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
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
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
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())
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
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)