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 fetch_protein(pdb_id: str) -> ProteinState:
# pull protein from PDB
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 data for phi/psi angles
structure = PDBParser().get_structure(pdb_id, pdb_file)
peptides = PPBuilder().build_peptides(structure)[0]
phi_psi_angles = list(
map(
lambda x: (180.0 if not x[0] else (x[0] * 180 / np.pi) % 360, 180.0
if not x[1] else (x[1] * 180 / np.pi) % 360),
peptides.get_phi_psi_list()))
protein_state = ProteinState(angles=np.array(phi_psi_angles).T)
return protein_state
