def run(self):
r = self.parse_cl()
if r != 0:
return
r = self.read_model_file()
if r != 0:
return
pi_params = self.get_pdb_interpretation_params()
model = mmtbx.model.manager(
model_input=self.pdb_inp,
# process_input = True,
build_grm=True,
stop_for_unknowns=False,
pdb_interpretation_params=pi_params,
restraint_objects=self.input_objects.cif_objects)
print("Model object created from file %s:" % \
getattr(self.work_params, self.pdbf_def), file=self.log)
# If needed, this could be wrapped in try...except to catch errors.
c = validate_H(model=model,
use_neutron_distances=pi_params.pdb_interpretation.
use_neutron_distances)
c.validate_inputs()
c.run()
results = c.get_results()
self.print_results(results)
def __init__(
self,
model,
pdb_hierarchy=None, # keep for mmtbx.validation_summary (multiple models)
fmodel=None,
fmodel_neutron=None,
sequences=None,
flags=None,
header_info=None,
raw_data=None,
unmerged_data=None,
keep_hydrogens=True,
nuclear=False,
save_probe_unformatted_file=None,
show_hydrogen_outliers=False,
min_cc_two_fofc=0.8,
n_bins_data=10,
count_anomalous_pairs_separately=False,
use_internal_variance=True,
outliers_only=True,
use_pdb_header_resolution_cutoffs=False,
file_name=None,
ligand_selection=None,
rotamer_library="8000",
map_params=None):
assert rotamer_library == "8000", "data_version given to RotamerEval not recognized."
for name in self.__slots__:
setattr(self, name, None)
# use objects from model
self.model = model
if (self.model is not None):
pdb_hierarchy = self.model.get_hierarchy()
xray_structure = self.model.get_xray_structure()
geometry_restraints_manager = self.model.get_restraints_manager(
).geometry
crystal_symmetry = self.model.crystal_symmetry()
all_chain_proxies = self.model.all_chain_proxies
else:
assert (pdb_hierarchy is not None)
xray_structure = None
geometry_restraints_manager = None
crystal_symmetry = None
all_chain_proxies = None
# very important - the i_seq attributes may be extracted later
pdb_hierarchy.atoms().reset_i_seq()
self.pdb_hierarchy = pdb_hierarchy
if (xray_structure is None):
if (fmodel is not None):
xray_structure = fmodel.xray_structure
elif (crystal_symmetry is not None):
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=crystal_symmetry)
self.crystal_symmetry = crystal_symmetry
if (crystal_symmetry is None) and (fmodel is not None):
self.crystal_symmetry = fmodel.f_obs().crystal_symmetry()
# use maps (fmodel is not used)
# run earlier since pdb_hierarchy gets modified
use_maps = False
if (map_params is not None):
use_maps = ((map_params.input.maps.map_file_name) or
((map_params.input.maps.map_coefficients_file_name) and
(map_params.input.maps.map_coefficients_label)))
if (use_maps):
if (flags.real_space):
self.real_space = experimental.real_space(
fmodel=None,
model=self.model,
cc_min=min_cc_two_fofc,
molprobity_map_params=map_params.input.maps)
if (flags.waters):
self.waters = waters.waters(
pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure,
fmodel=None,
collect_all=True,
molprobity_map_params=map_params.input.maps)
self.header_info = header_info
if (flags is None):
flags = molprobity_flags()
import mmtbx.model.statistics
self.model_statistics_geometry = mmtbx.model.statistics.geometry(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry_restraints_manager,
use_hydrogens=keep_hydrogens,
use_nuclear=nuclear)
self.model_statistics_geometry_result = \
self.model_statistics_geometry.result()
self.ramalyze = self.model_statistics_geometry_result.ramachandran.ramalyze
self.omegalyze = self.model_statistics_geometry_result.omega.omegalyze
self.rotalyze = self.model_statistics_geometry_result.rotamer.rotalyze
self.cbetadev = self.model_statistics_geometry_result.c_beta.cbetadev
self.clashes = self.model_statistics_geometry_result.clash.clashes
if pdb_hierarchy.contains_protein():
