org.jmol.viewer

Class Eval

class Eval extends Object

Nested Class Summary
static classEval.Context
classEval.Rpn
classEval.ScriptException
Field Summary
Token[][]aatoken
intcommandHistoryLevelMax
Compilercompiler
HashtablecontextVariables
booleancoordinatesAreFractional
ThreadcurrentThread
Object[]data
booleandebugScript
booleanerror
StringerrorMessage
static String[]errors
BooleanexecutionPaused
ObjectexpressionResult
static intERROR_axisExpected
static intERROR_badArgumentCount
static intERROR_badMillerIndices
static intERROR_badRGBColor
static intERROR_booleanExpected
static intERROR_booleanOrNumberExpected
static intERROR_booleanOrWhateverExpected
static intERROR_colorExpected
static intERROR_colorOrPaletteRequired
static intERROR_coordinateOrNameOrExpressionRequired
static intERROR_drawObjectNotDefined
static intERROR_endOfStatementUnexpected
static intERROR_expressionExpected
static intERROR_expressionOrIntegerExpected
static intERROR_filenameExpected
static intERROR_fileNotFoundException
static intERROR_incompatibleArguments
static intERROR_insufficientArguments
static intERROR_integerExpected
static intERROR_integerOutOfRange
static intERROR_invalidArgument
static intERROR_invalidParameterOrder
static intERROR_keywordExpected
static intERROR_multipleModelsNotOK
static intERROR_noUnitCell
static intERROR_numberExpected
static intERROR_numberMustBe
static intERROR_numberOutOfRange
static intERROR_objectNameExpected
static intERROR_propertyNameExpected
static intERROR_spaceGroupNotFound
static intERROR_stringExpected
static intERROR_stringOrIdentifierExpected
static intERROR_tooManyScriptLevels
static intERROR_unrecognizedAtomProperty
static intERROR_unrecognizedBondProperty
static intERROR_unrecognizedCommand
static intERROR_unrecognizedExpression
static intERROR_unrecognizedObject
static intERROR_unrecognizedParameter
static intERROR_unrecognizedParameterWarning
static intERROR_unrecognizedShowParameter
static intERROR_what
static StringEXPRESSION_KEY
Stringfilename
booleanfileOpenCheck
StringfullCommand
StringfunctionName
booleanhistoryDisabled
booleanignoreError
BooleaninterruptExecution
booleanisBondSet
booleanisExecuting
booleanisForCheck
booleanisScriptCheck
booleanisStateScript
booleanisSyntaxCheck
intiToken
intlastMoNumber
intlineEnd
int[]lineIndices
short[]lineNumbers
booleanlogMessages
StringBufferoutputBuffer
intpc
intpcEnd
Stringscript
intscriptLevel
static intscriptLevelMax
intscriptReportingLevel
Eval.Context[]stack
Token[]statement
intstatementLength
StringBufferstrbufLog
SymmetryInterfacesymmetry
static StringSCRIPT_COMPLETED
Token[]tempStatement
inttheTok
TokentheToken
StringthisCommand
longtimeBeginExecution
longtimeEndExecution
booleantQuiet
Hashtablevariables
Viewerviewer
Constructor Summary
Eval(Viewer viewer)
Method Summary
voidanimation()
voidanimationDirection()
voidanimationMode()
voidassignBitsetVariable(String variable, BitSet bs)
Point3fatomCenterOrCoordinateParameter(int i)
floatatomProperty(Atom atom, int tokWhat, boolean asInt)
voidaxes(int index)
voidbackground(int i)
ObjectbitsetTokenVector(Object v)
BitSetbitSetForModelFileNumber(int m)
voidbondorder()
booleanbooleanParameter(int i)
voidboundbox(int index)
voidcalculate()
voidcenter(int i)
voidcenterAt()
Point3fcenterParameter(int i)
booleanchangeElementColor(String str, int argb)
booleancheckContinue()
voidcheckLength(int length)
voidcheckLength(int length, int errorPt)
intcheckLength23()
voidcheckLength34()
ObjectcheckScriptSilent(String script)
booleancheckToken(int i)
voidclearDefinitionsAndLoadPredefined()
voidclearPredefined(String[] list)
voidclearState(boolean tQuiet)
voidcolor()
voidcolorObject(int tokObject, int index)
static intcolorPtToInt(Point3f pt)
voidcolorShape(int shapeType, int index, boolean isBackground)
BitSetcomparatorInstruction(int tokWhat, float[] data, int tokOperator, int comparisonValue, float comparisonFloat)
voidconfiguration()
