I've been trying to use the smarts facilities of CDK to detect
functional groups within SMILES strings. The
UniversalIsomorphismTester.getSubgraph*() methods seem to be what I
want. I can get the bond mapping to work but the
UniversalIsomorphismTest.getSubgraphAtomsMaps() method doesn't seem to
work. Below is some Jython code to illustrate my point. I hope it's
self explanitory even for those not familiar with python:
<jython-code>
import org.openscience.cdk as CDK
U = CDK.isomorphism.UniversalIsomorphismTester
mol = CDK.smiles.SmilesParser().parseSmiles('OCCC=CCO')
smarts = CDK.smiles.smarts.SMARTSParser.parse('CO')
bondMatches = U.getSubgraphMaps(mol, smarts)
for match in bondMatches:
print 'BondMatch:',
for rMap in match:
print '%d-%d' % (rMap.getId1(), rMap.getId2())
atomMatches = U.getSubgraphAtomsMaps(mol, smarts)
for match in atomMatches:
print 'AtomMatch: ', match
</jython-code>
<output>
BondMatch: 0-0
BondMatch: 5-0
AtomMatch: []
AtomMatch: []
</output>
The atom mapping are empty, even though the bond mappings are correct.
Am I missunderstanding the purpose of getSubgraphAtomsMaps()?
Converting from a bond mapping to an atom mapping doesn't look easy,
since a bond could match in either direction (e.g. above the first match
is an O-C bond, the second match is a C-O bond). Is there a facility in
CDK to do this?
Thanks,
Stephen
---
Stephen Pascoe 01235 445980
Climateprediction.net data scientist
Rutherford Appleton Laboratory, CCLRC
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