Hi Soren,
On Mon, Mar 30, 2015 at 11:37 PM, Soren Wacker <swac...@ucalgary.ca> wrote:
>
> I am wondering how RDKit handles molecule conformations and stereo-isomers.
> E.G. when I generate a chiral molecule from a smiles string, where
> chirality is not explicated.
> Does RDKit generate a random conformation, or no specific conformation in
> the first place?
>
By default no conformation is generated, but if you ask the RDKit to
generate a 3D conformation (or conformations), it will attempt to generate
one that matches whatever stereochemistry is specified.
So if you specify the chirality it attempts to preserve it:
In [17]: m = Chem.AddHs(Chem.MolFromSmiles('Cl[C@H](F)CC[C@H](C)Br'))
In [18]: AllChem.EmbedMultipleConfs(m,10)
Out[18]: <rdkit.rdBase._vecti at 0x7f6f9b3184d0>
In [19]: _=AllChem.UFFOptimizeMoleculeConfs(m,maxIters=1000)
In [20]: for conf in m.GetConformers():
tm = Chem.Mol(m,False,conf.GetId())
Chem.AssignAtomChiralTagsFromStructure(tm)
print Chem.FindMolChiralCenters(tm)
....:
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'S')]
But if you don't specify it, you get random stereoisomers:
In [21]: m = Chem.AddHs(Chem.MolFromSmiles('Cl[CH](F)CC[CH](C)Br'))
In [22]: AllChem.EmbedMultipleConfs(m,10)
Out[22]: <rdkit.rdBase._vecti at 0x7f6f9b318350>
In [23]: _=AllChem.UFFOptimizeMoleculeConfs(m,maxIters=1000)
In [24]: for conf in m.GetConformers():
tm = Chem.Mol(m,False,conf.GetId())
Chem.AssignAtomChiralTagsFromStructure(tm)
print Chem.FindMolChiralCenters(tm)
....:
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'R')]
[(1, 'S'), (5, 'S')]
[(1, 'S'), (5, 'R')]
[(1, 'R'), (5, 'S')]
[(1, 'R'), (5, 'S')]
[(1, 'R'), (5, 'S')]
[(1, 'S'), (5, 'S')]
[(1, 'R'), (5, 'R')]
[(1, 'R'), (5, 'S')]
Does that answer your question?
-greg
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