Hello, I have a question stereocenters in symmetrical compounds. I've found that if I take a flat, mapped, symmetrical compound and artificially set the chiral tag of the center carbon to form a stereocenter, it won't "correct itself" and remove the stereocenter when I run AssignStereochemistry:
s_mapped = [OH:1][CH2:2][CH:3]([OH:4])[CH2:5][OH:6] mol = Chem.MolFromSmiles(s_mapped) mol.GetAtomWithIdx(2).SetChiralTag(Chem.CHI_TETRAHEDRAL_CCW) Chem.AssignStereochemistry(mol, cleanIt=True, force=True) print(Chem.MolToSmiles(mol)) Output (still has the artifically introduced stereocenter): [OH:1][CH2:2][C@H:3]([OH:4])[CH2:5][OH:6] On the other hand, if I use an unmapped SMILES to create the mol and do the exact same steps, then AssignStereochemistry does successfully remove the artificially introduced stereocenter (which is what I want to happen with the mapped mol too). s_unmapped = 'OCC(O)CO' mol = Chem.MolFromSmiles(s_unmapped) mol.GetAtomWithIdx(2).SetChiralTag(Chem.CHI_TETRAHEDRAL_CCW) Chem.AssignStereochemistry(mol, cleanIt=True, force=True) print(Chem.MolToSmiles(mol)) OCC(O)CO Is this normal rdkit behavior (to have this difference between using an unmapped vs mapped mol)? How can I get it so that the mapped mol doesn't have that chiral tag anymore? Thanks for the help. Phil
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