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How to replicate results? #224
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I have also encountered this issue, and even after upgrading Biopython to the latest version 1.84, there are still numerous warnings stating '{entity_id} defined twice' |
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My error
Generate the ESM2 embeddings for the proteins:
I downloaded the BindingMOAD dataset and extracted it into the "/data/BindingMOAD_2020_ab_processed_biounit" directory.
I ran "datasets/esm_embedding_preparation.py", But file run error "NotADirectoryError: [Errno 20] Not a directory: '/mnt/data/sjb/chem/DiffDock/DiffDock-main//data/BindingMOAD_2020_ab_processed_biounit/pdb_protein/._1xq6_1_protein.pdb/ _1xq6_1_protein.pdb_protein.pdb'".
I modified the default code to use moad and found that after the MOAD dataset set was decompressed, some files started with '.', I modified line 73 of "esm_embedding_preparation.py". From "names = [n[:6] for n in names]" to "names = [n[:6] for n in names if not n.startswith('.')]", the error that the file cannot be found is no longer reported.
But there are new problems, the following is all the errors:
Dear Author How should this be resolved?If you can answer, thank you very much for your help
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