voidconnect()
voidconsole()
StringcontextTrace()
voiddata()
voiddataFrame(int datatype)
voiddefine()
voiddelay()
voiddelay(long millis)
voiddelete()
voiddeleteAtomsInVariables(BitSet bsDeleted)
voiddipole()
voiddisplay(boolean isDisplay)
voiddots(int iShape)
voiddraw()
voidecho(int index, boolean isImage)
voidellipsoid()
voiderror(int error)
voiderror(int error, String value)
voiderror(int error, String value, String more)
booleanerror(int error, String value, String more, boolean warningOnly)
voidevalError(String message)
static ObjectevaluateExpression(Viewer viewer, Object expr)
a general-use method to evaluate a "SET" type expression.
BitSetexpression(int index)
BitSetexpression(Token[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted)
StringextractCommandOption(String name)
voidfile()
floatfloatParameter(int i, float min, float max)
floatfloatParameter(int index)
intfloatParameterSet(int i, float[] fparams)
floatfloatSetting(int pt, float min, float max)
floatfloatSetting(int pt)
voidflowControl(int tok)
voidfont(int shapeType, float fontsize)
voidframe(int offset)
voidframeControl(int i, boolean isSubCmd)
voidfrank(int index)
voidfunction()
intgetArgbParam(int index)
intgetArgbParam(int index, boolean allowNone)
intgetArgbParamLast(int index, boolean allowNone)
BitSetgetAtomBits(int tokType, Object specInfo)
static BitSetgetAtomBitSet(Eval e, Viewer viewer, Object atomExpression)
static VectorgetAtomBitSetVector(Eval e, Viewer viewer, Object atomExpression)
StringgetBitsetIdent(BitSet bs, String label, Object tokenValue, boolean useAtomMap)
protected ObjectgetBitsetProperty(BitSet bs, int tok, Point3f ptRef, Point4f planeRef, Object tokenValue, Object opValue, boolean useAtomMap, int ptAtom)
TokengetBitsetPropertySelector(int i, boolean mustBeSettable)
intgetColorTriad(int i)
StringgetCommand(int pc)
TokengetContextVariableAsToken(String var)
Vector3fgetDrawObjectAxis(String axisID)
Point3fgetDrawObjectCenter(String axisID)
StringgetErrorMessage()
intgetExecutionWalltime()
StringgetFullPathName()
FunctiongetFunction(String name)
StringgetFunctionCalls(String selectedFunction)
TokengetFunctionReturn(String name, Vector params)
StringgetIsosurfaceJvxl()
intgetLinenumber()
intgetMadParameter()
MinimizerInterfacegetMinimizer()
StringgetMoJvxl(int ptMO)
StringgetNextComment()
ObjectgetNumericParameter(String var)
ObjectgetParameter(String var, boolean asToken)
StringgetParameterEscaped(String var)
Point3fgetPoint3f(int i, boolean allowFractional)
Point4fgetPoint4f(int i)
ObjectgetPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim)
voidgetProperty()
StringgetScript()
static intgetSeqCode(Token instruction)
intgetSetAxesTypeMad(int index)
StringgetShapeNameParameter(int i)
intgetShapeType(int tok)
StringgetState()
ObjectgetStringObjectAsToken(String s, String key)
SymmetryInterfacegetSymmetry()
TokengetToken(int i)
floatgetTranslucentLevel(int i)
floatgetZoomFactor(int i, int ptCenter, float radius, float factor0)
voidgotocmd()
voidhaltExecution()
voidhbond(boolean isCommand)
voidhelp()
voidhistory(int pt)
Point4fhklParameter(int i)
voidhover()
booleanifCmd()
voidinitIsosurface(int iShape)
booleaninsertArrayValue(String key, Token result)
voidinstructionDispatchLoop(boolean doList)
voidintegerOutOfRange(int min, int max)
intintParameter(int index)
intintParameter(int i, int min, int max)
intintSetting(int pt, int val, int min, int max)
intintSetting(int pt)
voidinvertSelected()
booleanisCenterParameter(int i)
booleanisColorParam(int i)
booleanisExecutionPaused()
booleanisFloatParameter(int index)
voidisosurface(int iShape)
booleanisPoint3f(int i)
booleanisScriptExecuting()
voidlabel(int index)
voidlcaoCartoon()
booleanlistIsosurface(int iShape)
voidload()
booleanloadError(String msg)
booleanloadFunction(String name, Vector params)
booleanloadScript(String filename, String script, boolean debugCompiler)
booleanloadScriptFile(String filename, boolean tQuiet)
