def run(args, params=None, out=sys.stdout, log=sys.stderr):
if (((len(args) == 0) and (params is None)) or
((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help")))):
show_usage()
return
if (params is None):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="file_name")
work_params = pcl.work.extract()
# or use parameters defined by GUI
else:
work_params = params
pdb_inp = iotbx.pdb.input(file_name=work_params.file_name)
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params(
)
pdb_int_params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=pdb_int_params,
build_grm=True)
fixed_pdb_h = model.get_hierarchy().deep_copy()
fixed_pdb_h.reset_atom_i_seqs()
fixed_pdb_h = fix_rotamer_outliers(
model=model,
radius=work_params.radius,
)
res_pdb_str = model.model_as_pdb()
with open("%s.pdb" % work_params.output_prefix, "w") as f:
f.write(res_pdb_str)
def run(args, params=None, out=sys.stdout, log=sys.stderr):
if ( ((len(args) == 0) and (params is None)) or
((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help"))) ):
show_usage()
return
if (params is None):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="file_name")
work_params = pcl.work.extract()
# or use parameters defined by GUI
else:
work_params = params
pdb_files = work_params.file_name
mon_lib_srv = mmtbx.monomer_library.server.server()
ppf_srv = mmtbx.utils.process_pdb_file_srv(
crystal_symmetry = None,
pdb_interpretation_params = None,
stop_for_unknowns = False,
log = log,
cif_objects = None, # need to figure out how to get them
mon_lib_srv = mon_lib_srv,
ener_lib = None,
use_neutron_distances = False)
processed_pdb_file, pdb_inp = ppf_srv.process_pdb_files(
pdb_file_names = pdb_files)
cs = ppf_srv.crystal_symmetry
xrs = processed_pdb_file.xray_structure(show_summary = True)
if(xrs is None):
raise Sorry("Cannot extract xray_structure.")
grm = get_geometry_restraints_manager(
processed_pdb_file=processed_pdb_file,
xray_structure=xrs,
log=log)
pdb_h = processed_pdb_file.all_chain_proxies.pdb_hierarchy
fixed_pdb_h = pdb_h.deep_copy()
fixed_pdb_h.reset_atom_i_seqs()
rotamer_manager = RotamerEval(mon_lib_srv=mon_lib_srv)
fixed_pdb_h = fix_rotamer_outliers(
pdb_hierarchy=fixed_pdb_h,
grm=grm.geometry,
xrs=xrs,
radius=work_params.radius,
mon_lib_srv=mon_lib_srv,
rotamer_manager=rotamer_manager,
asc=None)
iotbx.pdb.write_whole_pdb_file(
file_name="%s.pdb" % work_params.output_prefix,
processed_pdb_file=processed_pdb_file,
pdb_hierarchy=fixed_pdb_h,
crystal_symmetry=cs)
def exercise_2():
model = get_necessary_inputs(pdb_str_2)
pdb_h = fix_rotamer_outliers(model=model, radius=5)
rotamers = []
for res in pdb_h.only_chain().only_conformer().residues():
rotamers.append(model.get_rotamer_manager().evaluate_residue(res))
assert rotamers == [
'mtt180', 'tttt', 'm-30', 'pt', 'p', 'mt-10', 'm-40', 'EXCEPTION',
'tt', 'tttt'
], rotamers
def exercise_1():
""" 58 is outlier """
model = get_necessary_inputs(pdb_str_1)
# pdb_h.write_pdb_file("fix_rot_out_ex1_start.pdb")
pdb_h = fix_rotamer_outliers(model=model, radius=5)
rotamers = []
# pdb_h.write_pdb_file("fix_rot_out_ex1_end.pdb")
for res in pdb_h.only_chain().only_conformer().residues():
rotamers.append(model.get_rotamer_manager().evaluate_residue(res))
# print rotamers
assert rotamers == ['m-80', 'p'], rotamers
def exercise_2(mon_lib_srv, ener_lib, rotamer_manager):
