org.jmol.scriptext

Class SmilesExt

java.lang.Object

org.jmol.scriptext.SmilesExt

All Implemented Interfaces:

JmolSmilesExtension

public class SmilesExt
extends java.lang.Object
implements JmolSmilesExtension

Field Summary

Fields

Modifier and Type	Field and Description
private ScriptEval	e
private SmilesMatcherInterface	sm

Constructor Summary

Constructors

Constructor and Description
SmilesExt()

Method Summary

Modifier and Type	Method and Description
float[]	getFlexFitList(BS bs1, BS bs2, java.lang.String smiles1, boolean isSmarts)
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 isSmarts, boolean asMap, int[][] mapSet, javajs.util.P3 center, boolean firstMatchOnly, boolean bestMap) 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, BS bsSelected, BS bsMatch3D, boolean isSmarts, boolean asOneBitset)
private static void	getTorsions(Atom[] atoms, int[][] bondMap, float[][] diff, int pt)
JmolSmilesExtension	init(java.lang.Object se)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

e

private ScriptEval e

sm

private SmilesMatcherInterface sm

Constructor Detail

SmilesExt

public SmilesExt()

Method Detail

init

public JmolSmilesExtension init(java.lang.Object se)

Specified by:

init in interface JmolSmilesExtension

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 isSmarts,
                                  boolean asMap,
                                  int[][] mapSet,
                                  javajs.util.P3 center,
                                  boolean firstMatchOnly,
                                  boolean bestMap)
                           throws ScriptException

The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.

Specified by:

getSmilesCorrelation in interface JmolSmilesExtension

Parameters:

bsA -

bsB -

smiles -

ptsA -

ptsB -

m4 -

vReturn -

isSmarts -

asMap -

mapSet -

center -

firstMatchOnly -

bestMap -

Returns:

standard deviation

Throws:

ScriptException

getSmilesMatches

public java.lang.Object getSmilesMatches(java.lang.String pattern,
                                         java.lang.String smiles,
                                         BS bsSelected,
                                         BS bsMatch3D,
                                         boolean isSmarts,
                                         boolean asOneBitset)
                                  throws ScriptException

Specified by:

getSmilesMatches in interface JmolSmilesExtension

Throws:

ScriptException

getFlexFitList

public float[] getFlexFitList(BS bs1,
                              BS bs2,
                              java.lang.String smiles1,
                              boolean isSmarts)
                       throws ScriptException

Specified by:

getFlexFitList in interface JmolSmilesExtension

Throws:

ScriptException

getTorsions

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