def run_tst_xrs_and_hierarchy():
# Check if scatterers in xrs are neutral after calling function
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
model = mmtbx.model.manager(model_input=pdb_inp, log=null_out())
model.neutralize_scatterers()
xrs = model.get_xray_structure()
for scatterer in xrs.scatterers():
assert (scatterer.scattering_type in neutral_atoms_list)
# Check if pdb_hierarchy has neutral atoms as well
pdb_str_neutralized = model.model_as_pdb()
pdb_inp_neutralized = iotbx.pdb.input(source_info=None,
lines=pdb_str_neutralized)
model_neutralized = mmtbx.model.manager(model_input=pdb_inp_neutralized,
log=null_out())
xrs_neutralized = model_neutralized.get_xray_structure()
for scatterer in xrs_neutralized.scatterers():
assert (scatterer.scattering_type in neutral_atoms_list)
def run_tst_grm_after_neutralize_scatterers():
# Look at nonbonded interaction CB - OE2 in Glu
# OE2 has negative charge
# vdw distance is 2.560 A when OE2 is neutral
# vdw distance is 2.752 A when OE1 has O1- charge
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_2)
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=True)
atoms = model.get_hierarchy().atoms()
grm = model.get_restraints_manager()
# with open('1.geo', 'w') as f:
# f.write(model.restraints_as_geo())
nonbonded_proxies = grm.geometry.pair_proxies().nonbonded_proxies.simple
for nb_proxy in nonbonded_proxies:
iseq, jseq = nb_proxy.i_seqs
if (iseq == 4 and jseq == 8):
vdw_distance1 = nb_proxy.vdw_distance
assert (atoms[iseq].name.strip() == 'CB')
assert (atoms[jseq].name.strip() == 'OE2')
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=False)
model.neutralize_scatterers()
model.process_input_model(make_restraints=True)
atoms2 = model.get_hierarchy().atoms()
grm2 = model.get_restraints_manager()
# with open('2.geo', 'w') as f:
# f.write(model.restraints_as_geo())
nonbonded_proxies2 = grm2.geometry.pair_proxies().nonbonded_proxies.simple
for nb_proxy in nonbonded_proxies2:
iseq, jseq = nb_proxy.i_seqs
if (iseq == 4 and jseq == 8):
vdw_distance2 = nb_proxy.vdw_distance
assert (atoms2[iseq].name.strip() == 'CB')
assert (atoms2[jseq].name.strip() == 'OE2')
assert (vdw_distance1 != vdw_distance2)