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
>
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
> http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk_______________________________________________
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
