Package org.jmol.script
Class ScriptParam
- java.lang.Object
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- org.jmol.script.ScriptError
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- org.jmol.script.ScriptParam
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- All Implemented Interfaces:
JmolScriptEvaluator
- Direct Known Subclasses:
ScriptExpr
public abstract class ScriptParam extends ScriptError
The ScriptParam class holds methods used to parse parameters in Jmol scripts.
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Field Summary
Fields Modifier and Type Field Description java.util.Map<java.lang.String,ScriptFunction>
contextFunctions
java.util.Map<java.lang.String,SV>
contextVariables
boolean
coordinatesAreFractional
set in getPointOrPlanejavajs.util.P3
fractionalPoint
set in getPointOrPlaneboolean
isBondSet
int
iToken
static int
MODE_P_ALLOW_FRACTIONAL
protected static int
MODE_P_CONVERT_TO_CARTESIAN
protected static int
MODE_P_IMPLICIT_FRACTIONAL
protected static int
MODE_P_INT_ONLY
protected static int
MODE_P_NULL_ON_ERROR
static int
MODE_P3
static int
MODE_P34
protected static int
MODE_P4
int
slen
T[]
st
int
theTok
T
theToken
ScriptContext
thisContext
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Fields inherited from class org.jmol.script.ScriptError
chk, error, ERROR_axisExpected, ERROR_backgroundModelError, ERROR_badArgumentCount, ERROR_badMillerIndices, ERROR_badRGBColor, ERROR_booleanExpected, ERROR_booleanOrNumberExpected, ERROR_booleanOrWhateverExpected, ERROR_cannotSet, ERROR_colorExpected, ERROR_colorOrPaletteRequired, ERROR_commandExpected, ERROR_coordinateOrNameOrExpressionRequired, ERROR_drawObjectNotDefined, ERROR_endOfStatementUnexpected, ERROR_expressionExpected, ERROR_expressionOrIntegerExpected, ERROR_filenameExpected, ERROR_fileNotFoundException, ERROR_incompatibleArguments, ERROR_insufficientArguments, ERROR_integerExpected, ERROR_integerOutOfRange, ERROR_invalidArgument, ERROR_invalidParameterOrder, ERROR_keywordExpected, ERROR_moCoefficients, ERROR_moIndex, ERROR_moModelError, ERROR_moOccupancy, ERROR_moOnlyOne, ERROR_multipleModelsDisplayedNotOK, ERROR_multipleModelsNotOK, ERROR_noData, ERROR_noPartialCharges, ERROR_noUnitCell, ERROR_numberExpected, ERROR_numberMustBe, ERROR_numberOutOfRange, ERROR_objectNameExpected, ERROR_planeExpected, ERROR_propertyNameExpected, ERROR_spaceGroupNotFound, ERROR_stringExpected, ERROR_stringOrIdentifierExpected, ERROR_tooManyPoints, ERROR_tooManyScriptLevels, ERROR_unrecognizedAtomProperty, ERROR_unrecognizedBondProperty, ERROR_unrecognizedCommand, ERROR_unrecognizedExpression, ERROR_unrecognizedObject, ERROR_unrecognizedParameter, ERROR_unrecognizedParameterWarning, ERROR_unrecognizedShowParameter, ERROR_what, ERROR_writeWhat, errorMessage, errorMessageUntranslated, errorType, iCommandError, ignoreError, vwr
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Constructor Summary
Constructors Constructor Description ScriptParam()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description javajs.util.P3
atomCenterOrCoordinateParameter(int i, java.lang.Object[] ret)
javajs.util.P3
centerParameter(int i, java.lang.Object[] ret)
protected javajs.util.P3
centerParameterForModel(int i, int modelIndex, java.lang.Object[] ret)
javajs.util.T3
checkHKL(javajs.util.T3 pt)
Note - this check does not allow a 0 for h, k, or l.int
checkLast(int i)
int
checkLength(int length)
int
checkLength23()
protected int
checkLength34()
int
checkLengthErrorPt(int length, int errorPt)
protected boolean
checkToken(int i)
float
floatParameter(int index)
protected float
floatParameterRange(int i, float min, float max)
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 inputint
getArgbParam(int index)
protected int
getArgbParamLast(int index, boolean allowNone)
int
getArgbParamOrNone(int index, boolean allowNone)
javajs.util.BS
getAtomsStartingAt(int i)
static int
getBondOrderFromString(java.lang.String s)
private int
getColorTriad(int i)
SV
getContextVariableAsVariable(java.lang.String var, boolean isLocal)
(package private) 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.javajs.util.T3
getFractionalPoint(int i)
Could return a P4 for large 1100100100 type indicatorsjavajs.util.P4
getHklPlane(javajs.util.T3 pt, float offset, javajs.util.Lst<javajs.util.P3> pts)
int
getMadParameter()
java.lang.Object
getParameter(java.lang.String key, int tokType, boolean nullAsString)
static int
getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger)
reads standard n.m float-as-integer n*1000000 + m and returns (n % 7) << 5 + (m % 0x1F)private static int
getPartialBondOrderFromString(java.lang.String s)
javajs.util.P3
getPoint3f(int i, boolean allowFractional, boolean throwE)
Get an {x,y,z} value, possibly fractional, with option to throw an error.javajs.util.P4
getPoint4f(int i)
javajs.util.P3[]
getPointArray(int i, int nPoints, boolean allowNull)
may return null values in some casesjavajs.util.Lst<javajs.util.P3>
getPointOrCenterVector(T t)
javajs.util.T3
getPointOrPlane(int index, int mode)
Get the point or plane at an indexjavajs.util.Lst<javajs.util.P3>
getPointVector(T t, int i)
javajs.util.Quat
getQuaternionParameter(int i, javajs.util.BS bsAtoms, boolean divideByCurrent)
T
getToken(int i)
protected java.lang.Object
getVarParameter(java.lang.String var, boolean orReturnName)
