Loads protein from pdb into SCNProtein.

scn_from_pdb.py

import prody
import sidechainnet as scn
from sidechainnet.utils.download import get_resolution_from_pdbid

def from_pdb(filename, pdbid="", include_resolution=False):
    """Create a SCNProtein from a PDB file. Warning: does not support gapped proteins!!
    Args:
        filename (str): Path to existing PDB file.
        pdbid (str): 4-letter string representing the PDB Identifier.
        include_resolution (bool, default=False): If True, query the PDB for the protein
            structure resolution based off of the given pdb_id.
    Returns:
        A SCNProtein object containing the coorinates, angles, and sequence parsed
        from the PDB file.
    """
    # TODO: Raise an alarm if the user is working with files that have gaps
    # First, use Prody to parse the PDB file
    chain = prody.parsePDB(filename)
    # Next, use SidechainNet to make the relevant measurements given the Prody chain obj
    (dihedrals_np, coords_np, observed_sequence, unmodified_sequence,
     is_nonstd) = scn.utils.measure.get_seq_coords_and_angles(chain,
                                                              replace_nonstd=True)
    scndata = {
        "coordinates": coords_np.reshape(len(observed_sequence), -1, 3),
        "angles": dihedrals_np,
        "sequence": observed_sequence,
        "unmodified_seq": unmodified_sequence,
        "mask": "+" * len(observed_sequence),
        "is_modified": is_nonstd,
        "id": pdbid,
    }
    # If requested, look up the resolution of the given PDB ID
    if include_resolution:
        assert pdbid, "You must provide a PDB ID to look up the resolution."
        scndata['resolution'] = get_resolution_from_pdbid(pdbid)
    return scn.SCNProtein(**scndata)