RDkit error

[hwidong-na]

Hi,

Thanks for sharing your work.

I got this error after fixing issue #2.

  File "/home/leona/anaconda3/envs/chemprop/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/leona/anaconda3/envs/chemprop/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/home/leona/anaconda3/envs/chemprop/lib/python3.8/site-packages/molevol-0.0.1-py3.8.egg/MolEvol/local_search/local_searcher_explain.py", line 114, in local_for_one_molecule
    subgraph_smiles = extract_selected_subgraph_for_gcn(smiles, selected_atoms)
  File "/home/leona/anaconda3/envs/chemprop/lib/python3.8/site-packages/molevol-0.0.1-py3.8.egg/MolEvol/common/fingerprint.py", line 163, in extract_selected_subgraph_for_gcn
    minimum_smiles, _ = extract_subgraph(smiles, selected_atoms)
  File "/home/leona/github.sec.samsung.net/multiobj-rationale/multiobj_rationale/fuseprop/chemutils.py", line 259, in extract_subgraph
    subgraph = Chem.MolToSmiles(subgraph, kekuleSmiles=True)
rdkit.Chem.rdchem.AtomKekulizeException: Aromatic bonds on non aromatic atom 10

I think this is related to the rdkit version. Which version did you used?

Bests regards,
Hwidong

[binghong-ml]

We used Rdkit 2020.03.4. Will upload a Conda env requirement soon. Thanks!

[hwidong-na]

Thanks for your prompt reply! The error doesn't appear with rdkit version you mentioned.