def get_model_stat(file_name):
grm = restraints.get_grm(file_name = file_name)
r = model_statistics.geometry(
pdb_hierarchy = grm.pdb_hierarchy,
restraints_manager = grm.restraints_manager,
molprobity_scores = True)
# XXX very runtime inefficient
distances = flex.double()
xyz = grm.pdb_hierarchy.atoms().extract_xyz()
bond_proxies_simple = grm.restraints_manager.geometry.pair_proxies(
sites_cart = xyz).bond_proxies.simple
for i, site_i in enumerate(xyz):
for j, site_j in enumerate(xyz):
if(j>i):
bonded = False
for proxy in bond_proxies_simple:
p1 = list(proxy.i_seqs)
p2 = [i,j]
p1.sort()
p2.sort()
if(p1==p2): bonded=True
if(not bonded):
dist_ij = math.sqrt(
(site_i[0]-site_j[0])**2+
(site_i[1]-site_j[1])**2+
(site_i[2]-site_j[2])**2)
distances.append(dist_ij)
min_nonbonded_distance = flex.min(distances)
# bond(rmsd), bond(max), angle(rmsd), angle(max), etc..
#print r.b_mean, r.b_max, r.a_min, r.a_max, r.clashscore, min_nonbonded_distance
return min_nonbonded_distance, r.b_max , r.a_max
def get_model_stat(pdb_file_name=None, pdb_hierarchy=None,
crystal_symmetry=None, show=True):
mon_lib_srv = mmtbx.monomer_library.server.server()
ener_lib = mmtbx.monomer_library.server.ener_lib()
params = mmtbx.monomer_library.pdb_interpretation.master_params.extract()
params.use_neutron_distances = True
params.restraints_library.cdl = False
params.sort_atoms = False
params.clash_guard.nonbonded_distance_threshold=None
#
assert [pdb_file_name, pdb_hierarchy].count(None)==1
assert [crystal_symmetry, pdb_hierarchy].count(None) in [0,2]
if(pdb_file_name is not None):
pdb_inp = iotbx.pdb.input(file_name=pdb_file_name)
crystal_symmetry = pdb_inp.crystal_symmetry()
pdb_hierarchy = \
iotbx.pdb.input(file_name=pdb_file_name).construct_hierarchy()
# XXX centralize. 3rd copy-paste!
params = monomer_library.pdb_interpretation.master_params.extract()
params.clash_guard.nonbonded_distance_threshold=None
params.disable_uc_volume_vs_n_atoms_check=False
params.use_neutron_distances = True
params.restraints_library.cdl = False
processed_pdb_file = mmtbx.monomer_library.pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
params = params,
pdb_inp = pdb_hierarchy.as_pdb_input(),
strict_conflict_handling = False,
crystal_symmetry = crystal_symmetry,
force_symmetry = True,
log = null_out())
xrs = processed_pdb_file.xray_structure()
sctr_keys = xrs.scattering_type_registry().type_count_dict().keys()
has_hd = "H" in sctr_keys or "D" in sctr_keys
#
restraints_manager = processed_pdb_file.geometry_restraints_manager(
show_energies = False,
assume_hydrogens_all_missing = not has_hd,
plain_pairs_radius = 5.0)
#
stats = model_statistics.geometry(
pdb_hierarchy = pdb_hierarchy,
restraints_manager = restraints_manager,
molprobity_scores = True)
if(show):
print("-"*79)
stats.show(out=sys.stdout)
print("-"*79)
#
return stats
def show(self, prefix="", log=None):
self.assert_pdb_hierarchy_xray_structure_sync()
if(log is None): log = sys.stdout
fmt = """%s Map CC (whole unit cell): %-6.3f
%s Map CC (around atoms): %-6.3f
%s rmsd (bonds): %-s
%s rmsd (angles): %-s
%s Dist. moved from start: %-6.3f
%s Dist. moved from previous: %-6.3f
%s All-atom clashscore %-s
%s Ramachandran plot:
%s outliers: %-s %%
%s allowed: %-s %%
%s favored: %-s %%
%s Rotamer outliers: %-s %%
%s C-beta deviations: %-s
"""
if(self.geometry_restraints_manager is not None):
mso = model_statistics.geometry(
pdb_hierarchy = self.pdb_hierarchy,
molprobity_scores = libtbx.env.has_module("probe"),
restraints_manager = self.geometry_restraints_manager)
print >> log, fmt%(
prefix, self.map_cc_whole_unit_cell,
prefix, self.map_cc_around_atoms,
prefix, format_value("%-6.2f", self.rmsd_b).strip(),
prefix, format_value("%-6.2f", self.rmsd_a).strip(),
prefix, self.dist_from_start,
prefix, self.dist_from_previous,
prefix, format_value("%-6.2f", mso.clashscore),
prefix,
prefix, format_value("%-5.2f", mso.ramachandran_outliers),
prefix, format_value("%-5.2f", mso.ramachandran_allowed),
prefix, format_value("%-5.2f", mso.ramachandran_favored),
