Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

2017-02-10 Thread Greg Landrum
To close the loop on this: the bug fix is now merged onto master. The ring stereochemistry code now handles spiro centers. Here's the little demo of that: In [2]: print(Chem.CanonSmiles('O[C@H]1CC[C@]11CC[C@@](Cl)(Br)CC1')) O[C@H]1CC[C@]12CC[C@@](Cl)(Br)CC2 Unlike previously (see the bug report)

Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

2017-02-08 Thread Greg Landrum
SetIsotope(0) > > sdf.write(mol) > > > > > > GIST is updated to include this: https://gist.github.com/jepdavidson/ > fdfbf6366a17f4829de3d4de22f3b442 > > > > Kind regards > > > > James > > > > > > *From:* Greg Landrum [mailto:greg

Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

2017-02-08 Thread James Davidson
2017 03:45 To: James Davidson Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?) Hi James, This is definitely a bug. The problem seems to be connected to the way what the RDKit calls "ring stereochemistry" i

Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

2017-02-07 Thread Greg Landrum
Hi James, This is definitely a bug. The problem seems to be connected to the way what the RDKit calls "ring stereochemistry" is handled when there are spiro linkages. Here's the github issue: https://github.com/rdkit/rdkit/issues/1294 I'll take a look. Best, -greg On Tue, Feb 7, 2017 at