def exercise_3():
pdb_raw = """\
ATOM 1 CA GLY A 1 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 2 CA GLY A 2 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 3 CA GLY A 3 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 4 CA GLY A 4 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 5 CA GLY A 5 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 6 CA GLY A 6 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 7 CA GLY A 7 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 8 CA GLY A 8 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 9 CA GLY A 9 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 10 CA GLY A 10 -0.227 9.888 -15.197 1.00 54.04 C
HETATM 11 N SEP A 11 -2.112 0.368 -0.991 1.00 20.00 A N
HETATM 12 CA SEP A 11 -0.692 0.284 -0.951 1.00 20.00 A C
HETATM 13 CB SEP A 11 -0.234 0.166 0.485 1.00 20.00 A C
HETATM 14 OG SEP A 11 1.130 -0.184 0.515 1.00 20.00 A O
HETATM 15 C SEP A 11 -0.237 -0.930 -1.727 1.00 20.00 A C
HETATM 16 O SEP A 11 -0.767 -2.051 -1.509 1.00 20.00 A O
HETATM 18 P SEP A 11 1.922 -0.008 1.871 1.00 20.00 A P
HETATM 19 O1P SEP A 11 2.139 1.462 2.140 1.00 20.00 A O
HETATM 20 O2P SEP A 11 3.259 -0.703 1.767 1.00 20.00 A O-1
HETATM 21 O3P SEP A 11 1.127 -0.614 3.002 1.00 20.00 A O-1
END"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
ligand_sel = pdb_in.hierarchy.atom_selection_cache().selection(
"resname SEP")
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ligand_selection=ligand_sel,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert (mstats.n_protein == 10)
assert ("Ligands:" in out.getvalue())
assert approx_equal(mstats.macromolecules.b_mean, 54.04)
# now with just the raw selection string
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ligand_selection="resname SEP",
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert (mstats.n_protein == 10)
assert ("Ligands:" in out.getvalue())
def exercise_3 () :
pdb_raw = """\
ATOM 1 CA GLY A 1 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 2 CA GLY A 2 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 3 CA GLY A 3 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 4 CA GLY A 4 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 5 CA GLY A 5 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 6 CA GLY A 6 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 7 CA GLY A 7 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 8 CA GLY A 8 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 9 CA GLY A 9 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 10 CA GLY A 10 -0.227 9.888 -15.197 1.00 54.04 C
HETATM 11 N SEP A 11 -2.112 0.368 -0.991 1.00 20.00 A N
HETATM 12 CA SEP A 11 -0.692 0.284 -0.951 1.00 20.00 A C
