScriptExecuting
public boolean isScriptExecuting()
- Specified by:
isScriptExecuting
in classJmolViewer
-
haltScriptExecution
public void haltScriptExecution()
- Specified by:
haltScriptExecution
in classJmolViewer
-
pauseScriptExecution
public void pauseScriptExecution()
-
resolveDatabaseFormat
java.lang.String resolveDatabaseFormat(java.lang.String fileName)
-
hasDatabasePrefix
public static boolean hasDatabasePrefix(java.lang.String fileName)
-
isDatabaseCode
public static boolean isDatabaseCode(char ch)
-
setLoadFormat
public java.lang.Object setLoadFormat(java.lang.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. Starting with Jmol 13.1.13, we allow a generalized search using =xxx= where xxx is a known or user-specified database designation.- Parameters:
name
-type
-withPrefix
-- Returns:
- String or String[]
-
getStandardLabelFormat
public java.lang.String getStandardLabelFormat(int type)
-
getAdditionalHydrogens
public javajs.util.P3[] getAdditionalHydrogens(javajs.util.BS bsAtoms, boolean doAll, boolean justCarbon, javajs.util.Lst<Atom> vConnections)
-
setMarBond
public void setMarBond(short marBond)
- Specified by:
setMarBond
in classJmolViewer
-
setHoverLabel
public void setHoverLabel(java.lang.String strLabel)
-
setHoverEnabled
private void setHoverEnabled(boolean tf)
-
hoverOn
void hoverOn(int atomIndex, boolean isLabel)
-
hoverOnPt
public void hoverOnPt(int x, int y, java.lang.String text, java.lang.String id, javajs.util.T3 pt)
Hover over an arbitrary point.- Parameters:
x
-y
-text
-id
- optional id to set _objecthovered topt
- optional pt to set "hovered" to
-
hoverOff
void hoverOff()
-
setDebugScript
public void setDebugScript(boolean debugScript)
- Specified by:
setDebugScript
in classJmolViewer
-
clearClickCount
void clearClickCount()
-
setCursor
public void setCursor(int cursor)
-
setPickingMode
void setPickingMode(java.lang.String strMode, int pickingMode)
-
getPickingMode
public int getPickingMode()
-
setPickingStyle
void setPickingStyle(java.lang.String style, int pickingStyle)
-
getDrawHover
public boolean getDrawHover()
-
getAtomInfo
public java.lang.String getAtomInfo(int atomOrPointIndex)
-
getAtomInfoXYZ
private java.lang.String getAtomInfoXYZ(int atomIndex, boolean useChimeFormat)
-
setSync
private void setSync()
-
setJmolCallbackListener
public void setJmolCallbackListener(JmolCallbackListener listener)
- Specified by:
setJmolCallbackListener
in classJmolViewer
-
setJmolStatusListener
public void setJmolStatusListener(JmolStatusListener listener)
- Specified by:
setJmolStatusListener
in classJmolViewer
-
getStatusChanged
public javajs.util.Lst<javajs.util.Lst<javajs.util.Lst<java.lang.Object>>> getStatusChanged(java.lang.String statusNameList)
-
menuEnabled
public boolean menuEnabled()
-
popupMenu
void popupMenu(int x, int y, char type)
-
setRotateBondIndex
public void setRotateBondIndex(int i)
-
getMenu
public java.lang.String getMenu(java.lang.String type)
-
getPopupMenu
private java.lang.Object getPopupMenu()
-
setMenu
public void setMenu(java.lang.String fileOrText, boolean isFile)
- Specified by:
setMenu
in classJmolViewer
-
setStatusFrameChanged
void setStatusFrameChanged(boolean isVib, boolean doNotify)
- Parameters:
isVib
-doNotify
- ignored; not implemented
-
doHaveJDX
private boolean doHaveJDX()
-
getJSV
JmolJSpecView getJSV()
-
getJDXBaseModelIndex
public 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. This might then allow pointing off a peak in JSpecView to switch to the model that is involved in HNMR or CNMR- Parameters:
modelIndex
-- Returns:
- modelIndex
-
getJspecViewProperties
public java.lang.Object getJspecViewProperties(java.lang.Object myParam)
-
scriptEcho
public void scriptEcho(java.lang.String strEcho)
-
isScriptQueued
private boolean isScriptQueued()
-
notifyError
public void notifyError(java.lang.String errType, java.lang.String errMsg, java.lang.String errMsgUntranslated)
-
jsEval
public java.lang.String jsEval(java.lang.String strEval)
-
jsEvalSV
public SV jsEvalSV(java.lang.String strEval)
-
setFileLoadStatus
private void setFileLoadStatus(FIL ptLoad, java.lang.String fullPathName, java.lang.String fileName, java.lang.String modelName, java.lang.String strError, java.lang.Boolean isAsync)
-
getZapName
public java.lang.String getZapName()
-
setStatusMeasuring
public void setStatusMeasuring(java.lang.String status, int intInfo, java.lang.String strMeasure, float value)
-
notifyMinimizationStatus
public void notifyMinimizationStatus()
-
setStatusAtomPicked
public void setStatusAtomPicked(int atomIndex, java.lang.String info, java.util.Map<java.lang.String,java.lang.Object> map, boolean andSelect)
-
setStatusDragDropped
public boolean setStatusDragDropped(int mode, int x, int y, java.lang.String fileName)
-
setStatusResized
public void setStatusResized(int width, int height)
-
scriptStatus
public void scriptStatus(java.lang.String strStatus)
-
scriptStatusMsg
public void scriptStatusMsg(java.lang.String strStatus, java.lang.String statusMessage)
