Package org.jmol.scriptext

Class SmilesExt

java.lang.Object
org.jmol.scriptext.SmilesExt
public class SmilesExt extends Object

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    private ScriptEval
    e
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    SmilesExt()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    float[]
    getFlexFitList(javajs.util.BS bs1, javajs.util.BS bs2, String smiles1, boolean isSmarts)
     
    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)
    The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.
    Object
    getSmilesMatches(String pattern, 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(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

  • Field Details

  • Constructor Details

    • SmilesExt

      public SmilesExt()

  • Method Details

    • init

      public SmilesExt init(Object se)

    • 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

    • getFlexFitList

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

    • getTorsions

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

    • mapPolyhedra

      public float mapPolyhedra(int i1, int i2, boolean isSmiles, javajs.util.M4 m) throws ScriptException
      Throws:
      ScriptException