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zaixizhang / MGSSL

Official implementation of NeurIPS'21 paper"Motif-based Graph Self-Supervised Learning for Molecular Property Prediction"
Apache License 2.0
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Are there some mistakes in tree decomposition modules? #7

Closed 1004766790 closed 1 year ago

1004766790 commented 1 year ago

Dear author, I run the mol_tree.py to preprocess the dataset and generate clique.txt, but it throws the KekulizeException for molecules such as Cc1c(/C=C/c2cc(Br)ccn2)c(O)n2c(nc3ccccc32)c1C#N. I use the decomposition modules on other datsets, it make the same exceptions, can you update the code or give some advice?

zaixizhang commented 1 year ago

Hi, thanks for your feedback! Depending on the rdkit version and the smiles format, there may be warnings such as KekulizeException in the motif extraction process. However, they do not influence the proper working of code based on my experience.

tengsaisai commented 1 year ago

But it's not a warning. The program won't work.