def exercise_2():
"""
Same as 1 but automatic NCS search procedure does not match short chains,
in this case chains B,C, so they left out of NCS.
Not clear if we should utilize MTRIX instead of searching for NCS
because currently we don't output them and in consecutive runs NCS
search would be utilized anyway, potentially yelding different groups.
"""
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_2)
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params(
)
pdb_int_params.pdb_interpretation.ncs_search.enabled = True
model = mmtbx.model.manager(model_input=inp,
pdb_interpretation_params=pdb_int_params,
process_input=True,
log=null_out())
# model.get_xray_structure()
ss = model.get_ss_annotation()
assert ss.get_n_helices() == 3
assert ss.get_n_sheets() == 3
assert not model.ncs_constraints_present()
assert model.get_ncs_obj() is not None
model.setup_ncs_constraints_groups()
# print model.get_ncs_obj()
assert model.ncs_constraints_present()
assert model.get_master_hierarchy().atoms_size() == 15
# print model.get_master_hierarchy().as_pdb_string()
assert list(model.get_master_selection()).count(True) == 15
def exercise_biomt():
inp = iotbx.pdb.input(lines=biomt_txt+ss_txt+atoms_txt, source_info=None)
model = mmtbx.model.manager(
model_input = inp)
assert model.get_number_of_atoms() == 300, model.get_number_of_atoms()
assert model.get_hierarchy().atoms_size() == 300
assert model.get_xray_structure().scatterers().size() == 300
ss_ann = model.get_ss_annotation()
assert ss_ann.get_n_helices() == 2
assert ss_ann.get_n_sheets() == 1
model.expand_with_BIOMT_records()
assert model.get_number_of_atoms() == 900, model.get_number_of_atoms()
assert model.get_hierarchy().atoms_size() == 900
assert model.get_xray_structure().scatterers().size() == 900, model.get_xray_structure().scatterers().size()
ss_ann = model.get_ss_annotation()
assert ss_ann.get_n_helices() == 6
assert ss_ann.get_n_sheets() == 3
def run(self):
# I'm guessing self.data_manager, self.params and self.logger
# are already defined here...
# this must be mmtbx.model.manager?
model = self.data_manager.get_model()
atoms = model.get_atoms()
all_bsel = flex.bool(atoms.size(), False)
for selection_string in self.params.atom_selection_program.inselection:
print("Selecting '%s'" % selection_string, file=self.logger)
isel = model.iselection(string=selection_string)
all_bsel.set_selected(isel, True)
if self.params.atom_selection_program.write_pdb_file is None:
print(" %d atom%s selected" % plural_s(isel.size()),
file=self.logger)
for atom in atoms.select(isel):
print(" %s" % atom.format_atom_record(),
file=self.logger)
print("", file=self.logger)
if self.params.atom_selection_program.write_pdb_file is not None:
print("Writing file:",
show_string(
self.params.atom_selection_program.write_pdb_file),
file=self.logger)
ss_ann = model.get_ss_annotation()
if not model.crystal_symmetry() or \
(not model.crystal_symmetry().unit_cell()):
model = shift_and_box_model(model, shift_model=False)
selected_model = model.select(all_bsel)
if (ss_ann is not None):
selected_model.set_ss_annotation(ss_ann.\
filter_annotation(
hierarchy=selected_model.get_hierarchy(),
asc=selected_model.get_atom_selection_cache(),
remove_short_annotations=False,
remove_3_10_helices=False,
remove_empty_annotations=True,
concatenate_consecutive_helices=False,
split_helices_with_prolines=False,
filter_sheets_with_long_hbonds=False))
if self.params.atom_selection_program.cryst1_replacement_buffer_layer is not None:
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=selected_model.get_atoms().extract_xyz(),
buffer_layer=self.params.atom_selection_program.
cryst1_replacement_buffer_layer)
sp = crystal.special_position_settings(box.crystal_symmetry())
sites_frac = box.sites_frac()
xrs_box = selected_model.get_xray_structure(
).replace_sites_frac(box.sites_frac())
xray_structure_box = xray.structure(sp, xrs_box.scatterers())
selected_model.set_xray_structure(xray_structure_box)
pdb_str = selected_model.model_as_pdb()
f = open(self.params.atom_selection_program.write_pdb_file, 'w')
f.write(pdb_str)
f.close()
print("", file=self.logger)
def exercise_mtrix():
inp = iotbx.pdb.input(lines=mtrix_txt+ss_txt+atoms_txt, source_info=None)
model = mmtbx.model.manager(
model_input = inp)
assert model.get_number_of_atoms() == 900, model.get_number_of_atoms()
assert model.get_hierarchy().atoms_size() == 900
assert model.get_xray_structure().scatterers().size() == 900
ss_ann = model.get_ss_annotation()
# print ss_ann.as_pdb_str()
assert ss_ann.get_n_helices() == 6
assert ss_ann.get_n_sheets() == 3
def exercise_1():
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1)
model = mmtbx.model.manager(
model_input = inp,
log = null_out())
assert model.get_number_of_atoms() == 21
assert model.get_hierarchy().atoms_size() == 21
assert model.get_xray_structure().scatterers().size() == 21
ss = model.get_ss_annotation()
# print ss.as_pdb_str()
# STOP()
assert ss.get_n_helices() == 3
# because the second strand contains chain B which is not in ATOM records
# whole sheet got discarded.
assert ss.get_n_sheets() == 0
rm = model.get_restraints_manager()
assert rm.geometry.pair_proxies().bond_proxies.simple.size() == 6
# since No NCS was set, these functions return the whole thing and no
# master selection
assert model.get_master_hierarchy().atoms_size() == 21
assert model.get_master_selection().size() == 0
# print model.model_as_pdb()
# print "="*40
# Here we set NCS constraints
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1)
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
pdb_int_params.pdb_interpretation.ncs_search.enabled=True
model = mmtbx.model.manager(
model_input = inp,
pdb_interpretation_params = pdb_int_params,
process_input=True,
log = null_out())
# model.get_xray_structure()
assert not model.ncs_constraints_present()
assert model.get_ncs_obj() is not None
model.setup_ncs_constraints_groups()
# print model.get_ncs_obj()
assert model.ncs_constraints_present()
assert model.get_master_hierarchy().atoms_size() == 7
# print model.get_master_hierarchy().as_pdb_string()
# print list(model.get_master_selection())
assert list(model.get_master_selection()).count(True) == 7
def show_ss_counts(model):
ss = model.get_ss_annotation()
print("Number of helices:", ss.get_n_helices())
print("Number of sheets :", ss.get_n_sheets())
