def summary(pdb_file=None, pdb_hierarchy=None, crystal_symmetry=None):
header_info = None
if (pdb_hierarchy is None):
assert (pdb_file is not None)
pdb_in = file_reader.any_file(pdb_file, force_type="pdb")
pdb_in.assert_file_type("pdb")
pdb_hierarchy = pdb_in.file_object.hierarchy
pdb_hierarchy.atoms().reset_i_seq()
header_info = molprobity.pdb_header_info(pdb_file=pdb_file)
crystal_symmetry = pdb_in.file_object.crystal_symmetry()
else:
assert (pdb_file is None)
#
cache = pdb_hierarchy.atom_selection_cache()
sel = cache.selection('protein')
pdb_hierarchy = pdb_hierarchy.select(sel)
#
model = mmtbx.model.manager(model_input=pdb_hierarchy.as_pdb_input())
if crystal_symmetry and model.crystal_symmetry() is None:
model.set_crystal_symmetry(
crystal_symmetry) # Somehow pdb_hiearchy lacks cs
if not model.crystal_symmetry():
aaa = bbb
return molprobity.molprobity(model=model,
keep_hydrogens=False,
header_info=header_info).summarize()
def analyze_fragment(pdb_str):
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
model = mmtbx.model.manager(pdb_in.input)
validation = molprobity.molprobity(model, outliers_only=False)
result = analyze_model.process_pdb_hierarchy(
pdb_hierarchy=model.get_hierarchy(),
validation=validation,
log=null_out())
return result
def analyze_fragment(pdb_str):
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
hierarchy = pdb_in.hierarchy
validation = molprobity.molprobity(pdb_hierarchy=hierarchy,
outliers_only=False)
result = analyze_model.process_pdb_hierarchy(pdb_hierarchy=hierarchy,
validation=validation,
log=null_out())
return result
def analyze_fragment (pdb_str) :
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_str)
hierarchy = pdb_in.hierarchy
validation = molprobity.molprobity(pdb_hierarchy=hierarchy,
outliers_only=False)
result = analyze_model.process_pdb_hierarchy(
pdb_hierarchy=hierarchy,
validation=validation,
log=null_out())
return result
def run():
result = []
for p in [True, False]:
for mr in [True, False]:
pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str)
hierarchy = pdb_inp.construct_hierarchy()
model = mmtbx.model.manager(model_input=pdb_inp, log=null_out())
if(p):
model.process(make_restraints=mr)
o = molprobity.molprobity(model = model)
result.append("%8.4f"%o.rms_bonds())
assert len(list(set(result)))==1
def __init__ (self,
fmodel,
pdb_hierarchy,
params=None,
processed_pdb_file=None,
geometry_restraints_manager=None,
cif_objects=(),
cif_files=(), # XXX bug
debug=None,
verbose=True,
out=sys.stdout) :
adopt_init_args(self, locals())
if (self.params is None) :
self.params = master_phil.extract().alt_confs
self.extract_selection()
self.refine_cycle = 1
self.map_file = None
self.r_work_start = fmodel.r_work()
self.r_free_start = fmodel.r_free()
t_start = time.time()
for i_cycle in range(params.macro_cycles) :
n_alts = self.build_residue_conformers(stop_if_none=(i_cycle==0))
if (n_alts == 0) :
if (i_cycle == 0) :
raise Sorry("No alternate conformations found.")
else :
self.refine(constrain_occupancies=False)
refine_again = self.params.refinement.constrain_correlated_occupancies
if (self.rejoin()) :
refine_again = True
self.refine(title="Refining final model")
make_header("Finished", out=out)
from mmtbx.validation import molprobity
validation = molprobity.molprobity(
pdb_hierarchy=self.pdb_hierarchy,
outliers_only=False)
print >> self.out, ""
validation.show_summary(out=self.out, prefix=" ")
make_sub_header("Analyzing final model", out=out)
analyze_model.process_pdb_hierarchy(
pdb_hierarchy=self.pdb_hierarchy,
validation=validation,
log=self.out).show(out=out, verbose=self.verbose)
print >> self.out, ""
print >> self.out, "Start: r_work=%6.4f r_free=%6.4f" % \
(self.r_work_start, self.r_free_start)
print >> self.out, "Final: r_work=%6.4f r_free=%6.4f" % \
(self.fmodel.r_work(), self.fmodel.r_free())
t_end = time.time()
print >> self.out, ""
print >> self.out, "Total runtime: %d s" % int(t_end - t_start)
print >> self.out, ""
def summary(pdb_file=None, pdb_hierarchy=None):
header_info = None
if (pdb_hierarchy is None):
assert (pdb_file is not None)
pdb_in = file_reader.any_file(pdb_file, force_type="pdb")
pdb_in.assert_file_type("pdb")
pdb_hierarchy = pdb_in.file_object.hierarchy
pdb_hierarchy.atoms().reset_i_seq()
header_info = molprobity.pdb_header_info(pdb_file=pdb_file)
else:
assert (pdb_file is None)
return molprobity.molprobity(None,
pdb_hierarchy=pdb_hierarchy,
keep_hydrogens=False,
header_info=header_info).summarize()
def summary (pdb_file=None, pdb_hierarchy=None) :
header_info = None
if (pdb_hierarchy is None) :
assert (pdb_file is not None)
pdb_in = file_reader.any_file(pdb_file, force_type="pdb")
pdb_in.assert_file_type("pdb")
pdb_hierarchy = pdb_in.file_object.hierarchy
pdb_hierarchy.atoms().reset_i_seq()
header_info = molprobity.pdb_header_info(
pdb_file=pdb_file)
else :
assert (pdb_file is None)
return molprobity.molprobity(
pdb_hierarchy=pdb_hierarchy,
keep_hydrogens=False,
header_info=header_info).summarize()
def filter_before_build (
pdb_hierarchy,
fmodel,
geometry_restraints_manager,
selection=None,
params=None,
verbose=True,
log=sys.stdout) :
"""
Pick residues suitable for building alternate conformations - by default,
this means no MolProbity/geometry outliers, good fit to map, no missing
atoms, and no pre-existing alternates, but with significant difference
density nearby.
