On Mon, Dec 5, 2011 at 7:42 PM, JP <[email protected]> wrote: > Monday stereochemistry blues,
sounds bad. ;-) > Using RDKit 2011.09.01 on Ubuntu GNU Linux 10.10. > > When generating smiles via the "AssignAtomChiralTagsFromStructure" > method not all stereo centres are defined as highlighted in the > following (and attached) example: > > Expected smiles (including stereo) > O=C1N2[C@@H](C(=O)[O-])C(C)(C)[S@](=O)[C@@H]2[C@@H]1NC(=O)Cc1ccccc1 > > Actual smiles (including stereo) > c1ccc(CC(N[C@@H]2C(=O)N3[C@@H](C([O-])=O)C(C)(C)S(=O)[C@@H]32)=O)cc1 > > The S atom is a chiral centre (it has lone pairs), but has no > stereochemistry defined. The RDKit does not recognize three-coordinate sulfur as a stereogenic atom; it should. This is a bug (https://sourceforge.net/tracker/?func=detail&aid=3453172&group_id=160139&atid=814650). I'm not really sure how much effort this is going to be to fix, so I'm not sure it will be fixed before the next release. -greg ------------------------------------------------------------------------------ Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
