On Feb 8, 2016, at 7:03 PM, Paolo Tosco wrote: > ... there is a "ghost" atom involved in determining the sulfur chirality, > which is the sulfur lone pair. Even if this is not in the Daylight specs, the > lone-pair is usually treated as an implicit hydrogen, and therefore > considered as the first atom in the clockwise or anticlockwise accounting:
Thanks for the explanation. Interestingly, I see that two different RDKit versions give two different answers. Which is correct? == most recent version appears to swap the chirality == >>> import rdkit >>> rdkit.__version__ '2016.03.1.dev1' >>> Chem.CanonSmiles("CN[S@](c1ccccc1)=O") 'CN[S@@](=O)c1ccccc1' >>> Chem.CanonSmiles("CN[S@]2=O.c12ccccc1") 'CN[S@](=O)c1ccccc1' == older version gives the answer I expect == >>> import rdkit >>> rdkit.__version__ '2015.09.1.dev1' >>> Chem.CanonSmiles("CN[S@](c1ccccc1)=O") 'CN[S@@](=O)c1ccccc1' >>> Chem.CanonSmiles("CN[S@]2=O.c12ccccc1") 'CN[S@@](=O)c1ccccc1' I think the older version is correct because the SMILES chirality depends on the bond ordering, not the lexical position. I don't see anything in the milestone:2016_03_1 issues related to this specific item, so I wonder if this change was deliberate. Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss