def __call__(self,
atom_group,
log,
window_size=2,
backbone_sample_angle=10,
anneal=False,
annealing_temperature=1000,
use_chi1_sampling=False):
import iotbx.pdb.hierarchy
from scitbx.array_family import flex
assert (atom_group is not None)
pdb_hierarchy = self.pdb_hierarchy.deep_copy()
xray_structure = self.xray_structure.deep_copy_scatterers()
geometry_restraints_manager = self.geometry_restraints_manager
# FIXME this doesn't work - can't recover the atom_group afterwards!
#hd_sel = xray_structure.hd_selection()
#n_hydrogen = hd_sel.count(True)
#if (n_hydrogen > 0):
# non_hd_sel = ~hd_sel
# pdb_hierarchy = pdb_hierarchy.select(non_hd_sel)
# xray_structure = xray_structure.select(non_hd_sel)
# geometry_restraints_manager = geometry_restraints_manager.select(
# non_hd_sel)
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
isel = building.extract_iselection([atom_group])
atom_group = pdb_atoms[isel[0]].parent()
atom_group_start = atom_group.detached_copy()
needs_rebuild = not building.is_stub_residue(atom_group)
residue_group = atom_group.parent()
assert (len(residue_group.atom_groups()) == 1)
sel_residues = building.get_window_around_residue(
residue=atom_group, window_size=window_size)
# get rid of sidechains for surrounding residues only
adjacent_residues = []
for other_rg in sel_residues:
if (other_rg != residue_group):
adjacent_residues.append(other_rg)
building.remove_sidechain_atoms(adjacent_residues)
pdb_atoms = pdb_hierarchy.atoms()
adjacent_trimmed_atom_names = pdb_atoms.extract_name()
adjacent_trimmed_sel = pdb_atoms.extract_i_seq()
xrs_adjacent_trimmed = xray_structure.select(adjacent_trimmed_sel)
grm_adjacent_trimmed = geometry_restraints_manager.select(
adjacent_trimmed_sel)
pdb_atoms.reset_i_seq()
# get rid of central sidechain and refine mainchain for entire window
truncate = (not atom_group.resname in ["GLY", "ALA"]) # XXX PRO?
if (truncate):
building.remove_sidechain_atoms([atom_group])
pdb_atoms = pdb_hierarchy.atoms()
all_mc_sel = pdb_atoms.extract_i_seq()
xrs_mc = xrs_adjacent_trimmed.select(all_mc_sel)
pdb_atoms.reset_i_seq()
window_mc_sel = building.extract_iselection(sel_residues)
selection = flex.bool(pdb_atoms.size(),
False).set_selected(window_mc_sel, True)
restraints_manager = grm_adjacent_trimmed.select(all_mc_sel)
box = building.box_build_refine_base(
xray_structure=xrs_mc,
pdb_hierarchy=pdb_hierarchy,
selection=selection,
processed_pdb_file=None,
target_map=self.target_map,
geometry_restraints_manager=restraints_manager.geometry,
d_min=self.d_min,
out=null_out(),
debug=True)
box.restrain_atoms(selection=box.others_in_box, reference_sigma=0.1)
box.real_space_refine(selection=box.selection_in_box)
sites_new = box.update_original_coordinates()
pdb_atoms.set_xyz(sites_new)
