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futianfan / DST

(differentiable) gradient-based optimization on a chemical graph for de novo molecule design/optimization (ICLR 2022)
https://openreview.net/forum?id=w_drCosT76&referrer=%5BAuthor%20Console%5D(%2Fgroup%3Fid%3DICLR.cc%2F2022%2FConference%2FAuthors%23your-submissions)
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Error run vocabulary.py #2

Open VincentH23 opened 2 years ago

VincentH23 commented 2 years ago

Hi! I'm very interesting in your works. I would like to reproduce your results but I have a problem when I run vocabulary.py error :"rdkit.Chem.rdchem.KekulizeException: Can't kekulize mol. Unkekulized atoms: 23"

Could you help me please ?

futianfan commented 2 years ago

hi Vincent,

sorry for late response! I didn't get the same error. But I think you can use the extracted vocabulary to run DST, which is available in this repository.

Also, the latest DST version is in the benchmark, where we train the GNN model online to save oracle calls. you can run DST based on one-line code: "python run.py DST --task production --n_runs 5 --oracles qed".

free feel to raise an issue if it doesn't work. thanks for your interest!

bbjy commented 2 years ago

Hi! I'm very interesting in your works. I would like to reproduce your results but I have a problem when I run vocabulary.py error :"rdkit.Chem.rdchem.KekulizeException: Can't kekulize mol. Unkekulized atoms: 23"

Could you help me please ?

Hi Vincent,

I met the same error using rdkit==2022.03.5. I reinstall the rdkit with version 2020.09.1.0 as the article said, and the error is fixed.

If you are stilled confused by this problem, I hope this will help you.

futianfan commented 2 years ago

thanks for clarify this @bbjy