Re: [Rdkit-discuss] SMILES validation question

[Yutong Z. <pro...@gm...>]

This one is tricky and I bumped into something similar not too long ago.
What happened is that by default:

[2] mol = Chem.MolFromSmiles("O=C(CC1SCCC1)c1coooo1N")

automatically has sanitize set to True. One of the steps is aromaticity
sanitization. Since I don't think the mol satisfies 4n+2, sanitization
removed aromaticity from the ring.
You can verify this with: print([a.GetIsAromatic() for a in mol.GetAtoms()])

[3] smi = Chem.MolToSmiles(mol)

Then generates: 'NO1OOOC=C1C(=O)CC1CCCS1', which results in a neutral
oxygen with 3 explicit valences.

Unfortunately AFAIK, RDKit can only catchErrors when a certain sanitization
step failed but not if it succeeded (as in this case). Maybe Greg or Brian
has a better solution?