Field Detail

• e

  private ScriptEval e

• sm

  private SmilesMatcherInterface sm

Constructor Detail

• SmilesExt

  public SmilesExt()

Method Detail

• init

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

• getSmilesCorrelation

  public float getSmilesCorrelation​(BS bsA,
                                    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<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,
                                           BS bsSelected,
                                           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​(BS bs1,
                                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)