I think getSubgraphAtomsMaps() calls makeAtomsMapsOfBondsMaps(). However, your
email gave me an idea. It appears you need at least 3 atoms in the smarts
string for the atom mapping to work:
<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('CCO')
bondMatches = U.getSubgraphMaps(mol, smarts)
for match in bondMatches:
print 'BondMatch:',
for rMap in match:
print '%d-%d' % (rMap.getId1(), rMap.getId2()),
print
atomMatches = U.getSubgraphAtomsMaps(mol, smarts)
for match in atomMatches:
print 'AtomMatch: ', match
</jython-code>
<output>
BondMatch: 0-1 1-0
BondMatch: 4-0 5-1
AtomMatch: [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED]
AtomMatch: [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED]
</output>
Stephen.
---
Stephen Pascoe 01235 445980
Climateprediction.net data scientist
Rutherford Appleton Laboratory, CCLRC
-----Original Message-----
From: Nina Jeliazkova [mailto:[EMAIL PROTECTED]
Sent: 20 December 2005 15:11
To: Pascoe, S (Stephen)
Cc: [email protected]
Subject: Re: [Cdk-user] Using UniversalIsomorphismTester to detect functional
groups
Hi,
There are two static methods in UniversalIsomorphismTester class which can be
used to convert bond maps to atom maps.
public static List makeAtomsMapsOfBondsMaps(List l, AtomContainer g1,
AtomContainer g2) public static List makeAtomsMapOfBondsMap(List l,
AtomContainer g1, AtomContainer g2)
Haven't tried with jython, but works nice from java.
Regards,
Nina
"Pascoe, S (Stephen)" <[EMAIL PROTECTED]> wrote:
> 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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--
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* * Institute for Parallel Processing
* * Bulgarian Academy of Sciences
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* The Bulgarian NREN * 1113 Sofia, Bulgaria
* * Tel: +359 886 802011
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