Ejemplo n.º 1
0
def neighbours(atom, test_atoms, distance):
  results = []
  for test_atom in test_atoms:
    if v3.distance(test_atom.pos, atom.pos) < distance:
      if abs(test_atom.res_num - atom.res_num) > 2:
        results.append(test_atom)
  return results
Ejemplo n.º 2
0
def neighbours(atom, test_atoms, distance):
    results = []
    for test_atom in test_atoms:
        if v3.distance(test_atom.pos, atom.pos) < distance:
            if abs(test_atom.res_num - atom.res_num) > 2:
                results.append(test_atom)
    return results
Ejemplo n.º 3
0
def in_contact(res1, res2):
  for a1 in res1.atoms():
    for a2 in res2.atoms():
      if v3.distance(a1.pos, a2.pos) < 4:
        return True
  return False
Ejemplo n.º 4
0
  results = []
  for test_atom in test_atoms:
    if v3.distance(test_atom.pos, atom.pos) < distance:
      if abs(test_atom.res_num - atom.res_num) > 2:
        results.append(test_atom)
  return results

atoms = soup.atoms()
nitrogens = filter(lambda a: a.element=="N", atoms)
oxygens = filter(lambda a: a.element=="O", atoms)

print "Hydrogen bonds:"
for oxygen in oxygens:
  bonded_nitrogens = neighbours(oxygen, nitrogens, 3.5)
  for nitrogen in bonded_nitrogens:
    d = v3.distance(oxygen.pos, nitrogen.pos)
    print (str(oxygen), str(nitrogen)), "%.2f" % d 



# find surface residues/set b-factor using the inbuilt
# accessible surface-area calculator with a water probe radius
# of 1.4 angstroms. writes out PDB file to be viewed:
#     >> pdbshow -b 1be9.asa.pdb
# And:
#     >> pdbshow -b 1be9.res.asa.pdb

atoms = []
for res in soup.residues():
  if res.type not in data.solvent_res_types:
    atoms.extend(res.atoms())
Ejemplo n.º 5
0
def in_contact(res1, res2):
    for a1 in res1.atoms():
        for a2 in res2.atoms():
            if v3.distance(a1.pos, a2.pos) < 4:
                return True
    return False
Ejemplo n.º 6
0
    for test_atom in test_atoms:
        if v3.distance(test_atom.pos, atom.pos) < distance:
            if abs(test_atom.res_num - atom.res_num) > 2:
                results.append(test_atom)
    return results


atoms = soup.atoms()
nitrogens = filter(lambda a: a.element == "N", atoms)
oxygens = filter(lambda a: a.element == "O", atoms)

print "Hydrogen bonds:"
for oxygen in oxygens:
    bonded_nitrogens = neighbours(oxygen, nitrogens, 3.5)
    for nitrogen in bonded_nitrogens:
        d = v3.distance(oxygen.pos, nitrogen.pos)
        print(str(oxygen), str(nitrogen)), "%.2f" % d

# find surface residues/set b-factor using the inbuilt
# accessible surface-area calculator with a water probe radius
# of 1.4 angstroms. writes out PDB file to be viewed:
#     >> pdbshow -b 1be9.asa.pdb
# And:
#     >> pdbshow -b 1be9.res.asa.pdb

atoms = []
for res in soup.residues():
    if res.type not in data.solvent_res_types:
        atoms.extend(res.atoms())
pdbatoms.add_radii(atoms)
areas = asa.calculate_asa(atoms, 1.4)