Package org.jmol.script

Class ScriptParam

java.lang.Object
org.jmol.script.ScriptError
org.jmol.script.ScriptParam
All Implemented Interfaces:
JmolScriptEvaluator
Direct Known Subclasses:
ScriptEval
public abstract class ScriptParam extends ScriptError
The ScriptParam class holds methods used to parse parameters in Jmol scripts.

  • Field Details

    • contextVariables

      public Map<String,SV> contextVariables

    • contextFunctions

      public Map<String,ScriptFunction> contextFunctions

    • thisContext

      public ScriptContext thisContext

    • iToken

      public int iToken

    • theTok

      public int theTok

    • theToken

      public T theToken

    • st

      public T[] st

    • slen

      public int slen

    • fractionalPoint

      public P3 fractionalPoint
      set in getPointOrPlane

    • coordinatesAreFractional

      public boolean coordinatesAreFractional
      set in getPointOrPlane

    • isBondSet

      public boolean isBondSet

    • MODE_P3

      public static final int MODE_P3
      See Also:

    • MODE_P4

      protected static final int MODE_P4
      See Also:

    • MODE_P34

      public static final int MODE_P34
      See Also:

    • MODE_P_INT_ONLY

      protected static final int MODE_P_INT_ONLY
      See Also:

    • MODE_P_ALLOW_FRACTIONAL

      public static final int MODE_P_ALLOW_FRACTIONAL
      See Also:

    • MODE_P_CONVERT_TO_CARTESIAN

      protected static final int MODE_P_CONVERT_TO_CARTESIAN
      See Also:

    • MODE_P_IMPLICIT_FRACTIONAL

      protected static final int MODE_P_IMPLICIT_FRACTIONAL
      See Also:

    • MODE_P_NULL_ON_ERROR

      protected static final int MODE_P_NULL_ON_ERROR
      See Also:

  • Constructor Details

    • ScriptParam

      public ScriptParam()

  • Method Details

    • getToken

      public T getToken(int i) throws ScriptException
      Throws:
      ScriptException

    • tokAt

      public int tokAt(int i)

    • checkToken

      protected boolean checkToken(int i)

    • getParameter

      public Object getParameter(String key, int tokType, boolean nullAsString)

    • getVarParameter

      protected Object getVarParameter(String var, boolean orReturnName)

    • getContextVariableAsVariable

      public SV getContextVariableAsVariable(String var, boolean isLocal)

    • paramAsStr

      public String paramAsStr(int i) throws ScriptException
      Throws:
      ScriptException

    • stringParameter

      public String stringParameter(int index) throws ScriptException
      Throws:
      ScriptException

    • stringParameterSet

      public String[] stringParameterSet(int i) throws ScriptException
      Throws:
      ScriptException

    • objectNameParameter

      public String objectNameParameter(int index) throws ScriptException
      Throws:
      ScriptException

    • atomCenterOrCoordinateParameter

      public P3 atomCenterOrCoordinateParameter(int i, 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)

    • centerParameter

      public P3 centerParameter(int i, Object[] ret) throws ScriptException
      Throws:
      ScriptException

    • centerParameterForModel

      protected P3 centerParameterForModel(int i, int modelIndex, Object[] ret) throws ScriptException
      Throws:
      ScriptException

    • planeParameter

      public P4 planeParameter(int i, boolean isBest) throws ScriptException
      Throws:
      ScriptException

    • getAtomsStartingAt

      public BS getAtomsStartingAt(int i) throws ScriptException
      Throws:
      ScriptException

    • getPointOrCenterVector

      public Lst<P3> getPointOrCenterVector(T t) throws ScriptException
      Throws:
      ScriptException

    • hklParameter

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

    • getHklPlane

      public P4 getHklPlane(T3 pt, float offset, Lst<P3> pts)

    • getPointOrPlane

      public 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 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 T3 getFractionalPoint(int i) throws ScriptException
      Could return a P4 for large 1100100100 type indicators
      Parameters:
      i -
      Returns:
      P3 or P4
      Throws:
      ScriptException

    • getPoint4f

      public P4 getPoint4f(int i) throws ScriptException
      Throws:
      ScriptException

    • getPoint4fNoError

      public P4 getPoint4fNoError(int i) throws ScriptException
      Throws:
      ScriptException

