FileNotFoundError: [Errno 2] No such file or directory: 'data/BindingMOAD_2020_ab_processed_biounit/moad_sequences_new'

gcorso / DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

https://arxiv.org/abs/2210.01776

MIT License

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FileNotFoundError: [Errno 2] No such file or directory: 'data/BindingMOAD_2020_ab_processed_biounit/moad_sequences_new' #202

Closed srilekha1993 closed 3 months ago

srilekha1993 commented 3 months ago

Hi, This URL i have referred for https://zenodo.org/records/10656052 for downloading BindingMOAD_2020_ab_processed dataset. But there is no moad_sequences_new folder inside BindingMOAD_2020_ab_processed. Can anyone please provide the correct link for the above dataset?

haotianteng commented 1 month ago

the generated sequence fasta is default prepared_for_esm.fasta not pdbbind_sequences.fasta in README.md, so should run this command instead: python scripts/extract.py esm2_t33_650M_UR50D ${DIFFDOCK_BASE}/data/prepared_for_esm.fasta embeddings_output --repr_layers 33 --include per_tok --truncation_seq_length 4096

Notice this command should be run at the facebook esm repository, not the DIFFDOCK repository.

README.md needs some correction. @gcorso