def bond_angle_outliers(self):
get_class = common_residue_names_get_class
rc = restraints.combined(
pdb_hierarchy = self.pdb_hierarchy,
xray_structure = self.model.get_xray_structure(),
geometry_restraints_manager = self.model.get_restraints_manager().\
geometry,
ignore_hd = False, # important
outliers_only = False,
use_segids_in_place_of_chainids = False)
bond_mean_delta, n_bonds, bond_mean = 0, 0, 0
# bond outliers involving hydrogens
outliers_bonds = []
for result in rc.bonds.results:
atom_info_hd = get_atom_info_if_hd(atoms_info=result.atoms_info)
# Consider only H/D atoms
if atom_info_hd is not None:
# Calculate mean bond length and delta for non-water
# --> used to get rough idea if H are at X-ray or neutron bond lengths.
if (get_class(name=atom_info_hd.resname) != 'common_water'):
bond_mean_delta = bond_mean_delta + result.delta
bond_mean = bond_mean + result.model
n_bonds += 1
if result.is_outlier():
atoms_str = mp_geo.get_atoms_str(
atoms_info=result.atoms_info)
outliers_bonds.append(
(atom_info_hd.id_str(), atoms_str, result.model,
result.delta, result.target, atom_info_hd.xyz))
self.outliers_bonds = outliers_bonds
bond_mean_delta = bond_mean_delta / n_bonds
bond_mean = bond_mean / n_bonds
xray_distances_used = False
# value 0.08 was obtained by checking all 123 neutron models deposited
# until Sep 2017 and by analysing delta
if (bond_mean_delta >= 0.08 and self.use_neutron_distances):
xray_distances_used = True
self.bond_results = group_args(bond_mean_delta=bond_mean_delta,
bond_mean=bond_mean,
xray_distances_used=xray_distances_used)
# angle outliers involving hydrogens
outliers_angles = []
for result in rc.angles.results:
atom_info_hd = get_atom_info_if_hd(atoms_info=result.atoms_info)
# Consider only H/D atoms
if atom_info_hd is not None:
if result.is_outlier():
atoms_str = mp_geo.get_atoms_str(
atoms_info=result.atoms_info)
outliers_angles.append([
atom_info_hd.id_str(), atoms_str, result.model,
result.delta, result.target, atom_info_hd.xyz
])
self.outliers_angles = outliers_angles
def get_bond_and_angle_outliers(pdb_hierarchy,
xray_structure,
geometry_restraints_manager,
use_segids,
outliers_only=False,
type=None):
rc = restraints.combined(
pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure,
geometry_restraints_manager=geometry_restraints_manager,
ignore_hd=True,
outliers_only=outliers_only,
use_segids_in_place_of_chainids=use_segids)
return rc
def run_validation(pdb_file, ignore_hd=True):
from mmtbx.validation import restraints
import mmtbx.command_line
cmdline = mmtbx.command_line.load_model_and_data(
args=[pdb_file],
master_phil=mmtbx.command_line.generic_simple_input_phil(),
process_pdb_file=True,
require_data=False,
out=null_out())
validation = restraints.combined(
pdb_hierarchy=cmdline.pdb_hierarchy,
xray_structure=cmdline.xray_structure,
geometry_restraints_manager=cmdline.geometry,
ignore_hd=ignore_hd)
return validation
def run_validation (pdb_file, ignore_hd=True) :
from mmtbx.validation import restraints
import mmtbx.command_line
cmdline = mmtbx.command_line.load_model_and_data(
args=[pdb_file],
master_phil=mmtbx.command_line.generic_simple_input_phil(),
process_pdb_file=True,
require_data=False,
out=null_out())
validation = restraints.combined(
pdb_hierarchy=cmdline.pdb_hierarchy,
xray_structure=cmdline.xray_structure,
geometry_restraints_manager=cmdline.geometry,
ignore_hd=ignore_hd)
return validation
def get_bond_and_angle_outliers(
pdb_hierarchy,
xray_structure,
geometry_restraints_manager,
use_segids,
outliers_only=False,
type=None):
rc = restraints.combined(
pdb_hierarchy=pdb_hierarchy,
xray_structure=xray_structure,
geometry_restraints_manager=geometry_restraints_manager,
ignore_hd=True,
outliers_only=outliers_only,
use_segids_in_place_of_chainids=use_segids)
return rc
def run (args, log=sys.stdout) :
processed_pdb_file = pdb_interpretation.run(
args=args,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log=log)
xray_structure = processed_pdb_file.xray_structure()
if xray_structure is None :
raise Sorry("Could not calculate X-ray structure from this PDB file. "+
"This is probably due to missing symmetry information (CRYST1 record.")
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
chain_proxies = processed_pdb_file.all_chain_proxies
pdb_hierarchy = chain_proxies.pdb_hierarchy
result = restraints.combined(
pdb_hierarchy=chain_proxies.pdb_hierarchy,
xray_structure=xray_structure,
geometry_restraints_manager=geometry,
ignore_hd=True)
result.show(out=log, prefix=" ")
def run(args, log=sys.stdout):
processed_pdb_file = pdb_interpretation.run(
args=args,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log=log)
xray_structure = processed_pdb_file.xray_structure()
if xray_structure is None:
raise Sorry(
"Could not calculate X-ray structure from this PDB file. " +
"This is probably due to missing symmetry information (CRYST1 record."
)
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
chain_proxies = processed_pdb_file.all_chain_proxies
pdb_hierarchy = chain_proxies.pdb_hierarchy
result = restraints.combined(pdb_hierarchy=chain_proxies.pdb_hierarchy,
xray_structure=xray_structure,
geometry_restraints_manager=geometry,
ignore_hd=True)
result.show(out=log, prefix=" ")
def run_geometry_validation(self) :
from mmtbx.validation import restraints
restraints = restraints.combined(
pdb_hierarchy=self.cmdline.pdb_hierarchy,
xray_structure=self.cmdline.xray_structure,
geometry_restraints_manager=self.cmdline.geometry,
ignore_hd=True,
cdl=False)
restraints.angles.show()
# get bond legth outlier data
for result in restraints.bonds.results :
#print >> sys.stderr, dir(result)
# Since this is a bond length there are two atoms involved
reskey0,name0 = self.get_res_key_and_atom(result.atoms_info[0])
reskey1,name1 = self.get_res_key_and_atom(result.atoms_info[1])
self.residues[reskey0].add_bondlength_result(result,reskey0,name0,
reskey1,name1)
if reskey0 != reskey1 :
self.residues[reskey1].add_bondlength_result(result,reskey1,name1,
reskey0,name0)
for result in restraints.angles.results :
#print >> sys.stderr, dir(result)
# Since this is a angle there are three atoms involved
reskey0,name0 = self.get_res_key_and_atom(result.atoms_info[0])
reskey1,name1 = self.get_res_key_and_atom(result.atoms_info[1])
reskey2,name2 = self.get_res_key_and_atom(result.atoms_info[2])
# The logic that follows inserts the angle outlier info into the
# two or one residue[s] involved. At least two of the three residues
# will be the same residue.
self.residues[reskey0].add_angle_result(result,reskey0,name0,
reskey1,name1,
reskey2,name2)
if reskey0 != reskey1 :
self.residues[reskey1].add_angle_result(result,reskey1,name1,
reskey0,name0,
reskey2,name2)
elif reskey0 != reskey2 :
self.residues[reskey2].add_angle_result(result,reskey2,name2,
reskey1,name1,
reskey0,name0)
def __init__(self,
pdb_hierarchy,
xray_structure=None,
fmodel=None,
fmodel_neutron=None,
geometry_restraints_manager=None,
crystal_symmetry=None,
sequences=None,
flags=None,
header_info=None,
raw_data=None,
unmerged_data=None,
all_chain_proxies=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)
# 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,
pdb_hierarchy=pdb_hierarchy,
crystal_symmetry=self.crystal_symmetry,
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(
fmodel=fmodel,
pdb_hierarchy=pdb_hierarchy,
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()
def __init__ (self,
pdb_hierarchy,
xray_structure=None,
fmodel=None,
fmodel_neutron=None,
geometry_restraints_manager=None,
crystal_symmetry=None,
sequences=None,
flags=None,
header_info=None,
raw_data=None,
unmerged_data=None,
all_chain_proxies=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)
# 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()
self.header_info = header_info
if (flags is None) :
flags = molprobity_flags()
if pdb_hierarchy.contains_protein() :
if (flags.ramalyze) :
self.ramalyze = ramalyze.ramalyze(
pdb_hierarchy=pdb_hierarchy,
outliers_only=outliers_only,
out=null_out(),
quiet=True)
##### omegalyze ################################################################
if (flags.omegalyze) :
self.omegalyze = omegalyze.omegalyze(
pdb_hierarchy=pdb_hierarchy,
nontrans_only=outliers_only,
out=null_out(),
quiet=True)
##### omegalyze ################################################################
if (flags.rotalyze) :
self.rotalyze = rotalyze.rotalyze(
pdb_hierarchy=pdb_hierarchy,
data_version=rotamer_library,
outliers_only=outliers_only,
out=null_out(),
quiet=True)
if (flags.cbetadev) :
self.cbetadev = cbetadev.cbetadev(
pdb_hierarchy=pdb_hierarchy,
outliers_only=outliers_only,
out=null_out(),
quiet=True)
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.clashscore) :
self.clashes = clashscore.clashscore(
pdb_hierarchy=pdb_hierarchy,
save_probe_unformatted_file=save_probe_unformatted_file,
nuclear=nuclear,
keep_hydrogens=keep_hydrogens,
out=null_out(),
verbose=False)
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)
# use maps (fmodel is not used)
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,
pdb_hierarchy=pdb_hierarchy,
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)
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(
fmodel=fmodel,
pdb_hierarchy=pdb_hierarchy,
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)
def __init__(self,
model,
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(not self.model.processed()):
self.model.process(make_restraints=True)
if(self.model is None and pdb_hierarchy is not None):
import mmtbx.model
self.model = mmtbx.model.manager(
model_input = pdb_hierarchy.as_pdb_input())
self.model.process(make_restraints=True)
pdb_hierarchy = self.model.get_hierarchy()
if(nuclear):
self.model.setup_scattering_dictionaries(scattering_table="neutron")
if (self.model is not None):
if(self.model.get_restraints_manager() is None):
self.model.process(make_restraints=True)
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 = None
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()
self.model_statistics_geometry = self.model.geometry_statistics(
use_hydrogens=keep_hydrogens, condensed_probe=False, fast_clash=False)
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 (self.model is not None):
# keep for backwards compatibility
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)
# ligand_selection is no longer available
self.model_stats_new = self.model.composition()
self.adp_stats = self.model.adp_statistics()
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)
fmodel.update_all_scales()
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))