On 20 February 2010 13:35, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: >> http://my.cdash.org/index.php?project=Open%20Babel > > Here's another failure. This is on the SMILES/SMARTS match test (i.e., all of > these SMILES should match themselves when turned into SMARTS). > > O([P@@](N)(=O)c1ccccc1)CC > > When I read this in as a SMILES and output as a SMILES, I lose chirality: > > O(P(=O)(N)c1ccccc1)CC > > Now if I look at the smartsmatch results > (http://my.cdash.org/testDetails.php?test=1816390&build=49366) I can see that > each of the failing molecules has a "chiral" non-carbon atom like > "c...@]1[c@@H](CCC1)[C@@H]1CCCNC1". > > In previous versions, we retained these chiral specifiers. I can certainly > understand "N" being ignored, but "P" and "S" can definitely be chiral. Does > the new stereo analysis ignore all non-carbon atoms for chirality?
I think the answer is probably "yes". I'll look into it. I have a feeling that there is some corner case where a lone pair is involved in the chirality, but it should be relatively to deal with the general case. > Thanks, > -Geoff > > (Two tests with clear analysis, two tests "failing" due to bug-fixes which > have been updated, one left) > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