-
setScriptStatus
public void setScriptStatus(java.lang.String strStatus, java.lang.String statusMessage, int msWalltime, java.lang.String strErrorMessageUntranslated)
-
showUrl
public void showUrl(java.lang.String urlString)
- Specified by:
showUrl
in classJmolViewer
-
setMeshCreator
public void setMeshCreator(java.lang.Object meshCreator)
an external applet or app with class that extends org.jmol.jvxl.MeshCreator might execute: org.jmol.viewer.Viewer vwr = applet.getViewer(); vwr.setMeshCreator(this); then that class's updateMesh(String id) method will be called whenever a mesh is rendered.- Parameters:
meshCreator
-
-
showConsole
public void showConsole(boolean showConsole)
-
getConsole
public JmolAppConsoleInterface getConsole()
-
getParameter
public java.lang.Object getParameter(java.lang.String key)
- Specified by:
getParameter
in classJmolViewer
-
getP
public java.lang.Object getP(java.lang.String key)
-
getPOrNull
public java.lang.Object getPOrNull(java.lang.String key)
-
unsetProperty
public void unsetProperty(java.lang.String key)
-
notifyStatusReady
public void notifyStatusReady(boolean isReady)
- Specified by:
notifyStatusReady
in classJmolViewer
-
getBooleanProperty
public boolean getBooleanProperty(java.lang.String key)
- Specified by:
getBooleanProperty
in classJmolViewer
-
getInt
public int getInt(int tok)
- Specified by:
getInt
in classJmolViewer
-
getDelayMaximumMs
public int getDelayMaximumMs()
-
getHermiteLevel
public int getHermiteLevel()
-
getHoverDelay
public int getHoverDelay()
-
getBoolean
public boolean getBoolean(int tok)
- Specified by:
getBoolean
in classJmolViewer
-
allowEmbeddedScripts
public boolean allowEmbeddedScripts()
-
getDragSelected
boolean getDragSelected()
-
getBondsPickable
boolean getBondsPickable()
-
useMinimizationThread
public boolean useMinimizationThread()
-
getFloat
public float getFloat(int tok)
- Specified by:
getFloat
in classJmolViewer
-
setStringProperty
public void setStringProperty(java.lang.String key, java.lang.String value)
- Specified by:
setStringProperty
in classJmolViewer
-
setStringPropertyTok
private void setStringPropertyTok(java.lang.String key, int tok, java.lang.String value)
-
setFloatProperty
public void setFloatProperty(java.lang.String key, float value)
- Specified by:
setFloatProperty
in classJmolViewer
-
setFloatPropertyTok
private void setFloatPropertyTok(java.lang.String key, int tok, float value)
-
setIntProperty
public void setIntProperty(java.lang.String key, int value)
- Specified by:
setIntProperty
in classJmolViewer
-
setIntPropertyTok
private void setIntPropertyTok(java.lang.String key, int tok, int value)
-
checkIntRange
private static int checkIntRange(int value, int min, int max)
-
checkFloatRange
private static float checkFloatRange(float value, float min, float max)
-
setBooleanProperty
public void setBooleanProperty(java.lang.String key, boolean value)
- Specified by:
setBooleanProperty
in classJmolViewer
-
setBooleanPropertyTok
private void setBooleanPropertyTok(java.lang.String key, int tok, boolean value)
-
setModelKitMode
private void setModelKitMode(boolean value)
-
setSmilesString
public void setSmilesString(java.lang.String s)
-
removeUserVariable
public void removeUserVariable(java.lang.String key)
-
jmolTest
private void jmolTest()
-
showParameter
public void showParameter(java.lang.String key, boolean ifNotSet, int nMax)
-
showString
public void showString(java.lang.String str, boolean isPrint)
-
getAllSettings
public java.lang.String getAllSettings(java.lang.String prefix)
-
getBindingInfo
public java.lang.String getBindingInfo(java.lang.String qualifiers)
-
getIsosurfacePropertySmoothing
public int getIsosurfacePropertySmoothing(boolean asPower)
-
setNavigationDepthPercent
public void setNavigationDepthPercent(float percent)
-
getShowNavigationPoint
public boolean getShowNavigationPoint()
-
getCurrentSolventProbeRadius
public float getCurrentSolventProbeRadius()
-
setPerspectiveDepth
public void setPerspectiveDepth(boolean perspectiveDepth)
- Specified by:
setPerspectiveDepth
in classJmolViewer
-
setAxesOrientationRasmol
public void setAxesOrientationRasmol(boolean TF)
- Specified by:
setAxesOrientationRasmol
in classJmolViewer
-
setAxesScale
private void setAxesScale(int tok, float val)
-
setAxesMode
void setAxesMode(int mode)
-
getSelectionHalosEnabled
public boolean getSelectionHalosEnabled()
-
setSelectionHalosEnabled
public void setSelectionHalosEnabled(boolean TF)
-
getShowSelectedOnce
public boolean getShowSelectedOnce()
-
setStrandCount
private void setStrandCount(int type, int value)
-
getStrandCount
public int getStrandCount(int type)
-
setNavigationMode
public void setNavigationMode(boolean TF)
-
setAutoBond
public void setAutoBond(boolean TF)
- Specified by:
setAutoBond
in classJmolViewer
-
makeConnections
public int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.BS bsBonds, boolean isBonds, boolean addGroup, float energy)
-
rebond
public void rebond()
- Specified by:
rebond
in classJmolViewer