prefix, format_value("%6.2f", mso.rotamer_outliers).strip(),
prefix, format_value("%-3d", mso.c_beta_dev))
else:
print >> log, fmt%(
prefix, self.map_cc_whole_unit_cell,
prefix, self.map_cc_around_atoms,
prefix, "None",
prefix, "None",
prefix, self.dist_from_start,
prefix, self.dist_from_previous,
prefix, "None",
prefix,
prefix, "None",
prefix, "None",
prefix, "None",
prefix, "None",
prefix, "None")
def show(self, prefix="", log=None):
self.assert_pdb_hierarchy_xray_structure_sync()
if (log is None): log = sys.stdout
fmt = """%s Map CC (whole unit cell): %-6.3f
%s Map CC (around atoms): %-6.3f
%s rmsd (bonds): %-s
%s rmsd (angles): %-s
%s Dist. moved from start: %-6.3f
%s Dist. moved from previous: %-6.3f
%s All-atom clashscore %-s
%s Ramachandran plot:
%s outliers: %-s %%
%s allowed: %-s %%
%s favored: %-s %%
%s Rotamer outliers: %-s %%
%s C-beta deviations: %-s
"""
if (self.geometry_restraints_manager is not None):
mso = model_statistics.geometry(
pdb_hierarchy=self.pdb_hierarchy,
molprobity_scores=libtbx.env.has_module("probe"),
restraints_manager=self.geometry_restraints_manager)
print >> log, fmt % (
prefix, self.map_cc_whole_unit_cell, prefix,
self.map_cc_around_atoms, prefix,
format_value("%-6.2f", self.rmsd_b).strip(), prefix,
format_value("%-6.2f", self.rmsd_a).strip(), prefix,
self.dist_from_start, prefix, self.dist_from_previous, prefix,
format_value("%-6.2f", mso.clashscore), prefix, prefix,
format_value("%-5.2f", mso.ramachandran_outliers), prefix,
format_value("%-5.2f", mso.ramachandran_allowed), prefix,
format_value("%-5.2f", mso.ramachandran_favored), prefix,
format_value("%6.2f", mso.rotamer_outliers).strip(), prefix,
format_value("%-3d", mso.c_beta_dev))
else:
print >> log, fmt % (
prefix, self.map_cc_whole_unit_cell, prefix,
self.map_cc_around_atoms, prefix, "None", prefix, "None",
prefix, self.dist_from_start, prefix, self.dist_from_previous,
prefix, "None", prefix, prefix, "None", prefix, "None", prefix,
"None", prefix, "None", prefix, "None")
def show_geometry(
xray_structures,
processed_pdb_file,
scattering_table,
hierarchy,
model_selections,
show_geometry_statistics,
mvd_obj,
atom_selections):
if(len(xray_structures)>1):
tmp = xray_structures[0]
for xi in xray_structures[1:]:
tmp = tmp.concatenate(xi)
xray_structures = tmp
else:
xray_structures = xray_structures[0]
##
utils.assert_xray_structures_equal(
x1 = xray_structures,
x2 = processed_pdb_file.xray_structure(),
sites = True,
adp = False,
occupancies = True)
##
hd_sel_all = xray_structures.hd_selection()
if(show_geometry_statistics):
sctr_keys = \
xray_structures.scattering_type_registry().type_count_dict().keys()
has_hd = "H" in sctr_keys or "D" in sctr_keys
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies = False,
plain_pairs_radius = 5.0,
assume_hydrogens_all_missing = not has_hd)
restraints_manager_all = mmtbx.restraints.manager(
geometry = geometry,
normalization = True)
models = hierarchy.models()
geometry_statistics = []
n_residues_in_altlocs = None
for i_seq, model_selection in enumerate(model_selections):
hierarchy_i_seq = pdb.hierarchy.root()
hierarchy_i_seq.append_model(models[i_seq].detached_copy())
#
overall_counts_i_seq = hierarchy_i_seq.overall_counts()
n_residues_in_altlocs = \
overall_counts_i_seq.n_alt_conf_pure + \
overall_counts_i_seq.n_alt_conf_proper + \
overall_counts_i_seq.n_alt_conf_improper
#
resname_classes = []
for k,v in zip(overall_counts_i_seq.resname_classes.keys(),
overall_counts_i_seq.resname_classes.values()):
resname_classes.append(" ".join([k.replace("common_",""), str(v)]))
#
xray_structure = xray_structures.select(model_selection)
assert hierarchy_i_seq.atoms().size() == xray_structure.scatterers().size()
hd_sel = xray_structure.hd_selection()
def select_atom_selections(selection = model_selection,
atom_selections = atom_selections):
result = group_args()
result.all = atom_selections.all .select(selection)
result.macromolecule = atom_selections.macromolecule.select(selection)
