Class SmilesExt

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

  • Constructor Details

    • SmilesExt

      public SmilesExt()

  • Method Details

    • init

      public SmilesExt init(Object se)

    • getSmilesCorrelation

      public float getSmilesCorrelation(BS bsA, BS bsB, String smiles, Lst<P3> ptsA, Lst<P3> ptsB, M4 m4, Lst<BS> vReturn, boolean asMap, int[][] mapSet, 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(Object patternObj, Object smilesObj, BS bsSelected, BS bsMatch3D, int flags, boolean asOneBitset, boolean firstMatchOnly) throws ScriptException
      Parameters:
      patternObj - String or SmilesSearch
      smilesObj - String or SmilesSearch
      bsSelected -
      bsMatch3D -
      flags -
      asOneBitset -
      firstMatchOnly -
      Returns:
      Object
      Throws:
      ScriptException

    • getFlexFitList

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

    • mapPolyhedra

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