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java.lang.Objectorg.jmol.smiles.PatternMatcher
public class PatternMatcher
A class to match a SMILES pattern with a Jmol molecule.
The SMILES specification can been found at the SMILES Home Page.
An example on how to use it:
PatternMatcher matcher = new PatternMatcher(jmolViewer);
try {
BitSet bitSet = matcher.getSubstructureSet(smilesString);
// Use bitSet...
} catch (InvalidSmilesException e) {
// Exception management
}
SmilesMolecule
Field Summary | |
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private int |
atomCount
|
private ModelSet |
modelSet
|
Constructor Summary | |
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PatternMatcher()
Constructs a PatternMatcher . |
Method Summary | |
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java.util.BitSet |
getSubstructureSet(SmilesMolecule pattern)
Returns a vector of bits indicating which atoms match the pattern. |
java.util.BitSet |
getSubstructureSet(java.lang.String smiles)
Returns a vector of bits indicating which atoms match the pattern. |
private void |
searchMatch(java.util.BitSet bs,
SmilesMolecule pattern,
int atomNum)
Recursively search matches. |
private void |
searchMatch(java.util.BitSet bs,
SmilesMolecule pattern,
SmilesAtom patternAtom,
int atomNum,
int i)
Recursively search matches. |
void |
setViewer(Viewer viewer)
|
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private int atomCount
private ModelSet modelSet
Constructor Detail |
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public PatternMatcher()
PatternMatcher
.
Method Detail |
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public void setViewer(Viewer viewer)
setViewer
in interface SmilesMatcherInterface
public java.util.BitSet getSubstructureSet(java.lang.String smiles) throws java.lang.Exception
getSubstructureSet
in interface SmilesMatcherInterface
smiles
- SMILES pattern.
java.lang.Exception
- Raised if smiles
is not a valid SMILES pattern.public java.util.BitSet getSubstructureSet(SmilesMolecule pattern)
pattern
- SMILES pattern.
private void searchMatch(java.util.BitSet bs, SmilesMolecule pattern, int atomNum)
bs
- Resulting BitSet (each atom in a structure is set to 1).pattern
- SMILES pattern.atomNum
- Current atom of the pattern.private void searchMatch(java.util.BitSet bs, SmilesMolecule pattern, SmilesAtom patternAtom, int atomNum, int i)
bs
- Resulting BitSet (each atom in a structure is set to 1).pattern
- SMILES pattern.patternAtom
- Atom of the pattern that is currently tested.atomNum
- Current atom of the pattern.i
- Atom number of the atom that is currently tested to match patternAtom
.
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