Chem.Kekulize(mol) error

[Nokimann]

rdkit version: 2021.03.3
(didn't check in other versions)

Doing
python get_vocab.py --ncpu 16 < aromatic.txt > vocab.txt with aromatic SMILES,
an error occurs because of Chem.Kekulize function.

In chemutils.py,

Before:

def get_mol(smiles):
    mol = Chem.MolFromSmiles(smiles)
    if mol is not None: Chem.Kekulize(mol)
    return mol

After: adding clearAromaticFlags=True

def get_mol(smiles):
    mol = Chem.MolFromSmiles(smiles)
    if mol is not None: Chem.Kekulize(mol, clearAromaticFlags=True)
    return mol

Solved.

[HarreyJia]

Thank you SO much! I have been stuck in the error for a long time.

However, I still want to know whether something different would happen in the later judgement if I changed the code.

[purplerainf]

Hi, I think I had the same issue. The error message I've got was
"rdkit.Chem.rdchem.KekulizeException: Can't kekulize mol. Unkekulized atoms: 5 6 7 8 9 10 18 26 27"

Nokimann's suggestion works for me as well, but it would be great if the author or others confirm it.

[marshallcase]

Just had the same issue as @purplerainf and @Nokimann's suggestion seemed to fix the issue. Thanks!