[Rdkit-discuss] trying to figure out what an rdkit warning means

[Bennion, B. <ben...@ll...>]

Hello,
Below I show a smiles string from MOE and the smiles string calculated from RDKit and the InChI string calculated by RDkit(2020_1).

The error on conversion to inchi string is confusing me after entering both smiles strings into a viewer I don't see any undefined stereo center.

O=C(/C=C/c1ccccc1)c1ccc(OC/C=C(/CC/C=C(\C)/C)\C)cc1
CC(C)=CCC/C(C)=C/COc1ccc(C(=O)/C=C/c2ccccc2)cc1
[18:10:42] WARNING: Omitted undefined stereo
InChI=1S/C25H28O2/c1-20(2)8-7-9-21(3)18-19-27-24-15-13-23(14-16-24)25(26)17-12-22-10-5-4-6-11-22/h4-6,8,10-18H,7,9,19H2,1-3H3


   while len(line) != 0:
        fields = line.replace('","',' ').split()
        mol1 = fields[0].replace('"','')
        mol_name = fields[1]

        try:
            mol = Chem.MolFromSmiles(mol1,sanitize=False) #, removeHs=False)
        except:
            mol = None
        if mol is None:
            print("mol1 failed:",mol1)
            output.write("mol1 failes:",mol1)
        else:
            rkditsmiout.write('\"'+Chem.MolToSmiles(mol, isomericSmiles=True)+'\"\n')
            print(Chem.MolToSmiles(mol, isomericSmiles=True))
            rkditsmiout.write('\"'+Chem.inchi.MolToInchi(mol)+'\"\n')
            print(Chem.inchi.MolToInchi(mol))
            count += 1
            print(count)