booleanloadScriptFileInternal(String filename)
booleanloadScriptString(String script, boolean tQuiet)
voidlogDebugScript(int ifLevel)
BitSetlookupIdentifierValue(String identifier)
BitSetlookupValue(String variable, boolean plurals)
voidmessage()
voidminimize()
booleanmo(boolean isInitOnly)
intmodelNumberParameter(int index)
voidmonitor()
intmoOffset(int index)
voidmove()
voidmoveto()
voidnavigate()
voidnumberOutOfRange(float min, float max)
StringobjectNameParameter(int index)
StringoptParameterAsString(int i)
StringparameterAsString(int i)
ObjectparameterExpression(int pt, int ptMax, String key, boolean asVector)
ObjectparameterExpression(int pt, int ptMax, String key, boolean asVector, int ptAtom, Hashtable localVars, String localVar)
voidpause()
voidpauseExecution()
voidplaneExpected()
Point4fplaneParameter(int i)
voidpmesh()
voidpointGroup()
voidpolyhedra()
voidpopContext()
voidpredefine(String script)
voidprint()
voidproteinShape(int shapeType)
voidpushContext(Function function)
floatradiusParameter(int index, float defaultValue)
Based on the form of the parameters, returns and encoded radius as follows: script meaning range encoded +1.2 offset [0 - 10] x -1.2 offset 0) x 1.2 absolute (0 - 10] x + 10 -30% 70% (-100 - 0) x + 200 +30% 130% (0 x + 200 80% percent (0 x + 100 in each case, numbers can be integer or float
voidrefresh()
voidreset()
voidrestore()
voidrestrict()
voidrestrictSelected(boolean doInvert)
voidresumePausedExecution()
voidreturnCmd()
voidrotate(boolean isSpin, boolean isSelected)
voidrunEval(boolean checkScriptOnly, boolean openFiles, boolean historyDisabled, boolean listCommands)
voidrunScript(String script)
voidrunScript(String script, StringBuffer outputBuffer)
voidsave()
voidscript(int tok)
voidscriptStatus(String s)
voidselect()
voidselectionHalo(int pt)
voidset()
voidsetAtomShapeSize(int shape, int defOn)
voidsetBitsetProperty(BitSet bs, int tok, int iValue, float fValue, Token tokenValue)
voidsetBondmode()
voidsetBooleanProperty(String key, boolean value)
StringsetColorOptions(int index, int iShape, int nAllowed)
voidsetDebugging()
voidsetEcho()
static StringsetErrorLineMessage(String filename, int lineCurrent, int pcCurrent, String lineInfo)
voidsetErrorMessage(String err)
static voidsetErrorMessages()
booleansetFloatProperty(String key, float value)
voidsetHbond()
booleansetIntProperty(String key, int value)
booleansetLabel(String str)
booleansetMeasurementUnits(String units)
booleansetMeshDisplayProperty(int shape, int i, int tok)
voidsetMoData(int shape, int moNumber, int offset, int modelIndex, String title)
voidsetMonitor()
StringsetObjectProperty()
booleansetParameter(String key, int intVal, boolean isJmolSet, boolean showing)
voidsetPicking()
voidsetPickingStyle()
voidsetProperty()
intsetShapeId(int iShape, int i, boolean idSeen)
voidsetShapeProperty(int shapeType, String propertyName, Object propertyValue)
voidsetShapeSize(int shapeType, int size)
voidsetShapeTranslucency(int shapeType, String prefix, String translucency, float translucentLevel, BitSet bs)
voidsetSpin(String key, int value)
voidsetSsbond()
booleansetStatement(int pc)
voidsetStringProperty(String key, String value)
voidsetUserColors()
voidsetVariable(int pt, int ptMax, String key, boolean showing)
voidshow()
voidshowString(String str)
voidslab(boolean isDepth)
voidssbond()
StringstatementAsString()
voidstereo()
StringstringParameter(int index)
StringstringSetting(int pt, boolean isJmolSet)
voidstructure()
voidsubset()
voidsync()
inttokAt(int i)
inttokAt(int i, Token[] args)
TokentokenAt(int i, Token[] args)
TokentokenSetting(int pt)
StringtoString()
voidtranslate()
voidtranslateSelected()
voidunitcell(int index)
voidvector()
voidvibration()
booleanwarning(int error, String value, String more)
voidwireframe()
Stringwrite(Token[] args)
Point3fxypParameter(int index)
voidzap(boolean isZapCommand)
voidzoom(boolean isZoomTo)

Field Detail

aatoken

private Token[][] aatoken

commandHistoryLevelMax

private int commandHistoryLevelMax

compiler

private Compiler compiler

contextVariables

private Hashtable contextVariables

coordinatesAreFractional

private boolean coordinatesAreFractional

currentThread

private Thread currentThread

data

private Object[] data

debugScript

private boolean debugScript

error

private boolean error

errorMessage

private String errorMessage

errors

static String[] errors

executionPaused

private Boolean executionPaused

expressionResult

private Object expressionResult

ERROR_axisExpected

static final int ERROR_axisExpected

ERROR_badArgumentCount

static final int ERROR_badArgumentCount

ERROR_badMillerIndices

static final int ERROR_badMillerIndices

ERROR_badRGBColor

static final int ERROR_badRGBColor

ERROR_booleanExpected

static final int ERROR_booleanExpected

ERROR_booleanOrNumberExpected

static final int ERROR_booleanOrNumberExpected

ERROR_booleanOrWhateverExpected

static final int ERROR_booleanOrWhateverExpected

ERROR_colorExpected

static final int ERROR_colorExpected

ERROR_colorOrPaletteRequired

static final int ERROR_colorOrPaletteRequired

ERROR_coordinateOrNameOrExpressionRequired

static final int ERROR_coordinateOrNameOrExpressionRequired

ERROR_drawObjectNotDefined

static final int ERROR_drawObjectNotDefined

ERROR_endOfStatementUnexpected

static final int ERROR_endOfStatementUnexpected

ERROR_expressionExpected

static final int ERROR_expressionExpected

ERROR_expressionOrIntegerExpected

static final int ERROR_expressionOrIntegerExpected

ERROR_filenameExpected

static final int ERROR_filenameExpected

ERROR_fileNotFoundException

static final int ERROR_fileNotFoundException

ERROR_incompatibleArguments

static final int ERROR_incompatibleArguments

ERROR_insufficientArguments

static final int ERROR_insufficientArguments

ERROR_integerExpected

static final int ERROR_integerExpected

ERROR_integerOutOfRange

static final int ERROR_integerOutOfRange

ERROR_invalidArgument

static final int ERROR_invalidArgument

ERROR_invalidParameterOrder

static final int ERROR_invalidParameterOrder

ERROR_keywordExpected

static final int ERROR_keywordExpected

ERROR_multipleModelsNotOK

static final int ERROR_multipleModelsNotOK

ERROR_noUnitCell

static final int ERROR_noUnitCell

ERROR_numberExpected

static final int ERROR_numberExpected

ERROR_numberMustBe

static final int ERROR_numberMustBe

ERROR_numberOutOfRange

static final int ERROR_numberOutOfRange

ERROR_objectNameExpected

static final int ERROR_objectNameExpected

ERROR_propertyNameExpected

static final int ERROR_propertyNameExpected

ERROR_spaceGroupNotFound

static final int ERROR_spaceGroupNotFound

ERROR_stringExpected

static final int ERROR_stringExpected

ERROR_stringOrIdentifierExpected

static final int ERROR_stringOrIdentifierExpected

ERROR_tooManyScriptLevels

static final int ERROR_tooManyScriptLevels

ERROR_unrecognizedAtomProperty

static final int ERROR_unrecognizedAtomProperty

ERROR_unrecognizedBondProperty

static final int ERROR_unrecognizedBondProperty

ERROR_unrecognizedCommand

static final int ERROR_unrecognizedCommand

ERROR_unrecognizedExpression

static final int ERROR_unrecognizedExpression

ERROR_unrecognizedObject

static final int ERROR_unrecognizedObject

ERROR_unrecognizedParameter

static final int ERROR_unrecognizedParameter

ERROR_unrecognizedParameterWarning

static final int ERROR_unrecognizedParameterWarning

