def tst_3():
'''
Test if the modification works also when cif_objects are supplied
(meaning there is a ligand cif file)
'''
pdb_inp = iotbx.pdb.input(lines=pdb_str2.split("\n"), source_info=None)
cif_object = iotbx.cif.reader(input_string=cif_str2).model()
# bla.cif does not exist, but cif_objects needs a filename in first position
# of the tuple
cif_objects = [('bla.cif', cif_object)]
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.use_neutron_distances = False
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
restraint_objects=cif_objects,
log=null_out())
# request neutron bond lengths
model.set_hydrogen_bond_length(use_neutron_distances=True,
show=False,
log=sys.stdout)
compare_XH_bond_length_to_ideal(model=model)
# request X-ray bond lengths
model.set_hydrogen_bond_length(use_neutron_distances=False,
show=False,
log=sys.stdout)
compare_XH_bond_length_to_ideal(model=model)
def tst_1():
'''
input model: bond lengths close to neutron but not quite
input grm: neutron bond lengths
'''
pdb_inp = iotbx.pdb.input(lines=pdb_str1.split("\n"), source_info=None)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.use_neutron_distances = True
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
# request neutron bond lengths
model.set_hydrogen_bond_length(use_neutron_distances=True,
show=False,
log=sys.stdout)
model.process_input_model(make_restraints=True)
compare_XH_bond_length_to_ideal(model=model)
#STOP()
# request X-ray bond lengths
pdb_inp = iotbx.pdb.input(lines=pdb_str1.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=False)
model.set_hydrogen_bond_length(use_neutron_distances=False,
show=False,
log=sys.stdout)
compare_XH_bond_length_to_ideal(model=model)
def tst_2():
'''
input model: bond lengths close to neutron but not quite
input grm: X-ray bond lengths
'''
pdb_inp = iotbx.pdb.input(lines=pdb_str1.split("\n"), source_info=None)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.use_neutron_distances = False
model = mmtbx.model.manager(
model_input = pdb_inp,
log = null_out())
model.process(pdb_interpretation_params = params)
#
# Check if selected individual bond lengths are correct
atoms = model.get_hierarchy().atoms()
assert (atoms[4].id_str() == 'pdb=" CB ARG A 74 "')
assert (atoms[18].id_str() == 'pdb=" HB2 ARG A 74 "')
assert approx_equal(atoms[4].distance(atoms[18]), 1.08, eps = 0.005)
assert (atoms[10].id_str() == 'pdb=" NH2 ARG A 74 "')
assert (atoms[15].id_str() == 'pdb="DH21 ARG A 74 "')
assert approx_equal(atoms[10].distance(atoms[15]), 0.99, eps = 0.005)
# request neutron bond lengths
model.set_hydrogen_bond_length(use_neutron_distances=True,
show=False,
log=sys.stdout)
# Check if bond lengths are equal to ideal
compare_XH_bond_length_to_ideal(model = model)
# Check if selected individual bond lengths are correct
atoms = model.get_hierarchy().atoms()
assert approx_equal(atoms[4].distance(atoms[18]), 1.09, eps = 0.005)
assert approx_equal(atoms[10].distance(atoms[15]), 1.02, eps = 0.005)
# request X-ray bond lengths
model.set_hydrogen_bond_length(use_neutron_distances=False,
show=False,
log=sys.stdout)
compare_XH_bond_length_to_ideal(model = model)
# Check if selected individual bond lengths are correct
atoms = model.get_hierarchy().atoms()
assert approx_equal(atoms[4].distance(atoms[18]), 0.97, eps = 0.005)
assert approx_equal(atoms[10].distance(atoms[15]), 0.86, eps = 0.005)