Confirm - I’ll look into it tonight.
For now if you don’t need the SMARTS stereochemistry you can actually use the
Pattern directly with the query container. This gives the correct answer:
Pattern pattern = Pattern.findSubstructure(SMARTSParser.parse(smarts, blr));
for (IAtomContainer ring : ringSet.atomContainers()) {
System.out.println(pattern.matches(ring));
}
On 7 Feb 2014, at 16:03, Nick Vandewiele <nick.vandewi...@ugent.be> wrote:
> Hi,
>
> I am using CDK 1.5.4 and detected some behavior of the SMARTS matcher that I
> didn’t quite understand.
> When I search for a SMARTS pattern in one of the rings detected using the
> SSSRFinder algorithm, the success of finding the pattern in the ring depends
> on whether implicit hydrogens were converted to explicit ones, or not.
> If explicit hydrogens are present, the pattern is not found. If only implicit
> hydrogens are present, the pattern IS found.
>
> This code was used:
>
> String smiles = "C1C(O)CCC1";
> IChemObjectBuilder blr =
> SilentChemObjectBuilder.getInstance();
> SmilesParser smipar = new SmilesParser(blr);
> IAtomContainer m = smipar.parseSmiles(smiles);
> String smarts = "C1-C-C-C-C1";
> SMARTSQueryTool sqt = new SMARTSQueryTool(smarts, blr);
>
> AtomContainerManipulator.convertImplicitToExplicitHydrogens(m);
> IRingSet ringSet = new SSSRFinder(m).findSSSR();//find SSSR rings
>
> for(IAtomContainer ring : ringSet.atomContainers()){
> boolean found = sqt.matches(ring);//false (should be true)
> }
>
> Although the release notes of 1.5.4 are very informative, I couldn’t find an
> answer explaining this behavior.
>
> So my question is two-fold:
> 1) how do I ensure that the pattern is found, even when explicit
> hydrogens are used in the atomcontainer?
> 2) What is happening underneath the hood here? Is this behavior normal?
>
> Regards,
> Nick
>
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