ERROR_unrecognizedShowParameter

static final int ERROR_unrecognizedShowParameter

ERROR_what

static final int ERROR_what

EXPRESSION_KEY

private static final String EXPRESSION_KEY

filename

private String filename

fileOpenCheck

private boolean fileOpenCheck

fullCommand

private String fullCommand

functionName

private String functionName

historyDisabled

private boolean historyDisabled

ignoreError

private boolean ignoreError

interruptExecution

private Boolean interruptExecution

isBondSet

private boolean isBondSet

isExecuting

private boolean isExecuting

isForCheck

boolean isForCheck

isScriptCheck

boolean isScriptCheck

isStateScript

private boolean isStateScript

isSyntaxCheck

boolean isSyntaxCheck

iToken

int iToken

lastMoNumber

private int lastMoNumber

lineEnd

private int lineEnd

lineIndices

private int[] lineIndices

lineNumbers

private short[] lineNumbers

logMessages

boolean logMessages

outputBuffer

private StringBuffer outputBuffer

pc

private int pc

pcEnd

private int pcEnd

script

private String script

scriptLevel

private int scriptLevel

scriptLevelMax

private static final int scriptLevelMax

scriptReportingLevel

private int scriptReportingLevel

stack

private Eval.Context[] stack

statement

private Token[] statement

statementLength

private int statementLength

strbufLog

private final StringBuffer strbufLog

symmetry

private SymmetryInterface symmetry

SCRIPT_COMPLETED

static final String SCRIPT_COMPLETED

tempStatement

private Token[] tempStatement

theTok

private int theTok

theToken

private Token theToken

thisCommand

private String thisCommand

timeBeginExecution

private long timeBeginExecution

timeEndExecution

private long timeEndExecution

tQuiet

private boolean tQuiet

variables

private Hashtable variables

viewer

Viewer viewer

Constructor Detail

Eval

Eval(Viewer viewer)

Method Detail

animation

private void animation()

animationDirection

private void animationDirection()

animationMode

private void animationMode()

assignBitsetVariable

private void assignBitsetVariable(String variable, BitSet bs)

atomCenterOrCoordinateParameter

private Point3f atomCenterOrCoordinateParameter(int i)

atomProperty

private float atomProperty(Atom atom, int tokWhat, boolean asInt)

axes

private void axes(int index)

background

private void background(int i)

bitsetTokenVector

Object bitsetTokenVector(Object v)

bitSetForModelFileNumber

BitSet bitSetForModelFileNumber(int m)

bondorder

private void bondorder()

booleanParameter

private boolean booleanParameter(int i)

boundbox

private void boundbox(int index)

calculate

private void calculate()

center

private void center(int i)

centerAt

private void centerAt()

centerParameter

private Point3f centerParameter(int i)

changeElementColor

private boolean changeElementColor(String str, int argb)

checkContinue

private boolean checkContinue()

checkLength

private void checkLength(int length)

checkLength

private void checkLength(int length, int errorPt)

checkLength23

private int checkLength23()

checkLength34

private void checkLength34()

checkScriptSilent

Object checkScriptSilent(String script)

checkToken

private boolean checkToken(int i)

clearDefinitionsAndLoadPredefined

void clearDefinitionsAndLoadPredefined()

clearPredefined

private void clearPredefined(String[] list)

clearState

private void clearState(boolean tQuiet)

color

private void color()

colorObject

private void colorObject(int tokObject, int index)