pdb_h, grm, xrs = get_necessary_inputs(pdb_str_2, mon_lib_srv, ener_lib)
pdb_h = fix_rotamer_outliers(
pdb_hierarchy=pdb_h,
grm=grm,
xrs=xrs,
radius=5,
mon_lib_srv=mon_lib_srv,
rotamer_manager=rotamer_manager,
asc=None)
rotamers = []
for res in pdb_h.only_chain().only_conformer().residues():
rotamers.append(rotamer_manager.evaluate_residue(res))
assert rotamers == ['mtt180', 'tttt', 'm-30', 'pt', 'p', 'mt-10', 'm-40',
'EXCEPTION', 'tt', 'tttt'], rotamers
def exercise_2(mon_lib_srv, ener_lib, rotamer_manager):
pdb_h, grm, xrs = get_necessary_inputs(pdb_str_2, mon_lib_srv, ener_lib)
pdb_h = fix_rotamer_outliers(pdb_hierarchy=pdb_h,
grm=grm,
xrs=xrs,
radius=5,
mon_lib_srv=mon_lib_srv,
rotamer_manager=rotamer_manager,
asc=None)
rotamers = []
for res in pdb_h.only_chain().only_conformer().residues():
rotamers.append(rotamer_manager.evaluate_residue(res))
assert rotamers == [
'mtt180', 'tttt', 'm-30', 'pt', 'p', 'mt-10', 'm-40', 'EXCEPTION',
'tt', 'tttt'
], rotamers
def exercise_1(mon_lib_srv, ener_lib, rotamer_manager):
""" 58 is outlier """
pdb_h, grm, xrs = get_necessary_inputs(pdb_str_1, mon_lib_srv, ener_lib)
# pdb_h.write_pdb_file("fix_rot_out_ex1_start.pdb")
pdb_h = fix_rotamer_outliers(pdb_hierarchy=pdb_h,
grm=grm,
xrs=xrs,
radius=5,
mon_lib_srv=mon_lib_srv,
rotamer_manager=rotamer_manager,
asc=None)
rotamers = []
# pdb_h.write_pdb_file("fix_rot_out_ex1_end.pdb")
for res in pdb_h.only_chain().only_conformer().residues():
rotamers.append(rotamer_manager.evaluate_residue(res))
# print rotamers
assert rotamers == ['m-80', 'p'], rotamers
def exercise_1(mon_lib_srv, ener_lib, rotamer_manager):
""" 58 is outlier """
pdb_h, grm, xrs = get_necessary_inputs(pdb_str_1, mon_lib_srv, ener_lib)
# pdb_h.write_pdb_file("fix_rot_out_ex1_start.pdb")
pdb_h = fix_rotamer_outliers(
pdb_hierarchy=pdb_h,
grm=grm,
xrs=xrs,
radius=5,
mon_lib_srv=mon_lib_srv,
rotamer_manager=rotamer_manager,
asc=None)
rotamers = []
# pdb_h.write_pdb_file("fix_rot_out_ex1_end.pdb")
for res in pdb_h.only_chain().only_conformer().residues():
rotamers.append(rotamer_manager.evaluate_residue(res))
# print rotamers
assert rotamers == ['m-80', 'p'], rotamers
def run(self):
t_0 = time()
ncs_obj = iotbx.ncs.input(
hierarchy=self.whole_pdb_h,
chain_max_rmsd=4.0,
chain_similarity_threshold=0.99,
residue_match_radius=999.0)
print >> self.log, "Found NCS groups:"
ncs_obj.show(format='phil', log=self.log)
ncs_restr_group_list = ncs_obj.get_ncs_restraints_group_list(
raise_sorry=False)
self.using_ncs = False
total_ncs_selected_atoms = 0
master_sel = flex.size_t([])
filtered_ncs_restr_group_list = self.filter_ncs_restraints_group_list(
self.whole_pdb_h, ncs_restr_group_list)
if len(filtered_ncs_restr_group_list) > 0:
self.using_ncs = True
master_sel = flex.bool(self.whole_pdb_h.atoms_size(), True)
for ncs_gr in filtered_ncs_restr_group_list:
for copy in ncs_gr.copies:
master_sel.set_selected(copy.iselection, False)
self.master_pdb_h = self.whole_pdb_h.select(master_sel)
self.master_sel=master_sel
self.master_pdb_h.reset_atom_i_seqs()
if self.using_ncs:
self.master_pdb_h.write_pdb_file("%s_master_h.pdb" % self.params.output_prefix)
self.working_pdb_h = self.master_pdb_h
else:
self.working_pdb_h = self.whole_pdb_h
self.working_pdb_h.reset_atom_i_seqs()
self.ann = ioss.annotation.from_phil(
phil_helices=self.params.secondary_structure.protein.helix,
