Hi Noel, Thanks for the update, and also for the slides! Great presentation! Also I appreciate you mentioned our study, as you pointed out this is a win-win situation for both cheminformatic tool developers and database maintainers. We will probably get back with more test results very soon.
Regarding PubChem molecule 12040015, I just sent a mail to the inchi-discuss list, as this is indeed an InChI issue I think and it is responsible for several InChI mismatches from the 878 cases. All the best, Robert >-----Original Message----- >From: Noel O'Boyle [mailto:baoille...@gmail.com] >Sent: Monday, August 29, 2011 5:45 PM >To: Róbert Kiss >Cc: openbabel-discuss@lists.sourceforge.net >Subject: Re: [Open Babel] SDF conversion test results > >Hi Robert, > >I've gotten the figure down to 120. > >69 of the remaining problems (as far as I can tell) are due to >differences between how the InChI code and Open Babel handle the >situation where you have a tetrahedral center where two of the three >non-stereo bonds are very close (in angle) to each other. If the angle >is within 4 degrees (or so), then the InChI binary will mark it as >ambiguous stereochemistry. Open Babel does not do this - it just works >out the angle and ploughs ahead. I don't regard this as a bug in Open >Babel. > >An example of this is 12040015. I guess the source of the problem is >with the depiction or structure generation - the two bonds should not >have been placed so close together (GIGO). Note that this is >reasonable behaviour by the InChI code, but it would have been useful >if there were an option to turn this off. > >I still have some work to do on the bonds marked "4", but fixing this >will have little effect on your test set (as you pointed out). > >- Noel > >On 23 August 2011 11:29, Noel O'Boyle <baoille...@gmail.com> wrote: >> I note that Chris has fixed some problems with metals, and we're down >> to 146 failures. Of these 57 have a particular substructure that >> appears to confuse OB. >> >> - Noel >> ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
