def fetch_protein(pdb_id: str) -> Tuple[List[str], np.ndarray]:
# retrieve pdb file from Protein Data Bank
pdb_file = f"{pdb_id}.pdb"
pdb_file_path = os.path.join(os.getcwd(), pdb_file)
protein_url = f"https://files.rcsb.org/download/{pdb_file}"
req = requests.get(protein_url)
with open(pdb_file_path, "w") as f:
f.write(req.text)
# parse pdb file
structure = PDBParser().get_structure(pdb_id, pdb_file)
peptides = PPBuilder().build_peptides(structure)[0]
# extract amino acid sequence and phi/psi angles
aa_sequence = list(peptides.get_sequence())
phi_psi_angles = np.array(
list(
map(
lambda x: (180 if not x[0] else np.rad2deg(x[0]), 180
if not x[1] else np.rad2deg(x[1])),
peptides.get_phi_psi_list()))).T
# remove pdb file
subprocess.check_output(["rm", pdb_file])
return aa_sequence, phi_psi_angles
def find_pdb_limits(pdb_path):
""""""
pdb = PDBParser().get_structure('', pdb_path)
# takes the first (and only) polypeptide
pp = PPBuilder().build_peptides(pdb)[0]
start = pp[0].get_id()[1]
end = pp[-1].get_id()[1]
seq = pp.get_sequence()
return (start, end, seq)