phil_sheets=self.params.secondary_structure.protein.sheet,
pdb_hierarchy=self.whole_pdb_h)
self.working_xrs = self.working_pdb_h.extract_xray_structure(crystal_symmetry=self.cs)
if self.using_ncs:
self.whole_xrs = self.whole_pdb_h.extract_xray_structure(crystal_symmetry=self.cs)
else:
self.whole_xrs = self.working_xrs
if self.params.use_map_for_reference:
# self.prepare_reference_map(xrs=self.whole_xrs, pdb_h=self.whole_pdb_h)
# self.prepare_reference_map_2(xrs=self.whole_xrs, pdb_h=self.whole_pdb_h)
self.prepare_reference_map_3(xrs=self.whole_xrs, pdb_h=self.whole_pdb_h)
# STOP()
if self.ann.get_n_helices() + self.ann.get_n_sheets() == 0:
self.ann = self.pdb_input.extract_secondary_structure()
self.original_ann = None
self.filtered_whole_ann = None
if self.ann is not None:
self.original_ann = self.ann.deep_copy()
print >> self.log, "Original SS annotation"
print >> self.log, self.original_ann.as_pdb_str()
self.ann.remove_short_annotations()
self.filtered_whole_ann = self.ann.deep_copy()
self.ann.remove_empty_annotations(
hierarchy=self.working_pdb_h)
self.filtered_whole_ann.remove_empty_annotations(
hierarchy=self.whole_pdb_h)
# self.ann.concatenate_consecutive_helices()
self.ann.split_helices_with_prolines(
hierarchy=self.working_pdb_h,
asc=None)
self.filtered_whole_ann.split_helices_with_prolines(
hierarchy=self.whole_pdb_h,
asc=None)
# print >> self.log, "Splitted SS annotation"
# print >> self.log, ann.as_pdb_str()
print >> self.log, "Filtered SS annotation"
print >> self.log, self.ann.as_pdb_str()
# getting grm with SS restraints
self.get_grm()
if (self.ann is None or
self.ann.get_n_helices() + self.ann.get_n_sheets() == 0 or
not self.params.ss_idealization.enabled):
print >> self.log, "No secondary structure annotations found or SS idealization is disabled."
print >> self.log, "Secondary structure substitution step will be skipped"
self.log.flush()
# here we want to do geometry minimization anyway!
negate_selection = None
if self.reference_map is None:
outlier_selection_txt = mmtbx.building.loop_closure.utils. \
rama_outliers_selection(self.working_pdb_h, self.rama_manager, 1)
print >> self.log, "outlier_selection_txt", outlier_selection_txt
negate_selection = "all"
if outlier_selection_txt != "" and outlier_selection_txt is not None:
negate_selection = "not (%s)" % outlier_selection_txt
self.minimize(
hierarchy=self.whole_pdb_h,
xrs=self.whole_xrs,
original_pdb_h=self.whole_pdb_h,
grm=self.whole_grm,
ncs_restraints_group_list=filtered_ncs_restr_group_list,
excl_string_selection=negate_selection,
ss_annotation=self.ann,
reference_map=self.reference_map)
# self.original_boxed_hierarchy.write_pdb_file(file_name="original_boxed_h_1.pdb")
else:
self.params.ss_idealization.file_name_before_regularization = \
"%s_ss_before_reg.pdb" % self.params.output_prefix
ssb.substitute_ss(
real_h=self.working_pdb_h,
xray_structure=self.working_xrs,
ss_annotation=self.ann,
params=self.params.ss_idealization,
grm=self.working_grm,
fix_rotamer_outliers=True,
cif_objects=self.cif_objects,
verbose=True,
reference_map=self.reference_map,
rotamer_manager=self.rotamer_manager,
log=self.log)
self.log.flush()
self.after_ss_idealization = geometry_no_grm(
pdb_hierarchy=iotbx.pdb.input(
source_info=None,
lines=self.working_pdb_h.as_pdb_string()).construct_hierarchy(),
molprobity_scores=True)
