org.jmol.script

Class ScriptEvaluator

java.lang.Object

org.jmol.script.ScriptEvaluator

public class ScriptEvaluator
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	ScriptEvaluator.ScriptException

Field Summary

Fields

Modifier and Type	Field and Description
private Token[][]	aatoken
private int	commandHistoryLevelMax
protected ScriptCompiler	compiler
private java.lang.String	contextPath
private java.util.Map<java.lang.String,ScriptVariable>	contextVariables
private boolean	coordinatesAreFractional
private java.lang.Thread	currentThread
private java.lang.Object[]	data
private boolean	debugScript
private java.util.Map<java.lang.String,java.lang.Object>	definedAtomSets
private boolean	error
(package private) static int	ERROR_axisExpected
(package private) static int	ERROR_backgroundModelError
(package private) static int	ERROR_badArgumentCount
(package private) static int	ERROR_badMillerIndices
(package private) static int	ERROR_badRGBColor
(package private) static int	ERROR_booleanExpected
(package private) static int	ERROR_booleanOrNumberExpected
(package private) static int	ERROR_booleanOrWhateverExpected
(package private) static int	ERROR_colorExpected
(package private) static int	ERROR_colorOrPaletteRequired
(package private) static int	ERROR_commandExpected
(package private) static int	ERROR_coordinateOrNameOrExpressionRequired
(package private) static int	ERROR_drawObjectNotDefined
(package private) static int	ERROR_endOfStatementUnexpected
(package private) static int	ERROR_expressionExpected
(package private) static int	ERROR_expressionOrIntegerExpected
(package private) static int	ERROR_filenameExpected
(package private) static int	ERROR_fileNotFoundException
(package private) static int	ERROR_incompatibleArguments
(package private) static int	ERROR_insufficientArguments
(package private) static int	ERROR_integerExpected
(package private) static int	ERROR_integerOutOfRange
(package private) static int	ERROR_invalidArgument
(package private) static int	ERROR_invalidParameterOrder
(package private) static int	ERROR_keywordExpected
(package private) static int	ERROR_moCoefficients
(package private) static int	ERROR_moIndex
(package private) static int	ERROR_moModelError
(package private) static int	ERROR_moOccupancy
(package private) static int	ERROR_moOnlyOne
(package private) static int	ERROR_multipleModelsDisplayedNotOK
(package private) static int	ERROR_multipleModelsNotOK
(package private) static int	ERROR_noData
(package private) static int	ERROR_noPartialCharges
(package private) static int	ERROR_noUnitCell
(package private) static int	ERROR_numberExpected
(package private) static int	ERROR_numberMustBe
(package private) static int	ERROR_numberOutOfRange
(package private) static int	ERROR_objectNameExpected
(package private) static int	ERROR_planeExpected
(package private) static int	ERROR_propertyNameExpected
(package private) static int	ERROR_spaceGroupNotFound
(package private) static int	ERROR_stringExpected
(package private) static int	ERROR_stringOrIdentifierExpected
(package private) static int	ERROR_tooManyPoints
(package private) static int	ERROR_tooManyScriptLevels
(package private) static int	ERROR_unrecognizedAtomProperty
(package private) static int	ERROR_unrecognizedBondProperty
(package private) static int	ERROR_unrecognizedCommand
(package private) static int	ERROR_unrecognizedExpression
(package private) static int	ERROR_unrecognizedObject
(package private) static int	ERROR_unrecognizedParameter
(package private) static int	ERROR_unrecognizedParameterWarning
(package private) static int	ERROR_unrecognizedShowParameter
(package private) static int	ERROR_what
(package private) static int	ERROR_writeWhat
private java.lang.String	errorMessage
protected java.lang.String	errorMessageUntranslated
protected java.lang.String	errorType
private boolean	executionPaused
private boolean	executionStepping
private static java.lang.String	EXPRESSION_KEY
private java.lang.Object	expressionResult
private java.lang.String	filename
private boolean	forceNoAddHydrogens
private javax.vecmath.Point3f	fractionalPoint
private java.lang.String	fullCommand
private java.lang.String	functionName
private boolean	historyDisabled
protected int	iCommandError
private boolean	ignoreError
private boolean	interruptExecution
(package private) static int	iProcess
private boolean	isBondSet
private boolean	isCmdLine_C_Option
protected boolean	isCmdLine_c_or_C_Option
private boolean	isExecuting
private boolean	isStateScript
protected boolean	isSyntaxCheck
private int	iToken
private int	lineEnd
private int[][]	lineIndices
private short[]	lineNumbers
protected boolean	logMessages
private java.lang.StringBuffer	outputBuffer
private ParallelProcessor	parallelProcessor
protected int	pc
private int	pcEnd
private java.lang.String	script
static java.lang.String	SCRIPT_COMPLETED
private java.lang.String	scriptExtensions
(package private) int	scriptLevel
private static int	scriptLevelMax
private int	scriptReportingLevel
(package private) ShapeManager	shapeManager
private Token[]	statement
private int	statementLength
private Token[]	tempStatement
private static java.lang.Object	testData
private static java.lang.Object	testData2
private int	theTok
private Token	theToken
private java.lang.String	thisCommand
protected ScriptContext	thisContext
private long	timeBeginExecution
private long	timeEndExecution
private boolean	tQuiet
protected Viewer	viewer
private java.util.List<Token[]>	vProcess

Constructor Summary

Constructors

Constructor and Description
ScriptEvaluator(Viewer viewer)