-
rebondState
public void rebondState(boolean isStateScript)
-
setPercentVdwAtom
public void setPercentVdwAtom(int value)
- Specified by:
setPercentVdwAtom
in classJmolViewer
-
getMadBond
public short getMadBond()
- Specified by:
getMadBond
in classJmolViewer
-
setShowHydrogens
public void setShowHydrogens(boolean TF)
- Specified by:
setShowHydrogens
in classJmolViewer
-
setShowBbcage
public void setShowBbcage(boolean value)
-
getShowBbcage
public boolean getShowBbcage()
-
setShowUnitCell
public void setShowUnitCell(boolean value)
-
getShowUnitCell
public boolean getShowUnitCell()
-
setShowAxes
public void setShowAxes(boolean value)
-
getShowAxes
public boolean getShowAxes()
-
setFrankOn
public void setFrankOn(boolean TF)
- Specified by:
setFrankOn
in classJmolViewer
-
getShowFrank
public boolean getShowFrank()
-
setShowMeasurements
public void setShowMeasurements(boolean TF)
- Specified by:
setShowMeasurements
in classJmolViewer
-
setUnits
public void setUnits(java.lang.String units, boolean isDistance)
-
setRasmolDefaults
public void setRasmolDefaults()
- Specified by:
setRasmolDefaults
in classJmolViewer
-
setJmolDefaults
public void setJmolDefaults()
- Specified by:
setJmolDefaults
in classJmolViewer
-
setDefaultsType
private void setDefaultsType(java.lang.String type)
-
setAntialias
private void setAntialias(int tok, boolean TF)
-
allocTempPoints
public javajs.util.P3[] allocTempPoints(int size)
-
freeTempPoints
public void freeTempPoints(javajs.util.P3[] tempPoints)
-
allocTempScreens
public javajs.util.P3i[] allocTempScreens(int size)
-
freeTempScreens
public void freeTempScreens(javajs.util.P3i[] tempScreens)
-
allocTempEnum
public STR[] allocTempEnum(int size)
-
freeTempEnum
public void freeTempEnum(STR[] temp)
-
getFont3D
public Font getFont3D(java.lang.String fontFace, java.lang.String fontStyle, float fontSize)
-
getAtomGroupQuaternions
public javajs.util.Quat[] getAtomGroupQuaternions(javajs.util.BS bsAtoms, int nMax)
-
setStereoMode
public void setStereoMode(int[] twoColors, STER stereoMode, float degrees)
-
getChimeInfo
public java.lang.String getChimeInfo(int tok)
-
getModelFileInfo
public java.lang.String getModelFileInfo()
-
getModelFileInfoAll
public java.lang.String getModelFileInfoAll()
-
getProperty
public java.lang.Object getProperty(java.lang.String returnType, java.lang.String infoType, java.lang.Object paramInfo)
- Specified by:
getProperty
in classJmolViewer
- Parameters:
returnType
- "JSON", "string", "readable", and anything else returns the Java object.- Returns:
- property data -- see org.jmol.viewer.PropertyManager.java
-
showEditor
public void showEditor(java.lang.String[] file_text)
-
getPropertyManager
private JmolPropertyManager getPropertyManager()
-
setTainted
public void setTainted(boolean TF)
-
notifyMouseClicked
public int notifyMouseClicked(int x, int y, int action, int mode)
-
checkObjectClicked
java.util.Map<java.lang.String,java.lang.Object> checkObjectClicked(int x, int y, int modifiers)
-
checkObjectHovered
public boolean checkObjectHovered(int x, int y)
-
checkObjectDragged
boolean checkObjectDragged(int prevX, int prevY, int x, int y, int action)
-
rotateAxisAngleAtCenter
public boolean rotateAxisAngleAtCenter(JmolScriptEvaluator eval, javajs.util.P3 rotCenter, javajs.util.V3 rotAxis, float degreesPerSecond, float endDegrees, boolean isSpin, javajs.util.BS bsSelected)
-
rotateAboutPointsInternal
public boolean rotateAboutPointsInternal(JmolScriptEvaluator eval, javajs.util.P3 point1, javajs.util.P3 point2, float degreesPerSecond, float endDegrees, boolean isSpin, javajs.util.BS bsSelected, javajs.util.V3 translation, javajs.util.Lst<javajs.util.P3> finalPoints, float[] dihedralList, javajs.util.M4 m4)
-
startSpinningAxis
public void startSpinningAxis(javajs.util.T3 pt1, javajs.util.T3 pt2, boolean isClockwise)
-
getModelDipole
public javajs.util.V3 getModelDipole()
-
calculateMolecularDipole
public javajs.util.V3 calculateMolecularDipole(javajs.util.BS bsAtoms) throws java.lang.Exception
- Throws:
java.lang.Exception
-
setDefaultLattice
public void setDefaultLattice(javajs.util.P3 p)
-
getDefaultLattice
public javajs.util.P3 getDefaultLattice()
-
getModelExtract
public java.lang.String getModelExtract(java.lang.Object atomExpression, boolean doTransform, boolean isModelKit, java.lang.String type)
V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR- Parameters:
atomExpression
-doTransform
-isModelKit
-type
-- Returns:
- full file data
-
getData
public java.lang.String getData(java.lang.String atomExpression, java.lang.String type)
- Specified by:
getData
in classJmolViewer
-
getModelFileData
public java.lang.String getModelFileData(java.lang.String atomExpression, java.lang.String type, boolean allTrajectories)
- Parameters:
atomExpression
- -- will be wrapped in { } and evaluatedtype
- -- lower case means "atom data only; UPPERCASE returns full file dataallTrajectories
-- Returns:
- full or atom-only data formatted as specified
-
getModelCml
