def _setup_model_h(self):
if self.model_h is not None:
return
if not self.model.has_hd():
# runs reduce internally
assert (libtbx.env.has_module(name="reduce"))
assert (libtbx.env.has_module(name="elbow"))
self.model_h = ready_set_model_interface(
model=self.model,
params=[
"add_h_to_water=False",
"optimise_final_geometry_of_hydrogens=False"
],
)
else:
self.model_h = self.model.deep_copy()
params_h = mmtbx.model.manager.get_default_pdb_interpretation_params()
params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation
# customization for model with H
params_h.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
params_h.pdb_interpretation.max_reasonable_bond_distance = None
params_h.pdb_interpretation.use_neutron_distances = True
params_h.pdb_interpretation.ncs_search = self.params_for_model.pdb_interpretation.ncs_search
params_h.pdb_interpretation.ncs_search.exclude_selection = "water"
self.model_h.set_pdb_interpretation_params(params_h)
self.model_h.get_restraints_manager()
self.model_h.idealize_h_riding()
self.model_h.setup_ncs_constraints_groups(filter_groups=True)
self.model_h._update_master_sel()
if self.params.debug:
self.shift_and_write_result(model=self.model_h,
fname_suffix="model_h")
def get_readyset_model_with_grm(self):
'''
Run ready set by default (to get ligand cif and/or add H atoms)
TODO: Once it it refactored, make running it optional
Complicated case is when cif is input for one ligand, but missing
for another ligand
'''
self.readyset_model = None
#if not self.model.has_hd():
if (self.params.place_hydrogens):
params = [
"add_h_to_water=False",
"optimise_final_geometry_of_hydrogens=False", "--silent"
]
else:
params = [
"add_h_to_water=False", "hydrogens=False",
"optimise_final_geometry_of_hydrogens=False", "--silent"
]
assert (libtbx.env.has_module(name="reduce"))
assert (libtbx.env.has_module(name="elbow"))
# runs reduce internally
self.readyset_model = ready_set_model_interface(model=self.model,
params=params)
self.readyset_model.set_log(null_out())
def run(self):
pdb_fn = self.data_manager.get_default_model_name()
print('Using model file:', pdb_fn, file=self.logger)
restraint_objects = list()
if self.data_manager.has_restraints():
print('Using restraints files',
self.data_manager.get_restraint_names(),
file=self.logger)
for filename in self.data_manager.get_restraint_names():
restraint_objects.append(
(filename, self.data_manager.get_restraint(filename)))
model = self.data_manager.get_model()
pi_params = model.get_default_pdb_interpretation_params()
pi_params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
# TODO: below are some non-defaults for pdb_interpretation,
# but they cannot be changed
# Do we need the non-defaults?
# assume_hydrogens_all_missing --> default is False, but becomes True if H are present
# hard_minimum_nonbonded_distance --> default is 0.001 but is 0 in NBO
# substitute_non_crystallographic_unit_cell_if_necessary --> not necessary
# add H atoms with readyset
params = [
"add_h_to_water=False",
"optimise_final_geometry_of_hydrogens=False"
]
assert (libtbx.env.has_module(name="reduce"))
assert (libtbx.env.has_module(name="elbow"))
readyset_model = ready_set_model_interface(
model=model, params=params, keep_temp=self.params.keep_temp)
readyset_model.set_pdb_interpretation_params(pi_params)
readyset_model.set_restraint_objects(restraint_objects)
readyset_model.get_restraints_manager()
# TODO: do we need macro_mol_sel, do we care?
# If we use model.select(), we don't need it.
proxies = readyset_model.all_chain_proxies
cache = proxies.pdb_hierarchy.atom_selection_cache()
macro_mol_sel = proxies.selection(cache=cache,
string='protein or dna or rna')
#t0 = time.time()
nb_overlaps = nbo.info(model=readyset_model,
macro_molecule_selection=macro_mol_sel)
#t1 = time.time()
nb_overlaps.show(log=self.logger, nbo_type='all', normalized_nbo=True)
#t2 = time.time()
processed_nbps = pnp.manager(model=readyset_model)
clashes = processed_nbps.get_clashes()
#t3 = time.time()
clashes.show(log=self.logger)
hbonds = processed_nbps.get_hbonds()
hbonds.show(log=self.logger)
def _setup_model_h(self):
if self.model_h is not None:
return
if not self.model.has_hd():
self.model_h = ready_set_model_interface(
model=self.model,
params=[
"add_h_to_water=False",
"optimise_final_geometry_of_hydrogens=False"
],
)
else:
self.model_h = self.model.deep_copy()
params_h = mmtbx.model.manager.get_default_pdb_interpretation_params()
params_h.pdb_interpretation.use_neutron_distances = True
params_h.pdb_interpretation.ncs_search = self.params_for_model.pdb_interpretation.ncs_search
params_h.pdb_interpretation.ncs_search.exclude_selection = "water"
self.model_h.set_pdb_interpretation_params(params_h)
self.model_h.get_restraints_manager()
self.model_h.idealize_h_riding()
self.model_h.setup_ncs_constraints_groups(filter_groups=True)
self.model_h._update_master_sel()