Method Summary

Methods

Modifier and Type	Method and Description
private void	addProcess(int pc, int pt, boolean isStart)
private void	addShapeProperty(java.util.List<java.lang.Object[]> propertyList, java.lang.String key, java.lang.Object value)
private void	animation()
private void	animationDirection()
private void	animationMode()
private void	assign()
private javax.vecmath.Point3f	atomCenterOrCoordinateParameter(int i)
private java.util.BitSet	atomExpression(int index)
private java.util.BitSet	atomExpression(Token[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted)
private void	axes(int index)
private void	background(int i)
private void	bind()
(package private) java.util.BitSet	bitSetForModelFileNumber(int m)
(package private) java.util.List<ScriptVariable>	bitsetVariableVector(java.lang.Object v)
private void	bondorder()
private boolean	booleanParameter(int i)
private void	boundbox(int index)
private void	breakCmd(int pt)
private void	calculate()
private void	cd()
private void	center(int i)
private void	centerAt()
private javax.vecmath.Point3f	centerParameter(int i)
private javax.vecmath.Point3f	centerParameter(int i, int modelIndex)
private boolean	changeElementColor(java.lang.String str, int argb)
private boolean	checkContinue() checks to see if there is a pause condition, during which commands can still be issued, but with the ! first.
private int	checkLast(int i)
private int	checkLength(int length)
private int	checkLength(int length, int errorPt)
private int	checkLength23()
private int	checkLength34()
ScriptContext	checkScriptSilent(java.lang.String script) a method for just checking a script
private TickInfo	checkTicks(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst)
private boolean	checkToken(int i)
private void	clearDefinedVariableAtomSets()
private void	clearState(boolean tQuiet)
private void	color()
private void	colorShape(int shapeType, int index, boolean isBackground)
private void	colorShape(int shapeType, int typeMask, int argb, java.lang.String translucency, float translucentLevel, java.util.BitSet bs)
private void	compare()
private java.util.BitSet	compareFloat(int tokWhat, float[] data, int tokOperator, float comparisonFloat)
private static boolean	compareFloat(int tokOperator, float propertyFloat, float comparisonFloat)
protected java.util.BitSet	compareInt(int tokWhat, int tokOperator, int comparisonValue)
private java.util.BitSet	compareString(int tokWhat, int tokOperator, java.lang.String comparisonString)
private boolean	compareString(int tokOperator, java.lang.String propertyValue, java.lang.String comparisonValue)
private boolean	compileScript(java.lang.String filename, java.lang.String strScript, boolean debugCompiler)
boolean	compileScriptFile(java.lang.String filename, boolean tQuiet)
private boolean	compileScriptFileInternal(java.lang.String filename, java.lang.String localPath, java.lang.String remotePath, java.lang.String scriptPath)
boolean	compileScriptString(java.lang.String script, boolean tQuiet)
private void	configuration()
private void	connect(int index)
private void	console()
private void	contact()
private java.lang.Object[]	createFunction(java.lang.String fname, java.lang.String xyz, java.lang.String ret) for the ISOSURFACE command
private void	data()
private void	define()
private void	defineAtomSet(java.lang.String script)
private void	defineSets() support for @xxx or define xxx commands
private void	delay()
private void	delay(long millis)
private void	delete()
void	deleteAtomsInVariables(java.util.BitSet bsDeleted)
private void	dipole()
private void	display(boolean isDisplay)
private void	dots(int iShape)
private void	draw()
private void	echo(int index, boolean isImage)
private void	ellipsoid()
private RadiusData	encodeRadiusParameter(int index, boolean isOnly, boolean allowAbsolute)
(package private) void	error(int iError)
(package private) void	error(int iError, int i)
(package private) void	error(int iError, java.lang.String value)
(package private) void	error(int iError, java.lang.String value, java.lang.String more)
(package private) void	error(int iError, java.lang.String value, java.lang.String more, java.lang.String more2)
(package private) void	error(int iError, java.lang.String value, java.lang.String more, java.lang.String more2, boolean warningOnly)
(package private) static java.lang.String	errorString(int iError, java.lang.String value, java.lang.String more, java.lang.String more2, boolean translated)
(package private) void	evalError(java.lang.String message, java.lang.String strUntranslated)
float	evalFunctionFloat(java.lang.Object func, java.lang.Object params, float[] values)
void	evaluateCompiledScript(boolean isCmdLine_c_or_C_Option, boolean isCmdLine_C_Option, boolean historyDisabled, boolean listCommands, java.lang.StringBuffer outputBuffer)
static boolean	evaluateContext(Viewer viewer, ScriptContext context, ShapeManager shapeManager)
static java.lang.Object	evaluateExpression(Viewer viewer, java.lang.Object expr, boolean asVariable) a general-use method to evaluate a "SET" type expression.
private java.lang.String	extractCommandOption(java.lang.String name)
private void	file()
private void	fixed()
private java.lang.String	fixScriptPath(java.lang.String strScript, java.lang.String filename)
private float[][]	floatArraySet(int i, int nX, int nY)
private float[][][]	floatArraySet(int i, int nX, int nY, int nZ)
private float	floatParameter(int index)
private float	floatParameter(int i, float min, float max)
private float[]	floatParameterSet(int i, int nMin, int nMax) process a general string or set of parameters as an array of floats, allowing for relatively free form input
private float	floatSetting(int pt)
private boolean	flowControl(int tok, boolean isForCheck)
private void	font(int shapeType, float fontsize)
private void	frame(int offset)
private void	frameControl(int i)
private void	frank(int index)
private void	function()
private int	getArgbParam(int index)
private int	getArgbParam(int index, boolean allowNone)
private int	getArgbParamLast(int index, boolean allowNone)
private java.util.BitSet	getAtomBits(int tokType, java.lang.Object specInfo)
static java.util.BitSet	getAtomBitSet(ScriptEvaluator e, java.lang.Object atomExpression) a general method to evaluate a string representing an atom set.
static java.util.List<java.lang.Integer>	getAtomBitSetVector(ScriptEvaluator e, int atomCount, java.lang.Object atomExpression) just provides a vector list of atoms in a string-based expression
(package private) java.util.BitSet	getAtomsNearSurface(float distance, java.lang.String surfaceId)
(package private) java.lang.Object	getBitsetIdent(java.util.BitSet bs, java.lang.String label, java.lang.Object tokenValue, boolean useAtomMap, int index, boolean isExplicitlyAll)
protected java.lang.Object	getBitsetProperty(java.util.BitSet bs, int tok, javax.vecmath.Point3f ptRef, javax.vecmath.Point4f planeRef, java.lang.Object tokenValue, java.lang.Object opValue, boolean useAtomMap, int index, boolean asVectorIfAll)
private float[]	getBitsetPropertyFloat(java.util.BitSet bs, int tok, float min, float max)
private ScriptVariable	getBitsetPropertySelector(int i, boolean mustBeSettable)
static int	getBondOrderFromString(java.lang.String s)
private java.lang.Object	getCapSlabObject(int i, boolean isLcaoCartoon)
private java.lang.String	getColorRange(int i)
private int	getColorTriad(int i)
private java.lang.String	getCommand(int pc, boolean allThisLine, boolean addSemi) used for recall of commands in the application console
private java.lang.String	getContext(boolean withVariables)
private ScriptVariable	getContextVariableAsVariable(java.lang.String var)
java.util.Map<java.lang.String,ScriptVariable>	getContextVariables()
private javax.vecmath.Vector3f	getDrawObjectAxis(java.lang.String axisID, int index)
java.lang.String	getErrorMessage()
java.lang.String	getErrorMessageUntranslated()
int	getExecutionWalltime()
static int	getFloatEncodedInt(java.lang.String strDecimal) Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders.
private java.lang.String	getFullPathName()
private java.util.Map<java.lang.String,java.lang.Object>	getHash(int i)
protected javax.vecmath.Point4f	getHklPlane(javax.vecmath.Point3f pt)
private java.lang.String	getIsosurfaceDataRange(int iShape, java.lang.String sep)
private java.lang.String	getIsosurfaceJvxl(boolean asMesh, int iShape)
private int	getLinenumber(ScriptContext c)
private int	getMadParameter()
private static float	getMinMax(float[] data, boolean isMax, int tok)
private java.lang.String	getMoJvxl(int ptMO)
private java.lang.String	getNextComment()
java.lang.String	getNextStatement() when paused, indicates what statement will be next
private java.lang.Object	getNumericParameter(java.lang.String var)
private javax.vecmath.Point3f[]	getObjectBoundingBox(java.lang.String id)
private javax.vecmath.Point3f	getObjectCenter(java.lang.String axisID, int index, int modelIndex)
private java.lang.Object	getParameter(java.lang.String key, int tokType)
private java.lang.String	getParameterEscaped(java.lang.String var)
static int	getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger) reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)
static int	getPartialBondOrderFromString(java.lang.String s)
private javax.vecmath.Point3f	getPoint3f(int i, boolean allowFractional)
private javax.vecmath.Point4f	getPoint4f(int i)
private javax.vecmath.Point3f[]	getPointArray(int i, int nPoints)
private java.lang.Object	getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim)
(package private) java.util.List<javax.vecmath.Point3f>	getPointVector(Token t, int i)
private void	getProperty()