result.solvent = atom_selections.solvent .select(selection)
result.ligand = atom_selections.ligand .select(selection)
result.backbone = atom_selections.backbone .select(selection)
result.sidechain = atom_selections.sidechain .select(selection)
return result
atom_selections_i_model = select_atom_selections(
selection = model_selection,
atom_selections = atom_selections)
if(hd_sel.count(True) > 0 and scattering_table != "neutron"):
xray_structure_stat = show_xray_structure_statistics(
xray_structure = xray_structure,
hd_sel = hd_sel,
atom_selections = atom_selections_i_model)
else:
xray_structure_stat = show_xray_structure_statistics(
xray_structure = xray_structure,
atom_selections=atom_selections_i_model)
model_statistics_geometry_macromolecule = None
model_statistics_geometry_solvent = None
model_statistics_geometry_ligand = None
model_statistics_geometry_all = None
molprobity_stats_i_seq = None
rms_b_iso_or_b_equiv_bonded = None
if(show_geometry_statistics):
# exclude hydrogens
if(hd_sel.count(True) > 0 and scattering_table != "neutron"):
xray_structure = xray_structure.select(~hd_sel)
model_selection = model_selection.select(~hd_sel)
hierarchy_i_seq = hierarchy_i_seq.select(~hd_sel)
geometry = restraints_manager_all.geometry.select(selection=~hd_sel_all)
atom_selections_i_model = select_atom_selections(selection =~hd_sel_all,
atom_selections = atom_selections_i_model)
model_selection_as_bool = flex.bool(xray_structures.scatterers().size(),
model_selection)
geometry = restraints_manager_all.geometry.select(selection =
model_selection_as_bool)
restraints_manager = mmtbx.restraints.manager(
geometry = geometry,
normalization = True)
restraints_manager.geometry.pair_proxies(sites_cart =
xray_structure.sites_cart())
###
model_statistics_geometry_all = model_statistics.geometry(
pdb_hierarchy = hierarchy_i_seq,
molprobity_scores = True,
restraints_manager = restraints_manager)
#
if(atom_selections.macromolecule.count(True)>0):
mac_sel = atom_selections_i_model.macromolecule
model_statistics_geometry_macromolecule = model_statistics.geometry(
pdb_hierarchy = hierarchy_i_seq.select(mac_sel),
molprobity_scores = True,
restraints_manager = restraints_manager.select(mac_sel))
#
if(atom_selections.solvent.count(True)>0):
sol_sel = atom_selections_i_model.solvent
model_statistics_geometry_solvent = model_statistics.geometry(
pdb_hierarchy = hierarchy_i_seq.select(sol_sel),
molprobity_scores = True,
restraints_manager = restraints_manager.select(sol_sel))
#
if(atom_selections.ligand.count(True)>0):
lig_sel = atom_selections_i_model.ligand
model_statistics_geometry_ligand = model_statistics.geometry(
pdb_hierarchy = hierarchy_i_seq.select(lig_sel),
molprobity_scores = True,
restraints_manager = restraints_manager.select(lig_sel))
###
rms_b_iso_or_b_equiv_bonded = utils.rms_b_iso_or_b_equiv_bonded(
restraints_manager = restraints_manager,
xray_structure = xray_structure)
#
molprobity_stats_i_seq = molprobity_stats(
model_statistics_geometry = model_statistics_geometry_all,
resname_classes = overall_counts_i_seq.resname_classes)
geometry_statistics.append(group_args(
n_residues_in_altlocs = n_residues_in_altlocs,
resname_classes = resname_classes,
xray_structure_stat = xray_structure_stat,
rms_b_iso_or_b_equiv_bonded = rms_b_iso_or_b_equiv_bonded,
geometry_all = model_statistics_geometry_all,
geometry_macromolecule = model_statistics_geometry_macromolecule,
geometry_solvent = model_statistics_geometry_solvent,
geometry_ligand = model_statistics_geometry_ligand,
molprobity = molprobity_stats_i_seq))
mvd_obj.collect(models = geometry_statistics)
return geometry_statistics
def run(args, log=sys.stdout):
print >> log, "-"*79
print >> log, legend
print >> log, "-"*79
inputs = mmtbx.utils.process_command_line_args(args = args,
master_params = master_params())
params = inputs.params.extract()
# estimate resolution
d_min = params.resolution
broadcast(m="Map resolution:", log=log)
if(d_min is None):
raise Sorry("Resolution is required.")
