[Rdkit-discuss] EnumerateStereoisomers fails without notice after using MolStandardize.Standardizer()

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.

Re: [Rdkit-discuss] EnumerateStereoisomers fails without notice after using MolStandardize.Standardizer()

Hi Zhenting, It looks like you need to reassign stereochemistry after calling fragment_parent: smi = 'CC(F)Cl' mol1 = Chem.MolFromSmiles(smi) s = MolStandardize.Standardizer() mol2 = s.fragment_parent(mol1) Chem.AssignStereochemistry(mol2, True, True, True) mol3 = Chem.AddHs(mol2) isomers1 =