private Quaternion	getQuaternionParameter(int i)
java.lang.String	getScript()
ScriptContext	getScriptContext()
private java.lang.String	getScriptID(ScriptContext context)
private static int	getSeqCode(Token instruction)
private int	getSetAxesTypeMad(int index)
private java.lang.String	getShapeNameParameter(int i)
private java.lang.Object	getShapeProperty(int shapeType, java.lang.String propertyName)
private java.lang.Object	getShapeProperty(int shapeType, java.lang.String propertyName, int index)
private boolean	getShapeProperty(int shapeType, java.lang.String propertyName, java.lang.Object[] data)
private int	getShapeType(int tok)
(package private) float	getSmilesCorrelation(java.util.BitSet bsA, java.util.BitSet bsB, java.lang.String smiles, java.util.List<javax.vecmath.Point3f> ptsA, java.util.List<javax.vecmath.Point3f> ptsB, javax.vecmath.Matrix4f m, java.util.List<java.util.BitSet> vReturn, boolean isSmarts, boolean asMap)
(package private) java.lang.Object	getSmilesMatches(java.lang.String pattern, java.lang.String smiles, java.util.BitSet bsSelected, java.util.BitSet bsMatch3D, boolean isSmarts, boolean asOneBitset)
private java.lang.Object	getStringObjectAsVariable(java.lang.String s, java.lang.String key)
private java.lang.String	getStringParameter(java.lang.String var, boolean orReturnName)
private Token	getToken(int i)
private float	getTranslucentLevel(int i)
private void	getWithinDistanceVector(java.util.List<java.lang.Object[]> propertyList, float distance, javax.vecmath.Point3f ptc, java.util.BitSet bs, boolean isShow)
private float	getZoom(int i, java.util.BitSet bs, float currentZoom)
private void	gotoCmd(java.lang.String strTo)
void	haltExecution()
private void	hbond()
private void	help()
private void	history(int pt)
private javax.vecmath.Point4f	hklParameter(int i)
private void	hover()
private boolean	ifCmd()
private java.lang.String	initIsosurface(int iShape)
private void	instructionDispatchLoop(boolean doList) here we go -- everything else in this class is called by this method or one of its subsidiary methods.
private void	integerOutOfRange(int min, int max)
private int	intParameter(int index)
private int	intParameter(int i, int min, int max)
private int	intSetting(int pt)
private void	invertSelected()
private boolean	isArrayParameter(int i)
private boolean	isCenterParameter(int i)
private boolean	isColorParam(int i)
private boolean	isCommandDisplayable(int i) provides support for the script editor
boolean	isExecutionPaused()
boolean	isExecutionStepping()
private boolean	isFloatParameter(int index)
private void	isosurface(int iShape)
private boolean	isPoint3f(int i)
boolean	isScriptExecuting()
private void	label(int index)
private void	lcaoCartoon()
private boolean	listIsosurface(int iShape)
private void	load()
private void	log()
private void	logDebugScript(int ifLevel)
private void	logLoadInfo(java.lang.String msg)
private java.util.BitSet	lookupIdentifierValue(java.lang.String identifier)
private java.util.BitSet	lookupValue(java.lang.String setName, boolean plurals)
private void	mapProperty()
private void	measure()
private void	message()
private void	minimize()
private boolean	mo(boolean isInitOnly)
private int	modelNumberParameter(int index)
private int	moOffset(int index)
private void	move()
private void	moveto()
private void	navigate()
private void	numberOutOfRange(float min, float max)
private java.lang.String	objectNameParameter(int index)
private java.lang.String	optParameterAsString(int i)
private java.lang.String	parameterAsString(int i)
private java.lang.Object	parameterExpression(int pt, int ptMax, java.lang.String key, boolean ignoreComma, boolean asVector, int ptAtom, boolean isArrayItem, java.util.Map localVars, java.lang.String localVar) This is the primary driver of the RPN (reverse Polish notation) expression processor.
private boolean	parameterExpressionBoolean(int pt, int ptMax)
private java.util.List<ScriptVariable>	parameterExpressionList(int pt, int ptAtom, boolean isArrayItem)
private java.lang.String	parameterExpressionString(int pt, int ptMax)
private ScriptVariable	parameterExpressionToken(int pt)
private boolean	pause()
void	pauseExecution(boolean withDelay)
private void	planeExpected()
private javax.vecmath.Point4f	planeParameter(int i)
private java.lang.String	plot(Token[] args)
private void	pointGroup()
private void	polyhedra()
(package private) void	popContext(boolean isFlowCommand, boolean statementOnly)
private void	print()
private void	processShapeCommand(int tok)
private void	prompt()
private void	proteinShape(int shapeType)
private void	pushContext(ContextToken token)
private void	refresh()
private void	reset()
private void	restore()
private void	restoreScriptContext(ScriptContext context, boolean isPopContext, boolean isFlowCommand, boolean statementOnly)
private void	restrict()
private void	restrictSelected(boolean isBond, boolean doInvert)
void	resumePausedExecution()
private void	returnCmd(ScriptVariable tv)
private void	rotate(boolean isSpin, boolean isSelected)
private void	runFunction(ScriptFunction function, java.util.List<ScriptVariable> params, ScriptVariable tokenAtom)
(package private) ScriptVariable	runFunction(ScriptFunction function, java.lang.String name, java.util.List<ScriptVariable> params, ScriptVariable tokenAtom, boolean getReturn, boolean setContextPath)
void	runScript(java.lang.String script)
void	runScript(java.lang.String script, java.lang.StringBuffer outputBuffer) runs a script and sends selected output to a provided StringBuffer
private void	save()
private void	script(int tok, java.lang.String filename, boolean listCommands)
private void	scriptStatusOrBuffer(java.lang.String s)
private void	select(int i)
private void	selectionHalo(int pt)
private void	set()
private void	setAtomShapeSize(int shape, float scale)
private void	setBitsetProperty(java.util.BitSet bs, int tok, int iValue, float fValue, Token tokenValue)
private void	setBondmode()
private void	setBooleanProperty(java.lang.String key, boolean value)
private java.lang.String	setColorOptions(java.lang.StringBuffer sb, int index, int iShape, int nAllowed)
(package private) java.util.BitSet	setContactBitSets(java.util.BitSet bsA, java.util.BitSet bsB, boolean localOnly, float distance, RadiusData rd, boolean warnMultiModel)
private void	setCursorWait(boolean TF)
void	setDebugging()
private void	setEcho()
(package private) static java.lang.String	setErrorLineMessage(java.lang.String functionName, java.lang.String filename, int lineCurrent, int pcCurrent, java.lang.String lineInfo)
private void	setErrorMessage(java.lang.String err)
private boolean	setFloatProperty(java.lang.String key, float value)
private void	setHbond()
private boolean	setIntProperty(java.lang.String key, int value)
private boolean	setLabel(java.lang.String str)
private boolean	setMeasurementUnits(java.lang.String units)
private boolean	setMeshDisplayProperty(int shape, int i, int tok)
private void	setMoData(java.util.List<java.lang.Object[]> propertyList, int moNumber, float[] linearCombination, int offset, boolean isNegOffset, int modelIndex, java.lang.String title)
private void	setMonitor()
private void	setObjectArgb(java.lang.String str, int argb)
private void	setObjectMad(int iShape, java.lang.String name, int mad)
private java.lang.String	setObjectProperty()
private void	setPicking()
private void	setPickingStyle()
private int	setScriptExtensions()
private java.lang.String	setShapeId(int iShape, int i, boolean idSeen)
private void	setShapeProperty(int shapeType, java.lang.String propertyName, java.lang.Object propertyValue)
private void	setShapeProperty(int iShape, java.lang.String propertyName, java.lang.Object propertyValue, java.util.BitSet bs)
private void	setShapeSize(int shapeType, int size, java.util.BitSet bs)
private void	setShapeSize(int shapeType, RadiusData rd)
private void	setShapeTranslucency(int shapeType, java.lang.String prefix, java.lang.String translucency, float translucentLevel, java.util.BitSet bs)
private void	setSsbond()
private boolean	setStatement(int pc) provides support for @x and @{....} in statements.
private void	setStringProperty(java.lang.String key, java.lang.String value)
private void	setUserColors()
private void	setVariable(int pt, int ptMax, java.lang.String key, int setType)
private void	setZslab()
private void	show()
private void	showString(java.lang.String str)
private void	showString(java.lang.String str, boolean isPrint)
private void	slab(boolean isDepth)
private void	ssbond()
(package private) static java.lang.String	statementAsString(Token[] statement, int iTok, boolean doLogMessages)
void	stepPausedExecution()
private void	stereo()
private java.lang.String	stringParameter(int index)
private java.lang.String[]	stringParameterSet(int i)
private java.lang.String	stringSetting(int pt, boolean isJmolSet)
private void	structure()
private void	struts()
private void	subset()
private int	switchCmd(ContextToken c, int tok)
private void	sync()
private void	timeout(int index)
private int	tokAt(int i)
private int	tokAt(int i, Token[] args)
private Token	tokenAt(int i, Token[] args)
java.lang.String	toString()
private void	translate(boolean isSelected)
private void	unbind()
private void	undoRedoMove()
private void	unitcell(int index)
private void	vector()
private void	vibration()
private void	warning(int iError, java.lang.String value, java.lang.String more)
private void	wireframe()
(package private) java.lang.String	write(Token[] args)
private javax.vecmath.Point3f	xypParameter(int index)
private void	zap(boolean isZapCommand)
private void	zoom(boolean isZoomTo)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