print >> log, " d_min: %6.4f"%d_min
# model
broadcast(m="Input PDB:", log=log)
file_names = inputs.pdb_file_names
if(len(file_names) != 1): raise Sorry("PDB file has to given.")
if(inputs.crystal_symmetry is None):
raise Sorry("No crystal symmetry defined.")
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv = monomer_library.server.server(),
ener_lib = monomer_library.server.ener_lib(),
file_name = file_names[0],
crystal_symmetry = inputs.crystal_symmetry,
force_symmetry = True,
log = None)
ph = processed_pdb_file.all_chain_proxies.pdb_hierarchy
if(len(ph.models())>1):
raise Sorry("Only one model allowed.")
xrs = processed_pdb_file.xray_structure()
xrs.scattering_type_registry(table = params.scattering_table)
xrs.show_summary(f=log, prefix=" ")
# restraints
sctr_keys = xrs.scattering_type_registry().type_count_dict().keys()
has_hd = "H" in sctr_keys or "D" in sctr_keys
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies = False,
assume_hydrogens_all_missing = not has_hd,
plain_pairs_radius = 5.0)
# map
broadcast(m="Input map:", log=log)
if(inputs.ccp4_map is None): raise Sorry("Map file has to given.")
inputs.ccp4_map.show_summary(prefix=" ")
map_data = inputs.ccp4_map.map_data()
print >> log, " Actual map (min,max,mean):", \
map_data.as_1d().min_max_mean().as_tuple()
make_sub_header("Histogram of map values", out=log)
md = map_data.as_1d()
show_histogram(data=md, n_slots=10, data_min=flex.min(md),
data_max=flex.max(md), log=log)
# shift origin if needed
shift_needed = not \
(map_data.focus_size_1d() > 0 and map_data.nd() == 3 and
map_data.is_0_based())
if(shift_needed):
N = map_data.all()
O=map_data.origin()
map_data = map_data.shift_origin()
# apply same shift to the model
a,b,c = xrs.crystal_symmetry().unit_cell().parameters()[:3]
sites_cart = xrs.sites_cart()
sx,sy,sz = a/N[0]*O[0], b/N[1]*O[1], c/N[2]*O[2]
sites_cart_shifted = sites_cart-\
flex.vec3_double(sites_cart.size(), [sx,sy,sz])
xrs.set_sites_cart(sites_cart_shifted)
####
# Compute and show all stats
####
broadcast(m="Model statistics:", log=log)
make_sub_header("Overall", out=log)
ms = model_statistics.geometry(
pdb_hierarchy = ph,
restraints_manager = geometry,
molprobity_scores = True)
ms.show()
make_sub_header("Histogram of devations from ideal bonds", out=log)
show_histogram(data=ms.bond_deltas, n_slots=10, data_min=0, data_max=0.2,
log=log)
#
make_sub_header("Histogram of devations from ideal angles", out=log)
show_histogram(data=ms.angle_deltas, n_slots=10, data_min=0, data_max=30.,
log=log)
#
make_sub_header("Histogram of non-bonded distances", out=log)
show_histogram(data=ms.nonbonded_distances, n_slots=10, data_min=0,
data_max=5., log=log)
#
make_sub_header("Histogram of ADPs", out=log)
bs = xrs.extract_u_iso_or_u_equiv()*adptbx.u_as_b(1.)