colorPtToInt

static int colorPtToInt(Point3f pt)

colorShape

private void colorShape(int shapeType, int index, boolean isBackground)

comparatorInstruction

private BitSet comparatorInstruction(int tokWhat, float[] data, int tokOperator, int comparisonValue, float comparisonFloat)

configuration

private void configuration()

connect

private void connect()

console

private void console()

contextTrace

String contextTrace()

data

private void data()

dataFrame

private void dataFrame(int datatype)

define

private void define()

delay

private void delay()

delay

private void delay(long millis)

delete

private void delete()

deleteAtomsInVariables

void deleteAtomsInVariables(BitSet bsDeleted)

dipole

private void dipole()

display

private void display(boolean isDisplay)

dots

private void dots(int iShape)

draw

private void draw()

echo

private void echo(int index, boolean isImage)

ellipsoid

private void ellipsoid()

error

void error(int error)

error

void error(int error, String value)

error

void error(int error, String value, String more)

error

boolean error(int error, String value, String more, boolean warningOnly)

evalError

void evalError(String message)

evaluateExpression

static Object evaluateExpression(Viewer viewer, 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

expression

private BitSet expression(int index)

expression

private BitSet expression(Token[] code, int pcStart, int pcStop, boolean allowRefresh, boolean allowUnderflow, boolean mustBeBitSet, boolean andNotDeleted)

extractCommandOption

private String extractCommandOption(String name)

file

private void file()

floatParameter

private float floatParameter(int i, float min, float max)

floatParameter

private float floatParameter(int index)

floatParameterSet

private int floatParameterSet(int i, float[] fparams)

floatSetting

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

floatSetting

private float floatSetting(int pt)

flowControl

private void flowControl(int tok)

font

private void font(int shapeType, float fontsize)

frame

private void frame(int offset)

frameControl

private void frameControl(int i, boolean isSubCmd)

frank

private void frank(int index)

function

private void function()

getArgbParam

private int getArgbParam(int index)

getArgbParam

private int getArgbParam(int index, boolean allowNone)

getArgbParamLast

private int getArgbParamLast(int index, boolean allowNone)

getAtomBits

private BitSet getAtomBits(int tokType, Object specInfo)

getAtomBitSet

static BitSet getAtomBitSet(Eval e, Viewer viewer, Object atomExpression)

getAtomBitSetVector

static Vector getAtomBitSetVector(Eval e, Viewer viewer, Object atomExpression)

getBitsetIdent

String getBitsetIdent(BitSet bs, String label, Object tokenValue, boolean useAtomMap)

getBitsetProperty

protected Object getBitsetProperty(BitSet bs, int tok, Point3f ptRef, Point4f planeRef, Object tokenValue, Object opValue, boolean useAtomMap, int ptAtom)

getBitsetPropertySelector

private Token getBitsetPropertySelector(int i, boolean mustBeSettable)

getColorTriad

private int getColorTriad(int i)

getCommand

private String getCommand(int pc)

getContextVariableAsToken

private Token getContextVariableAsToken(String var)

getDrawObjectAxis

private Vector3f getDrawObjectAxis(String axisID)

getDrawObjectCenter

private Point3f getDrawObjectCenter(String axisID)

getErrorMessage

String getErrorMessage()

getExecutionWalltime

int getExecutionWalltime()

getFullPathName

private String getFullPathName()

getFunction

private Function getFunction(String name)

getFunctionCalls

private String getFunctionCalls(String selectedFunction)

getFunctionReturn

Token getFunctionReturn(String name, Vector params)

getIsosurfaceJvxl

private String getIsosurfaceJvxl()

getLinenumber

private int getLinenumber()

getMadParameter

private int getMadParameter()

getMinimizer

private MinimizerInterface getMinimizer()

getMoJvxl

private String getMoJvxl(int ptMO)

getNextComment

private String getNextComment()

getNumericParameter

private Object getNumericParameter(String var)

getParameter

private Object getParameter(String var, boolean asToken)

getParameterEscaped

private String getParameterEscaped(String var)

getPoint3f

private Point3f getPoint3f(int i, boolean allowFractional)

getPoint4f

private Point4f getPoint4f(int i)