SCRIPT_COMPLETED

public static final java.lang.String SCRIPT_COMPLETED

See Also:

Constant Field Values

tQuiet

private boolean tQuiet

isSyntaxCheck

protected boolean isSyntaxCheck

isCmdLine_C_Option

private boolean isCmdLine_C_Option

isCmdLine_c_or_C_Option

protected boolean isCmdLine_c_or_C_Option

historyDisabled

private boolean historyDisabled

logMessages

protected boolean logMessages

debugScript

private boolean debugScript

interruptExecution

private boolean interruptExecution

executionPaused

private boolean executionPaused

executionStepping

private boolean executionStepping

isExecuting

private boolean isExecuting

timeBeginExecution

private long timeBeginExecution

timeEndExecution

private long timeEndExecution

EXPRESSION_KEY

private static final java.lang.String EXPRESSION_KEY

See Also:

Constant Field Values

shapeManager

ShapeManager shapeManager

scriptLevelMax

private static final int scriptLevelMax

See Also:

Constant Field Values

currentThread

private java.lang.Thread currentThread

viewer

protected Viewer viewer

compiler

protected ScriptCompiler compiler

definedAtomSets

private java.util.Map<java.lang.String,java.lang.Object> definedAtomSets

outputBuffer

private java.lang.StringBuffer outputBuffer

contextPath

private java.lang.String contextPath

filename

private java.lang.String filename

functionName

private java.lang.String functionName

isStateScript

private boolean isStateScript

scriptLevel

int scriptLevel

scriptReportingLevel

private int scriptReportingLevel

commandHistoryLevelMax

private int commandHistoryLevelMax

aatoken

private Token[][] aatoken

lineNumbers

private short[] lineNumbers

lineIndices

private int[][] lineIndices

contextVariables

private java.util.Map<java.lang.String,ScriptVariable> contextVariables

script

private java.lang.String script

pc

protected int pc

thisCommand

private java.lang.String thisCommand

fullCommand

private java.lang.String fullCommand

statement

private Token[] statement

statementLength

private int statementLength

iToken

private int iToken

lineEnd

private int lineEnd

pcEnd

private int pcEnd

scriptExtensions

private java.lang.String scriptExtensions

forceNoAddHydrogens

private boolean forceNoAddHydrogens

parallelProcessor

private ParallelProcessor parallelProcessor

thisContext

protected ScriptContext thisContext

error

private boolean error

errorMessage

private java.lang.String errorMessage

errorMessageUntranslated

protected java.lang.String errorMessageUntranslated

errorType

protected java.lang.String errorType

iCommandError

protected int iCommandError

ignoreError

private boolean ignoreError

ERROR_axisExpected

static final int ERROR_axisExpected

See Also:

Constant Field Values

ERROR_backgroundModelError

static final int ERROR_backgroundModelError

See Also:

Constant Field Values

ERROR_badArgumentCount

static final int ERROR_badArgumentCount

See Also:

Constant Field Values

ERROR_badMillerIndices

static final int ERROR_badMillerIndices

See Also:

Constant Field Values

ERROR_badRGBColor

static final int ERROR_badRGBColor

See Also:

Constant Field Values

ERROR_booleanExpected

static final int ERROR_booleanExpected

See Also:

Constant Field Values

ERROR_booleanOrNumberExpected

static final int ERROR_booleanOrNumberExpected

See Also:

Constant Field Values

ERROR_booleanOrWhateverExpected

static final int ERROR_booleanOrWhateverExpected

See Also:

Constant Field Values

ERROR_colorExpected

static final int ERROR_colorExpected

See Also:

Constant Field Values

ERROR_colorOrPaletteRequired

static final int ERROR_colorOrPaletteRequired

See Also:

Constant Field Values

ERROR_commandExpected

static final int ERROR_commandExpected

See Also:

Constant Field Values

ERROR_coordinateOrNameOrExpressionRequired

static final int ERROR_coordinateOrNameOrExpressionRequired

See Also:

Constant Field Values

ERROR_drawObjectNotDefined

static final int ERROR_drawObjectNotDefined

See Also:

Constant Field Values

ERROR_endOfStatementUnexpected

static final int ERROR_endOfStatementUnexpected

See Also:

Constant Field Values

ERROR_expressionExpected

static final int ERROR_expressionExpected

See Also:

Constant Field Values

ERROR_expressionOrIntegerExpected

static final int ERROR_expressionOrIntegerExpected

See Also:

Constant Field Values

ERROR_filenameExpected

static final int ERROR_filenameExpected

See Also:

Constant Field Values

ERROR_fileNotFoundException

static final int ERROR_fileNotFoundException

See Also:

Constant Field Values

ERROR_incompatibleArguments

static final int ERROR_incompatibleArguments

See Also:

Constant Field Values

ERROR_insufficientArguments

static final int ERROR_insufficientArguments

See Also:

Constant Field Values

ERROR_integerExpected

static final int ERROR_integerExpected

See Also:

Constant Field Values

ERROR_integerOutOfRange

static final int ERROR_integerOutOfRange

See Also:

Constant Field Values

ERROR_invalidArgument

static final int ERROR_invalidArgument

See Also:

Constant Field Values

ERROR_invalidParameterOrder

static final int ERROR_invalidParameterOrder

See Also:

Constant Field Values

ERROR_keywordExpected

static final int ERROR_keywordExpected

See Also:

Constant Field Values

ERROR_moCoefficients

static final int ERROR_moCoefficients

See Also:

Constant Field Values

ERROR_moIndex

static final int ERROR_moIndex

See Also:

Constant Field Values

ERROR_moModelError

static final int ERROR_moModelError

See Also:

Constant Field Values

ERROR_moOccupancy

static final int ERROR_moOccupancy

See Also:

Constant Field Values

ERROR_moOnlyOne

static final int ERROR_moOnlyOne

See Also:

Constant Field Values

ERROR_multipleModelsDisplayedNotOK

static final int ERROR_multipleModelsDisplayedNotOK

See Also:

Constant Field Values

ERROR_noData

static final int ERROR_noData

See Also:

Constant Field Values

ERROR_noPartialCharges

static final int ERROR_noPartialCharges

See Also:

Constant Field Values

ERROR_noUnitCell

static final int ERROR_noUnitCell

See Also:

Constant Field Values

ERROR_numberExpected

static final int ERROR_numberExpected

See Also:

Constant Field Values

ERROR_numberMustBe

static final int ERROR_numberMustBe

See Also:

Constant Field Values

ERROR_numberOutOfRange

static final int ERROR_numberOutOfRange

See Also:

Constant Field Values

ERROR_objectNameExpected

static final int ERROR_objectNameExpected

See Also:

Constant Field Values

ERROR_planeExpected

static final int ERROR_planeExpected

See Also:

Constant Field Values

ERROR_propertyNameExpected

static final int ERROR_propertyNameExpected

See Also:

Constant Field Values

ERROR_spaceGroupNotFound

static final int ERROR_spaceGroupNotFound

See Also:

Constant Field Values

ERROR_stringExpected

static final int ERROR_stringExpected

See Also:

Constant Field Values

ERROR_stringOrIdentifierExpected

static final int ERROR_stringOrIdentifierExpected

See Also:

Constant Field Values

ERROR_tooManyPoints

static final int ERROR_tooManyPoints

See Also:

Constant Field Values

ERROR_tooManyScriptLevels

static final int ERROR_tooManyScriptLevels

See Also:

Constant Field Values

ERROR_unrecognizedAtomProperty

static final int ERROR_unrecognizedAtomProperty

See Also:

Constant Field Values

ERROR_unrecognizedBondProperty

static final int ERROR_unrecognizedBondProperty

See Also:

Constant Field Values

ERROR_unrecognizedCommand

static final int ERROR_unrecognizedCommand

See Also:

Constant Field Values

ERROR_unrecognizedExpression

static final int ERROR_unrecognizedExpression

See Also:

Constant Field Values

ERROR_unrecognizedObject

static final int ERROR_unrecognizedObject

See Also:

Constant Field Values

ERROR_unrecognizedParameter

static final int ERROR_unrecognizedParameter

See Also:

Constant Field Values

ERROR_unrecognizedParameterWarning

static final int ERROR_unrecognizedParameterWarning

See Also:

Constant Field Values

ERROR_unrecognizedShowParameter

static final int ERROR_unrecognizedShowParameter

See Also:

Constant Field Values

ERROR_what

static final int ERROR_what

See Also:

Constant Field Values

ERROR_writeWhat

static final int ERROR_writeWhat

See Also:

Constant Field Values

ERROR_multipleModelsNotOK

static final int ERROR_multipleModelsNotOK

See Also:

Constant Field Values

tempStatement

private Token[] tempStatement

isBondSet

private boolean isBondSet

expressionResult

private java.lang.Object expressionResult

theTok

private int theTok

theToken

private Token theToken

coordinatesAreFractional

private boolean coordinatesAreFractional

fractionalPoint

private javax.vecmath.Point3f fractionalPoint

vProcess

private java.util.List<Token[]> vProcess

iProcess

static int iProcess

data

private java.lang.Object[] data

testData

private static java.lang.Object testData

testData2

private static java.lang.Object testData2

Constructor Detail

ScriptEvaluator

public ScriptEvaluator(Viewer viewer)

Method Detail

compileScriptString

public boolean compileScriptString(java.lang.String script,
                          boolean tQuiet)

createFunction

private java.lang.Object[] createFunction(java.lang.String fname,
                                java.lang.String xyz,
                                java.lang.String ret)

for the ISOSURFACE command

Parameters:

fname -

xyz -

ret -

Returns:

[ ScriptFunction, Params ]

compileScriptFile

public boolean compileScriptFile(java.lang.String filename,
                        boolean tQuiet)

evaluateCompiledScript

public void evaluateCompiledScript(boolean isCmdLine_c_or_C_Option,
                          boolean isCmdLine_C_Option,
                          boolean historyDisabled,
                          boolean listCommands,
                          java.lang.StringBuffer outputBuffer)

runScript

public void runScript(java.lang.String script,
             java.lang.StringBuffer outputBuffer)
               throws ScriptEvaluator.ScriptException

runs a script and sends selected output to a provided StringBuffer

Parameters:

script -

outputBuffer -

Throws:

ScriptEvaluator.ScriptException

checkScriptSilent

public ScriptContext checkScriptSilent(java.lang.String script)

a method for just checking a script

Parameters:

script -

Returns:

a ScriptContext that indicates errors and provides a tokenized version of the script that has passed all syntax checking, both in the compiler and the evaluator

setDebugging

public void setDebugging()

getExecutionWalltime

public int getExecutionWalltime()

haltExecution

public void haltExecution()

pauseExecution

public void pauseExecution(boolean withDelay)

stepPausedExecution

public void stepPausedExecution()

resumePausedExecution

public void resumePausedExecution()

isScriptExecuting

public boolean isScriptExecuting()

isExecutionPaused

public boolean isExecutionPaused()

isExecutionStepping

public boolean isExecutionStepping()

getNextStatement

public java.lang.String getNextStatement()

when paused, indicates what statement will be next

Returns:

a string indicating the statement

getCommand

private java.lang.String getCommand(int pc,
                          boolean allThisLine,
                          boolean addSemi)

used for recall of commands in the application console

Parameters:

pc -

allThisLine -

addSemi -

Returns:

a string representation of the command

logDebugScript

private void logDebugScript(int ifLevel)

evaluateExpression

public static java.lang.Object evaluateExpression(Viewer viewer,
                                  java.lang.Object expr,
                                  boolean asVariable)

a general-use method to evaluate a "SET" type expression.

Parameters:

viewer -

expr -

asVariable - TODO

Returns:

an object of one of the following types: Boolean, Integer, Float, String, Point3f, BitSet

evaluateContext

public static boolean evaluateContext(Viewer viewer,
                      ScriptContext context,
                      ShapeManager shapeManager)

getAtomBitSet

public static java.util.BitSet getAtomBitSet(ScriptEvaluator e,
                             java.lang.Object atomExpression)

a general method to evaluate a string representing an atom set.

Parameters:

e -

atomExpression -

Returns:

is a bitset indicating the selected atoms

getAtomBitSetVector

public static java.util.List<java.lang.Integer> getAtomBitSetVector(ScriptEvaluator e,
                                                    int atomCount,
                                                    java.lang.Object atomExpression)

just provides a vector list of atoms in a string-based expression

Parameters:

e -

atomCount -

atomExpression -

Returns:

vector list of selected atoms

parameterExpressionList

private java.util.List<ScriptVariable> parameterExpressionList(int pt,
                                                     int ptAtom,
                                                     boolean isArrayItem)
                                                        throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

parameterExpressionString

private java.lang.String parameterExpressionString(int pt,
                                         int ptMax)
                                            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

parameterExpressionBoolean

private boolean parameterExpressionBoolean(int pt,
                                 int ptMax)
                                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

parameterExpressionToken

private ScriptVariable parameterExpressionToken(int pt)
                                         throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

parameterExpression

private java.lang.Object parameterExpression(int pt,
                                   int ptMax,
                                   java.lang.String key,
                                   boolean ignoreComma,
                                   boolean asVector,
                                   int ptAtom,
                                   boolean isArrayItem,
                                   java.util.Map localVars,
                                   java.lang.String localVar)
                                      throws ScriptEvaluator.ScriptException

This is the primary driver of the RPN (reverse Polish notation) expression processor. It handles all math outside of a "traditional" Jmol SELECT/RESTRICT context. [Object atomExpression() takes care of that, and also uses the RPN class.]

Parameters:

pt - token index in statement start of expression

ptMax - token index in statement end of expression

key - variable name for debugging reference only -- null indicates return Boolean -- "" indicates return String

ignoreComma - TODO

asVector - a flag passed on to RPN;

ptAtom - this is a for() or select() function with a specific atom selected

isArrayItem - we are storing A[x] = ... so we need to deliver "x" as well

localVars - see below -- lists all nested for(x, {exp}, select(y, {ex},...)) variables

localVar - x or y in above for(), select() examples

Returns:

either a vector or a value, caller's choice.

Throws:

ScriptEvaluator.ScriptException - errors are thrown directly to the Eval error system.

getHash

private java.util.Map<java.lang.String,java.lang.Object> getHash(int i)
                                                          throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

bitsetVariableVector

java.util.List<ScriptVariable> bitsetVariableVector(java.lang.Object v)

getBitsetIdent

java.lang.Object getBitsetIdent(java.util.BitSet bs,
                              java.lang.String label,
                              java.lang.Object tokenValue,
                              boolean useAtomMap,
                              int index,
                              boolean isExplicitlyAll)

getBitsetPropertySelector

private ScriptVariable getBitsetPropertySelector(int i,
                                       boolean mustBeSettable)
                                          throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getBitsetPropertyFloat

private float[] getBitsetPropertyFloat(java.util.BitSet bs,
                             int tok,
                             float min,
                             float max)
                                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getBitsetProperty

protected java.lang.Object getBitsetProperty(java.util.BitSet bs,
                                 int tok,
                                 javax.vecmath.Point3f ptRef,
                                 javax.vecmath.Point4f planeRef,
                                 java.lang.Object tokenValue,
                                 java.lang.Object opValue,
                                 boolean useAtomMap,
                                 int index,
                                 boolean asVectorIfAll)
                                      throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setBitsetProperty

private void setBitsetProperty(java.util.BitSet bs,
                     int tok,
                     int iValue,
                     float fValue,
                     Token tokenValue)
                        throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getContextVariables