HETATM 13 CB SEP A 11 -0.234 0.166 0.485 1.00 20.00 A C
HETATM 14 OG SEP A 11 1.130 -0.184 0.515 1.00 20.00 A O
HETATM 15 C SEP A 11 -0.237 -0.930 -1.727 1.00 20.00 A C
HETATM 16 O SEP A 11 -0.767 -2.051 -1.509 1.00 20.00 A O
HETATM 18 P SEP A 11 1.922 -0.008 1.871 1.00 20.00 A P
HETATM 19 O1P SEP A 11 2.139 1.462 2.140 1.00 20.00 A O
HETATM 20 O2P SEP A 11 3.259 -0.703 1.767 1.00 20.00 A O-1
HETATM 21 O3P SEP A 11 1.127 -0.614 3.002 1.00 20.00 A O-1
END"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
ligand_sel = pdb_in.hierarchy.atom_selection_cache().selection("resname SEP")
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ligand_selection=ligand_sel,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert (mstats.n_protein == 10)
assert ("Ligands:" in out.getvalue())
assert approx_equal(mstats.macromolecules.b_mean, 54.04)
# now with just the raw selection string
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ligand_selection="resname SEP",
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert (mstats.n_protein == 10)
assert ("Ligands:" in out.getvalue())
def get_mstats(pdb_raw):
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=True)
return mstats
def exercise_2 () :
pdb_raw = """\
ATOM 6407 N GLY A 388 -0.783 9.368 -16.436 1.00 51.96 N
ATOM 6408 CA GLY A 388 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 6409 C GLY A 388 -0.637 11.320 -14.897 1.00 55.86 C
ATOM 6410 O GLY A 388 -1.728 11.738 -15.347 1.00 56.70 O
ATOM 6411 OXT GLY A 388 0.129 12.024 -14.203 1.00 56.98 O
ATOM 6412 D GLY A 388 -0.460 9.727 -17.309 1.00 51.44 D
ATOM 6413 HA2 GLY A 388 -0.561 9.258 -14.385 1.00 54.07 H
ATOM 6414 HA3 GLY A 388 0.843 9.835 -15.243 1.00 54.13 H
TER 6415 GLY A 388
HETATM 6416 D D8U A 401 -12.236 -13.695 -42.992 1.00 15.23 D
HETATM 6417 O DOD A1001 -4.151 -5.107 -38.592 1.00 13.40 O
HETATM 6418 D1 DOD A1001 -4.760 -5.026 -39.326 1.00 15.45 D
HETATM 6419 D2 DOD A1001 -4.625 -4.741 -37.845 1.00 14.81 D
"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert ("Ligands:" in out.getvalue())
assert ("B_iso: mean = 15.2 max = 15.2 min = 15.2" in out.getvalue())
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 exercise_1 () :
pdb_raw = """\
ATOM 1134 N LYS A 82 5.933 36.285 21.572 1.00 70.94 N
ATOM 1135 CA LYS A 82 6.564 37.423 20.931 1.00 76.69 C
ATOM 1136 C LYS A 82 5.553 38.547 20.756 1.00 78.75 C
ATOM 1137 O LYS A 82 5.325 39.038 19.654 1.00 86.47 O
ATOM 1138 CB LYS A 82 7.179 37.024 19.583 1.00 82.32 C
ATOM 1139 CG LYS A 82 8.190 38.035 19.048 0.00 70.34 C
ATOM 1140 CD LYS A 82 9.429 38.129 19.944 0.00 67.69 C
ATOM 1141 CE LYS A 82 9.983 39.545 20.014 0.00 64.44 C
ATOM 1142 NZ LYS A 82 10.933 39.832 18.908 0.00 61.45 N
