public class SmilesExt extends java.lang.Object implements JmolSmilesExtension
Modifier and Type | Field and Description |
---|---|
private ScriptEval |
e |
private SmilesMatcherInterface |
sm |
Constructor and Description |
---|
SmilesExt() |
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) |
private ScriptEval e
private SmilesMatcherInterface sm
public JmolSmilesExtension init(java.lang.Object se)
init
in interface JmolSmilesExtension
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
getSmilesCorrelation
in interface JmolSmilesExtension
bsA
- bsB
- smiles
- ptsA
- ptsB
- m4
- vReturn
- isSmarts
- asMap
- mapSet
- center
- firstMatchOnly
- bestMap
- ScriptException
public java.lang.Object getSmilesMatches(java.lang.String pattern, java.lang.String smiles, BS bsSelected, BS bsMatch3D, boolean isSmarts, boolean asOneBitset) throws ScriptException
getSmilesMatches
in interface JmolSmilesExtension
ScriptException
public float[] getFlexFitList(BS bs1, BS bs2, java.lang.String smiles1, boolean isSmarts) throws ScriptException
getFlexFitList
in interface JmolSmilesExtension
ScriptException
private static void getTorsions(Atom[] atoms, int[][] bondMap, float[][] diff, int pt)