From: SourceForge.net <no...@so...> - 2011-02-24 12:10:19
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Patches item #3183552, was opened at 2011-02-16 10:15 Message generated for change (Comment added) made by mark_rynbeek You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3183552&group_id=20024 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: master Group: Needs Review Status: Open Resolution: None Priority: 5 Private: No Submitted By: Mark Rijnbeek (mark_rynbeek) Assigned to: Nobody/Anonymous (nobody) Summary: Tautomer generation based on InChI Initial Comment: This patch is for a class to generate tautomers, based on a paper which describes an InChI based algorithm (see: http://pubs.acs.org/doi/abs/10.1021/ci1001179) The patch contains a class to generate tautomers, a test class and some minor changes to make the ant build/test work. I put the new class in its own module 'tautomer'. ---------------------------------------------------------------------- Comment By: Mark Rijnbeek (mark_rynbeek) Date: 2011-02-24 12:10 Message: Thanks Gilleain. Could you update your patches so that they work in case they're outdated? By the way, Egon mentioned warfarin earlier. I have added it as a unit test, you get six tautomers. The mobile hydrogens for warfarin are set only if you set flag KET for the InChI generation (https://sourceforge.net/mailarchive/forum.php?forum_name=inchi-discuss) ---------------------------------------------------------------------- Comment By: gilleain maclean torrance (gilleain) Date: 2011-02-24 11:58 Message: Ah. I just made some patches for a couple of possible changes. They're probably outdated, but they are : a) Narrowing the thrown Exception to CDKException/CloneNotSupported b) Slightly faster duplicate removal code I'll attach the patches anyway, to show what I mean. ---------------------------------------------------------------------- Comment By: Mark Rijnbeek (mark_rynbeek) Date: 2011-02-24 11:51 Message: Thanks, I removed the IMoleculeSet (which seemed an approriate class, is it 'deprecated'?) and replaced it with List<IAtomContainer>. The IAtomContainer is more practical than IMolecule, as I pass them into SMSD which works on atom containers. I also added more test cases. ---------------------------------------------------------------------- Comment By: Rajarshi Guha (rajarshi) Date: 2011-02-19 14:23 Message: Looks good. My only comment is that I'd rather see List<IMolecule> used as the return type than IMoleculeSet in getTautomers() and elsewhere. Otherwise I think it can be applied ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2011-02-16 10:18 Message: Cool! ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3183552&group_id=20024 |