show_histogram(data=bs, n_slots=10, data_min=flex.min(bs),
data_max=flex.max(bs), log=log)
#
# Compute FSC(map, model)
broadcast(m="Map-model FSC:", log=log)
mmtbx.maps.correlation.fsc_model_map(
xray_structure=xrs, map=map_data, d_min=d_min, log=log)
#
# various CC
cc_calculator = mmtbx.maps.correlation.from_map_and_xray_structure_or_fmodel(
xray_structure = xrs,
map_data = map_data,
d_min = d_min)
broadcast(m="Map-model CC:", log=log)
print >> log, "Overall (entire box): %6.4f"%cc_calculator.cc()
print >> log, "Around atoms (masked): %6.4f"%cc_calculator.cc(
selection=flex.bool(xrs.scatterers().size(), True))
# per chain
print >> log, "Per chain:"
for chain in ph.chains():
print >> log, " chain %s: %6.4f"%(chain.id, cc_calculator.cc(
selection=chain.atoms().extract_i_seq()))
# per residue
print >> log, "Per residue:"
for rg in ph.residue_groups():
cc = cc_calculator.cc(selection=rg.atoms().extract_i_seq())
print >> log, " chain id: %s resid %s: %6.4f"%(
rg.parent().id, rg.resid(), cc)
# per residue detailed counts
print >> log, "Per residue (histogram):"
crystal_gridding = maptbx.crystal_gridding(
unit_cell = xrs.unit_cell(),
space_group_info = xrs.space_group_info(),
pre_determined_n_real = map_data.accessor().all())
f_calc = xrs.structure_factors(d_min=d_min).f_calc()
fft_map = miller.fft_map(
crystal_gridding = crystal_gridding,
fourier_coefficients = f_calc)
fft_map.apply_sigma_scaling()
map_model = fft_map.real_map_unpadded()
sites_cart = xrs.sites_cart()
cc_per_residue = flex.double()
for rg in ph.residue_groups():
cc = mmtbx.maps.correlation.from_map_map_atoms(
map_1 = map_data,
map_2 = map_model,
sites_cart = sites_cart.select(rg.atoms().extract_i_seq()),
unit_cell = xrs.unit_cell(),
radius = 2.)
cc_per_residue.append(cc)
show_histogram(data=cc_per_residue, n_slots=10, data_min=-1., data_max=1.0,
log=log)
def show_geometry(xray_structures, processed_pdb_file, scattering_table,
hierarchy, model_selections, show_geometry_statistics,
mvd_obj, atom_selections):
if (len(xray_structures) > 1):
tmp = xray_structures[0]
for xi in xray_structures[1:]:
tmp = tmp.concatenate(xi)
xray_structures = tmp
else:
xray_structures = xray_structures[0]
##
utils.assert_xray_structures_equal(x1=xray_structures,
x2=processed_pdb_file.xray_structure(),
sites=True,
adp=False,
occupancies=True)
##
hd_sel_all = xray_structures.hd_selection()
if (show_geometry_statistics):
sctr_keys = \
xray_structures.scattering_type_registry().type_count_dict().keys()
has_hd = "H" in sctr_keys or "D" in sctr_keys
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies=False,
plain_pairs_radius=5.0,
assume_hydrogens_all_missing=not has_hd)
restraints_manager_all = mmtbx.restraints.manager(geometry=geometry,
normalization=True)
models = hierarchy.models()
geometry_statistics = []
n_residues_in_altlocs = None
for i_seq, model_selection in enumerate(model_selections):
hierarchy_i_seq = pdb.hierarchy.root()
hierarchy_i_seq.append_model(models[i_seq].detached_copy())
#
overall_counts_i_seq = hierarchy_i_seq.overall_counts()
n_residues_in_altlocs = \
overall_counts_i_seq.n_alt_conf_pure + \
overall_counts_i_seq.n_alt_conf_proper + \
overall_counts_i_seq.n_alt_conf_improper
#
resname_classes = []
for k, v in zip(overall_counts_i_seq.resname_classes.keys(),
overall_counts_i_seq.resname_classes.values()):
resname_classes.append(" ".join([k.replace("common_", ""),
str(v)]))
#
xray_structure = xray_structures.select(model_selection)
assert hierarchy_i_seq.atoms_size() == xray_structure.scatterers(
).size()
hd_sel = xray_structure.hd_selection()
def select_atom_selections(selection=model_selection,
atom_selections=atom_selections):
result = group_args()
