Hi RDKit community,
I’m using RDKit (version 2020.09.4) to read and manipulate CXSMILES with
enhanced stereochemistry group definitions. I’d like to read in a CXSMILES with
“OR” stereo groups and to change the “OR” to “absolute” within the graph mol,
before outputting the new CXSMILES. I have found the methods:
RWMol.SetStereoGroups and rdchem.CreateStereoGroups, which I assume should
provide the functionality I need, however I’m struggling to use them. Are any
of the following options in the example code possible? And if so, please can
someone advise how to implement them?
Example code:
cxsmiles = 'Cl[C@@H](F)(Br) |o1:1|'
mol = Chem.MolFromSmiles(cxsmiles)
editable_mol = Chem.RWMol(mol)
orig_stereo_grps = editable_mol.GetStereoGroups()
# option 1 - can I change the stereo group type from STEREO_OR to
STEREO_ABSOLUTE by editing an the StereoGroup object itself?
for grp in orig_stereo_grps:
print([atom.GetIdx() for atom in grp.GetAtoms()])
print(grp.GetGroupType())
# option 2 - can I construct a StereoGroup_vect object with the STEREO_ABSOLUTE
type and feed this into the SetStereoGroups command?
stereo_grps = Chem.StereoGroup_vect()
editable_mol.SetStereoGroups(list(stereo_grps))
# option 3 - can I use Chem.CreateStereoGroup to change the stereo group type?
Chem.CreateStereoGroup(Chem.StereoGroupType.STEREO_ABSOLUTE, editable_mol, [1])
print(Chem.MolToCXSmiles(editable_mol)) # no change seen in output
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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