That solves my problem, thank you very much. On Wed, Jan 29, 2014 at 6:19 AM, Greg Landrum <[email protected]> wrote: > > 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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