Package org.jmol.script

Class ScriptParam

  • 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.

    • Field Detail

      • contextVariables

        public java.util.Map<java.lang.String,​SV> contextVariables

      • contextFunctions

        public java.util.Map<java.lang.String,​ScriptFunction> contextFunctions

      • iToken

        public int iToken

      • theTok

        public int theTok

      • theToken

        public T theToken

      • st

        public T[] st

      • slen

        public int slen

      • fractionalPoint

        public javajs.util.P3 fractionalPoint
        set in getPointOrPlane

      • coordinatesAreFractional

        public boolean coordinatesAreFractional
        set in getPointOrPlane

      • isBondSet

        public boolean isBondSet

      • MODE_P_ALLOW_FRACTIONAL

        public static final int MODE_P_ALLOW_FRACTIONAL
        See Also:
        Constant Field Values

      • MODE_P_CONVERT_TO_CARTESIAN

        protected static final int MODE_P_CONVERT_TO_CARTESIAN
        See Also:
        Constant Field Values

      • MODE_P_IMPLICIT_FRACTIONAL

        protected static final int MODE_P_IMPLICIT_FRACTIONAL
        See Also:
        Constant Field Values

    • Constructor Detail

      • ScriptParam

        public ScriptParam()

    • Method Detail

      • tokAt

        public int tokAt​(int i)

      • checkToken

        protected boolean checkToken​(int i)

      • getParameter

        public java.lang.Object getParameter​(java.lang.String key,
                                     int tokType,
                                     boolean nullAsString)

      • getVarParameter

        protected java.lang.Object getVarParameter​(java.lang.String var,
                                           boolean orReturnName)

      • getContextVariableAsVariable

        public SV getContextVariableAsVariable​(java.lang.String var,
                                       boolean isLocal)

      • 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

      • isCenterParameter

        public boolean isCenterParameter​(int i)

      • centerParameterForModel

        protected javajs.util.P3 centerParameterForModel​(int i,
                                                 int modelIndex,
                                                 java.lang.Object[] ret)
                                          throws ScriptException
        Throws:
        ScriptException

      • hklParameter

        public javajs.util.P4 hklParameter​(int i,
                                   javajs.util.Lst<javajs.util.P3> pts,
                                   boolean allowOffset)
                            throws ScriptException
        Throws:
        ScriptException

      • getHklPlane

        public javajs.util.P4 getHklPlane​(javajs.util.T3 pt,
                                  float offset,
                                  javajs.util.Lst<javajs.util.P3> pts)

      • 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

      • isPoint3f

        public boolean isPoint3f​(int i)

      • 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

      • 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

      • isFloatParameter

        public boolean isFloatParameter​(int index)

      • 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 points
        allowNull - if allowing null values (as in setting atom properties such as vxyz or xyz)
        Returns:
        array of P3, with possible null values
        Throws:
        ScriptException

      • listParameter

        public javajs.util.Lst<java.lang.Object> listParameter​(int i,
                                                       int nMin,
                                                       int nMax)
                                                throws ScriptException
        Throws:
        ScriptException

      • listParameter4

        public javajs.util.Lst<java.lang.Object> listParameter4​(int i,
                                                        int nMin,
                                                        int nMax,
                                                        boolean allowString)
                                                 throws ScriptException
        Throws:
        ScriptException

      • 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

      • isArrayParameter

        public boolean isArrayParameter​(int i)

      • getQuaternionParameter

        public javajs.util.Quat getQuaternionParameter​(int i,
                                               javajs.util.BS bsAtoms,
                                               boolean divideByCurrent)
                                        throws ScriptException
        Throws:
        ScriptException

      • 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

      • 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

      • getBondOrderFromString

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

      • getPartialBondOrderFromString

        private static int getPartialBondOrderFromString​(java.lang.String s)

      • isColorParam

        public boolean isColorParam​(int i)

      • tickParamAsStr

        public TickInfo tickParamAsStr​(int index,
                               boolean allowUnitCell,
                               boolean allowScale,
                               boolean allowFirst)
                        throws ScriptException
        Parameters:
        index -
        allowUnitCell - IGNORED
        allowScale -
        allowFirst -
        Returns:
        TickInfo
        Throws:
        ScriptException

      • setBooleanProperty

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

      • setIntProperty

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

      • setFloatProperty

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

      • setStringProperty

        protected void setStringProperty​(java.lang.String key,
                                 java.lang.String value)

      • 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

      • planeValue

        public javajs.util.P4 planeValue​(T x)