On 10/18/10 8:54 AM, Noel O'Boyle wrote: > 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?
The rules you describe for SMILES sound exactly right. I don't remember the number 12 specifically, but I do remember debating this point while we were writing the SMILES toolkit at Daylight and we came up with this rule. Craig > > 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
