def __init__(self, xray_structure, params, pdb_hierarchy, log=None):
self.log = log
self.pdb_hierarchy = pdb_hierarchy
self.crystal_symmetry = xray_structure.crystal_symmetry()
if (self.log is None): self.log = sys.stdout
self.xray_structure = xray_structure
self.params = params
asc = self.pdb_hierarchy.atom_selection_cache(
special_position_settings=crystal.special_position_settings(
crystal_symmetry=self.crystal_symmetry))
if (self.params.random_seed is not None):
random.seed(self.params.random_seed)
flex.set_random_seed(self.params.random_seed)
self.top_selection = flex.smart_selection(
flags=flex.bool(xray_structure.scatterers().size(), True))
if (self.params.selection is not None):
self.top_selection = flex.smart_selection(
flags=asc.selection(self.params.selection))
self._rotate_about_axis()
self._process_adp()
self._process_sites()
self._process_occupancies()
self._put_in_box()
self._change_of_basis()
# Up to this point we are done with self.xray_structure
self.pdb_hierarchy.adopt_xray_structure(self.xray_structure)
# Now only manipulations that use self.pdb_hierarchy are done
if (self.params.set_chemical_element_simple_if_necessary
or self.params.rename_chain_id.old_id
or self.params.renumber_residues
or self.params.increment_resseq
or self.params.convert_semet_to_met
or self.params.convert_met_to_semet
or self.params.set_charge.charge
or self.params.truncate_to_polyala
or self.params.truncate_to_polygly
or self.params.remove_alt_confs or self.params.move_waters_last
or self.params.remove_fraction or self.params.keep
or self.params.remove):
del self.xray_structure # it is invalide below this point
self._set_chemical_element_simple_if_necessary()
self._rename_chain_id()
self._renumber_residues()
self._convert_semet_to_met()
self._convert_met_to_semet()
self._set_atomic_charge()
self._truncate_to_poly_ala()
self._truncate_to_poly_gly()
self._remove_alt_confs()
self._move_waters()
self._remove_atoms()
self._apply_keep_remove()
def _process_occupancies(self):
def check_if_already_modified():
if(self.top_selection): return
if (self._occupancies_modified):
raise Sorry("Can't modify occupancies (already modified).")
else:
self._occupancies_modified = True
for occ in self.params.occupancies:
if(occ.atom_selection is None):
selection = self.top_selection
else:
asc = self.pdb_hierarchy.atom_selection_cache(
special_position_settings=crystal.special_position_settings(
crystal_symmetry = self.crystal_symmetry))
sel = asc.selection(occ.atom_selection)
selection = flex.smart_selection(flags=sel)
if(occ.randomize):
self._print_action(
text = "Randomizing occupancies",
selection = selection)
check_if_already_modified()
self.xray_structure.shake_occupancies(selection=selection.flags)
if(occ.set is not None):
self._print_action(
text = "Setting occupancies to: %8.3f"%occ.set, selection = selection)
check_if_already_modified()
self.xray_structure.set_occupancies(
value = occ.set,
selection = selection.flags)
def _process_sites(self):
for sites in self.params.sites:
if (sites.atom_selection is None):
selection = self.top_selection
else:
asc = self.pdb_hierarchy.atom_selection_cache(
special_position_settings=crystal.special_position_settings(
crystal_symmetry = self.crystal_symmetry))
sel = asc.selection(sites.atom_selection)
selection = flex.smart_selection(flags=sel)
self._shake_sites(selection=selection, rms_difference=sites.shake)
self._switch_rotamers(selection=selection, mode=sites.switch_rotamers)
self._rb_shift(
selection=selection,
translate=sites.translate,
rotate=sites.rotate,
euler_angle_convention=sites.euler_angle_convention)
def _process_adp(self):
for adp in self.params.adp:
if (adp.atom_selection is None):
selection = self.top_selection
else:
asc = self.pdb_hierarchy.atom_selection_cache(
