pdb.py

from Bio.Seq import Seq
import Bio.PDB
import Bio.SeqUtils

pdb_filename = '../inputs/1qo7.pdb'
structure = Bio.PDB.PDBParser().get_structure(pdb_code, pdb_filename)
model = structure[0]
pdb_seq = [residue.resname for residue in model['B']]
pdb_seq = ''.join([Bio.SeqUtils.seq1(s) for s in pdb_seq])
ca_coord = np.array([residue['CA'].coord for residue in model['A'] if 'CA' in residue])


def get_contacts(d, cutoff):
    contacts = np.argwhere(d < cutoff)
    lower = np.array([c[0] < c[1] for c in contacts])
    contacts = contacts[lower]
    return [tuple(c) for c in contacts]

c50 = get_contacts(d, 5.0)
c45 = get_contacts(d, 4.5)