On Mon, Aug 24, 2015 at 3:31 AM, S.L. Chan <[email protected]> wrote:
>
> I got two conformers of a molecule. It looks like they have the same
> chirality (S, I believe). But RDKit perceives them as different. Is it a
> bug, or did I miss anything?
>
>
Yes, this appears to be a bug:
In [27]: m = Chem.MolFromMolFile('r3.sdf',removeHs=False)
In [28]: m2 = Chem.MolFromMolFile('b1.sdf',removeHs=False)
In [29]: Chem.AssignAtomChiralTagsFromStructure(m)
In [30]: Chem.AssignAtomChiralTagsFromStructure(m2)
In [31]: Chem.MolToSmiles(m,isomericSmiles=True)
Out[31]: '[H]C(=O)[C@
]([H])(C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[N+]([H])([H])[H]'
In [32]: Chem.MolToSmiles(m2,isomericSmiles=True)
Out[32]: '[H]C(=O)[C@
]([H])(C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[N+]([H])([H])[H]'
In [33]: Chem.FindMolChiralCenters(m)
Out[33]: [(1, 'S')]
In [34]: Chem.FindMolChiralCenters(m2)
Out[34]: [(1, 'R')]
I will investigate.
-greg
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