On Sat, Dec 18, 2010 at 6:27 AM, Greg Landrum <[email protected]> wrote: > > > For 'classic' aliphatic systems, double-bonds in > > 3-7-membered rings can only sensibly exist in the cis orientation, so > > 'ignoring' them would be ok. However, for 8-membered and above, cis or > > trans are certainly both possible, so it becomes more important to keep > > track - particularly if canonical smiles are being used to check for > > unique structures, as my colleague was doing with the geldanamycin > > example above. > > yeah, that's clear: for larger ring systems the information should be > preserved. That's very easy to do. The more difficult part is going to > be making sure the output is actually canonical. I've entered a bug > for this > (https://sourceforge.net/tracker/?func=detail&aid=3139534&group_id=160139&atid=814650) > and I'll take a look to try and get it fixed (and correct).
I just checked in a set of changes that should get this (mostly) working correctly. Here's a demonstration with Geldanamycin: In [7]: smi=r'NC(=O)o...@h]1c(/C)=C/[...@h](C)[C@@H](O)[C@@H](OC)c...@h](C)C\C2=C(/OC)C(=O)\C=C(\NC(=O)C(\C)=C\C=C/[C@@H]1OC)C2=O' In [8]: print Chem.CanonSmiles(smi) COC1=C2C[C@@H](C)c...@h](OC)[...@h](O)[C@@H](C)/C=C(\C)[...@h](OC(N)=O)[C@@H](OC)/C=C\C=C(/C)C(=O)NC(=CC1=O)C2=O At least according to Marvin, those two structures are the same. One very important caveat: I have not modified the depiction code to generate correct coordinates for trans bonds in cycles. All coordinates for ring systems still have all cis bonds. This has an impact if you write an SD (or mol) file : the stereochemistry captured in that file will be incorrect. I've entered a bug report for this (https://sourceforge.net/tracker/?func=detail&aid=3147014&group_id=160139&atid=814650) so that it doesn't get lost, but I suspect this is going to be a tough one to fix and not at all sure when it will done. It would be *really* useful to have some more real-world cases like this one to use as tests. So if you happen to have others you can send I would be quite happy to have them. Best Regards, -greg ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
