From: <a.s...@ch...> - 2006-07-07 14:57:13
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Hi all, there is a bug in the SmilesParser for the SMILES c%101ccccc1.O%10 (dot-connected phenole). The problem is probably, that the first ring opening is read as %101 instead of %10 and thus the second ring opening (with symbol 1) is never found. The reformated SMILES c1%10ccccc1.O%10 works. According to the Daylight theory manual, percent sign ring closures must be two digits only. I noticed the bug since after parsing the smiles, the StructureDiagramGenerator throws the following exception: org.openscience.cdk.exception.CDKException: Molecule not connected. Use ConnectivityChecker.partitionIntoMolecules() and do the layout for every single component. I didn't want to file a but report yet, since I don't know whether this bug will still exist in Todd's new SmilesParser. cheers, Andreas -- PhD student in the research group of Prof. Dr. Gisbert Schneider Institute for Organic Chemistry and Chemical Biology Chair for Chemo- and Bioinformatics Beilstein-endowed Chair for Chemoinformatics Johann Wolfgang Goethe University Siesmayerstr. 70 60323 Frankfurt am Main Germany Tel.: +49-69-798-24879 Fax: +49-69-798-24880 http://www.modlab.de/ |
From: Egon W. <e.w...@sc...> - 2006-07-08 11:42:49
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On Friday 07 July 2006 16:44, Andreas Sch=FCller wrote: > I didn't want to file a but report yet, since I don't know whether this > bug will still exist in Todd's new SmilesParser. Yes, I think it will. Todd's patch is mostly concerned with addressing the= =20 find-the-correct-bond-order-distribution problem. I've just filed it as a b= ug=20 report. Egon =2D-=20 e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |