Can you replicate this for other cases with an explicit [H].
On Wed, Nov 4, 2009 at 11:23 AM, Mark Rijnbeek <ma...@ebi.ac.uk> wrote:
>
> Hello,
>
> for my Orchem project I'm looking into CDK SMARTS matching inside the
> database. Things work pretty well, I just now encountered a particular
> (non aromatic) compound that does not seem to match against itself. It
> seems the hydrogen is the reason, example below.
>
> The standalone program creates an atom container based on SMILES, and a
> SMARTS query tool using that same smiles, then looks if the SMILES
> container matches itself as a SMARTS query.
> It doesn't work, but does work if you remove the [H]. The Universal
> Isomorphism Tester looks to be the culprit, getSubgraphMaps does not
> give a list back. I was wondering if this is expected behaviour.
>
> thanks,
> Mark
> ___________________________
>
>
> Output
> ------
> smiles is:[H][C@@]1(CCC(C)=CC1=O)C(C)=C
> smarts is:[H][C@@]1(CCC(C)=CC1=O)C(C)=C
> no match
>
> smiles is:[C@@]1(CCC(C)=CC1=O)C(C)=C
> smarts is:[C@@]1(CCC(C)=CC1=O)C(C)=C
> match
>
>
>
> Class
> -----
> package uk.ac.ebi.orchem.scratch;
>
> import org.openscience.cdk.interfaces.IMolecule;
> import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
> import org.openscience.cdk.smiles.SmilesParser;
> import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
> import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
>
> public class UITTest {
> public static void main(String[] args) throws Exception {
>
> test("[H][C@@]1(CCC(C)=CC1=O)C(C)=C");
> test("[C@@]1(CCC(C)=CC1=O)C(C)=C");
>
> }
> public static void test (String smiles ) throws Exception {
> System.out.println("smiles is:"+smiles);
> SmilesParser sp = new SmilesParser
> (NoNotificationChemObjectBuilder.getInstance());
>
> IMolecule mol = sp.parseSmiles(smiles);
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
>
> SMARTSQueryTool querytool = new SMARTSQueryTool(smiles);
> System.out.println("smarts is:"+querytool.getSmarts());
>
> if (querytool.matches(mol))
> System.out.println("match");
> else {
> System.out.println("no match");
> }
>
> }
> }
>
>
>
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--
Rajarshi Guha
NIH Chemical Genomics Center
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