def run(pdb_str, expected_ids):
get_class = iotbx.pdb.common_residue_names_get_class
mon_lib_srv = mmtbx.monomer_library.server.server()
rotamer_manager = RotamerEval()
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
pdb_hierarchy = pdb_inp.construct_hierarchy()
result_ids = []
for residue_group in pdb_hierarchy.residue_groups():
for conformer in residue_group.conformers():
for residue in conformer.residues():
sites_cart = residue.atoms().extract_xyz()
rotamer_name = rotamer_manager.evaluate_residue(
residue=residue)
print residue.resname, residue.resseq, rotamer_name
result_ids.append(rotamer_name)
if (get_class(residue.resname) == "common_amino_acid"):
rotamer_iterator = mon_lib_srv.rotamer_iterator(
fine_sampling=True,
comp_id=residue.resname,
atom_names=residue.atoms().extract_name(),
sites_cart=sites_cart)
if (rotamer_iterator is None
or rotamer_iterator.problem_message is not None
or rotamer_iterator.rotamer_info is None):
rotamer_iterator = None
if (rotamer_iterator is not None):
d1_min, d2_min = 1.e+9, 1.e+9
for r, rotamer_sites_cart in rotamer_iterator:
sites_cart_rot = rotamer_manager.nearest_rotamer_sites_cart(
residue=residue)
d1 = flex.mean(
flex.sqrt((sites_cart - sites_cart_rot).dot()))
d2 = flex.mean(
flex.sqrt(
(sites_cart - rotamer_sites_cart).dot()))
if (d1 < d1_min):
d1_min = d1
if (d2 < d2_min):
d2_min = d2
assert approx_equal(d1_min, d2_min)
assert result_ids == expected_ids
def run(pdb_str, expected_ids):
get_class = iotbx.pdb.common_residue_names_get_class
mon_lib_srv = mmtbx.monomer_library.server.server()
rotamer_manager = RotamerEval()
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
pdb_hierarchy = pdb_inp.construct_hierarchy()
result_ids = []
for residue_group in pdb_hierarchy.residue_groups():
for conformer in residue_group.conformers():
for residue in conformer.residues():
sites_cart = residue.atoms().extract_xyz()
rotamer_name = rotamer_manager.evaluate_residue(residue=residue)
print residue.resname, residue.resseq, rotamer_name
result_ids.append(rotamer_name)
if(get_class(residue.resname) == "common_amino_acid"):
rotamer_iterator = mon_lib_srv.rotamer_iterator(
fine_sampling = True,
comp_id = residue.resname,
atom_names = residue.atoms().extract_name(),
sites_cart = sites_cart)
if(rotamer_iterator is None or
rotamer_iterator.problem_message is not None or
rotamer_iterator.rotamer_info is None):
rotamer_iterator = None
if(rotamer_iterator is not None):
d1_min, d2_min = 1.e+9, 1.e+9
for r, rotamer_sites_cart in rotamer_iterator:
sites_cart_rot = rotamer_manager.nearest_rotamer_sites_cart(
residue=residue)
d1= flex.mean(flex.sqrt((sites_cart - sites_cart_rot).dot()))
d2= flex.mean(flex.sqrt((sites_cart - rotamer_sites_cart).dot()))
if(d1 < d1_min):
d1_min = d1
if(d2 < d2_min):
d2_min = d2
assert approx_equal(d1_min, d2_min)
assert result_ids == expected_ids
