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
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