fetchprotein

A Python package to fetch a protein 3D Structure / MSA / FASTA file from the PDB, UniProt or AlphaFold-DB (depending on the protein_filename extension).

Supports extensions:

• pdb: for 3D structure from PDB or AlphaFold-DB
• cif: for 3D structure from PDB or AlphaFold-DB
• fasta: for FASTA from PDB or UniProt
• a3m: for MSA from AlphaFold-DB (API is currently unavailable)

Installation and Usage

Install with pip:

pip install fetchprotein

CLI usage:

fetchprotein --help
fetchprotein 6m0j.pdb
fetchprotein Q9LW00.cif
fetchprotein Q9LW00.a3m # might be currently unavailable
fetchprotein Q9LW00.fasta
fetchprotein 6m0j.fasta

Python usage:
WARNING: Fetch for AlphaFold-DB MSA is currently unavailable.

# Imports
from fetchprotein.fetch import fetchprotein
from fetchprotein.fetch import fetch_structure, fetch_sequence, fetch_msa

# Use generic fetch function
path = fetchprotein('6M0J.pdb', output_dir='./test_data/')     # fetch 3D structure from PDB
path = fetchprotein('Q9LW00.cif', output_dir='./test_data/')   # fetch 3D structure from AlphaFold-DB
path = fetchprotein('Q9LW00.a3m', output_dir='./test_data/')   # fetch MSA from AlphaFold-DB
path = fetchprotein('Q9LW00.fasta', output_dir='./test_data/') # fetch FASTA from UniProt
path = fetchprotein('6M0J.fasta', output_dir='./test_data/')   # fetch FASTA from PDB

# Use specific fetch functions
path = fetch_structure('6M0J', extension="cif", output_dir='./test_data/')
path = fetch_structure('Q9LW00', extension="pdb", output_dir='./test_data/')

path = fetch_sequence('6M0J', extension="fasta", output_dir='./test_data/')
path = fetch_sequence('Q9LW00', extension="fasta", output_dir='./test_data/')

path = fetch_msa('Q9LW00', extension="a3m", output_dir='./test_data/')