Doh - of course. So the SMARTS has a quirk that ‘C1’ matches the
‘CDKConstants.ISINRING’ flag.
We can fix this without a patch - just add this before you match. The
SMARTSQueryTool should be doing it already - not sure why it isn’t though….
(that’s the bug)
> SmartsMatchers.prepare(ring, true);
On 7 Feb 2014, at 17:03, John May <john...@ebi.ac.uk> wrote:
> No problem,
>
> master, but nothing should have changed…
>
> J
>
> On 7 Feb 2014, at 16:47, Nick Vandewiele <nick.vandewi...@ugent.be> wrote:
>
>> John,
>>
>> Thanks for the fast response!
>>
>> However: adding or removing dashes in the SMARTS string doesn’t change the
>> outcome when I try it.
>>
>> Also, using your proposed alternative, eg:
>> Pattern pattern = Ullmann.findSubstructure(SMARTSParser.parse(smarts, blr));
>>
>> for (IAtomContainer ring : ringSet.atomContainers()) {
>> System.out.println(pattern.matches(ring));
>> }
>>
>> Does not change the outcome (ie false) for me neither.
>> Are you using the 1.5.4 or master branch?
>>
>> Regards,
>> Nick
>>
>> From: John May [mailto:john...@ebi.ac.uk]
>> Sent: Friday, February 07, 2014 5:28 PM
>> To: Nick Vandewiele
>> Cc: cdk-user@lists.sourceforge.net
>> Subject: Re: [Cdk-user] SMARTS matching after implicit to explict hydrogen
>> conversion and SSSRing finder
>>
>> Okay it’s the bond matching… C-1-C-C-C-C1 works but C1-C-C-C-C1 doesn’t.
>>
>> Should be an easy fix.
>>
>> J
>>
>> 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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