special_position_settings=crystal.special_position_settings(
crystal_symmetry = self.crystal_symmetry))
sel = asc.selection(adp.atom_selection)
selection = flex.smart_selection(flags=sel)
if (adp.convert_to_isotropic):
self._convert_to_isotropic(selection=selection)
if (adp.convert_to_anisotropic):
self._convert_to_anisotropic(selection=selection)
self._set_b_iso(selection=selection, b_iso=adp.set_b_iso)
self._scale_adp(selection=selection, factor=adp.scale_adp)
self._shift_b_iso(selection=selection, shift=adp.shift_b_iso)
if (adp.randomize):
self._randomize_adp(selection=selection)
def __init__(self, model, params, log = None):
self.log = log
self.params = params
self.model = model
self._neutralize_scatterers()
if not model.crystal_symmetry() or not model.crystal_symmetry().unit_cell():
# Make it up
from cctbx.maptbx.box import shift_and_box_model
model = shift_and_box_model(model, shift_model=False)
self.pdb_hierarchy = model.get_hierarchy()
self.crystal_symmetry = model.crystal_symmetry()
if(self.log is None): self.log = sys.stdout
self.xray_structure = model.get_xray_structure()
asc = self.pdb_hierarchy.atom_selection_cache(
special_position_settings=crystal.special_position_settings(
crystal_symmetry = self.crystal_symmetry))
if(self.params.random_seed is not None):
random.seed(self.params.random_seed)
flex.set_random_seed(self.params.random_seed)
self.top_selection = flex.smart_selection(
flags=flex.bool(self.xray_structure.scatterers().size(), True))
if(self.params.selection is not None):
self.top_selection = flex.smart_selection(
flags=asc.selection(self.params.selection))
self._rotate_about_axis()
self._process_adp()
self._process_sites()
self._process_occupancies()
self._put_in_box()
self._change_of_basis()
# Up to this point we are done with self.xray_structure
self.model.set_xray_structure(self.xray_structure)
self.pdb_hierarchy = self.model.get_hierarchy()
# Now only manipulations that use self.pdb_hierarchy are done
### segID manipulations
if (params.set_seg_id_to_chain_id):
if (params.clear_seg_id):
raise Sorry("Parameter conflict - set_seg_id_to_chain_id=True and "+
"clear_seg_id=True. Please choose only one of these options.")
for atom in self.pdb_hierarchy.atoms():
labels = atom.fetch_labels()
atom.segid = "%-4s" % labels.chain_id
elif (params.clear_seg_id):
for atom in self.pdb_hierarchy.atoms():
atom.segid = " "
if(self.params.set_chemical_element_simple_if_necessary or
self.params.rename_chain_id.old_id or
self.params.renumber_residues or self.params.increment_resseq or
self.params.convert_semet_to_met or
self.params.convert_met_to_semet or
self.params.set_charge.charge or
self.params.truncate_to_polyala or
self.params.truncate_to_polygly or
self.params.remove_alt_confs or
self.params.move_waters_last or
self.params.remove_fraction or
self.params.keep or
self.params.remove):
# del self.xray_structure # it is invalide below this point
self._set_chemical_element_simple_if_necessary()
self._rename_chain_id()
self._renumber_residues()
self._convert_semet_to_met()
self._convert_met_to_semet()
self._set_atomic_charge()
self._truncate_to_poly_ala()
self._truncate_to_poly_gly()
self._remove_alt_confs()
self._move_waters()
self._remove_atoms()
self._apply_keep_remove()
# Here goes really nasty hack. Never repeat it.
# It is here because I don't have clear idea about how to handle
# such dramatic changes in number of atoms etc that just was performed
# for hierarchy.
self.pdb_hierarchy.reset_atom_i_seqs()
self.pdb_hierarchy.atoms_reset_serial()
self.model._pdb_hierarchy = self.pdb_hierarchy
self.model._xray_structure = self.pdb_hierarchy.extract_xray_structure(
crystal_symmetry=self.model.crystal_symmetry())
self.model._update_atom_selection_cache()
self.model._update_has_hd()
self.model.get_hierarchy().atoms().reset_i_seq()
