Closed zw-SIMM closed 1 month ago
Hi,
Thank you for your interest!
Here,
alphafold_enzymes.p
would be a set of protein (UniProt) IDs that have an alpha-fold structure saved locally (this is only used in the skip_sample
method to save time from checking whether the path exists with something like os.path.exists
)uniprot2sequence_standard_set_structs.p
: is a dict mapping a protein ID to its sequence, similar to the uniprot2sequence.p
file. Thanks for pointing out the --load_wln_cache_in_dataset
flag. This should be False / not used. We will fix it in the next code update as well!
Hi,
Thank you for your interest!
Here,
alphafold_enzymes.p
would be a set of protein (UniProt) IDs that have an alpha-fold structure saved locally (this is only used in the method to save time from checking whether the path exists with something likeskip_sample``os.path.exists
)uniprot2sequence_standard_set_structs.p
: is a dict mapping a protein ID to its sequence, similar to the file.uniprot2sequence.p
Thanks for pointing out the flag. This should be False / not used. We will fix it in the next code update as well!
--load_wln_cache_in_dataset
Many thanks for your reply! The simplest method seems to comment them in load_dataset
method and skip_sample
method ?
Yes I think that should work. I'll also just clean up because some code is unused in the final version.
Nice work and beautiful codes! But some question about file path. What is the file
alphafold_enzymes.p
anduniprot2sequence_standard_set_structs.p
inclipzyme/datasets/enzyme_screening.py
? How to generate these files?Additionally,
args.load_wln_cache_in_dataset
seems missing.