On Tue, Jan 28, 2014 at 1:20 PM, Michał Nowotka <[email protected]> wrote:
> Look at this code:
>
> from rdkit import Chem
> mol =
> Chem.MolFromSmiles('O=C(O)C2N3C(=O)C(NC(=O)C(c1ccc(O)cc1)NC(=O)C(N)CC(=O)NC)C3SC2(C)C')
> Chem.AssignStereochemistry(mol, flagPossibleStereoCenters=True)
> [atom.HasProp('_ChiralityPossible') for atom in mol.GetAtoms()]
>
> >>> [0,0,0, ... only zeros ...]
>
> I believe this compound contains 5 possible stereo centers (picture
> attached). How can I get them detected by RDKit?
>
Because AssignStereochemistry() is an expensive operation, when you call it
the code checks to see if it has already been run. If so, the default
behavior is to immediately return. The SMILES parser calls
AssignStereochemistry without the flagPossibleStereoCenters argument set,
so when you call it nothing happens. You can force the calculation using
the force keyword. Here's your example:
In [8]: mol =
Chem.MolFromSmiles('O=C(O)C2N3C(=O)C(NC(=O)C(c1ccc(O)cc1)NC(=O)C(N)CC(=O)NC)C3SC2(C)C')
In [9]: Chem.AssignStereochemistry(mol,flagPossibleStereoCenters=True)
In [10]: [atom.GetIdx() for atom in mol.GetAtoms() if
atom.HasProp('_ChiralityPossible')]
Out[10]: []
In [11]:
Chem.AssignStereochemistry(mol,flagPossibleStereoCenters=True,force=True)
In [12]: [atom.GetIdx() for atom in mol.GetAtoms() if
atom.HasProp('_ChiralityPossible')]
Out[12]: [3, 7, 11, 22, 29]
This is the intended behavior, but I admit that it is somewhat confusing.
Since it doesn't add compute time, I will modify the molecule parsers to
use the flagPossibleStereoCenters argument.
Best,
-greg
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