A Python 3 protein structure fetcher. Retrieves the cif or pdb files from either the RCSB Protein Data Bank (PDB, using pypdb) or Alphafold using the Uniprot ID.
Please install the latest version of PyPDB using:
$ pip install git+git://github.com/williamgilpin/pypdb
Install profet using pip:
$ pip install profet
To install the development version, which contains the latest features and fixes, install directly from GitHub using
$ pip install git+git://github.com/alan-turing-institute/profet
Test the installation, navigate to the root directory and run
$ pytest
This code has been designed and tested for Python 3.
This package can be used to retrieve the available protein structure from any Uniprot ID.
The Fetcher class can search the IDs in both PDB and Alphafold, and saves the search results in a dictionary.
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.
set_default_db changes the default database into the given one between 'pdb' and 'alphafold'.
set_directory changes the directory where the files are saved. Files save as <directory>/<id>.<filetype>.
Run search_history() to see the search history of the fetcher.
If you run into an issue, or if you find a workaround for an existing issue, we would very much appreciate it if you could post your question or code as a GitHub issue.