    • xypParameter

      public P3 xypParameter(int index) throws ScriptException
      Throws:
      ScriptException

    • xyzpParameter

      public P4 xyzpParameter(int index) throws ScriptException
      Throws:
      ScriptException

    • optParameterAsString

      public String optParameterAsString(int i) throws ScriptException
      Throws:
      ScriptException

    • intParameter

      public int intParameter(int index) throws ScriptException
      Throws:
      ScriptException

    • isFloatParameter

      public boolean isFloatParameter(int index)

    • floatParameter

      public float floatParameter(int index) throws ScriptException
      Throws:
      ScriptException

    • getPointArray

      public P3[] getPointArray(int i, int nPoints, boolean allowNull, boolean throwException) 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)
      throwException -
      Returns:
      array of P3, with possible null values
      Throws:
      ScriptException

    • listParameter

      public Lst<Object> listParameter(int i, int nMin, int nMax) throws ScriptException
      Throws:
      ScriptException

    • listParameter4

      public Lst<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 Quat getQuaternionParameter(int i, BS bsAtoms, boolean divideByCurrent) throws ScriptException
      Throws:
      ScriptException

    • checkLast

      public int checkLast(int i) throws ScriptException
      Throws:
      ScriptException

    • checkLength

      public int checkLength(int length) throws ScriptException
      Throws:
      ScriptException

    • checkLengthErrorPt

      public int checkLengthErrorPt(int length, int errorPt) throws ScriptException
      Throws:
      ScriptException

    • checkLength23

      public int checkLength23() throws ScriptException
      Throws:
      ScriptException

    • checkLength34

      protected int checkLength34() throws ScriptException
      Throws:
      ScriptException

    • modelNumberParameter

      public int modelNumberParameter(int index) throws ScriptException
      Throws:
      ScriptException

    • getMadParameter

      public int getMadParameter() throws ScriptException
      Throws:
      ScriptException

    • intParameterRange

      public int intParameterRange(int i, int min, int max) throws ScriptException
      Throws:
      ScriptException

    • floatParameterRange

      protected float floatParameterRange(int i, float min, float max) throws ScriptException
      Throws:
      ScriptException

    • getPointVector

      public Lst<P3> getPointVector(T t, int i) throws ScriptException
      Throws:
      ScriptException

    • isColorParam

      public boolean isColorParam(int i)

    • getArgbParam

      public int getArgbParam(int index) throws ScriptException
      Throws:
      ScriptException

    • getArgbParamLast

      protected int getArgbParamLast(int index, boolean allowNone) throws ScriptException
      Throws:
      ScriptException

    • getArgbParamOrNone

      public int getArgbParamOrNone(int index, boolean allowNone) throws ScriptException
      Throws:
      ScriptException

    • 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(String key, boolean value)

    • setIntProperty

      protected boolean setIntProperty(String key, int value)

    • setFloatProperty

      protected boolean setFloatProperty(String key, float value)

    • setStringProperty

      protected void setStringProperty(String key, String value)

    • checkHKL

      public T3 checkHKL(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 P4 planeValue(T x)

    • transformPoints

      public static Lst<P3> transformPoints(Lst<P3> vPts, M4 m4, P3 center)

    • getTransformMatrix4

      public static double getTransformMatrix4(Lst<P3> ptsA, Lst<P3> ptsB, M4 m, P3 centerA)
      Fills a 4x4 matrix with rotation-translation of mapped points A to B. If centerA is null, this is a standard 4x4 rotation-translation matrix; otherwise, this 4x4 matrix is a rotation around a vector through the center of ptsA, and centerA is filled with that center; Prior to Jmol 14.3.12_2014.02.14, when used from the JmolScript compare() function, this method returned the second of these options instead of the first.
      Parameters:
      ptsA -
      ptsB -
      m - 4x4 matrix to be returned
      centerA - return center of rotation; if null, then standard 4x4 matrix is returned
      Returns:
      stdDev

    • setScriptArguments

      protected void setScriptArguments(Object params, boolean isCallback)
      Parameters:
      params -
      isCallback - unused to date

    • getCallbackParameter

      public SV getCallbackParameter(int n)

    • getMatrixParam

      protected M34 getMatrixParam(int i, int dim, boolean throwError) throws ScriptException
      Throws:
      ScriptException