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<mailto: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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