Dear all, Just a quick update for the list on the below exchange:
On Fri, Oct 26, 2012 at 7:22 AM, Greg Landrum <[email protected]> wrote: > > On Fri, Oct 26, 2012 at 12:10 AM, TJ O'Donnell <[email protected]> wrote: >> >> In a recent list of about 100,000 smiles, I ran into 512 that caused >> some problems. >> Basically, the stereochemistry of the canonicalized (isomericSmiles=True) >> smiles >> gets reversed. I saw some discussion of this topic a while back, but it >> seems >> it had not been resolved. >> [15:07:50] Warning: ring stereochemistry detected. The output SMILES >> is not canonical. >> Any help or input on this? > > From looking at your output, I believe this is a known > canonicalization problem (thus the warning above), not one of > correctness. > <snip> > The last time I looked at stereochemistry canonicalization, I was > unable to devise a scheme that handled these systems correctly while > still reliably canonicalizing things. It's worth revisiting this at > some point, but this is probably one of those "requires a long block > of uninterrupted concentration" things that are difficult for me to > schedule. At some point during the week a possible solution to this long-standing problem came to me. I checked a fix in yesterday and TJ has verified that it works for his molecules. I'm going to run some more canonicalization torture tests, but it's looking like I will actually be able to finally close a bug that was originally opened in early 2008: http://sourceforge.net/p/rdkit/bugs/40/ . That's got to make me smile. :-) -greg ------------------------------------------------------------------------------ LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
