Hi Ivan,
Thank you for the information! That’s very helpful.
Thanks,
Lauren
Dr Lauren Reid
Computational Chemist / Developer
MedChemica Ltd
Medchemica Ltd is a company registered in England and Wales with company number
8162245
> On 8 Nov 2022, at 16:58, Ivan Tubert-Brohman
> <ivan.tubert-broh...@schrodinger.com> wrote:
>
> 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
> <mailto: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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