# Write resulting pdb file.
self.shift_and_write_result(
hierarchy=self.working_pdb_h,
fname_suffix="ss_ideal",
grm=self.working_grm)
# STOP()
self.params.loop_idealization.minimize_whole = not self.using_ncs
# self.params.loop_idealization.enabled = False
# self.params.loop_idealization.variant_search_level = 0
loop_ideal = loop_idealization(
pdb_hierarchy=self.working_pdb_h,
params=self.params.loop_idealization,
secondary_structure_annotation=self.ann,
reference_map=self.reference_map,
crystal_symmetry=self.working_xrs.crystal_symmetry(),
grm=self.working_grm,
rama_manager=self.rama_manager,
rotamer_manager=self.rotamer_manager,
log=self.log,
verbose=True)
self.log.flush()
# STOP()
self.shift_and_write_result(
hierarchy=loop_ideal.resulting_pdb_h,
fname_suffix="rama_ideal",
grm=self.working_grm)
self.after_loop_idealization = geometry_no_grm(
pdb_hierarchy=iotbx.pdb.input(
source_info=None,
lines=loop_ideal.resulting_pdb_h.as_pdb_string()).construct_hierarchy(),
molprobity_scores=True)
# fixing remaining rotamer outliers
fixed_rot_pdb_h = loop_ideal.resulting_pdb_h.deep_copy()
fixed_rot_pdb_h.reset_atom_i_seqs()
if (self.params.additionally_fix_rotamer_outliers and
self.after_loop_idealization.rotamer_outliers > 0.004):
print >> self.log, "Processing pdb file again for fixing rotamers..."
self.log.flush()
print >> self.log, "Fixing rotamers..."
self.log.flush()
self.shift_and_write_result(
hierarchy=fixed_rot_pdb_h,
fname_suffix="just_before_rota")
fixed_rot_pdb_h = fix_rotamer_outliers(
pdb_hierarchy=fixed_rot_pdb_h,
grm=self.working_grm.geometry,
xrs=self.working_xrs,
map_data=self.reference_map,
mon_lib_srv=self.mon_lib_srv,
rotamer_manager=self.rotamer_manager,
verbose=True)
self.shift_and_write_result(
hierarchy=fixed_rot_pdb_h,
fname_suffix="rota_ideal",
grm=self.working_grm)
cs_to_write = self.cs if self.shift_vector is None else None
self.after_rotamer_fixing = geometry_no_grm(
pdb_hierarchy=iotbx.pdb.input(
source_info=None,
lines=fixed_rot_pdb_h.as_pdb_string()).construct_hierarchy(),
molprobity_scores=True)
ref_hierarchy_for_final_gm = self.original_boxed_hierarchy
if not self.params.use_starting_model_for_final_gm:
ref_hierarchy_for_final_gm = self.whole_pdb_h
ref_hierarchy_for_final_gm.reset_atom_i_seqs()
if self.params.additionally_fix_rotamer_outliers:
ssb.set_xyz_smart(self.working_pdb_h, fixed_rot_pdb_h)
if self.using_ncs:
print >> self.log, "Using ncs"
# multiply back and do geometry_minimization for the whole molecule
for ncs_gr in ncs_restr_group_list:
master_h = self.whole_pdb_h.select(ncs_gr.master_iselection)
for c in ncs_gr.copies:
new_sites = master_h.atoms().extract_xyz()
new_c_sites = c.r.elems * new_sites + c.t
self.whole_pdb_h.select(c.iselection).atoms().set_xyz(new_c_sites)
self.log.flush()
else:
# still need to run gm if rotamers were fixed
print >> self.log, "Not using ncs"
