From: Christoph S. <ste...@eb...> - 2009-01-14 22:37:57
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Nikolay Kochev wrote: >> I really think we should read in what we get, not more but also not less. >> If we start validating things inside the SMILES parser, we get into a >> lot of trouble and a never ending story. >> So, I think c1ccc1 should result in a 4-membered ring with all >> aromaticity flags set. >> It might be an error or someone wants to tell us something he considers >> important. :-) >> Again, afterwards, there can be a Validator running over what the SMILES >> parser returned. >> This concept is modular and removes decencies. >> > > > c1ccc1 is not aromatic. As far as I can remember it anti-aromatic. As I said above, detecting it as aromatic is an error (as in "wrong"). > In SMILES "c" - does not mean aromatic. It means sp2 carbon (and it might > be aromatic or not aromatic) That has been discussed again and again and there is no normative source for one or the other. 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.. |