public java.util.Map<java.lang.String,ScriptVariable> getContextVariables()

getScript

public java.lang.String getScript()

compileScript

private boolean compileScript(java.lang.String filename,
                    java.lang.String strScript,
                    boolean debugCompiler)

fixScriptPath

private java.lang.String fixScriptPath(java.lang.String strScript,
                             java.lang.String filename)

setScriptExtensions

private int setScriptExtensions()

runScript

public void runScript(java.lang.String script)
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

compileScriptFileInternal

private boolean compileScriptFileInternal(java.lang.String filename,
                                java.lang.String localPath,
                                java.lang.String remotePath,
                                java.lang.String scriptPath)

getParameter

private java.lang.Object getParameter(java.lang.String key,
                            int tokType)

getParameterEscaped

private java.lang.String getParameterEscaped(java.lang.String var)

getStringParameter

private java.lang.String getStringParameter(java.lang.String var,
                                  boolean orReturnName)

getNumericParameter

private java.lang.Object getNumericParameter(java.lang.String var)

getContextVariableAsVariable

private ScriptVariable getContextVariableAsVariable(java.lang.String var)

getStringObjectAsVariable

private java.lang.Object getStringObjectAsVariable(java.lang.String s,
                                         java.lang.String key)

evalFunctionFloat

public float evalFunctionFloat(java.lang.Object func,
                      java.lang.Object params,
                      float[] values)

runFunction

ScriptVariable runFunction(ScriptFunction function,
                         java.lang.String name,
                         java.util.List<ScriptVariable> params,
                         ScriptVariable tokenAtom,
                         boolean getReturn,
                         boolean setContextPath)
                     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

runFunction

private void runFunction(ScriptFunction function,
               java.util.List<ScriptVariable> params,
               ScriptVariable tokenAtom)
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

clearDefinedVariableAtomSets

private void clearDefinedVariableAtomSets()

defineSets

private void defineSets()

support for @xxx or define xxx commands

defineAtomSet

private void defineAtomSet(java.lang.String script)

lookupIdentifierValue

private java.util.BitSet lookupIdentifierValue(java.lang.String identifier)
                                        throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

lookupValue

private java.util.BitSet lookupValue(java.lang.String setName,
                           boolean plurals)
                              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

deleteAtomsInVariables

public void deleteAtomsInVariables(java.util.BitSet bsDeleted)

setStatement

private boolean setStatement(int pc)
                      throws ScriptEvaluator.ScriptException

provides support for @x and @{....} in statements. The compiler passes on these, because they must be integrated with the statement dynamically.

Parameters:

pc -

Returns:

a fixed token set -- with possible overrun of unused null tokens

Throws:

ScriptEvaluator.ScriptException

clearState

private void clearState(boolean tQuiet)

pushContext

private void pushContext(ContextToken token)
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getScriptContext

public ScriptContext getScriptContext()

popContext

void popContext(boolean isFlowCommand,
              boolean statementOnly)

restoreScriptContext

private void restoreScriptContext(ScriptContext context,
                        boolean isPopContext,
                        boolean isFlowCommand,
                        boolean statementOnly)

getContext

private java.lang.String getContext(boolean withVariables)

getLinenumber

private int getLinenumber(ScriptContext c)

getScriptID

private java.lang.String getScriptID(ScriptContext context)

getErrorMessage

public java.lang.String getErrorMessage()

getErrorMessageUntranslated

public java.lang.String getErrorMessageUntranslated()

setErrorMessage

private void setErrorMessage(java.lang.String err)

planeExpected

private void planeExpected()
                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

integerOutOfRange

private void integerOutOfRange(int min,
                     int max)
                        throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

numberOutOfRange

private void numberOutOfRange(float min,
                    float max)
                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

error

void error(int iError,
         int i)
     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

error

void error(int iError)
     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

error

void error(int iError,
         java.lang.String value)
     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

error

void error(int iError,
         java.lang.String value,
         java.lang.String more)
     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

error

void error(int iError,
         java.lang.String value,
         java.lang.String more,
         java.lang.String more2)
     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

warning

private void warning(int iError,
           java.lang.String value,
           java.lang.String more)
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

error

void error(int iError,
         java.lang.String value,
         java.lang.String more,
         java.lang.String more2,
         boolean warningOnly)
     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

evalError

void evalError(java.lang.String message,
             java.lang.String strUntranslated)
         throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

errorString

static java.lang.String errorString(int iError,
                           java.lang.String value,
                           java.lang.String more,
                           java.lang.String more2,
                           boolean translated)

Parameters:

iError -

value -

more -

more2 -

translated -

Returns:

constructed error string

setErrorLineMessage

static java.lang.String setErrorLineMessage(java.lang.String functionName,
                                   java.lang.String filename,
                                   int lineCurrent,
                                   int pcCurrent,
                                   java.lang.String lineInfo)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

statementAsString

static java.lang.String statementAsString(Token[] statement,
                                 int iTok,
                                 boolean doLogMessages)

getShapeProperty

private java.lang.Object getShapeProperty(int shapeType,
                                java.lang.String propertyName)

getShapeProperty

private boolean getShapeProperty(int shapeType,
                       java.lang.String propertyName,
                       java.lang.Object[] data)

getShapeProperty

private java.lang.Object getShapeProperty(int shapeType,
                                java.lang.String propertyName,
                                int index)

addShapeProperty

private void addShapeProperty(java.util.List<java.lang.Object[]> propertyList,
                    java.lang.String key,
                    java.lang.Object value)

setObjectMad

private void setObjectMad(int iShape,
                java.lang.String name,
                int mad)

setObjectArgb

private void setObjectArgb(java.lang.String str,
                 int argb)

setShapeProperty

private void setShapeProperty(int shapeType,
                    java.lang.String propertyName,
                    java.lang.Object propertyValue)

setShapeProperty

private void setShapeProperty(int iShape,
                    java.lang.String propertyName,
                    java.lang.Object propertyValue,
                    java.util.BitSet bs)

setShapeSize

private void setShapeSize(int shapeType,
                int size,
                java.util.BitSet bs)

setShapeSize

private void setShapeSize(int shapeType,
                RadiusData rd)

setBooleanProperty

private void setBooleanProperty(java.lang.String key,
                      boolean value)

setIntProperty

private boolean setIntProperty(java.lang.String key,
                     int value)

setFloatProperty

private boolean setFloatProperty(java.lang.String key,
                       float value)

setStringProperty

private void setStringProperty(java.lang.String key,
                     java.lang.String value)

showString

private void showString(java.lang.String str)

showString

private void showString(java.lang.String str,
              boolean isPrint)

scriptStatusOrBuffer

private void scriptStatusOrBuffer(java.lang.String s)

atomExpression

private java.util.BitSet atomExpression(int index)
                                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

atomExpression

private java.util.BitSet atomExpression(Token[] code,
                              int pcStart,
                              int pcStop,
                              boolean allowRefresh,
                              boolean allowUnderflow,
                              boolean mustBeBitSet,
                              boolean andNotDeleted)
                                 throws ScriptEvaluator.ScriptException

Parameters:

code -

pcStart -

pcStop -

allowRefresh -

allowUnderflow -

mustBeBitSet -

andNotDeleted - IGNORED

Returns:

atom bitset

Throws:

ScriptEvaluator.ScriptException

compareFloat

private java.util.BitSet compareFloat(int tokWhat,
                            float[] data,
                            int tokOperator,
                            float comparisonFloat)

compareString

private java.util.BitSet compareString(int tokWhat,
                             int tokOperator,
                             java.lang.String comparisonString)
                                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

compareInt

protected java.util.BitSet compareInt(int tokWhat,
                          int tokOperator,
                          int comparisonValue)

compareString

private boolean compareString(int tokOperator,
                    java.lang.String propertyValue,
                    java.lang.String comparisonValue)
                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

compareFloat

private static boolean compareFloat(int tokOperator,
                   float propertyFloat,
                   float comparisonFloat)

getAtomBits

private java.util.BitSet getAtomBits(int tokType,
                           java.lang.Object specInfo)

getSeqCode

private static int getSeqCode(Token instruction)

checkLast

private int checkLast(int i)
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

checkLength

private int checkLength(int length)
                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

checkLength

private int checkLength(int length,
              int errorPt)
                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

checkLength23

private int checkLength23()
                   throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

checkLength34

private int checkLength34()
                   throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getToken

private Token getToken(int i)
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

tokAt

private int tokAt(int i)

tokAt

private int tokAt(int i,
        Token[] args)

tokenAt

private Token tokenAt(int i,
            Token[] args)

checkToken

private boolean checkToken(int i)

modelNumberParameter

private int modelNumberParameter(int index)
                          throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

optParameterAsString

private java.lang.String optParameterAsString(int i)
                                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

parameterAsString

private java.lang.String parameterAsString(int i)
                                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

intParameter

private int intParameter(int index)
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

intParameter

private int intParameter(int i,
               int min,
               int max)
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

isFloatParameter

private boolean isFloatParameter(int index)

floatParameter

private float floatParameter(int i,
                   float min,
                   float max)
                      throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

floatParameter

private float floatParameter(int index)
                      throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

floatParameterSet

private float[] floatParameterSet(int i,
                        int nMin,
                        int nMax)
                           throws ScriptEvaluator.ScriptException

process a general string or set of parameters as an array of floats, allowing for relatively free form input

Parameters:

i -

nMin -

nMax -

Returns:

array of floats

Throws:

ScriptEvaluator.ScriptException

isArrayParameter

private boolean isArrayParameter(int i)

getPointArray

private javax.vecmath.Point3f[] getPointArray(int i,
                                    int nPoints)
                                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

floatArraySet

private float[][] floatArraySet(int i,
                      int nX,
                      int nY)
                         throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

floatArraySet

private float[][][] floatArraySet(int i,
                        int nX,
                        int nY,
                        int nZ)
                           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

stringParameter

private java.lang.String stringParameter(int index)
                                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

stringParameterSet

private java.lang.String[] stringParameterSet(int i)
                                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

objectNameParameter

private java.lang.String objectNameParameter(int index)
                                      throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

booleanParameter

private boolean booleanParameter(int i)
                          throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

atomCenterOrCoordinateParameter

private javax.vecmath.Point3f atomCenterOrCoordinateParameter(int i)
                                                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

isCenterParameter

private boolean isCenterParameter(int i)

centerParameter

private javax.vecmath.Point3f centerParameter(int i)
                                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

centerParameter

private javax.vecmath.Point3f centerParameter(int i,
                                    int modelIndex)
                                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

planeParameter

private javax.vecmath.Point4f planeParameter(int i)
                                      throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

hklParameter

private javax.vecmath.Point4f hklParameter(int i)
                                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getHklPlane

protected javax.vecmath.Point4f getHklPlane(javax.vecmath.Point3f pt)

getMadParameter

private int getMadParameter()
                     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getSetAxesTypeMad

private int getSetAxesTypeMad(int index)
                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

isColorParam

private boolean isColorParam(int i)

getArgbParam

private int getArgbParam(int index)
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getArgbParamLast

private int getArgbParamLast(int index,
                   boolean allowNone)
                      throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getArgbParam

private int getArgbParam(int index,
               boolean allowNone)
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getColorTriad

private int getColorTriad(int i)
                   throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

isPoint3f

private boolean isPoint3f(int i)

getPoint3f

private javax.vecmath.Point3f getPoint3f(int i,
                               boolean allowFractional)
                                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getPoint4f

private javax.vecmath.Point4f getPoint4f(int i)
                                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getPointOrPlane

private java.lang.Object getPointOrPlane(int index,
                               boolean integerOnly,
                               boolean allowFractional,
                               boolean doConvert,
                               boolean implicitFractional,
                               int minDim,
                               int maxDim)
                                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

xypParameter

private javax.vecmath.Point3f xypParameter(int index)
                                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

isCommandDisplayable

private boolean isCommandDisplayable(int i)

provides support for the script editor

Parameters:

i -

Returns:

true if displayable

checkContinue

private boolean checkContinue()

checks to see if there is a pause condition, during which commands can still be issued, but with the ! first.

Returns:

false if there was a problem

instructionDispatchLoop

private void instructionDispatchLoop(boolean doList)
                              throws ScriptEvaluator.ScriptException

here we go -- everything else in this class is called by this method or one of its subsidiary methods.

Parameters:

doList -

Throws:

ScriptEvaluator.ScriptException

setCursorWait

private void setCursorWait(boolean TF)

processShapeCommand

private void processShapeCommand(int tok)
                          throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

flowControl

private boolean flowControl(int tok,
                  boolean isForCheck)
                     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

gotoCmd

private void gotoCmd(java.lang.String strTo)
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

breakCmd

private void breakCmd(int pt)

addProcess

private void addProcess(int pc,
              int pt,
              boolean isStart)

switchCmd

private int switchCmd(ContextToken c,
            int tok)
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

ifCmd

private boolean ifCmd()
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

returnCmd

private void returnCmd(ScriptVariable tv)
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

help

private void help()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

move

private void move()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

moveto

private void moveto()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

navigate

private void navigate()
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

bondorder

private void bondorder()
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

console

private void console()
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

centerAt

private void centerAt()
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

stereo

private void stereo()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

compare

private void compare()
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getSmilesCorrelation

float getSmilesCorrelation(java.util.BitSet bsA,
                         java.util.BitSet bsB,
                         java.lang.String smiles,
                         java.util.List<javax.vecmath.Point3f> ptsA,
                         java.util.List<javax.vecmath.Point3f> ptsB,
                         javax.vecmath.Matrix4f m,
                         java.util.List<java.util.BitSet> vReturn,
                         boolean isSmarts,
                         boolean asMap)
                     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getSmilesMatches

java.lang.Object getSmilesMatches(java.lang.String pattern,
                                java.lang.String smiles,
                                java.util.BitSet bsSelected,
                                java.util.BitSet bsMatch3D,
                                boolean isSmarts,
                                boolean asOneBitset)
                            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

connect

private void connect(int index)
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getTranslucentLevel

private float getTranslucentLevel(int i)
                           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getProperty

private void getProperty()
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

background

private void background(int i)
                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

center

private void center(int i)
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setObjectProperty

private java.lang.String setObjectProperty()
                                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

color

private void color()
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

changeElementColor

private boolean changeElementColor(java.lang.String str,
                         int argb)

colorShape

private void colorShape(int shapeType,
              int index,
              boolean isBackground)
                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

colorShape

private void colorShape(int shapeType,
              int typeMask,
              int argb,
              java.lang.String translucency,
              float translucentLevel,
              java.util.BitSet bs)

setShapeTranslucency

private void setShapeTranslucency(int shapeType,
                        java.lang.String prefix,
                        java.lang.String translucency,
                        float translucentLevel,
                        java.util.BitSet bs)

cd

private void cd()
         throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

mapProperty

private void mapProperty()
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

data

private void data()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

define

private void define()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

echo

private void echo(int index,
        boolean isImage)
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

message

private void message()
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

log

private void log()
          throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

label

private void label(int index)
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

hover

private void hover()
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

load

private void load()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

logLoadInfo

private void logLoadInfo(java.lang.String msg)

getFullPathName

private java.lang.String getFullPathName()
                                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

measure

private void measure()
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

plot

private java.lang.String plot(Token[] args)
                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getMinMax

private static float getMinMax(float[] data,
              boolean isMax,
              int tok)

pause

private boolean pause()
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

print

private void print()
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

prompt

private void prompt()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

refresh

private void refresh()

reset

private void reset()
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

restrict

private void restrict()
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

restrictSelected

private void restrictSelected(boolean isBond,
                    boolean doInvert)

rotate

private void rotate(boolean isSpin,
          boolean isSelected)
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getQuaternionParameter