# need to update SS manager for the whole model here.
if self.params.use_ss_restraints:
ss_manager = manager(
pdb_hierarchy=self.whole_pdb_h,
geometry_restraints_manager=self.whole_grm.geometry,
sec_str_from_pdb_file=self.filtered_whole_ann,
params=None,
mon_lib_srv=self.mon_lib_srv,
verbose=-1,
log=self.log)
self.whole_grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=self.whole_pdb_h,
log=self.log)
print >> self.log, "loop_ideal.ref_exclusion_selection", loop_ideal.ref_exclusion_selection
print >> self.log, "Minimizing whole model"
self.minimize(
hierarchy=self.whole_pdb_h,
xrs=self.whole_xrs,
grm=self.whole_grm,
ncs_restraints_group_list=filtered_ncs_restr_group_list,
original_pdb_h=ref_hierarchy_for_final_gm,
excl_string_selection=loop_ideal.ref_exclusion_selection,
ss_annotation=self.ann,
reference_map = self.reference_map)
self.shift_and_write_result(
hierarchy=self.whole_pdb_h,
fname_suffix="all_idealized",
grm=self.whole_grm)
self.final_model_statistics = geometry_no_grm(
pdb_hierarchy=iotbx.pdb.input(
source_info=None,
lines=self.whole_pdb_h.as_pdb_string()).construct_hierarchy(),
molprobity_scores=True)
# self.original_boxed_hierarchy.write_pdb_file(file_name="original_boxed_end.pdb")
self.time_for_run = time() - t_0
def run(self):
t_0 = time()
self.ann = self.model.get_ss_annotation()
self.get_grm()
self.model.setup_ncs_constraints_groups()
self.init_model_statistics = self.get_statistics(self.model)
# Here we are preparing maps if needed.
if self.user_supplied_map is not None:
self.prepare_user_map()
if self.reference_map is None and self.params.use_map_for_reference:
self.prepare_reference_map_3()
if self.params.run_minimization_first:
# running simple minimization and updating all
# self.master, self.working, etc...
# self.whole_pdb_h.reset_atom_i_seqs()
if self.init_ref_map is None:
self.prepare_init_reference_map()
print >> self.log, "Minimization first"
self.minimize(
model=self.model,
original_pdb_h=self.original_hierarchy,
excl_string_selection=None, # don't need if we have map
reference_map=self.init_ref_map,
)
self.init_gm_model_statistics = self.get_statistics(self.model)
if self.params.debug:
self.shift_and_write_result(
model = self.model,
fname_suffix="init_gm")
if (self.init_gm_model_statistics is not None
and self.init_gm_model_statistics.ramachandran.outliers == 0
and self.init_gm_model_statistics.omega.twisted_general <= 0.01
and self.init_gm_model_statistics.omega.twisted_proline <= 0.01
and self.init_gm_model_statistics.omega.cis_general <= 0.01
and self.init_gm_model_statistics.omega.cis_proline <= 0.01):
print >> self.log, "Simple minimization was enough"
# Early exit!!!
self.shift_and_write_result(
model=self.model,
fname_suffix="all_idealized")
self.final_model_statistics = self.get_statistics(self.model)
# self.original_boxed_hierarchy.write_pdb_file(file_name="original_boxed_end.pdb")
self.time_for_run = time() - t_0
if self.params.output_pkl:
easy_pickle.dump(
file_name="%s.pkl" % self.params.output_prefix,
obj = self.get_stats_obj())
return
self.filtered_whole_ann = None
if self.ann is not None:
self.filtered_whole_ann = self.ann.deep_copy()
print >> self.log, "Original SS annotation"
print >> self.log, self.ann.as_pdb_str()
if self.params.filter_input_ss:
self.filtered_whole_ann = self.ann.filter_annotation(
hierarchy=self.model.get_hierarchy(),
asc=self.model.get_atom_selection_cache())
print >> self.log, "Filtered SS annotation"
print >> self.log, self.filtered_whole_ann.as_pdb_str()
self.model.set_ss_annotation(self.filtered_whole_ann)
# getting grm with SS restraints
self.update_ss_in_grm(self.filtered_whole_ann)
if (self.ann is None or
self.ann.get_n_helices() + self.ann.get_n_sheets() == 0 or
not self.params.ss_idealization.enabled):
print >> self.log, "No secondary structure annotations found or SS idealization is disabled."
print >> self.log, "Secondary structure substitution step will be skipped"
self.log.flush()
# here we want to do geometry minimization anyway!
negate_selection = None
if self.reference_map is None:
outlier_selection_txt = mmtbx.building.loop_closure.utils. \
rama_score_selection(self.model, self.model.get_ramachandran_manager(), "outlier",1)
print >> self.log, "outlier_selection_txt", outlier_selection_txt
negate_selection = "all"
if outlier_selection_txt != "" and outlier_selection_txt is not None:
negate_selection = "not (%s)" % outlier_selection_txt
# if self.params.run_minimization_first:
# self.minimize(
# model=self.model,
# original_pdb_h=self.whole_pdb_h,
# ncs_restraints_group_list=self.filtered_ncs_restr_group_list,
# excl_string_selection=negate_selection,
# reference_map=self.reference_map)
# self.original_boxed_hierarchy.write_pdb_file(file_name="original_boxed_h_1.pdb")
else:
if self.params.debug:
self.params.ss_idealization.file_name_before_regularization = \
"%s_ss_before_reg.pdb" % self.params.output_prefix
self.params.ss_idealization.skip_good_ss_elements = True
ssb.substitute_ss(
model = self.model,
params=self.params.ss_idealization,
fix_rotamer_outliers=True,
verbose=self.params.verbose,
reference_map=self.master_map,
log=self.log)
self.log.flush()
# for_stat_h = self.get_intermediate_result_hierarchy()
self.after_ss_idealization = self.get_statistics(self.model)
self.shift_and_write_result(
model=self.model,
fname_suffix="ss_ideal_stat")
# Write resulting pdb file.
if self.params.debug:
self.shift_and_write_result(
model=self.model,
fname_suffix="ss_ideal",
)
self.params.loop_idealization.minimize_whole = not self.model.ncs_constraints_present() and self.params.loop_idealization.minimize_whole
self.params.loop_idealization.debug = self.params.debug or self.params.loop_idealization.debug
# self.params.loop_idealization.enabled = False
# self.params.loop_idealization.variant_search_level = 0
print >> self.log, "Starting loop idealization"
loop_ideal = loop_idealization(
self.model,
params=self.params.loop_idealization,
reference_map=self.master_map,
log=self.log,
verbose=True)
self.log.flush()
if self.params.debug:
self.shift_and_write_result(
model = self.model,
fname_suffix="rama_ideal")
self.after_loop_idealization = self.get_statistics(self.model)
if self.params.add_hydrogens:
print >> self.log, "Adding hydrogens"
assert 0, "not implemented anymore"
self.add_hydrogens()
# fixing remaining rotamer outliers
if (self.params.additionally_fix_rotamer_outliers and
self.after_loop_idealization.rotamer.outliers > 0.004):
print >> self.log, "Processing pdb file again for fixing rotamers..."
self.log.flush()
print >> self.log, "Fixing rotamers..."