ATOM 1143 H LYS A 82 5.139 36.115 21.291 1.00 85.12 H
ATOM 1144 HA LYS A 82 7.279 37.749 21.501 1.00 92.03 H
ATOM 1145 HB2 LYS A 82 6.469 36.939 18.928 1.00 98.78 H
ATOM 1146 HB3 LYS A 82 7.636 36.175 19.687 1.00 98.78 H
ATOM 1147 HG2 LYS A 82 8.476 37.762 18.163 0.00 84.41 H
ATOM 1148 HG3 LYS A 82 7.775 38.912 19.011 0.00 84.41 H
ATOM 1149 HD2 LYS A 82 9.193 37.853 20.843 0.00 81.23 H
ATOM 1150 HD3 LYS A 82 10.122 37.551 19.589 0.00 81.23 H
ATOM 1151 HE2 LYS A 82 9.249 40.177 19.952 0.00 77.33 H
ATOM 1152 HE3 LYS A 82 10.453 39.662 20.854 0.00 77.33 H
ATOM 1153 HZ1 LYS A 82 11.237 40.666 18.977 0.00 73.75 H
ATOM 1154 HZ2 LYS A 82 10.523 39.738 18.123 0.00 73.75 H
ATOM 1155 HZ3 LYS A 82 11.621 39.269 18.944 0.00 73.75 H
ATOM 1156 N LYS A 83 4.936 38.927 21.866 1.00 75.79 N
ATOM 1157 CA LYS A 83 4.177 40.172 21.966 1.00 82.80 C
ATOM 1158 C LYS A 83 4.081 40.508 23.460 1.00 86.23 C
ATOM 1159 O LYS A 83 2.978 40.521 24.017 1.00 79.81 O
ATOM 1160 CB LYS A 83 2.790 40.044 21.332 1.00 79.16 C
ATOM 1161 CG LYS A 83 2.038 41.342 21.175 0.00 70.42 C
ATOM 1162 CD LYS A 83 2.072 41.803 19.735 0.00 66.90 C
ATOM 1163 CE LYS A 83 1.295 43.089 19.552 0.00 62.46 C
ATOM 1164 NZ LYS A 83 1.004 43.350 18.118 0.00 60.73 N
ATOM 1165 H LYS A 83 4.940 38.470 22.594 1.00 90.95 H
ATOM 1166 HA LYS A 83 4.658 40.885 21.518 1.00 99.36 H
ATOM 1167 HB2 LYS A 83 2.251 39.459 21.887 1.00 95.00 H
ATOM 1168 HB3 LYS A 83 2.890 39.655 20.449 1.00 95.00 H
ATOM 1169 HG2 LYS A 83 1.113 41.213 21.435 0.00 84.51 H
ATOM 1170 HG3 LYS A 83 2.453 42.024 21.726 0.00 84.51 H
ATOM 1171 HD2 LYS A 83 2.992 41.962 19.471 0.00 80.28 H
ATOM 1172 HD3 LYS A 83 1.672 41.123 19.171 0.00 80.28 H
ATOM 1173 HE2 LYS A 83 0.452 43.024 20.027 0.00 74.95 H
ATOM 1174 HE3 LYS A 83 1.818 43.830 19.896 0.00 74.95 H
ATOM 1175 HZ1 LYS A 83 0.521 42.683 17.780 0.00 72.87 H
ATOM 1176 HZ2 LYS A 83 1.764 43.417 17.661 0.00 72.87 H
ATOM 1177 HZ3 LYS A 83 0.548 44.109 18.034 0.00 72.87 H
ATOM 3630 N ASN A 242 -5.454 -3.027 1.145 0.00 67.69 N
ATOM 3631 CA ASN A 242 -4.759 -2.535 -0.037 0.00 65.44 C
ATOM 3632 C ASN A 242 -5.734 -2.397 -1.208 0.00 63.57 C
ATOM 3633 O ASN A 242 -6.425 -3.357 -1.552 0.00 63.94 O
ATOM 3634 CB ASN A 242 -3.626 -3.503 -0.392 0.00 63.13 C
ATOM 3635 CG ASN A 242 -2.802 -3.044 -1.576 0.00 63.58 C
ATOM 3636 OD1 ASN A 242 -2.524 -1.862 -1.731 0.00 65.52 O
ATOM 3637 ND2 ASN A 242 -2.399 -3.988 -2.416 0.00 62.17 N
ATOM 3638 H ASN A 242 -5.562 -3.880 1.129 0.00 81.22 H
ATOM 3639 HA ASN A 242 -4.375 -1.665 0.151 0.00 78.53 H
ATOM 3640 HB2 ASN A 242 -3.032 -3.587 0.370 0.00 75.76 H
ATOM 3641 HB3 ASN A 242 -4.007 -4.368 -0.611 0.00 75.76 H
ATOM 3642 HD21 ASN A 242 -1.929 -3.779 -3.104 0.00 74.60 H
