org.jmol.script
Class ScriptEvaluator

java.lang.Object
  extended by org.jmol.script.ScriptEvaluator

public class ScriptEvaluator
extends java.lang.Object


Nested Class Summary
(package private)  class ScriptEvaluator.ScriptException
           
 
Field Summary
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
ScriptEvaluator(Viewer viewer)
           
 
Method Summary
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)
          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, float min, float max)
           
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  int intSetting(int pt, int val, int min, int max)
           
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)
a general-use method to evaluate a "SET" type expression.

Parameters:
viewer -
expr -
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,
                       int val,
                       int min,
                       int max)
                throws ScriptEvaluator.ScriptException
Throws:
ScriptEvaluator.ScriptException

intSetting

private int intSetting(int pt)
                throws ScriptEvaluator.ScriptException
Throws:
ScriptEvaluator.ScriptException

floatSetting

private float floatSetting(int pt,
                           float min,
                           float max)
                    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)