From: Christoph S. <ste...@eb...> - 2011-06-20 11:18:15
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Thanks for the correction. You are of course completely right. Cheers, Chris -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. On 19 Jun 2011, at 08:16, Egon Willighagen wrote: > On Thu, Jun 16, 2011 at 11:04 AM, Christoph Steinbeck > <ste...@eb...> wrote: >> Thanks, Andrew, for pointing this out. Seems so obvious but we always went for the over-engineered approach :-) > > No, I would not phrase it like that; the current aromaticity searching > reuses components, rather than reinventing the wheel. > > It uses the (fast) spanning tree to find fused ring systems, counts > the rings (using the SSSR), and if <= three and the rings are not > found aromatic yet, it uses the AllRingsFinder to larger aromatic > rings. > > The ring counting can be improved, using atom and bond count. And what > it should do, is not find fused ring systems, but find fused, > potentially aromatic ring systems. The latter is what I was talking > about, in reply to Andrew's suggestion. This will not remove the need > for the AllRingsFinder. > > If anything, introducing this will further engeneer things into a more > complex framework, rather than simplify it. Aromaticity is not a > concept that allows for simple algorithms. The most basic Hueckel > approach does, but is only defined for a single ring, ignoring > sprouting with double bonds etc. > > Andrew, maybe we should write up a review on aromaticity in > cheminformatics? Set up a simple test set of corner cases, describe > the algorithms around, and show their limitations, using Open Source > implementations? > > Egon > > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Institutet för miljömedicin > Karolinska Institutet (http://ki.se/imm) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |