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LPDI-EPFL / masif

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.
Apache License 2.0
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step 1 download pdf failed #3

Closed billryan closed 4 years ago

billryan commented 4 years ago

When I run ./data_prepare_one.sh 1MBN_A_ under data/masif_site, it failed to download and showed

WARNING: The default download format has changed from PDB to PDBx/mmCif
jaumebonet commented 4 years ago

@pablogainza, @FreyrS seems that there is a newer version of biopython than the one used in the repo and (at least) the retrieve_pdb_file function has been updated.

The fix should be as easy as add file_format='pdb' to the call to retrieve_pdb_file in source/data_preparation/00-pdb_download.py.

One should avoid this by adding fixed versions in the requirement.txt file, so that one won't need to keep updating the code at each update of each dependent library.

pablogainza commented 4 years ago

Thanks Jaume!!

Billyryan, I am also working on a docker container with MaSIF for easy reproduction of the results. I hope to have it on a week or two.

On Sun, Feb 9, 2020 at 9:56 AM Jaume Bonet notifications@github.com wrote:

@pablogainza https://github.com/pablogainza, @FreyrS https://github.com/FreyrS seems that there is a newer version of biopython than the one used in the repo and (at least) the retrieve_pdb_file https://biopython.org/DIST/docs/api/Bio.PDB.PDBList%27.PDBList-class.html#retrieve_pdb_file function has been updated.

The fix should be as easy as add file_format='pdb' to the call to retrieve_pdb_file in source/data_preparation/00-pdb_download.py.

One should avoid this by adding fixed versions in the requirement.txt file, so that one won't need to keep updating the code at each update of each dependent library.

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