On 2012-10-08 21:08, Reinis Danne wrote: > On Mon, Oct 08, 2012 at 07:40:51PM +0200, David van der Spoel wrote: >> On 2012-10-08 19:11, Reinis Danne wrote: >>> On Mon, Oct 08, 2012 at 03:00:30PM +0200, David van der Spoel wrote: >>>>> >>>>> It adds TWO H for InChi output, not for SDF output, but it only produces >>>>> two double bonds (out of three). I guess these are related? >>> >>> Yes, they are. It is bond order perception fail (together with >>> kekulization). More about it below. >>> >> Fulvene works with this patch, both pdb and gaussian. >> For Azulene and Tetracene pdb input work but not gaussian (double bonds >> in the wrong place). > > In wrong place? I saw just respectively one or two separate Cs, > so I think it didn't find optimal matching and ended up with one > less double bond. Tough I still have to check if it really was > the case. I have a new kekulization implementation (it is not > yet really in usable state) and it finds correct double bonds > for azulene and tetracene so I think there might be kekulization > at fault. Tough it still doesn't explain why now PDB works while > Gaussian output doesn't.
I would be happy to test it, have > 1500 small molecules that I need bondorders for. If I compare the sdf from the old and the new algorithm I can manually check those that are different. > >> >> Is the Gaussian parsing based on Z-matrix or coordinates? If it would be >> based on coordinates I don't see why pdb should work and gaussian not. >> If there is some other kind of tree algorithm based on the zmat that >> could explain the difference. > > No, looking at the sources (line 388 and below) looks like it > uses xyz coordinates. > >> >> Fulvene and Azulene are both resonant structures, but do not adhere to >> the (2n+2) rule, so not aromatic according to that definition. > > I presume you meant 4n+2 rule. So the answer is that one can't > count those two electrons. Interestingly a quick search turned > up a paper (DOI: 10.1039/C003686B) suggesting it can go from > antiaromatic to aromatic depending on substituents or electronic > excitation state (DOI: 10.1021/ja045729c). > > I ran a short HF calculation on the SMILES molecule and the > small ring turned out to be not planar when there are Hs, so I > guess that it makes the reference SMILES correct since planarity > is one of the conditions for aromaticity. Still have to figure > out why the tests fail. > Be careful interpreting such calculations, there are quite a few cases where the energy landscape is shallow and correlated methods plus very tight optimization is needed to get the right answer, e.g. aniline springs to mind. -- 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 ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