public java.lang.String getModelCml(javajs.util.BS bs, int nAtomsMax, boolean addBonds, boolean doTransform)
-
getPdbAtomData
public java.lang.String getPdbAtomData(javajs.util.BS bs, javajs.util.OC out, boolean asPQR, boolean doTransform)
-
isJmolDataFrame
public boolean isJmolDataFrame()
-
setFrameTitle
public void setFrameTitle(int modelIndex, java.lang.String title)
-
setFrameTitleObj
public void setFrameTitleObj(java.lang.Object title)
-
getFrameTitle
public java.lang.String getFrameTitle()
-
setAtomProperty
public void setAtomProperty(javajs.util.BS bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
-
checkCoordinatesChanged
public void checkCoordinatesChanged()
-
setAtomCoords
public void setAtomCoords(javajs.util.BS bs, int tokType, java.lang.Object xyzValues)
-
setAtomCoordsRelative
public void setAtomCoordsRelative(javajs.util.T3 offset, javajs.util.BS bs)
-
invertAtomCoordPt
public void invertAtomCoordPt(javajs.util.P3 pt, javajs.util.BS bs)
-
invertAtomCoordPlane
public void invertAtomCoordPlane(javajs.util.P4 plane, javajs.util.BS bs)
-
invertRingAt
public void invertRingAt(int atomIndex, boolean isClick)
-
invertSelected
public void invertSelected(javajs.util.P3 pt, javajs.util.P4 plane, int iAtom, javajs.util.BS bsAtoms)
-
moveAtoms
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, javajs.util.BS bsAtoms, boolean translationOnly)
-
moveSelected
public void moveSelected(int deltaX, int deltaY, int deltaZ, int x, int y, javajs.util.BS bsSelected, boolean isTranslation, boolean asAtoms, int modifiers)
-
highlightBond
public void highlightBond(int index, int closestAtomIndex, int x, int y)
from Sticks- Parameters:
index
-closestAtomIndex
-
-
highlight
public void highlight(javajs.util.BS bs)
-
refreshMeasures
public void refreshMeasures(boolean andStopMinimization)
-
functionXY
public float[][] functionXY(java.lang.String functionName, int nX, int nY)
fills an array with data -- if nX < 0 and this would involve JavaScript, then this reads a full set of Double[][] in one function call. Otherwise it reads the values using individual function calls, which each return Double. If the functionName begins with "file:" then data are read from a file specified after the colon. The sign of nX is not relevant in that case. The file may contain mixed numeric and non-numeric values; the non-numeric values will be skipped by Parser.parseFloatArray- Parameters:
functionName
-nX
-nY
-- Returns:
- nX by nY array of floating values
-
functionXYZ
public float[][][] functionXYZ(java.lang.String functionName, int nX, int nY, int nZ)
-
extractMolData
public java.lang.String extractMolData(java.lang.String what)
- Specified by:
extractMolData
in classJmolViewer
-
getNMRPredict
public java.lang.String getNMRPredict(java.lang.String type)
- Parameters:
type
- C13 or H1- Returns:
- null
-
getHelp
public void getHelp(java.lang.String what)
-
getChemicalInfo
public java.lang.String getChemicalInfo(java.lang.String smiles, java.lang.String info, javajs.util.BS bsAtoms)
-
addCommand
public void addCommand(java.lang.String command)
Adds one or more commands to the command history- Parameters:
command
- the command to add
-
pushState
public void pushState()
-
popState
public void popState()
-
removeCommand
public java.lang.String removeCommand()
Removes one command from the command history- Returns:
- command removed
-
getSetHistory
public java.lang.String getSetHistory(int howFarBack)
Options include: ; all n == Integer.MAX_VALUE ; n prev n >= 1 ; next n == -1 ; set max to -2 - n n <= -3 ; just clear n == -2 ; clear and turn off; return "" n == 0 ; clear and turn on; return "" n == Integer.MIN_VALUE;- Specified by:
getSetHistory
in classJmolViewer
- Parameters:
howFarBack
- number of lines (-1 for next line)- Returns:
- one or more lines of command history
-
historyFind
public java.lang.String historyFind(java.lang.String cmd, int dir)
-
setHistory
public void setHistory(java.lang.String fileName)
-
getOutputChannel
public javajs.util.OC getOutputChannel(java.lang.String localName, java.lang.String[] fullPath)
-
writeTextFile
public java.lang.String writeTextFile(java.lang.String fileName, java.lang.String data)
- Specified by:
writeTextFile
in classJmolViewer
-
clipImageOrPasteText
public java.lang.String clipImageOrPasteText(java.lang.String text)
- Specified by:
clipImageOrPasteText
in classJmolViewer
- Parameters:
text
- null here clips image; String pastes text- Returns:
- "OK image to clipboard: [width] * [height] or "OK text to clipboard: [length]
-
getClipboardText
public java.lang.String getClipboardText()
- Specified by:
getClipboardText
in classJmolViewer
-
processWriteOrCapture
public java.lang.String processWriteOrCapture(java.util.Map<java.lang.String,java.lang.Object> params)
from eval write command only includes option to write set of files- Parameters:
params
-- Returns:
- message starting with "OK" or an error message
-
createZip
public java.lang.Object createZip(java.lang.String fileName, java.lang.String type, java.util.Map<java.lang.String,java.lang.Object> params)