ATOM 3643 HD22 ASN A 242 -2.609 -4.810 -2.272 0.00 74.60 H
ATOM 2 CA ALYS A 32 10.574 8.177 11.768 0.40 71.49 C
ATOM 3 CB ALYS A 32 9.197 8.686 12.246 0.40 74.71 C
ATOM 2 CA BLYS A 32 10.574 8.177 11.768 0.40 71.49 C
ATOM 3 CB BLYS A 32 9.197 8.686 12.246 0.40 74.71 C
ATOM 5 CA AVAL A 33 11.708 5.617 14.332 0.50 71.42 C
ATOM 6 CB AVAL A 33 11.101 4.227 14.591 0.50 71.47 C
ATOM 5 CA BVAL A 33 11.708 5.617 14.332 0.40 71.42 C
ATOM 6 CB BVAL A 33 11.101 4.227 14.591 0.40 71.47 C
TER
ATOM 1 N GLU X 18 -13.959 12.159 -6.598 1.00260.08 N
ATOM 2 CA GLU X 18 -13.297 13.465 -6.628 1.00269.83 C
ATOM 3 C GLU X 18 -11.946 13.282 -7.309 1.00269.18 C
ATOM 4 CB GLU X 18 -13.128 14.035 -5.210 1.00261.96 C
ATOM 5 CG GLU X 18 -14.455 14.401 -4.522 1.00263.56 C
ATOM 6 CD GLU X 18 -14.291 15.239 -3.242 1.00264.89 C
ATOM 7 OE1 GLU X 18 -14.172 14.646 -2.143 1.00264.24 O
ATOM 8 OE2 GLU X 18 -14.309 16.498 -3.306 1.00264.37 O1-
HETATM 614 S SO4 B 101 14.994 20.601 10.862 0.00 7.02 S
HETATM 615 O1 SO4 B 101 14.234 20.194 12.077 0.00 7.69 O
HETATM 616 O2 SO4 B 101 14.048 21.062 9.850 0.00 9.28 O
HETATM 617 O3 SO4 B 101 15.905 21.686 11.261 0.00 8.01 O
HETATM 618 O4 SO4 B 101 15.772 19.454 10.371 0.00 8.18 O
TER
HETATM 122 O HOH S 1 5.334 8.357 8.032 1.00 0.00 O
HETATM 123 O HOH S 2 5.396 15.243 10.734 1.00202.95 O
HETATM 124 O HOH S 3 -25.334 18.357 18.032 0.00 20.00 O
"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
#print out.getvalue()
assert not show_diff(out.getvalue(), """\
Overall:
Number of atoms = 50 (anisotropic = 0)
B_iso: mean = 96.0 max = 269.8 min = 0.0
Occupancy: mean = 0.47 max = 1.00 min = 0.00
warning: 22 atoms with zero occupancy
67 total B-factor or occupancy problem(s) detected
Atoms or residues with zero occupancy:
LYS A 82 CG occ=0.00
LYS A 82 CD occ=0.00
LYS A 82 CE occ=0.00
LYS A 82 NZ occ=0.00
LYS A 83 CG occ=0.00
LYS A 83 CD occ=0.00
LYS A 83 CE occ=0.00
LYS A 83 NZ occ=0.00
ASN A 242 (all) occ=0.00
SO4 B 101 (all) occ=0.00
HOH S 3 O occ=0.00
Macromolecules:
Number of atoms = 42 (anisotropic = 0)
B_iso: mean = 108.0 max = 269.8 min = 60.7
Occupancy: mean = 0.51 max = 1.00 min = 0.00
warning: 16 atoms with zero occupancy
57 total B-factor or occupancy problem(s) detected
Ligands:
Number of atoms = 5 (anisotropic = 0)
B_iso: mean = 8.0 max = 9.3 min = 7.0
Occupancy: mean = 0.00 max = 0.00 min = 0.00
warning: 5 atoms with zero occupancy
6 total B-factor or occupancy problem(s) detected
Waters:
Number of atoms = 3 (anisotropic = 0)
B_iso: mean = 74.3 max = 202.9 min = 0.0
Occupancy: mean = 0.67 max = 1.00 min = 0.00
warning: 1 atoms with zero occupancy
4 total B-factor or occupancy problem(s) detected
(Hydrogen atoms not included in overall counts.)
""")
assert (len(mstats.all.bad_adps) == 1)
assert (mstats.all.n_zero_b == 1)
mstats2 = loads(dumps(mstats))
out1 = StringIO()
out2 = StringIO()
mstats.show(out=out1)
mstats2.show(out=out2)
assert (out1.getvalue() == out2.getvalue())
# now with ignore_hd=False
mstats3 = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=False)
out2 = StringIO()
mstats3.show(out=out2)
assert (out2.getvalue() != out.getvalue())
assert (""" LYS A 83 HZ3 occ=0.00""" in out2.getvalue())
outliers = mstats3.all.as_gui_table_data(include_zoom=True)
assert (len(outliers) == 84)
# test with all_chain_proxies undefined
mstats4 = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=None,
ignore_hd=False)
outliers = mstats4.all.as_gui_table_data(include_zoom=True)
assert (len(outliers) == 84)
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))
def exercise_1():
pdb_raw = """\
ATOM 1134 N LYS A 82 5.933 36.285 21.572 1.00 70.94 N
ATOM 1135 CA LYS A 82 6.564 37.423 20.931 1.00 76.69 C
ATOM 1136 C LYS A 82 5.553 38.547 20.756 1.00 78.75 C
ATOM 1137 O LYS A 82 5.325 39.038 19.654 1.00 86.47 O
ATOM 1138 CB LYS A 82 7.179 37.024 19.583 1.00 82.32 C
ATOM 1139 CG LYS A 82 8.190 38.035 19.048 0.00 70.34 C
ATOM 1140 CD LYS A 82 9.429 38.129 19.944 0.00 67.69 C
ATOM 1141 CE LYS A 82 9.983 39.545 20.014 0.00 64.44 C
ATOM 1142 NZ LYS A 82 10.933 39.832 18.908 0.00 61.45 N
ATOM 1143 H LYS A 82 5.139 36.115 21.291 1.00 85.12 H
ATOM 1144 HA LYS A 82 7.279 37.749 21.501 1.00 92.03 H
ATOM 1145 HB2 LYS A 82 6.469 36.939 18.928 1.00 98.78 H
ATOM 1146 HB3 LYS A 82 7.636 36.175 19.687 1.00 98.78 H
ATOM 1147 HG2 LYS A 82 8.476 37.762 18.163 0.00 84.41 H
ATOM 1148 HG3 LYS A 82 7.775 38.912 19.011 0.00 84.41 H
ATOM 1149 HD2 LYS A 82 9.193 37.853 20.843 0.00 81.23 H
ATOM 1150 HD3 LYS A 82 10.122 37.551 19.589 0.00 81.23 H
ATOM 1151 HE2 LYS A 82 9.249 40.177 19.952 0.00 77.33 H
ATOM 1152 HE3 LYS A 82 10.453 39.662 20.854 0.00 77.33 H
ATOM 1153 HZ1 LYS A 82 11.237 40.666 18.977 0.00 73.75 H
ATOM 1154 HZ2 LYS A 82 10.523 39.738 18.123 0.00 73.75 H
ATOM 1155 HZ3 LYS A 82 11.621 39.269 18.944 0.00 73.75 H
ATOM 1156 N LYS A 83 4.936 38.927 21.866 1.00 75.79 N
ATOM 1157 CA LYS A 83 4.177 40.172 21.966 1.00 82.80 C
ATOM 1158 C LYS A 83 4.081 40.508 23.460 1.00 86.23 C
ATOM 1159 O LYS A 83 2.978 40.521 24.017 1.00 79.81 O
ATOM 1160 CB LYS A 83 2.790 40.044 21.332 1.00 79.16 C
ATOM 1161 CG LYS A 83 2.038 41.342 21.175 0.00 70.42 C
ATOM 1162 CD LYS A 83 2.072 41.803 19.735 0.00 66.90 C
ATOM 1163 CE LYS A 83 1.295 43.089 19.552 0.00 62.46 C
