Fetch PDB from PDB code

[universvm]

Hi there!

I'm currently using ampal in a project. I need to download several PDBs to handle with ampal. I looked at the load_pdb function in pdb_parser, and was thinking about passing an optional argument eg. fetch_pdb = True and then have a condition right before the PdbParser to download the PDBs into a specific folder and pass the path to PdbParser.

The fetching logic could be something like:

import urllib
from pathlib import Path

PDB_REQUEST_URL = 'https://files.rcsb.org/download/'
PROTEIN_DATA_FOLDER = Path('protein_data')
PROTEIN_DATA_FOLDER.mkdir(parents=True, exist_ok=True)

def download_pdb(pdb_id, output_folder):
    """
    Downloads a specific pdb file into a specific folder. 
    """
    urllib.request.urlretrieve(PDB_REQUEST_URL + pdb_id + '.pdb1.gz', filename=PROTEIN_DATA_FOLDER / f'{pdb_id}.pdb1.gz')

download_pdb('3qy1', PROTEIN_DATA_FOLDER)

Let me know what you think :)

[ChrisWellsWood]

I'm in favour of this, but I think it should be a function along side load_pdb called fetch_pdb, which mirrors the command names in PyMol. I'd prefer PDBe as the endpoint rather than RSCB, mainly because we can fetch biological units from there.

[universvm]

I'll open a pull request in the next couple of days. I'll add a test case as well. While I'm at it, should I also fix the incorrect documentation in the tests or should I open another issue for that?

    def test_parse_1ek9(self):
        """Check that **3qy1** has been parsed correctly."""
        test_file_path = str(TEST_FILE_FOLDER / '1ek9.pdb')
        self.check_ampal_contents(test_file_path)

    def test_parse_2ht0(self):
        """Check that **3qy1** has been parsed correctly.""" 
        test_file_path = str(TEST_FILE_FOLDER / '2ht0.pdb')
        self.check_ampal_contents(test_file_path)

Ie. def test_parse_2ht0 should check 2ht0 rather than 3qy1