On 2013-03-14 13:57, Geoffrey Hutchison wrote: >> Is there a RESP module in OB? I have code that does this rather well, >> the only thing that does not work exactly as it should is symmetry >> detection (to find atoms that should have the same charge because of >> symmetry). > > There is not a RESP module. If you have code you'd like to contribute, I > suspect it would be *highly* used. My analysis is that the vast majority of > citation for Open Babel come through Gasteiger charges. :-) > >> I have previously asked some questions here about bond-order/atom type >> detection and we are now going through a dataset of ~2000 molecules >> manually to see whether double bonds generated by OB are in the right >> place. There a few systems, in particular with five-rings, where >> problems occur. It seems to me that these errors can be detected >> relatively easy (just looking for C with 3 bonds would help). > > If you can get me a set of such mistakes, I can certainly adjust the bond > order code. I've put a zip file with a bunch of more or less pathetic cases on http://folding.bmc.uu.se/OB-BondOrderProblems.zip Some common themes are hetero rings, fused rings with odd number of carbons, isocyano groups etc.
Thanks for looking into this. > >> Somebody here said he was working on a complete new algorithm for this >> purpose > > I haven't seen such a thread. I wrote the majority of the existing code, > based on Roger Sayle's "Cruft to Content" talk which you can find online. > > I've followed the literature and haven't found anything which appears > dramatically better. > > -Geoff > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