"""
from mmtbx.validation import molprobity
from mmtbx.rotamer import rotamer_eval
import mmtbx.monomer_library.server
from mmtbx import building
from iotbx.pdb import common_residue_names_get_class
from scitbx.array_family import flex
if (selection is None) :
selection = flex.bool(fmodel.xray_structure.scatterers().size(), True)
pdb_atoms = pdb_hierarchy.atoms()
assert (pdb_atoms.size() == fmodel.xray_structure.scatterers().size())
pdb_atoms.reset_i_seq()
full_validation = molprobity.molprobity(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
geometry_restraints_manager=geometry_restraints_manager,
outliers_only=False,
rotamer_library="8000")
if (verbose) :
full_validation.show(out=log)
multi_criterion = full_validation.as_multi_criterion_view()
if (params is None) :
params = libtbx.phil.parse(filter_params_str).extract()
mon_lib_srv = mmtbx.monomer_library.server.server()
two_fofc_map, fofc_map = building.get_difference_maps(fmodel=fmodel)
residues = []
filters = params.discard_outliers
make_sub_header("Identifying candidates for building", out=log)
# TODO parallelize
for chain in pdb_hierarchy.only_model().chains() :
if (not chain.is_protein()) :
continue
for residue_group in chain.residue_groups() :
atom_groups = residue_group.atom_groups()
id_str = residue_group.id_str()
i_seqs = residue_group.atoms().extract_i_seq()
residue_sel = selection.select(i_seqs)
if (not residue_sel.all_eq(True)) :
continue
if (len(atom_groups) > 1) :
print >> log, " %s is already multi-conformer" % id_str
continue
atom_group = atom_groups[0]
res_class = common_residue_names_get_class(atom_group.resname)
if (res_class != "common_amino_acid") :
print >> log, " %s: non-standard residue" % id_str
continue
missing_atoms = rotamer_eval.eval_residue_completeness(
residue=atom_group,
mon_lib_srv=mon_lib_srv,
ignore_hydrogens=True)
if (len(missing_atoms) > 0) :
# residues modeled as pseudo-ALA are allowed by default; partially
# missing sidechains are more problematic
if ((building.is_stub_residue(atom_group)) and
(not params.ignore_stub_residues)) :
pass
else :
print >> log, " %s: missing or incomplete sidechain" % \
(id_str, len(missing_atoms))
continue
validation = multi_criterion.get_residue_group_data(residue_group)
is_outlier = is_validation_outlier(validation, params)
if (is_outlier) :
print >> log, " %s" % str(validation)
continue
if (params.use_difference_map) :
i_seqs_no_hd = building.get_non_hydrogen_atom_indices(residue_group)
map_stats = building.local_density_quality(
fofc_map=fofc_map,
two_fofc_map=two_fofc_map,
atom_selection=i_seqs_no_hd,
xray_structure=fmodel.xray_structure,
radius=params.sampling_radius)
if ((map_stats.number_of_atoms_below_fofc_map_level() == 0) and
(map_stats.fraction_of_nearby_grid_points_above_cutoff()==0)) :
if (verbose) :
print >> log, " no difference density for %s" % id_str
continue
residues.append(residue_group.only_atom_group())
if (len(residues) == 0) :
raise Sorry("No residues passed the filtering criteria.")
print >> log, ""
print >> log, "Alternate conformations will be tried for %d residue(s):" % \
len(residues)
building.show_chain_resseq_ranges(residues, out=log, prefix=" ")
print >> log, ""
return residues