ATOM 1164 NZ LYS A 83 1.004 43.350 18.118 0.00 60.73 N
ATOM 1165 H LYS A 83 4.940 38.470 22.594 1.00 90.95 H
ATOM 1166 HA LYS A 83 4.658 40.885 21.518 1.00 99.36 H
ATOM 1167 HB2 LYS A 83 2.251 39.459 21.887 1.00 95.00 H
ATOM 1168 HB3 LYS A 83 2.890 39.655 20.449 1.00 95.00 H
ATOM 1169 HG2 LYS A 83 1.113 41.213 21.435 0.00 84.51 H
ATOM 1170 HG3 LYS A 83 2.453 42.024 21.726 0.00 84.51 H
ATOM 1171 HD2 LYS A 83 2.992 41.962 19.471 0.00 80.28 H
ATOM 1172 HD3 LYS A 83 1.672 41.123 19.171 0.00 80.28 H
ATOM 1173 HE2 LYS A 83 0.452 43.024 20.027 0.00 74.95 H
ATOM 1174 HE3 LYS A 83 1.818 43.830 19.896 0.00 74.95 H
ATOM 1175 HZ1 LYS A 83 0.521 42.683 17.780 0.00 72.87 H
ATOM 1176 HZ2 LYS A 83 1.764 43.417 17.661 0.00 72.87 H
ATOM 1177 HZ3 LYS A 83 0.548 44.109 18.034 0.00 72.87 H
ATOM 3630 N ASN A 242 -5.454 -3.027 1.145 0.00 67.69 N
ATOM 3631 CA ASN A 242 -4.759 -2.535 -0.037 0.00 65.44 C
ATOM 3632 C ASN A 242 -5.734 -2.397 -1.208 0.00 63.57 C
ATOM 3633 O ASN A 242 -6.425 -3.357 -1.552 0.00 63.94 O
ATOM 3634 CB ASN A 242 -3.626 -3.503 -0.392 0.00 63.13 C
ATOM 3635 CG ASN A 242 -2.802 -3.044 -1.576 0.00 63.58 C
ATOM 3636 OD1 ASN A 242 -2.524 -1.862 -1.731 0.00 65.52 O
ATOM 3637 ND2 ASN A 242 -2.399 -3.988 -2.416 0.00 62.17 N
ATOM 3638 H ASN A 242 -5.562 -3.880 1.129 0.00 81.22 H
ATOM 3639 HA ASN A 242 -4.375 -1.665 0.151 0.00 78.53 H
ATOM 3640 HB2 ASN A 242 -3.032 -3.587 0.370 0.00 75.76 H
ATOM 3641 HB3 ASN A 242 -4.007 -4.368 -0.611 0.00 75.76 H
ATOM 3642 HD21 ASN A 242 -1.929 -3.779 -3.104 0.00 74.60 H
ATOM 3643 HD22 ASN A 242 -2.609 -4.810 -2.272 0.00 74.60 H
ATOM 2 CA ALYS A 32 10.574 8.177 11.768 0.40 71.49 C
ATOM 3 CB ALYS A 32 9.197 8.686 12.246 0.40 74.71 C
ATOM 2 CA BLYS A 32 10.574 8.177 11.768 0.40 71.49 C
ATOM 3 CB BLYS A 32 9.197 8.686 12.246 0.40 74.71 C
ATOM 5 CA AVAL A 33 11.708 5.617 14.332 0.50 71.42 C
ATOM 6 CB AVAL A 33 11.101 4.227 14.591 0.50 71.47 C
ATOM 5 CA BVAL A 33 11.708 5.617 14.332 0.40 71.42 C
ATOM 6 CB BVAL A 33 11.101 4.227 14.591 0.40 71.47 C
TER
ATOM 1 N GLU X 18 -13.959 12.159 -6.598 1.00260.08 N
ATOM 2 CA GLU X 18 -13.297 13.465 -6.628 1.00269.83 C
ATOM 3 C GLU X 18 -11.946 13.282 -7.309 1.00269.18 C
ATOM 4 CB GLU X 18 -13.128 14.035 -5.210 1.00261.96 C
ATOM 5 CG GLU X 18 -14.455 14.401 -4.522 1.00263.56 C
ATOM 6 CD GLU X 18 -14.291 15.239 -3.242 1.00264.89 C
ATOM 7 OE1 GLU X 18 -14.172 14.646 -2.143 1.00264.24 O
ATOM 8 OE2 GLU X 18 -14.309 16.498 -3.306 1.00264.37 O1-
HETATM 614 S SO4 B 101 14.994 20.601 10.862 0.00 7.02 S
