Add AFDBList class for PDBList-like AlphaFold downloads (#3990)#5176
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Abdeltoto wants to merge 2 commits intobiopython:masterfrom
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Add AFDBList class for PDBList-like AlphaFold downloads (#3990)#5176Abdeltoto wants to merge 2 commits intobiopython:masterfrom
Abdeltoto wants to merge 2 commits intobiopython:masterfrom
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Add AFDBList class to Bio.PDB.alphafold_db with retrieve_pdb_file method for downloading AlphaFold structures by UniProt ID. Supports mmCIF and PDB formats. Switch API URL to alphafold.ebi.ac.uk. Export AFDBList from Bio.PDB. Closes biopython#3990 Made-with: Cursor
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Hi,
I worked on issue #3990. The idea was to add a PDBList-like interface for the AlphaFold database, so users can download predicted structures by UniProt ID in a familiar way.
I added an
AFDBListclass that mirrors the mainPDBListworkflow:__init__(server, pdb, verbose)– same pattern as PDBListretrieve_pdb_file(uniprot_id, pdir, file_format, overwrite)– same idea as PDBList’sretrieve_pdb_file, but for UniProt accessionsSupported formats are mmCIF (default) and PDB. When there are multiple models for a single accession (e.g. isoforms), the canonical one is preferred by default, with an optional
model_indexparameter to choose another.I also switched the API base URL from alphafold.com to alphafold.ebi.ac.uk (the official EBI server) and added the missing
AFDBListexport toBio.PDB.Example usage::
Closes #3990