Hi Lauren,
The enhanced stereochemistry is available, not as atom properties, but as
"stereo groups" of the Mol object. For example,
>>> mol = Chem.MolFromSmiles('C[C@H]1CCCNC1 |&1:1,r|')
>>> for group in mol.GetStereoGroups():
print([group.GetGroupType(),
[atom.GetIdx() for atom in group.GetAtoms()]])
[rdkit.Chem.rdchem.StereoGroupType.STEREO_AND, [1]]
So in this case you have a single "AND" group consisting of only one atom,
1.
Hope this helps,
Ivan
On Tue, Nov 8, 2022 at 11:46 AM Lauren Reid <lauren.r...@medchemica.com>
wrote:
> Hi RDKit users,
>
> I'm using RDKit to read in CXSMILES with enhanced stereochemistry
> information using:
>
> from rdkit import Chem
> parser_params = Chem.SmilesParserParams()
> parser_params.allowCXSMILES = True
> parser_params.strictCXSMILES = True
>
> mol = Chem.MolFromSmiles("C[C@H]1CCCNC1 |&1:1,r|", parser_params)
>
>
> I can’t find in the docs how I can access the enhanced stereochemistry
> information associated with the rdchem.Mol. Does anyone know if it is
> possible to iterate over the atoms in mol and receive the enhanced
> stereochemistry labels associated with each atom? E.g, Is there an atom
> property that stores the “&” label for atom 1?
>
> Thanks in advance for any help.
>
> Lauren
>
> Dr Lauren Reid
> Computational Chemist / Developer
> MedChemica Ltd
>
> Medchemica Ltd is a company registered in England and Wales with company
> number 8162245
>
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