javajs.util.P4
hklParameter(int i, javajs.util.Lst<javajs.util.P3> pts, boolean allowOffset)
int
intParameter(int index)
int
intParameterRange(int i, int min, int max)
boolean
isArrayParameter(int i)
boolean
isCenterParameter(int i)
boolean
isColorParam(int i)
boolean
isFloatParameter(int index)
boolean
isPoint3f(int i)
javajs.util.Lst<java.lang.Object>
listParameter(int i, int nMin, int nMax)
javajs.util.Lst<java.lang.Object>
listParameter4(int i, int nMin, int nMax, boolean allowString)
int
modelNumberParameter(int index)
java.lang.String
objectNameParameter(int index)
java.lang.String
optParameterAsString(int i)
java.lang.String
paramAsStr(int i)
javajs.util.P4
planeParameter(int i, boolean isBest)
javajs.util.P4
planeValue(T x)
void
setBooleanProperty(java.lang.String key, boolean value)
protected boolean
setFloatProperty(java.lang.String key, float value)
protected boolean
setIntProperty(java.lang.String key, int value)
protected void
setStringProperty(java.lang.String key, java.lang.String value)
java.lang.String
stringParameter(int index)
java.lang.String[]
stringParameterSet(int i)
TickInfo
tickParamAsStr(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst)
int
tokAt(int i)
javajs.util.P3
xypParameter(int index)
javajs.util.P4
xyzpParameter(int index)
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Methods inherited from class org.jmol.script.ScriptError
bad, error, errorMore, errorStr, errorStr2, errorString, evalError, getErrorLineMessage, getErrorMessage, getErrorMessageUntranslated, integerOutOfRange, invArg, numberOutOfRange, setCursorWait, setErrorMessage, showStringPrint, warning
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.jmol.api.JmolScriptEvaluator
checkScriptSilent, checkSelect, compileScriptFile, compileScriptString, deleteAtomsInVariables, evalFunctionFloat, evalParallel, evaluateCompiledScript, evaluateExpression, getAllowJSThreads, getAtomBitSet, getNextStatement, getScript, getScriptContext, getThisContext, haltExecution, isExecuting, isPaused, isStateScript, isStepping, isStopped, loadFileResourceAsync, notifyResumeStatus, pauseExecution, pushContextDown, resumeEval, resumePausedExecution, runScript, runScriptBuffer, setCompiler, setDebugging, setObjectPropSafe, setStatic, setViewer, stepPausedExecution, stopScriptThreads
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Field Detail
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contextVariables
public java.util.Map<java.lang.String,SV> contextVariables
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contextFunctions
public java.util.Map<java.lang.String,ScriptFunction> contextFunctions
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thisContext
public ScriptContext thisContext
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iToken
public int iToken
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theTok
public int theTok
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theToken
public T theToken
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st
public T[] st
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slen
public int slen
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fractionalPoint
public javajs.util.P3 fractionalPoint
set in getPointOrPlane
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coordinatesAreFractional
public boolean coordinatesAreFractional
set in getPointOrPlane
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isBondSet
public boolean isBondSet
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MODE_P3
public static final int MODE_P3
- See Also:
- Constant Field Values
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MODE_P4
protected static final int MODE_P4
- See Also:
- Constant Field Values
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MODE_P34
public static final int MODE_P34
- See Also:
- Constant Field Values
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MODE_P_INT_ONLY
protected static final int MODE_P_INT_ONLY
- See Also:
- Constant Field Values
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MODE_P_ALLOW_FRACTIONAL
public static final int MODE_P_ALLOW_FRACTIONAL
- See Also:
- Constant Field Values
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MODE_P_CONVERT_TO_CARTESIAN
protected static final int MODE_P_CONVERT_TO_CARTESIAN
- See Also:
- Constant Field Values
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MODE_P_IMPLICIT_FRACTIONAL
protected static final int MODE_P_IMPLICIT_FRACTIONAL
- See Also:
- Constant Field Values
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MODE_P_NULL_ON_ERROR
protected static final int MODE_P_NULL_ON_ERROR
- See Also:
- Constant Field Values
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Method Detail
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getToken
public T getToken(int i) throws ScriptException
- Throws:
ScriptException
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tokAt
public int tokAt(int i)
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checkToken
protected boolean checkToken(int i)
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getParameter
public java.lang.Object getParameter(java.lang.String key, int tokType, boolean nullAsString)
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getVarParameter
