Dear group members,
Before using RDkit to enumerate stereoisomers, I'd like to keep the largest
fragment of input SMILES. However, when MolStandardize.Standardizer() is
used to keep the largest fragment, EnumerateStereoisomers() does not
generate the correct isomers and does not show error.
Any idea?
Please check the following code:
smi = 'CC(F)Cl'
mol1 = Chem.MolFromSmiles(smi)
s = MolStandardize.Standardizer()
mol2 = Chem.AddHs(s.fragment_parent(mol1))
isomers1 = list(EnumerateStereoisomers(mol1))
print('{} isomers generated for mol1'.format(len(isomers1)))
isomers2 = list(EnumerateStereoisomers(mol2))
print('{} isomers generated for mol2'.format(len(isomers2)))
Output:
2 isomers generated for mol1
1 isomers generated for mol2
Best regards
Zhenting
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