getPointOrPlane

private Object getPointOrPlane(int index, boolean integerOnly, boolean allowFractional, boolean doConvert, boolean implicitFractional, int minDim, int maxDim)

getProperty

private void getProperty()

getScript

String getScript()

getSeqCode

private static int getSeqCode(Token instruction)

getSetAxesTypeMad

private int getSetAxesTypeMad(int index)

getShapeNameParameter

private String getShapeNameParameter(int i)

getShapeType

private int getShapeType(int tok)

getState

String getState()

getStringObjectAsToken

private Object getStringObjectAsToken(String s, String key)

getSymmetry

private SymmetryInterface getSymmetry()

getToken

private Token getToken(int i)

getTranslucentLevel

private float getTranslucentLevel(int i)

getZoomFactor

private float getZoomFactor(int i, int ptCenter, float radius, float factor0)

gotocmd

private void gotocmd()

haltExecution

void haltExecution()

hbond

private void hbond(boolean isCommand)

help

private void help()

history

private void history(int pt)

hklParameter

private Point4f hklParameter(int i)

hover

private void hover()

ifCmd

private boolean ifCmd()

initIsosurface

private void initIsosurface(int iShape)

insertArrayValue

private boolean insertArrayValue(String key, Token result)

instructionDispatchLoop

private void instructionDispatchLoop(boolean doList)

integerOutOfRange

private void integerOutOfRange(int min, int max)

intParameter

private int intParameter(int index)

intParameter

private int intParameter(int i, int min, int max)

intSetting

private int intSetting(int pt, int val, int min, int max)

intSetting

private int intSetting(int pt)

invertSelected

private void invertSelected()

isCenterParameter

private boolean isCenterParameter(int i)

isColorParam

private boolean isColorParam(int i)

isExecutionPaused

boolean isExecutionPaused()

isFloatParameter

private boolean isFloatParameter(int index)

isosurface

private void isosurface(int iShape)

isPoint3f

private boolean isPoint3f(int i)

isScriptExecuting

boolean isScriptExecuting()

label

private void label(int index)

lcaoCartoon

private void lcaoCartoon()

listIsosurface

private boolean listIsosurface(int iShape)

load

private void load()

loadError

private boolean loadError(String msg)

loadFunction

private boolean loadFunction(String name, Vector params)

loadScript

private boolean loadScript(String filename, String script, boolean debugCompiler)

loadScriptFile

boolean loadScriptFile(String filename, boolean tQuiet)

loadScriptFileInternal

private boolean loadScriptFileInternal(String filename)

loadScriptString

boolean loadScriptString(String script, boolean tQuiet)

logDebugScript

private void logDebugScript(int ifLevel)

lookupIdentifierValue

private BitSet lookupIdentifierValue(String identifier)

lookupValue

private BitSet lookupValue(String variable, boolean plurals)

message

private void message()

minimize

private void minimize()

mo

private boolean mo(boolean isInitOnly)

modelNumberParameter

private int modelNumberParameter(int index)

monitor

private void monitor()

moOffset

private int moOffset(int index)

move

private void move()

moveto

private void moveto()

navigate

private void navigate()

numberOutOfRange

private void numberOutOfRange(float min, float max)

objectNameParameter

private String objectNameParameter(int index)

optParameterAsString

private String optParameterAsString(int i)

parameterAsString

private String parameterAsString(int i)

parameterExpression

private Object parameterExpression(int pt, int ptMax, String key, boolean asVector)

parameterExpression

private Object parameterExpression(int pt, int ptMax, String key, boolean asVector, int ptAtom, Hashtable localVars, String localVar)

pause

private void pause()

pauseExecution

void pauseExecution()

planeExpected

private void planeExpected()

planeParameter

private Point4f planeParameter(int i)

pmesh

private void pmesh()

pointGroup

private void pointGroup()

polyhedra

private void polyhedra()

popContext

private void popContext()

predefine

private void predefine(String script)

print

private void print()

proteinShape

private void proteinShape(int shapeType)

pushContext

private void pushContext(Function function)

radiusParameter

private float radiusParameter(int index, float defaultValue)
Based on the form of the parameters, returns and encoded radius as follows: script meaning range encoded +1.2 offset [0 - 10] x -1.2 offset 0) x 1.2 absolute (0 - 10] x + 10 -30% 70% (-100 - 0) x + 200 +30% 130% (0 x + 200 80% percent (0 x + 100 in each case, numbers can be integer or float

