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 > <[email protected]> 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 <[email protected] > <mailto:[email protected]>> 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 > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > <mailto:[email protected]> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
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