Usage

This package can be used to retrieve the available protein structure from any Uniprot ID.

The profet.Fetcher class can search the IDs in both PDB and Alphafold, and saves the search results in a dictionary.

profet.Fetcher.get_file() returns the structure corresponding to uniprot_id in the defined filetype: (default as ‘pdb’, option as ‘cif’), searching first in the defaulted database db (default as ‘pdb’, option as ‘alphafold’). The files can be saved to a local file with filesave.

profet.Fetcher.set_default_db() changes the default database into the given one between ‘pdb’ and ‘alphafold’.

profet.Fetcher.set_directory() changes the directory where the files are saved. Files save as <directory>/<id>.<filetype>.

Run profet.Fetcher.search_history() to see the search history of the fetcher.

See the run_profet.ipynb notebook for usage examples.