Kekulization Error

[Yuvaraj7UV]

smiles = Chem.MolFragmentToSmiles(mol, atoms, kekuleSmiles=True)
rdkit.Chem.rdchem.KekulizeException: Can't kekulize mol. Unkekulized atoms: 6 8 12

How did you deal with this kekulization error?

[huangtinglin]

I also encounter the same problem. Have you fixed it?

[manurubo]

I'm having the same problem.

I have found that if you modify the next in chemutils.py it works:

1. set kekuleSmiles of .py to False (inside get_clique_mol and get_smiles)
2. add sanitize=False in get_mol
3. Comment Chem.Kekulize(mol) in get_mol.

But I'm not sure if the whole model is gonna be afected.

[cosmina98]

I ve just added:
'for atom in atoms:
mol.GetAtomWithIdx(atom).SetNumExplicitHs(4)'
at the beginning of get_clique_mol()
And did not modify anything else.
"rdkit/rdkit#3334"
I am too unsure about how this affects the quality of the generated data

[jianglikun]

this is because the version of rdkit:
pip install rdkit-pypi==2020.9.5.2