Class CmdExt

    • Constructor Detail

      • CmdExt

        public CmdExt()
    • Method Detail

      • dispatch

        public java.lang.String dispatch​(int iTok,
                                         boolean flag,
                                         T[] st)
                                  throws ScriptException
        The command dispatcher for the set of commands extended by this class. These commands can be from the Jmol command of their method name or another command or method working as though it were a command, with a non-GUI-generated compiled script.
        Specified by:
        dispatch in class ScriptExt
        Parameters:
        iTok - the current statement position, usually 1
        flag - a command-specific flag
        st - the compiled statement for this command
        Throws:
        ScriptException
      • evalParallel

        public boolean evalParallel​(ScriptContext context,
                                    ShapeManager shapeManager)
        used for TRY command
        Parameters:
        context -
        shapeManager -
        Returns:
        true if successful; false if not
      • getBitsetIdent

        public java.lang.Object getBitsetIdent​(javajs.util.BS bs,
                                               java.lang.String label,
                                               java.lang.Object tokenValue,
                                               boolean useAtomMap,
                                               int index,
                                               boolean isExplicitlyAll)
      • getBitsetIdentFull

        public java.lang.Object getBitsetIdentFull​(javajs.util.BS bs,
                                                   java.lang.String label,
                                                   java.lang.Object tokenValue,
                                                   boolean useAtomMap,
                                                   int index,
                                                   boolean isExplicitlyAll,
                                                   java.lang.String[] sout)
      • getLoadSymmetryParams

        public int getLoadSymmetryParams​(int i,
                                         javajs.util.SB sOptions,
                                         java.util.Map<java.lang.String,​java.lang.Object> htParams)
                                  throws ScriptException
        Throws:
        ScriptException
      • checkPacked

        private int checkPacked​(int i,
                                java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                javajs.util.SB sOptions)
                         throws ScriptException
        Process FILL and PACKED and all their variants.
        Parameters:
        i -
        htParams -
        sOptions -
        Returns:
        new token position
        Throws:
        ScriptException
      • compare

        private void compare()
                      throws ScriptException
        Compares one set of atoms to another, generating the matrix that takes that maps the first set's coordinates to the second's. Options TRANSLATE and ROTATE will generate an animation. See interactive documentation for more details.
        Throws:
        ScriptException
      • modulation

        private void modulation()
                         throws ScriptException
        Allows for setting one or more specific t-values as well as full unit-cell shifts (multiples of q).
        Throws:
        ScriptException
      • write

        private java.lang.String write​(T[] args)
                                throws ScriptException
        Parameters:
        args -
        Returns:
        string for write() function
        Throws:
        ScriptException
      • prepareBinaryOutput

        public javajs.util.Lst<java.lang.Object> prepareBinaryOutput​(SV tvar)
      • filterShow

        private java.lang.String filterShow​(java.lang.String msg,
                                            java.lang.String name)
      • getUVBoxFromHKL

        private javajs.util.P3[] getUVBoxFromHKL​(SymmetryInterface uc,
                                                 javajs.util.P4 hkl,
                                                 javajs.util.P4 plane)
                                          throws ScriptException
        create a uvw-space unit cell from an HKL plane
        Parameters:
        uc -
        hkl -
        plane -
        Returns:
        [o a b c]
        Throws:
        ScriptException
      • modelkit

        private void modelkit()
                       throws ScriptException
        Configure the ModelKitPopup for Crystallographic symmetry viewing and structure editing new 14.29.45 see modelkit.ModelKitPopup.java
        Throws:
        ScriptException
      • getContext

        private java.lang.String getContext​(boolean withVariables)
      • getIsosurfaceJvxl

        private java.lang.Object getIsosurfaceJvxl​(int iShape,
                                                   java.lang.String type)
      • getScriptID

        private java.lang.String getScriptID​(ScriptContext context)
      • tokenAt

        private T tokenAt​(int i,
                          T[] args)
      • tokAtArray

        private static int tokAtArray​(int i,
                                      T[] args)
      • getPlotMinMax

        private float getPlotMinMax​(float[] data,
                                    boolean isMax,
                                    int tok)
      • parseDataArray

        private java.lang.Object parseDataArray​(java.lang.String str,
                                                boolean is3D)
      • getBitsetPropertyFloat

        public float[] getBitsetPropertyFloat​(javajs.util.BS bs,
                                              int tok,
                                              java.lang.String property,
                                              float min,
                                              float max)
                                       throws ScriptException
        Throws:
        ScriptException