-
outputToFile
public java.lang.String outputToFile(java.util.Map<java.lang.String,java.lang.Object> params)
- Specified by:
outputToFile
in classJmolViewer
- Parameters:
params
- include type, fileName, text, bytes, quality, width, height- Returns:
- null (canceled) or a message starting with OK or an error message
-
getOutputManager
private OutputManager getOutputManager()
-
setSyncTarget
private void setSyncTarget(int mode, boolean TF)
-
syncScript
public void syncScript(java.lang.String script, java.lang.String applet, int port)
- Specified by:
syncScript
in classJmolViewer
-
getModelIndexFromId
public int getModelIndexFromId(java.lang.String id)
- Specified by:
getModelIndexFromId
in classJmolViewer
- Parameters:
id
- some_id, filename#id, or ~fileNo.modelNo added ".basemodel" indicates to get the first model in a series from a JDX-MOL file.- Returns:
- model index if found; -2 if file found but model not found -2 if no file indicated and no model found -1 if no such file
-
setSyncDriver
public void setSyncDriver(int mode)
-
setProteinType
public void setProteinType(STR type, javajs.util.BS bs)
-
getVanderwaalsMar
public int getVanderwaalsMar(int i)
-
getVanderwaalsMarType
public int getVanderwaalsMarType(int atomicAndIsotopeNumber, VDW type)
-
setVdwStr
void setVdwStr(java.lang.String name)
-
setUserVdw
void setUserVdw(VDW mode)
-
getDefaultVdwNameOrData
public java.lang.String getDefaultVdwNameOrData(int mode, VDW type, javajs.util.BS bs)
-
deleteAtoms
public int deleteAtoms(javajs.util.BS bsAtoms, boolean fullModels)
-
deleteModels
public int deleteModels(int modelIndex, javajs.util.BS bsAtoms)
called by ZAP {atomExpression} when atoms are present or the command is specific for a model, such as ZAP 2.1- Parameters:
modelIndex
-bsAtoms
-- Returns:
- number of atoms deleted
-
deleteBonds
public void deleteBonds(javajs.util.BS bsDeleted)
-
deleteModelAtoms
public void deleteModelAtoms(int modelIndex, int firstAtomIndex, int nAtoms, javajs.util.BS bsModelAtoms)
-
getQuaternionFrame
public char getQuaternionFrame()
-
loadImageData
public boolean loadImageData(java.lang.Object image, java.lang.String nameOrError, java.lang.String echoName, ScriptContext sc)
NOTE: This method is called from within a j2sNative block in awtjs2d.Platform.java as well as from FileManager.loadImage- Parameters:
image
- could be a byte arraynameOrError
-echoName
- if this is an echo rather than the backgroundsc
- delivered in JavaScript from Platform.java- Returns:
- false
-
cd
public java.lang.String cd(java.lang.String dir)
-
setErrorMessage
public java.lang.String setErrorMessage(java.lang.String errMsg, java.lang.String errMsgUntranslated)
-
getErrorMessage
public java.lang.String getErrorMessage()
- Specified by:
getErrorMessage
in classJmolViewer
-
getErrorMessageUn
public java.lang.String getErrorMessageUn()
- Specified by:
getErrorMessageUn
in classJmolViewer
-
setShapeErrorState
public void setShapeErrorState(int shapeID, java.lang.String state)
-
getShapeErrorState
public java.lang.String getShapeErrorState()
-
handleError
public void handleError(java.lang.Error er, boolean doClear)
-
getFunctions
public java.util.Map<java.lang.String,JmolScriptFunction> getFunctions(boolean isStatic)
-
removeFunction
public void removeFunction(java.lang.String name)
-
getFunction
public JmolScriptFunction getFunction(java.lang.String name)
-
isStaticFunction
private static boolean isStaticFunction(java.lang.String name)
-
isFunction
public boolean isFunction(java.lang.String name)
-
clearFunctions
public void clearFunctions()
-
addFunction
public void addFunction(JmolScriptFunction function)
-
getFunctionCalls
public java.lang.String getFunctionCalls(java.lang.String selectedFunction)
-
checkPrivateKey
public 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. When the image creator is used it requires both a vwr object and that vwr's private key. But the private key is private, so it is not possible to create a useable image creator without working through a vwr's own methods. Bob Hanson, 9/20/2009- Parameters:
privateKey
-- Returns:
- true if privateKey matches
-
bindAction
public void bindAction(java.lang.String desc, java.lang.String name)
-
unBindAction
public void unBindAction(java.lang.String desc, java.lang.String name)
-
calculateStruts
public int calculateStruts(javajs.util.BS bs1, javajs.util.BS bs2)
-
getPreserveState
public 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.- Returns:
- TRUE or FALSE
-
isKiosk
boolean isKiosk()
-
hasFocus
public boolean hasFocus()
-
setFocus
public void setFocus()
-
stopMinimization
void stopMinimization()
-
clearMinimization
void clearMinimization()
-
getMinimizationInfo
public java.lang.String getMinimizationInfo()
-
checkMinimization
private void checkMinimization()
-
minimize
public void minimize(JmolScriptEvaluator eval, int steps, float crit, javajs.util.BS bsSelected, javajs.util.BS bsFixed, float rangeFixed, boolean addHydrogen, boolean isOnly, boolean isSilent, boolean isLoad2D) throws java.lang.Exception
- Parameters:
eval
-steps
- Integer.MAX_VALUE --> use defaultscrit
- -1 --> use defaultsbsSelected
-bsFixed
-rangeFixed
-addHydrogen
-isOnly
-isSilent
-isLoad2D
-- Throws:
java.lang.Exception
-
setMotionFixedAtoms
public void setMotionFixedAtoms(javajs.util.BS bs)
-
getMotionFixedAtoms
public javajs.util.BS getMotionFixedAtoms()
-
getAtomicPropertyState
void getAtomicPropertyState(javajs.util.SB commands, byte type, javajs.util.BS bs, java.lang.String name, float[] data)
-
getCenterAndPoints
public javajs.util.P3[][] getCenterAndPoints(javajs.util.Lst<java.lang.Object[]> atomSets, boolean addCenter)
-
writeFileData
public java.lang.String writeFileData(java.lang.String fileName, java.lang.String type, int modelIndex, java.lang.Object[] parameters)
-
getPdbData
public java.lang.String getPdbData(int modelIndex, java.lang.String type, javajs.util.BS bsAtoms, java.lang.Object[] parameters, javajs.util.OC oc, boolean getStructure)
-
getGroupsWithin
public javajs.util.BS getGroupsWithin(int nResidues, javajs.util.BS bs)
-
setShapeSize
public void setShapeSize(int shapeID, int madOrMad10, javajs.util.BS bsSelected)
- Parameters:
shapeID
-madOrMad10
- for axes, unitcell, and boundbox 10*mad; otherwise milliangstrom diameterbsSelected
-
-
setShapeProperty
public void setShapeProperty(int shapeID, java.lang.String propertyName, java.lang.Object value)
-
getShapeProperty
public java.lang.Object getShapeProperty(int shapeType, java.lang.String propertyName)
-
getShapePropertyAsInt
private int getShapePropertyAsInt(int shapeID, java.lang.String propertyName)
-
setModelVisibility
public void setModelVisibility()
-
resetShapes
public void resetShapes(boolean andCreateNew)
-
setParallel
public boolean setParallel(boolean TF)
-
isParallel
public boolean isParallel()
-
undoClear
void undoClear()
-
undoMoveAction
public void undoMoveAction(int action, int n)
- Parameters:
action
- Token.undo or Token.redon
- number of steps to go back/forward; 0 for all; -1 for clear; -2 for clear BOTH
-
undoMoveActionClear
public void undoMoveActionClear(int taintedAtom, int type, boolean clearRedo)
-
moveAtomWithHydrogens
protected void moveAtomWithHydrogens(int atomIndex, int deltaX, int deltaY, int deltaZ, javajs.util.BS bsAtoms)
-
isModelPDB
public boolean isModelPDB(int i)
-
deleteMeasurement
public void deleteMeasurement(int i)
- Specified by:
deleteMeasurement
in classJmolViewer
-
getSmiles
public java.lang.String getSmiles(javajs.util.BS bs) throws java.lang.Exception
- Specified by:
getSmiles
in classJmolViewer
- Throws:
java.lang.Exception
-
getOpenSmiles
public java.lang.String getOpenSmiles(javajs.util.BS bs) throws java.lang.Exception
- Specified by:
getOpenSmiles
in classJmolViewer
- Throws:
java.lang.Exception
-
getBioSmiles
public java.lang.String getBioSmiles(javajs.util.BS bs) throws java.lang.Exception
- Throws:
java.lang.Exception
-
getSmilesOpt
public java.lang.String getSmilesOpt(javajs.util.BS bsSelected, int index1, int index2, int flags, java.lang.String options) throws java.lang.Exception
returns the SMILES string for a sequence or atom set does not include attached protons on groups- Parameters:
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/- Returns:
- SMILES string
- Throws:
java.lang.Exception
-
alert
public void alert(java.lang.String msg)
-
prompt
public java.lang.String prompt(java.lang.String label, java.lang.String data, java.lang.String[] list, boolean asButtons)
-
dialogAsk
public java.lang.String dialogAsk(java.lang.String type, java.lang.String fileName, java.util.Map<java.lang.String,java.lang.Object> params)
Ask for new file name when opening a file- Parameters:
type
-fileName
-params
-- Returns:
- new file name
-
initializeExporter
public JmolRendererInterface initializeExporter(java.util.Map<java.lang.String,java.lang.Object> params)
-
getMouseEnabled
public boolean getMouseEnabled()
-
calcAtomsMinMax
public void calcAtomsMinMax(javajs.util.BS bs, BoxInfo boxInfo)
- Specified by:
calcAtomsMinMax
in classJmolViewer
-
getObjectMap
public void getObjectMap(java.util.Map<java.lang.String,?> map, char c)
used in autocompletion in console using TAB- Parameters:
map
-c
-
-
setPicked
public void setPicked(int atomIndex, boolean andReset)
-
runScript
public java.lang.String runScript(java.lang.String script)
Run a script using the script function script("xxxxxx") using direct script tokens for script ( "xxxxxxx" )- Specified by:
runScript
in classJmolViewer
- Returns:
- string from ScriptEvaluator#outputBuffer
-
runScriptCautiously
public java.lang.String runScriptCautiously(java.lang.String script)
formerly runScript(), this method really can ONLY be called by the viewer being run from an already-running script. If it is invoked by a separate thread, it can wreak havoc on any queued thread, since they are not thread safe.- Overrides:
runScriptCautiously
in classJmolViewer
- Parameters:
script
-- Returns:
- output of the script.
-
setFrameDelayMs
public void setFrameDelayMs(long millis)
-
getBaseModelBitSet
public javajs.util.BS getBaseModelBitSet()
-
clearTimeouts
public void clearTimeouts()
-
setTimeout
public void setTimeout(java.lang.String name, int mSec, java.lang.String script)
-
triggerTimeout
public void triggerTimeout(java.lang.String name)
-
clearTimeout
public void clearTimeout(java.lang.String name)
-
showTimeout
public java.lang.String showTimeout(java.lang.String name)
-
getOrCalcPartialCharges
public float[] getOrCalcPartialCharges(javajs.util.BS bsSelected, javajs.util.BS bsIgnore) throws JmolAsyncException
- Throws:
JmolAsyncException
-
calculatePartialCharges
public void calculatePartialCharges(javajs.util.BS bsSelected) throws JmolAsyncException
- Throws:
JmolAsyncException
-
setCurrentModelID
public void setCurrentModelID(java.lang.String id)
-
cacheClear
public void cacheClear()
-
cachePut
public void cachePut(java.lang.String key, java.lang.Object data)
JSInterface -- allows saving files in memory for later retrieval- Parameters:
key
-data
-
-
cacheFileByName
public int cacheFileByName(java.lang.String fileName, boolean isAdd)
-
clearThreads
public void clearThreads()
-
getEvalContextAndHoldQueue
public ScriptContext getEvalContextAndHoldQueue(JmolScriptEvaluator eval)
-
resizeInnerPanel
public int[] resizeInnerPanel(int width, int height)
- Specified by:
resizeInnerPanel
in classJmolViewer
-
getDefaultPropertyParam
public java.lang.String getDefaultPropertyParam(int propertyID)
-
getPropertyNumber
public int getPropertyNumber(java.lang.String name)
-
checkPropertyParameter
public boolean checkPropertyParameter(java.lang.String name)
-
extractProperty
public java.lang.Object extractProperty(java.lang.Object property, java.lang.Object args, int pt)
-
addHydrogens
public javajs.util.BS addHydrogens(javajs.util.BS bsAtoms, boolean is2DLoad, boolean isSilent)
-
addHydrogensInline
public javajs.util.BS addHydrogensInline(javajs.util.BS bsAtoms, javajs.util.Lst<Atom> vConnections, javajs.util.P3[] pts) throws java.lang.Exception
- Throws:
java.lang.Exception
-
evalFunctionFloat
public float evalFunctionFloat(java.lang.Object func, java.lang.Object params, float[] values)
- Specified by:
evalFunctionFloat
in interfaceAtomDataServer
-
evalParallel
public boolean evalParallel(ScriptContext context, ShapeManager shapeManager)
-
evaluateExpression
public java.lang.Object evaluateExpression(java.lang.Object stringOrTokens)
synchronized here trapped the eventQueue; see also evaluateExpressionAsVariable- Specified by:
evaluateExpression
in classJmolViewer
-
evaluateExpressionAsVariable
public SV evaluateExpressionAsVariable(java.lang.Object stringOrTokens)
-
getAtomBitSet
public javajs.util.BS getAtomBitSet(java.lang.Object atomExpression)
-
getScriptContext
public ScriptContext getScriptContext(java.lang.String why)
-
getAtomDefs
public java.lang.String getAtomDefs(java.util.Map<java.lang.String,java.lang.Object> names)
-
setCGO
public void setCGO(javajs.util.Lst<java.lang.Object> info)
-
setModelSet
public void setModelSet(ModelSet modelSet)
-
setObjectProp
public java.lang.String setObjectProp(java.lang.String id, int tokCommand)
-
setDihedrals
public void setDihedrals(float[] dihedralList, javajs.util.BS[] bsBranches, float rate)
-
getChainID
public int getChainID(java.lang.String id, boolean isAssign)
Create a unique integer for any chain string. Note that if there are any chains that are more than a single character, chainCaseSensitive is automatically set TRUE- Parameters:
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 query- Returns:
- i
-
getChainIDStr
public java.lang.String getChainIDStr(int id)
-
getScriptQueueInfo
public java.lang.Boolean getScriptQueueInfo()
-
getNMRCalculation
public JmolNMRInterface getNMRCalculation()
-
getDistanceUnits
public java.lang.String getDistanceUnits(java.lang.String s)
-
calculateFormalCharges
public int calculateFormalCharges(javajs.util.BS bs)
-
setModulation
public void setModulation(javajs.util.BS bs, boolean isOn, javajs.util.P3 t1, boolean isQ)
-
checkInMotion
public void checkInMotion(int state)
-
checkMotionRendering
public boolean checkMotionRendering(int tok)
check motion for rendering during mouse movement, spin, vibration, and animation- Parameters:
tok
-- Returns:
- TRUE if allowed
-
openExportChannel
public javajs.util.OC openExportChannel(double privateKey, java.lang.String fileName, boolean asWriter) throws java.io.IOException
- Throws:
java.io.IOException
-
log
public void log(java.lang.String data)
- Specified by:
log
in interfaceAtomDataServer
-
getLogFileName
public java.lang.String getLogFileName()
-
getCommands
public java.lang.String getCommands(java.util.Map<java.lang.String,javajs.util.BS> htDefine, java.util.Map<java.lang.String,javajs.util.BS> htMore, java.lang.String select)
-
allowCapture
public boolean allowCapture()
-
compileExpr
public T[] compileExpr(java.lang.String expr)
-
getAnnotationInfo