HETATM 615 O1 SO4 B 101 14.234 20.194 12.077 0.00 7.69 O
HETATM 616 O2 SO4 B 101 14.048 21.062 9.850 0.00 9.28 O
HETATM 617 O3 SO4 B 101 15.905 21.686 11.261 0.00 8.01 O
HETATM 618 O4 SO4 B 101 15.772 19.454 10.371 0.00 8.18 O
TER
HETATM 122 O HOH S 1 5.334 8.357 8.032 1.00 0.00 O
HETATM 123 O HOH S 2 5.396 15.243 10.734 1.00202.95 O
HETATM 124 O HOH S 3 -25.334 18.357 18.032 0.00 20.00 O
"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
#print out.getvalue()
assert not show_diff(
out.getvalue(), """\
Overall:
Number of atoms = 50 (anisotropic = 0)
B_iso: mean = 96.0 max = 269.8 min = 0.0
Occupancy: mean = 0.47 max = 1.00 min = 0.00
warning: 22 atoms with zero occupancy
69 total B-factor or occupancy problem(s) detected
Atoms or residues with zero occupancy:
LYS A 82 CG occ=0.00
LYS A 82 CD occ=0.00
LYS A 82 CE occ=0.00
LYS A 82 NZ occ=0.00
LYS A 83 CG occ=0.00
LYS A 83 CD occ=0.00
LYS A 83 CE occ=0.00
LYS A 83 NZ occ=0.00
ASN A 242 (all) occ=0.00
SO4 B 101 (all) occ=0.00
HOH S 3 O occ=0.00
Macromolecules:
Number of atoms = 42 (anisotropic = 0)
B_iso: mean = 108.0 max = 269.8 min = 60.7
Occupancy: mean = 0.51 max = 1.00 min = 0.00
warning: 16 atoms with zero occupancy
59 total B-factor or occupancy problem(s) detected
Ligands:
Number of atoms = 5 (anisotropic = 0)
B_iso: mean = 8.0 max = 9.3 min = 7.0
Occupancy: mean = 0.00 max = 0.00 min = 0.00
warning: 5 atoms with zero occupancy
6 total B-factor or occupancy problem(s) detected
Waters:
Number of atoms = 3 (anisotropic = 0)
B_iso: mean = 74.3 max = 202.9 min = 0.0
Occupancy: mean = 0.67 max = 1.00 min = 0.00
warning: 1 atoms with zero occupancy
4 total B-factor or occupancy problem(s) detected
(Hydrogen atoms not included in overall counts.)
""")
assert (len(mstats.all.bad_adps) == 1)
assert (mstats.all.n_zero_b == 1)
mstats2 = loads(dumps(mstats))
out1 = StringIO()
out2 = StringIO()
mstats.show(out=out1)
mstats2.show(out=out2)
assert (out1.getvalue() == out2.getvalue())
# now with ignore_hd=False
mstats3 = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=False)
out2 = StringIO()
mstats3.show(out=out2)
assert (out2.getvalue() != out.getvalue())
assert (""" LYS A 83 HZ3 occ=0.00""" in out2.getvalue())
outliers = mstats3.all.as_gui_table_data(include_zoom=True)
assert (len(outliers) == 86)
# test with all_chain_proxies undefined
mstats4 = model_properties.model_statistics(pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=None,
ignore_hd=False)
outliers = mstats4.all.as_gui_table_data(include_zoom=True)
assert (len(outliers) == 86)