self.log.flush()
if self.params.debug:
self.shift_and_write_result(
model = self.model,
fname_suffix="just_before_rota")
fix_rotamer_outliers(
model = self.model,
map_data=self.master_map,
verbose=True,
log=self.log)
if self.params.debug:
self.shift_and_write_result(
model = self.model,
fname_suffix="rota_ideal")
cs_to_write = self.cs if self.shift_vector is None else None
self.after_rotamer_fixing = self.get_statistics(self.model)
ref_hierarchy_for_final_gm = self.original_boxed_hierarchy
if not self.params.use_starting_model_for_final_gm:
ref_hierarchy_for_final_gm = self.model.get_hierarchy().deep_copy()
ref_hierarchy_for_final_gm.reset_atom_i_seqs()
if self.model.ncs_constraints_present():
print >> self.log, "Using ncs"
# assert 0
else:
print >> self.log, "Not using ncs"
# assert 0
# need to update SS manager for the whole model here.
if self.params.use_ss_restraints:
ss_params = sec_str_master_phil.fetch().extract()
ss_params.secondary_structure.protein.remove_outliers = not self.params.ss_idealization.enabled
self.set_ss_restraints(
ss_annotation=self.filtered_whole_ann,
params=ss_params.secondary_structure)
if self.params.run_minimization_last:
print >> self.log, "loop_ideal.ref_exclusion_selection", loop_ideal.ref_exclusion_selection
print >> self.log, "Minimizing whole model"
self.minimize(
model = self.model,
original_pdb_h=ref_hierarchy_for_final_gm,
excl_string_selection=loop_ideal.ref_exclusion_selection,
reference_map = self.reference_map)
self.shift_and_write_result(
model = self.model,
fname_suffix="all_idealized")
self.final_model_statistics = self.get_statistics(self.model)
self.time_for_run = time() - t_0
if self.params.output_pkl or self.params.debug:
easy_pickle.dump(
file_name="%s.pkl" % self.params.output_prefix,
obj = self.get_stats_obj())
def run(args, params=None, out=sys.stdout, log=sys.stderr):
if (((len(args) == 0) and (params is None)) or
((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help")))):
show_usage()
return
if (params is None):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="file_name")
work_params = pcl.work.extract()
# or use parameters defined by GUI
else:
work_params = params
pdb_files = work_params.file_name
from mmtbx.monomer_library.pdb_interpretation import grand_master_phil_str
params = iotbx.phil.parse(input_string=grand_master_phil_str,
process_includes=True).extract()
params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
mon_lib_srv = mmtbx.monomer_library.server.server()
ppf_srv = mmtbx.utils.process_pdb_file_srv(
crystal_symmetry=None,
pdb_interpretation_params=params.pdb_interpretation,
stop_for_unknowns=False,
log=log,
cif_objects=None, # need to figure out how to get them
mon_lib_srv=mon_lib_srv,
ener_lib=None,
use_neutron_distances=False)
processed_pdb_file, pdb_inp = ppf_srv.process_pdb_files(
pdb_file_names=pdb_files)
cs = ppf_srv.crystal_symmetry
xrs = processed_pdb_file.xray_structure(show_summary=True)
if (xrs is None):
raise Sorry("Cannot extract xray_structure.")
grm = get_geometry_restraints_manager(
processed_pdb_file=processed_pdb_file, xray_structure=xrs, log=log)
pdb_h = processed_pdb_file.all_chain_proxies.pdb_hierarchy
fixed_pdb_h = pdb_h.deep_copy()
fixed_pdb_h.reset_atom_i_seqs()
rotamer_manager = RotamerEval(mon_lib_srv=mon_lib_srv)
fixed_pdb_h = fix_rotamer_outliers(pdb_hierarchy=fixed_pdb_h,
grm=grm.geometry,
xrs=xrs,
radius=work_params.radius,
mon_lib_srv=mon_lib_srv,
rotamer_manager=rotamer_manager,
asc=None)
iotbx.pdb.write_whole_pdb_file(file_name="%s.pdb" %
work_params.output_prefix,
processed_pdb_file=processed_pdb_file,
pdb_hierarchy=fixed_pdb_h,
crystal_symmetry=cs)