Class SmilesExt


  • public class SmilesExt
    extends java.lang.Object
    • Field Summary

      Fields 
      Modifier and Type Field Description
      private ScriptEval e  
    • Constructor Summary

      Constructors 
      Constructor Description
      SmilesExt()  
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      float[] getFlexFitList​(javajs.util.BS bs1, javajs.util.BS bs2, java.lang.String smiles1, boolean isSmarts)  
      float getSmilesCorrelation​(javajs.util.BS bsA, javajs.util.BS bsB, java.lang.String smiles, javajs.util.Lst<javajs.util.P3> ptsA, javajs.util.Lst<javajs.util.P3> ptsB, javajs.util.M4 m4, javajs.util.Lst<javajs.util.BS> vReturn, boolean asMap, int[][] mapSet, javajs.util.P3 center, boolean bestMap, int flags)
      The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.
      java.lang.Object getSmilesMatches​(java.lang.String pattern, java.lang.String smiles, javajs.util.BS bsSelected, javajs.util.BS bsMatch3D, int flags, boolean asOneBitset, boolean firstMatchOnly)  
      private static void getTorsions​(Atom[] atoms, int[][] bondMap, float[][] diff, int pt)  
      SmilesExt init​(java.lang.Object se)  
      float mapPolyhedra​(int i1, int i2, boolean isSmiles, javajs.util.M4 m)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • SmilesExt

        public SmilesExt()
    • Method Detail

      • init

        public SmilesExt init​(java.lang.Object se)
      • getSmilesCorrelation

        public float getSmilesCorrelation​(javajs.util.BS bsA,
                                          javajs.util.BS bsB,
                                          java.lang.String smiles,
                                          javajs.util.Lst<javajs.util.P3> ptsA,
                                          javajs.util.Lst<javajs.util.P3> ptsB,
                                          javajs.util.M4 m4,
                                          javajs.util.Lst<javajs.util.BS> vReturn,
                                          boolean asMap,
                                          int[][] mapSet,
                                          javajs.util.P3 center,
                                          boolean bestMap,
                                          int flags)
                                   throws ScriptException
        The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.
        Parameters:
        bsA -
        bsB -
        smiles -
        ptsA -
        ptsB -
        m4 -
        vReturn -
        asMap -
        mapSet -
        center -
        bestMap -
        flags -
        Returns:
        standard deviation
        Throws:
        ScriptException
      • getSmilesMatches

        public java.lang.Object getSmilesMatches​(java.lang.String pattern,
                                                 java.lang.String smiles,
                                                 javajs.util.BS bsSelected,
                                                 javajs.util.BS bsMatch3D,
                                                 int flags,
                                                 boolean asOneBitset,
                                                 boolean firstMatchOnly)
                                          throws ScriptException
        Parameters:
        pattern - e
        smiles -
        bsSelected -
        bsMatch3D -
        flags -
        asOneBitset -
        firstMatchOnly -
        Returns:
        Object
        Throws:
        ScriptException
      • getFlexFitList

        public float[] getFlexFitList​(javajs.util.BS bs1,
                                      javajs.util.BS bs2,
                                      java.lang.String smiles1,
                                      boolean isSmarts)
                               throws ScriptException
        Throws:
        ScriptException
      • getTorsions

        private static void getTorsions​(Atom[] atoms,
                                        int[][] bondMap,
                                        float[][] diff,
                                        int pt)