protected java.lang.Object getVarParameter(java.lang.String var, boolean orReturnName)
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getContextVariableAsVariable
public SV getContextVariableAsVariable(java.lang.String var, boolean isLocal)
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paramAsStr
public java.lang.String paramAsStr(int i) throws ScriptException
- Throws:
ScriptException
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stringParameter
public java.lang.String stringParameter(int index) throws ScriptException
- Throws:
ScriptException
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stringParameterSet
public java.lang.String[] stringParameterSet(int i) throws ScriptException
- Throws:
ScriptException
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objectNameParameter
public java.lang.String objectNameParameter(int index) throws ScriptException
- Throws:
ScriptException
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atomCenterOrCoordinateParameter
public javajs.util.P3 atomCenterOrCoordinateParameter(int i, java.lang.Object[] ret) throws ScriptException
- Parameters:
i
-ret
- return P3 or BS to ret[0]; on input, passing a BS as ret[1] indicates that it should be ANDED with this BS prior to calculation (SHOW/DRAW SYMOP)- Returns:
- point -- ORIGINAL, non-copied atom, if a single atom
- Throws:
ScriptException
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isCenterParameter
public boolean isCenterParameter(int i)
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centerParameter
public javajs.util.P3 centerParameter(int i, java.lang.Object[] ret) throws ScriptException
- Throws:
ScriptException
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centerParameterForModel
protected javajs.util.P3 centerParameterForModel(int i, int modelIndex, java.lang.Object[] ret) throws ScriptException
- Throws:
ScriptException
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planeParameter
public javajs.util.P4 planeParameter(int i, boolean isBest) throws ScriptException
- Throws:
ScriptException
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getAtomsStartingAt
public javajs.util.BS getAtomsStartingAt(int i) throws ScriptException
- Throws:
ScriptException
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getPointOrCenterVector
public javajs.util.Lst<javajs.util.P3> getPointOrCenterVector(T t) throws ScriptException
- Throws:
ScriptException
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hklParameter
public javajs.util.P4 hklParameter(int i, javajs.util.Lst<javajs.util.P3> pts, boolean allowOffset) throws ScriptException
- Throws:
ScriptException
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getHklPlane
public javajs.util.P4 getHklPlane(javajs.util.T3 pt, float offset, javajs.util.Lst<javajs.util.P3> pts)
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getPointOrPlane
public javajs.util.T3 getPointOrPlane(int index, int mode) throws ScriptException
Get the point or plane at an index- Parameters:
index
-mode
- some combination of MODE_P options- Returns:
- P3 or P4 or null
- Throws:
ScriptException
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isPoint3f
public boolean isPoint3f(int i)
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getPoint3f
public javajs.util.P3 getPoint3f(int i, boolean allowFractional, boolean throwE) throws ScriptException
Get an {x,y,z} value, possibly fractional, with option to throw an error. Will set fractionalCoords and coordinatesAreFractional- Parameters:
i
-allowFractional
-throwE
-- Returns:
- P3
- Throws:
ScriptException
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getFractionalPoint
public javajs.util.T3 getFractionalPoint(int i) throws ScriptException
Could return a P4 for large 1100100100 type indicators- Parameters:
i
-- Returns:
- P3 or P4
- Throws:
ScriptException
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getPoint4f
public javajs.util.P4 getPoint4f(int i) throws ScriptException
- Throws:
ScriptException
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xypParameter
public javajs.util.P3 xypParameter(int index) throws ScriptException
- Throws:
ScriptException
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xyzpParameter
public javajs.util.P4 xyzpParameter(int index) throws ScriptException
- Throws:
ScriptException
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optParameterAsString
public java.lang.String optParameterAsString(int i) throws ScriptException
- Throws:
ScriptException
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intParameter
public int intParameter(int index) throws ScriptException
- Throws:
ScriptException
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isFloatParameter
public boolean isFloatParameter(int index)
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floatParameter
public float floatParameter(int index) throws ScriptException
- Throws:
ScriptException
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getPointArray
public javajs.util.P3[] getPointArray(int i, int nPoints, boolean allowNull) throws ScriptException
may return null values in some cases- Parameters:
i
-nPoints
- -1 for unspecified number of pointsallowNull
- if allowing null values (as in setting atom properties such as vxyz or xyz)- Returns:
- array of P3, with possible null values
- Throws:
ScriptException