result.all = atom_selections.all.select(selection)
result.macromolecule = atom_selections.macromolecule.select(
selection)
result.solvent = atom_selections.solvent.select(selection)
result.ligand = atom_selections.ligand.select(selection)
result.backbone = atom_selections.backbone.select(selection)
result.sidechain = atom_selections.sidechain.select(selection)
return result
atom_selections_i_model = select_atom_selections(
selection=model_selection, atom_selections=atom_selections)
if (hd_sel.count(True) > 0 and scattering_table != "neutron"):
xray_structure_stat = show_xray_structure_statistics(
xray_structure=xray_structure,
hd_sel=hd_sel,
atom_selections=atom_selections_i_model)
else:
xray_structure_stat = show_xray_structure_statistics(
xray_structure=xray_structure,
atom_selections=atom_selections_i_model)
model_statistics_geometry_macromolecule = None
model_statistics_geometry_solvent = None
model_statistics_geometry_ligand = None
model_statistics_geometry_all = None
molprobity_stats_i_seq = None
rms_b_iso_or_b_equiv_bonded = None
if (show_geometry_statistics):
# exclude hydrogens
if (hd_sel.count(True) > 0 and scattering_table != "neutron"):
xray_structure = xray_structure.select(~hd_sel)
model_selection = model_selection.select(~hd_sel)
hierarchy_i_seq = hierarchy_i_seq.select(~hd_sel)
geometry = restraints_manager_all.geometry.select(
selection=~hd_sel_all)
atom_selections_i_model = select_atom_selections(
selection=~hd_sel_all,
atom_selections=atom_selections_i_model)
model_selection_as_bool = flex.bool(
xray_structures.scatterers().size(), model_selection)
geometry = restraints_manager_all.geometry.select(
selection=model_selection_as_bool)
restraints_manager = mmtbx.restraints.manager(geometry=geometry,
normalization=True)
restraints_manager.geometry.pair_proxies(
sites_cart=xray_structure.sites_cart())
###
model_statistics_geometry_all = model_statistics.geometry(
pdb_hierarchy=hierarchy_i_seq,
molprobity_scores=True,
restraints_manager=restraints_manager)
#
if (atom_selections.macromolecule.count(True) > 0):
mac_sel = atom_selections_i_model.macromolecule
model_statistics_geometry_macromolecule = model_statistics.geometry(
pdb_hierarchy=hierarchy_i_seq.select(mac_sel),
molprobity_scores=True,
restraints_manager=restraints_manager.select(mac_sel))
#
if (atom_selections.solvent.count(True) > 0):
sol_sel = atom_selections_i_model.solvent
model_statistics_geometry_solvent = model_statistics.geometry(
pdb_hierarchy=hierarchy_i_seq.select(sol_sel),
molprobity_scores=True,
restraints_manager=restraints_manager.select(sol_sel))
#
if (atom_selections.ligand.count(True) > 0):
lig_sel = atom_selections_i_model.ligand
model_statistics_geometry_ligand = model_statistics.geometry(
pdb_hierarchy=hierarchy_i_seq.select(lig_sel),
molprobity_scores=True,
restraints_manager=restraints_manager.select(lig_sel))
###
rms_b_iso_or_b_equiv_bonded = utils.rms_b_iso_or_b_equiv_bonded(
restraints_manager=restraints_manager,
xray_structure=xray_structure)
#
molprobity_stats_i_seq = molprobity_stats(
model_statistics_geometry=model_statistics_geometry_all,
resname_classes=overall_counts_i_seq.resname_classes)
geometry_statistics.append(
group_args(
n_residues_in_altlocs=n_residues_in_altlocs,
resname_classes=resname_classes,
xray_structure_stat=xray_structure_stat,
rms_b_iso_or_b_equiv_bonded=rms_b_iso_or_b_equiv_bonded,
geometry_all=model_statistics_geometry_all,
geometry_macromolecule=model_statistics_geometry_macromolecule,
geometry_solvent=model_statistics_geometry_solvent,
geometry_ligand=model_statistics_geometry_ligand,
molprobity=molprobity_stats_i_seq))
mvd_obj.collect(models=geometry_statistics)
return geometry_statistics
