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 run(args, command_name=libtbx.env.dispatcher_name):
parser = argparse.ArgumentParser(
prog=command_name,
usage='%s pdb_file "atom_selection" [...]' % command_name)
parser.add_argument("file_name",
nargs=1,
help="File name of the model file")
parser.add_argument(
"inselections",
help="Atom selection strings",
nargs='+',
)
parser.add_argument("--write-pdb-file",
action="store",
help="write selected atoms to new PDB file",
default=None)
parser.add_argument(
"--cryst1-replacement-buffer-layer",
action="store",
type=float,
help="replace CRYST1 with pseudo unit cell covering the selected"
" atoms plus a surrounding buffer layer",
default=None)
co = parser.parse_args(args)
pdb_inp = iotbx.pdb.input(file_name=co.file_name[0])
model = mmtbx.model.manager(model_input=pdb_inp, process_input=True)
atoms = model.get_atoms()
all_bsel = flex.bool(atoms.size(), False)
for selection_string in co.inselections:
print selection_string
isel = model.iselection(selstr=selection_string)
all_bsel.set_selected(isel, True)
if (not co.write_pdb_file):
print " %d atom%s selected" % plural_s(isel.size())
for atom in atoms.select(isel):
print " %s" % atom.format_atom_record()
print
if (co.write_pdb_file):
print "Writing file:", show_string(co.write_pdb_file)
selected_model = model.select(all_bsel)
if (co.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=co.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(co.write_pdb_file, 'w')
f.write(pdb_str)
f.close()
print
def run(self):
filename = os.path.basename(self.data_manager.get_model_names()[0])
model = self.data_manager.get_model()
atoms = model.get_atoms()
all_bsel = flex.bool(atoms.size(), False)
selection_string_list = []
for selection_string in self.params.atom_selection_program.inselection:
selection_string_list.append(selection_string)
probescore = probescore_ligand.probescore(model, selection_string_list, self.params.probescore.has_h, nuclear=False, out=self.logger)
if self.params.probescore.output == "digest":
probescore.print_as_digest()
elif self.params.probescore.output == "raw":
probescore.print_as_raw()
elif self.params.probescore.output == "oneline":
probescore.print_as_oneline(filename=filename)
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(selstr=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)
selected_model = model.select(all_bsel)
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)