self.find_missing_atoms(out=null_out())
if (flags.nqh):
self.nqh_flips = clashscore.nqh_flips(
pdb_hierarchy=pdb_hierarchy)
if (pdb_hierarchy.contains_rna() and flags.rna
and libtbx.env.has_module(name="suitename")):
if (geometry_restraints_manager is not None):
self.rna = rna_validate.rna_validation(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry_restraints_manager,
outliers_only=outliers_only,
params=None)
if (flags.model_stats) and (xray_structure is not None):
self.model_stats = model_properties.model_statistics(
pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure,
all_chain_proxies=all_chain_proxies,
ignore_hd=(not nuclear),
ligand_selection=ligand_selection)
if (geometry_restraints_manager is not None) and (flags.restraints):
assert (xray_structure is not None)
self.restraints = restraints.combined(
pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure,
geometry_restraints_manager=geometry_restraints_manager,
ignore_hd=(not nuclear),
cdl=getattr(all_chain_proxies, "use_cdl", None))
if (sequences is not None) and (flags.seq):
self.sequence = sequence.validation(
pdb_hierarchy=pdb_hierarchy,
sequences=sequences,
log=null_out(),
include_secondary_structure=True,
extract_coordinates=True)
if (fmodel is not None):
if (use_pdb_header_resolution_cutoffs) and (header_info
is not None):
fmodel = fmodel.resolution_filter(d_min=header_info.d_min,
d_max=header_info.d_max)
if (flags.rfactors):
self.data_stats = experimental.data_statistics(
fmodel,
raw_data=raw_data,
n_bins=n_bins_data,
count_anomalous_pairs_separately=
count_anomalous_pairs_separately)
if (not use_maps): # if maps are used, keep previous results
if (flags.real_space):
self.real_space = experimental.real_space(
model=model, fmodel=fmodel, cc_min=min_cc_two_fofc)
if (flags.waters):
self.waters = waters.waters(pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure,
fmodel=fmodel,
collect_all=True)
if (unmerged_data is not None):
self.merging = experimental.merging_and_model_statistics(
f_obs=fmodel.f_obs(),
f_model=fmodel.f_model(),
r_free_flags=fmodel.r_free_flags(),
unmerged_i_obs=unmerged_data,
anomalous=count_anomalous_pairs_separately,
use_internal_variance=use_internal_variance,
n_bins=n_bins_data)
if (flags.xtriage):
import mmtbx.scaling.xtriage
f_model = abs(
fmodel.f_model()).set_observation_type_xray_amplitude()
if (raw_data is not None):
f_model, obs = f_model.common_sets(other=raw_data)
else:
obs = fmodel.f_obs()
self.xtriage = mmtbx.scaling.xtriage.xtriage_analyses(
miller_obs=obs,
miller_calc=f_model,
unmerged_obs=unmerged_data, # XXX some redundancy here...
text_out=null_out())
if (fmodel_neutron is not None) and (flags.rfactors):
self.neutron_stats = experimental.data_statistics(
fmodel_neutron,
n_bins=n_bins_data,
count_anomalous_pairs_separately=False)
if (pdb_hierarchy.models_size() == 1):
self._multi_criterion = multi_criterion_view(pdb_hierarchy)
# wilson B
self.wilson_b = None
if (fmodel is not None):
self.wilson_b = fmodel.wilson_b()
elif (fmodel_neutron is not None):
self.wilson_b = fmodel_neutron.wilson_b()
# validate hydrogens
self.hydrogens = None
if ((self.model is not None) and (self.model.has_hd)):
# import here to avoid circular import issues
from mmtbx.hydrogens.validate_H import validate_H, validate_H_results
hydrogens = validate_H(model, nuclear)
hydrogens.validate_inputs()
hydrogens.run()
self.hydrogens = validate_H_results(hydrogens.get_results())
# write probe file if needed (CLI and GUI)
if (save_probe_unformatted_file is not None):
pcm = self.clashes.probe_clashscore_manager
try:
with open(save_probe_unformatted_file, 'w') as f:
f.write(pcm.probe_unformatted)
self.clashes.probe_file = save_probe_unformatted_file
except IOError as err:
raise Sorry('%s could not be written correctly.\n%s' %
(save_probe_unformatted_file, err))