Class SmilesExt


  • public class SmilesExt
    extends Object
    • Constructor Detail

      • SmilesExt

        public SmilesExt()
    • Method Detail

      • getSmilesCorrelation

        public float getSmilesCorrelation​(javajs.util.BS bsA,
                                          javajs.util.BS bsB,
                                          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 Object getSmilesMatches​(String pattern,
                                       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
      • getTorsions

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