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listParameter
public javajs.util.Lst<java.lang.Object> listParameter(int i, int nMin, int nMax) throws ScriptException
- Throws:
ScriptException
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listParameter4
public javajs.util.Lst<java.lang.Object> listParameter4(int i, int nMin, int nMax, boolean allowString) throws ScriptException
- Throws:
ScriptException
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floatParameterSet
public float[] floatParameterSet(int i, int nMin, int nMax) throws 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:
ScriptException
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isArrayParameter
public boolean isArrayParameter(int i)
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getQuaternionParameter
public javajs.util.Quat getQuaternionParameter(int i, javajs.util.BS bsAtoms, boolean divideByCurrent) throws ScriptException
- Throws:
ScriptException
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checkLast
public int checkLast(int i) throws ScriptException
- Throws:
ScriptException
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checkLength
public int checkLength(int length) throws ScriptException
- Throws:
ScriptException
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checkLengthErrorPt
public int checkLengthErrorPt(int length, int errorPt) throws ScriptException
- Throws:
ScriptException
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checkLength23
public int checkLength23() throws ScriptException
- Throws:
ScriptException
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checkLength34
protected int checkLength34() throws ScriptException
- Throws:
ScriptException
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modelNumberParameter
public int modelNumberParameter(int index) throws ScriptException
- Throws:
ScriptException
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getMadParameter
public int getMadParameter() throws ScriptException
- Throws:
ScriptException
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intParameterRange
public int intParameterRange(int i, int min, int max) throws ScriptException
- Throws:
ScriptException
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floatParameterRange
protected float floatParameterRange(int i, float min, float max) throws ScriptException
- Throws:
ScriptException
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getPointVector
public javajs.util.Lst<javajs.util.P3> getPointVector(T t, int i) throws ScriptException
- Throws:
ScriptException
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getFloatEncodedInt
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
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getPartialBondOrderFromFloatEncodedInt
public static int getPartialBondOrderFromFloatEncodedInt(int bondOrderInteger)
reads standard n.m float-as-integer n*1000000 + m and returns (n % 7) << 5 + (m % 0x1F)- Parameters:
bondOrderInteger
-- Returns:
- Bond order partial mask
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getBondOrderFromString
public static int getBondOrderFromString(java.lang.String s)
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getPartialBondOrderFromString
private static int getPartialBondOrderFromString(java.lang.String s)
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isColorParam
public boolean isColorParam(int i)
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getArgbParam
public int getArgbParam(int index) throws ScriptException
- Throws:
ScriptException
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getArgbParamLast
protected int getArgbParamLast(int index, boolean allowNone) throws ScriptException
- Throws:
ScriptException
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getArgbParamOrNone
public int getArgbParamOrNone(int index, boolean allowNone) throws ScriptException
- Throws:
ScriptException
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getColorTriad
private int getColorTriad(int i) throws ScriptException
- Throws:
ScriptException
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tickParamAsStr
public TickInfo tickParamAsStr(int index, boolean allowUnitCell, boolean allowScale, boolean allowFirst) throws ScriptException
- Parameters:
index
-allowUnitCell
- IGNOREDallowScale
-allowFirst
-- Returns:
- TickInfo
- Throws:
ScriptException
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setBooleanProperty
public void setBooleanProperty(java.lang.String key, boolean value)
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setIntProperty
protected boolean setIntProperty(java.lang.String key, int value)
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setFloatProperty
protected boolean setFloatProperty(java.lang.String key, float value)
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setStringProperty
protected void setStringProperty(java.lang.String key, java.lang.String value)
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checkHKL
public javajs.util.T3 checkHKL(javajs.util.T3 pt) throws ScriptException
Note - this check does not allow a 0 for h, k, or l.- Parameters:
pt
-- Returns:
- pt or throw invArg
- Throws:
ScriptException
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planeValue
public javajs.util.P4 planeValue(T x)
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