public java.lang.String getAnnotationInfo(SV d, java.lang.String match, int type)
-
getAtomValidation
public javajs.util.Lst<java.lang.Float> getAtomValidation(java.lang.String type, Atom atom)
-
getJzt
public javajs.api.GenericZipTools getJzt()
-
dragMinimizeAtom
void dragMinimizeAtom(int iAtom)
-
getJBR
public BioResolver getJBR()
-
checkMenuUpdate
public void checkMenuUpdate()
-
getChimeMessenger
public JmolChimeMessenger getChimeMessenger()
-
getAuxiliaryInfoForAtoms
public java.lang.Object getAuxiliaryInfoForAtoms(java.lang.Object atomExpression)
-
getJSJSONParser
private javajs.util.JSJSONParser getJSJSONParser()
-
parseJSON
public java.lang.Object parseJSON(java.lang.String str)
-
parseJSONMap
public java.util.Map<java.lang.String,java.lang.Object> parseJSONMap(java.lang.String jsonMap)
-
parseJSONArray
public javajs.util.Lst<java.lang.Object> parseJSONArray(java.lang.String jsonArray)
-
getSymTemp
public SymmetryInterface getSymTemp()
Retrieve a Symmetry object, possibly re-using an old one.- Returns:
- org.jmol.symmetry.Symmetry object
-
setWindowDimensions
public void setWindowDimensions(float[] dims)
-
getTriangulator
public Triangulator getTriangulator()
-
getCurrentModelAuxInfo
public java.util.Map<java.lang.String,java.lang.Object> getCurrentModelAuxInfo()
-
startNBO
public void startNBO(java.lang.String options)
-
startPlugin
public void startPlugin(java.lang.String plugin)
startup -U nbo option- Parameters:
plugin
-
-
connectNBO
public void connectNBO(java.lang.String type)
-
getNBOParser
private NBOParser getNBOParser()
-
getNBOAtomLabel
public java.lang.String getNBOAtomLabel(Atom atom)
-
calculateChirality
public java.lang.String calculateChirality(javajs.util.BS bsAtoms)
-
getSubstructureSetArray
public javajs.util.BS[] getSubstructureSetArray(java.lang.String pattern, javajs.util.BS bsSelected, int flags) throws java.lang.Exception
- Throws:
java.lang.Exception
-
getSubstructureSetArrayForNodes
public javajs.util.BS[] getSubstructureSetArrayForNodes(java.lang.String pattern, Node[] nodes, int flags) throws java.lang.Exception
- Throws:
java.lang.Exception
-
getPdbID
public java.lang.String getPdbID()
-
getModelInfo
public java.lang.Object getModelInfo(java.lang.String key)
get a value from the current model's Model.auxiliaryInfo- Parameters:
key
-- Returns:
- value, or null if there is no SINGLE current model
-
getSmilesAtoms
public Node[] getSmilesAtoms(java.lang.String smiles) throws java.lang.Exception
- Throws:
java.lang.Exception
-
calculateChiralityForSmiles
public java.lang.String[] calculateChiralityForSmiles(java.lang.String smiles)
-
getModelForAtomIndex
public Model getModelForAtomIndex(int iatom)
-
assignAtom
public void assignAtom(int atomIndex, java.lang.String element, javajs.util.P3 ptNew)
-
getModelkit
public ModelKitPopup getModelkit(boolean andShow)
-
notifyScriptEditor
public void notifyScriptEditor(int msWalltime, java.lang.Object[] data)
-
sendConsoleMessage
public void sendConsoleMessage(java.lang.String msg)
-
getModelkitProperty
public java.lang.Object getModelkitProperty(java.lang.Object nameOrData)
- Parameters:
nameOrData
- could be name or [name,value]- Returns:
- value
-
setModelkitProperty
public java.lang.Object setModelkitProperty(java.lang.String key, java.lang.Object value)
-
getSymmetryInfo
public java.lang.Object getSymmetryInfo(int iatom, java.lang.String xyz, int iOp, javajs.util.P3 pt1, javajs.util.P3 pt2, int type, java.lang.String desc, float scaleFactor, int nth, int options)
A general method for retrieving symmetry information with full capability of the symop() scripting function.- Parameters:
iatom
- atom index specifying the model set and used for pt1 if that is null and also for matching element type.xyz
- the desired Jones-Faithful representation of the symmetry operation or nulliOp
- the desired symmetry operation [1-n] or 0pt1
- the starting point, or null if to use iatom or otherwise unnecessarypt2
- the target point, if this is a point-to-point determination, or the offset if not and options is nonzerotype
- a token type such as T.list or T.arraydesc
- if type == T.nada (0), a name evaluating to a type, or one of the special names: "info", "description", "matrix", "axispoint", or "time" (as in time-reversal); otherwise, if type == T.draw, the root id given to a returned DRAW command setscaleFactor
- if nonzero and type == T.draw, a scaling factor to be applied to the rotational vectornth
- in the case of a point-to-point determination, the nth matching operator, or 0 for "all"options
- if nonzero, a option, currently just T.offset, indicating that pt1 is an {i j k} offset from cell 555- Returns:
- string, Object[], or Lst
-
setModelKitRotateBondIndex
public void setModelKitRotateBondIndex(int i)
- Parameters:
i
- Integer.MIN_VALUE initializes the bond index
-
getMacro
public java.lang.String getMacro(java.lang.String key)
retrieve macros.json from the directory- Parameters:
key
-- Returns:
- the macro path
-
-