private Quaternion getQuaternionParameter(int i)
                                   throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getPointVector

java.util.List<javax.vecmath.Point3f> getPointVector(Token t,
                                                   int i)
                                               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getObjectCenter

private javax.vecmath.Point3f getObjectCenter(java.lang.String axisID,
                                    int index,
                                    int modelIndex)

getObjectBoundingBox

private javax.vecmath.Point3f[] getObjectBoundingBox(java.lang.String id)

getDrawObjectAxis

private javax.vecmath.Vector3f getDrawObjectAxis(java.lang.String axisID,
                                       int index)

script

private void script(int tok,
          java.lang.String filename,
          boolean listCommands)
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

function

private void function()
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

sync

private void sync()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

history

private void history(int pt)
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

display

private void display(boolean isDisplay)
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

delete

private void delete()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

minimize

private void minimize()
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

select

private void select(int i)
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

subset

private void subset()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

invertSelected

private void invertSelected()
                     throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

translate

private void translate(boolean isSelected)
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

zap

private void zap(boolean isZapCommand)
          throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

zoom

private void zoom(boolean isZoomTo)
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getZoom

private float getZoom(int i,
            java.util.BitSet bs,
            float currentZoom)
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

delay

private void delay()
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

delay

private void delay(long millis)

slab

private void slab(boolean isDepth)
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

ellipsoid

private void ellipsoid()
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getShapeNameParameter

private java.lang.String getShapeNameParameter(int i)
                                        throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setShapeId

private java.lang.String setShapeId(int iShape,
                          int i,
                          boolean idSeen)
                             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setAtomShapeSize

private void setAtomShapeSize(int shape,
                    float scale)
                       throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

encodeRadiusParameter

private RadiusData encodeRadiusParameter(int index,
                               boolean isOnly,
                               boolean allowAbsolute)
                                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

structure

private void structure()
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

wireframe

private void wireframe()
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

ssbond

private void ssbond()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

struts

private void struts()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

hbond

private void hbond()
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

configuration

private void configuration()
                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

vector

private void vector()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

dipole

private void dipole()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

animationMode

private void animationMode()
                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

vibration

private void vibration()
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

animationDirection

private void animationDirection()
                         throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

calculate

private void calculate()
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

pointGroup

private void pointGroup()
                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

dots

private void dots(int iShape)
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

proteinShape

private void proteinShape(int shapeType)
                   throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

animation

private void animation()
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

assign

private void assign()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

file

private void file()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

fixed

private void fixed()
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

frame

private void frame(int offset)
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

bitSetForModelFileNumber

java.util.BitSet bitSetForModelFileNumber(int m)

frameControl

private void frameControl(int i)
                   throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getShapeType

private int getShapeType(int tok)
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

font

private void font(int shapeType,
        float fontsize)
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

set

private void set()
          throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setZslab

private void setZslab()
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setBondmode

private void setBondmode()
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setEcho

private void setEcho()
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

intSetting

private int intSetting(int pt)
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

floatSetting

private float floatSetting(int pt)
                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

stringSetting

private java.lang.String stringSetting(int pt,
                             boolean isJmolSet)
                                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setLabel

private boolean setLabel(java.lang.String str)
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setMonitor

private void setMonitor()
                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setMeasurementUnits

private boolean setMeasurementUnits(java.lang.String units)
                             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setSsbond

private void setSsbond()
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setHbond

private void setHbond()
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setPicking

private void setPicking()
                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setPickingStyle

private void setPickingStyle()
                      throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

timeout

private void timeout(int index)
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setUserColors

private void setUserColors()
                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setVariable

private void setVariable(int pt,
               int ptMax,
               java.lang.String key,
               int setType)
                  throws ScriptEvaluator.ScriptException

Parameters:

pt -

ptMax -

key -

setType -

Throws:

ScriptEvaluator.ScriptException

axes

private void axes(int index)
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

boundbox

private void boundbox(int index)
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

checkTicks

private TickInfo checkTicks(int index,
                  boolean allowUnitCell,
                  boolean allowScale,
                  boolean allowFirst)
                     throws ScriptEvaluator.ScriptException

Parameters:

index -

allowUnitCell - IGNORED

allowScale -

allowFirst -

Returns:

TickInfo

Throws:

ScriptEvaluator.ScriptException

unitcell

private void unitcell(int index)
               throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

frank

private void frank(int index)
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

selectionHalo

private void selectionHalo(int pt)
                    throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

save

private void save()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

restore

private void restore()
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

write

java.lang.String write(Token[] args)
                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

show

private void show()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getIsosurfaceJvxl

private java.lang.String getIsosurfaceJvxl(boolean asMesh,
                                 int iShape)

getMoJvxl

private java.lang.String getMoJvxl(int ptMO)
                            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

extractCommandOption

private java.lang.String extractCommandOption(java.lang.String name)

draw

private void draw()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

polyhedra

private void polyhedra()
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

contact

private void contact()
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setContactBitSets

java.util.BitSet setContactBitSets(java.util.BitSet bsA,
                                 java.util.BitSet bsB,
                                 boolean localOnly,
                                 float distance,
                                 RadiusData rd,
                                 boolean warnMultiModel)

lcaoCartoon

private void lcaoCartoon()
                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getCapSlabObject

private java.lang.Object getCapSlabObject(int i,
                                boolean isLcaoCartoon)
                                   throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

mo

private boolean mo(boolean isInitOnly)
            throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setColorOptions

private java.lang.String setColorOptions(java.lang.StringBuffer sb,
                               int index,
                               int iShape,
                               int nAllowed)
                                  throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

moOffset

private int moOffset(int index)
              throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

setMoData

private void setMoData(java.util.List<java.lang.Object[]> propertyList,
             int moNumber,
             float[] linearCombination,
             int offset,
             boolean isNegOffset,
             int modelIndex,
             java.lang.String title)
                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

initIsosurface

private java.lang.String initIsosurface(int iShape)
                                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getNextComment

private java.lang.String getNextComment()

listIsosurface

private boolean listIsosurface(int iShape)
                        throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

isosurface

private void isosurface(int iShape)
                 throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getColorRange

private java.lang.String getColorRange(int i)
                                throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getIsosurfaceDataRange

private java.lang.String getIsosurfaceDataRange(int iShape,
                                      java.lang.String sep)

getWithinDistanceVector

private void getWithinDistanceVector(java.util.List<java.lang.Object[]> propertyList,
                           float distance,
                           javax.vecmath.Point3f ptc,
                           java.util.BitSet bs,
                           boolean isShow)

setMeshDisplayProperty

private boolean setMeshDisplayProperty(int shape,
                             int i,
                             int tok)
                                throws ScriptEvaluator.ScriptException

Parameters:

shape -

i -

tok -

Returns:

true if successful

Throws:

ScriptEvaluator.ScriptException

bind

private void bind()
           throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

unbind

private void unbind()
             throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

undoRedoMove

private void undoRedoMove()
                   throws ScriptEvaluator.ScriptException

Throws:

ScriptEvaluator.ScriptException

getAtomsNearSurface

java.util.BitSet getAtomsNearSurface(float distance,
                                   java.lang.String surfaceId)

getFloatEncodedInt

public static int getFloatEncodedInt(java.lang.String strDecimal)

Encodes a string such as "2.10" as an integer instead of a float so as to distinguish "2.1" from "2.10" used for model numbers and partial bond orders. 2147483647 is maxvalue, so this allows loading simultaneously up to 2147 files, each with 999999 models (or trajectories)

Parameters:

strDecimal -

Returns:

float encoded as an integer

getPartialBondOrderFromFloatEncodedInt

public static final int getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger)

reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5 + (m % 0x1F)

Parameters:

bondOrderInteger -

Returns:

Bond order partial mask

getBondOrderFromString

public static final int getBondOrderFromString(java.lang.String s)

getPartialBondOrderFromString

public static int getPartialBondOrderFromString(java.lang.String s)