Hi all, Following some problems getting agreement with the InChI DLL as described at http://baoilleach.blogspot.com/2010/10/measuring-information-loss-in-file_07.html (specifally the CID15550 example), I've rewritten the handling of cis/trans stereochem a little bit. There's a little bit more to go, so I won't be checking it in today, but here's the before and after picture:
Before: (1) The current code does not perceive cis/trans stereo if a bond is in a ring (and removes it if specified in the input). After: (1) Double bonds in rings are now treated as cis/trans stereo centers. (2) If stereo is not specified for these bonds, they are considered implicitly *cis* if in rings of size <= 12 (3) When writing SMILES containing double bonds in rings, the cis/trans symbol is not written if in rings of size <= 12 (4) When writing InChIs containing double bonds in rings, the cis/trans stereodescriptor will not be written for rings of size <= 7 The value of 12 is set by inspection of Daylight Depict output. The assumption is that rings of size <= 12 cannot have a trans bond and thus are implicitly cis. The value of 7 is from the InChI technical manual. Any thoughts before I check it in? Should I hold off on merging this until after the release? It is worth noting the the SMILES on the PubChem page for the compound (http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=15550) does not show any stereo symbol - and neither will Open Babel. However, the InChI on that page is incorrect - it should show the stereochemistry at the double bonds as the ring is of size 8. - Noel ------------------------------------------------------------------------------ Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