Parameters: index defaultValue a default value or Float.NaN

Returns: one of the above possibilities

Throws: ScriptException

refresh

private void refresh()

reset

private void reset()

restore

private void restore()

restrict

private void restrict()

restrictSelected

private void restrictSelected(boolean doInvert)

resumePausedExecution

void resumePausedExecution()

returnCmd

private void returnCmd()

rotate

private void rotate(boolean isSpin, boolean isSelected)

runEval

void runEval(boolean checkScriptOnly, boolean openFiles, boolean historyDisabled, boolean listCommands)

runScript

private void runScript(String script)

runScript

void runScript(String script, StringBuffer outputBuffer)

save

private void save()

script

private void script(int tok)

scriptStatus

private void scriptStatus(String s)

select

private void select()

selectionHalo

private void selectionHalo(int pt)

set

private void set()

setAtomShapeSize

private void setAtomShapeSize(int shape, int defOn)

setBitsetProperty

private void setBitsetProperty(BitSet bs, int tok, int iValue, float fValue, Token tokenValue)

setBondmode

private void setBondmode()

setBooleanProperty

private void setBooleanProperty(String key, boolean value)

setColorOptions

private String setColorOptions(int index, int iShape, int nAllowed)

setDebugging

void setDebugging()

setEcho

private void setEcho()

setErrorLineMessage

static String setErrorLineMessage(String filename, int lineCurrent, int pcCurrent, String lineInfo)

setErrorMessage

private void setErrorMessage(String err)

setErrorMessages

static void setErrorMessages()

setFloatProperty

private boolean setFloatProperty(String key, float value)

setHbond

private void setHbond()

setIntProperty

private boolean setIntProperty(String key, int value)

setLabel

private boolean setLabel(String str)

setMeasurementUnits

private boolean setMeasurementUnits(String units)

setMeshDisplayProperty

private boolean setMeshDisplayProperty(int shape, int i, int tok)

setMoData

private void setMoData(int shape, int moNumber, int offset, int modelIndex, String title)

setMonitor

private void setMonitor()

setObjectProperty

private String setObjectProperty()

setParameter

private boolean setParameter(String key, int intVal, boolean isJmolSet, boolean showing)

setPicking

private void setPicking()

setPickingStyle

private void setPickingStyle()

setProperty

private void setProperty()

setShapeId

private int setShapeId(int iShape, int i, boolean idSeen)

setShapeProperty

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

setShapeSize

private void setShapeSize(int shapeType, int size)

setShapeTranslucency

private void setShapeTranslucency(int shapeType, String prefix, String translucency, float translucentLevel, BitSet bs)

setSpin

private void setSpin(String key, int value)

setSsbond

private void setSsbond()

setStatement

private boolean setStatement(int pc)

setStringProperty

private void setStringProperty(String key, String value)

setUserColors

private void setUserColors()

setVariable

private void setVariable(int pt, int ptMax, String key, boolean showing)

show

private void show()

showString

private void showString(String str)

slab

private void slab(boolean isDepth)

ssbond

private void ssbond()

statementAsString

private String statementAsString()

stereo

private void stereo()

stringParameter

private String stringParameter(int index)

stringSetting

private String stringSetting(int pt, boolean isJmolSet)

structure

private void structure()

subset

private void subset()

sync

private void sync()

tokAt

private int tokAt(int i)

tokAt

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

tokenAt

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

tokenSetting

private Token tokenSetting(int pt)

toString

public String toString()

translate

private void translate()

translateSelected

private void translateSelected()

unitcell

private void unitcell(int index)

vector

private void vector()

vibration

private void vibration()

warning

private boolean warning(int error, String value, String more)

wireframe

private void wireframe()

write

String write(Token[] args)

xypParameter

private Point3f xypParameter(int index)

zap

private void zap(boolean isZapCommand)

zoom

private void zoom(boolean isZoomTo)