# extend and replace existing residue. this is done in such a way that
# the original atom ordering for the central residue is preserved, which
# allows us to use the pre-existing geometry restraints instead of
# re-calculating them every time this function is called.
target_atom_group = self.ideal_dict[atom_group.resname.lower()].\
only_model().only_chain().only_residue_group().only_atom_group()
new_atom_group_base = extend_sidechains.extend_residue(
residue=atom_group,
target_atom_group=target_atom_group,
mon_lib_srv=self.mon_lib_srv)
new_atom_group = iotbx.pdb.hierarchy.atom_group(
resname=atom_group.resname)
for atom in atom_group_start.atoms():
for new_atom in new_atom_group_base.atoms():
if (new_atom.name == atom.name):
new_atom_group.append_atom(new_atom.detached_copy())
n_atoms_new = len(new_atom_group.atoms())
n_atoms_start = len(atom_group_start.atoms())
if (n_atoms_new != n_atoms_start):
raise RuntimeError(
("Inconsistent atom counts for residue %s after " +
"building (%d versus %d).") %
(atom_group.id_str(), n_atoms_start, n_atoms_new))
rg = atom_group.parent()
rg.remove_atom_group(atom_group)
rg.append_atom_group(new_atom_group)
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
new_names = pdb_atoms.extract_name()
assert new_names.all_eq(adjacent_trimmed_atom_names)
# get new box around this residue
residue_sel = building.extract_iselection([new_atom_group])
selection = flex.bool(pdb_atoms.size(),
False).set_selected(residue_sel, True)
xrs_adjacent_trimmed.set_sites_cart(pdb_atoms.extract_xyz())
box = building.box_build_refine_base(
xray_structure=xrs_adjacent_trimmed,
pdb_hierarchy=pdb_hierarchy,
selection=selection,
processed_pdb_file=None,
target_map=self.target_map,
geometry_restraints_manager=grm_adjacent_trimmed.geometry,
d_min=self.d_min,
out=null_out(),
debug=True)
# place sidechain using mmtbx.refinement.real_space.fit_residue
if ((atom_group.resname in rotatable_sidechain_atoms)
and (use_chi1_sampling)):
fit_chi1_simple(residue=box.only_residue(),
unit_cell=box.unit_cell_box,
target_map=box.target_map_box,
rotamer_eval=self.rotamer_eval)
box.update_sites_from_pdb_atoms()
else:
box.fit_residue_in_box(backbone_sample_angle=backbone_sample_angle)
if (anneal):
box.anneal(start_temperature=annealing_temperature)
#box.real_space_refine()
sites_new = box.update_original_coordinates()
pdb_hierarchy.atoms().set_xyz(sites_new)
return building.atom_group_as_hierarchy(new_atom_group)
def find_alternate_residue (residue,
pdb_hierarchy,
fmodel,
restraints_manager,
params,
verbose=False,
debug=None,
log=None) :
if (log is None) :
log = null_out()
t1 = time.time()
from scitbx.array_family import flex
selection = flex.size_t()
window = building.get_window_around_residue(residue,
window_size=params.window_size)
for pdb_object in window :
selection.extend(pdb_object.atoms().extract_i_seq())
assert (len(selection) > 0) and (not selection.all_eq(0))
occupancies = []
if (params.expected_occupancy is not None) :
assert (0.0 <= params.expected_occupancy <= 1.0)
occupancies = [ params.expected_occupancy ]
else :
occupancies = [ 0.2, 0.3, 0.4, 0.5 ]
trials = []
sites_start_1d = pdb_hierarchy.atoms().extract_xyz().as_double()
from mmtbx.rotamer import rotamer_eval
rotamer_manager = rotamer_eval.RotamerEval(data_version="8000")
id_str = residue.id_str()
delete_selection = None
if (params.omit_waters) :
delete_selection = building.get_nearby_water_selection(
pdb_hierarchy=pdb_hierarchy,
xray_structure=fmodel.xray_structure,
selection=selection)
for occupancy in occupancies :
prefix = "%s_%.2f" % (id_str.replace(" ", "_"), occupancy)
map_file_name = None
if (debug > 1) :
map_file_name = prefix + ".mtz"
two_fofc_map, fofc_map = alt_confs.get_partial_omit_map(
fmodel=fmodel.deep_copy(),
selection=selection,
selection_delete=delete_selection,
negate_surrounding=True,
map_file_name=map_file_name,
partial_occupancy=1.0 - occupancy)
rebuild = rebuild_residue(
target_map=fofc_map,
pdb_hierarchy=pdb_hierarchy,
xray_structure=fmodel.xray_structure,
geometry_restraints_manager=restraints_manager,
rotamer_eval=rotamer_manager,
d_min=fmodel.f_obs().d_min())
new_hierarchy = rebuild(atom_group=residue,
window_size=params.window_size,
backbone_sample_angle=params.backbone_sample_angle,
anneal=params.anneal,
annealing_temperature=params.annealing_temperature,
use_chi1_sampling=params.simple_chi1_sampling,
log=log)
trial = residue_trial(
residue=residue,
new_hierarchy=new_hierarchy,
occupancy=occupancy,
rotamer_eval=rotamer_manager,
fmodel=fmodel,
two_fofc_map=two_fofc_map,
fofc_map=fofc_map)
trials.append(trial)
if (debug > 1) :
open("%s.pdb" % prefix, "w").write(trial.new_hierarchy.as_pdb_string())
sites_end_1d = pdb_hierarchy.atoms().extract_xyz().as_double()
assert sites_start_1d.all_eq(sites_end_1d)
t2 = time.time()
if (debug > 1) :
print >> log, " %d build trials (%s): %.3fs" % (len(occupancies),
residue.id_str(), t2 - t1)
return trials
def find_alternate_residue(residue,
pdb_hierarchy,
fmodel,
restraints_manager,
params,
verbose=False,
debug=None,
log=None):
if (log is None):
log = null_out()
t1 = time.time()
from scitbx.array_family import flex
selection = flex.size_t()
window = building.get_window_around_residue(residue,
window_size=params.window_size)
for pdb_object in window:
selection.extend(pdb_object.atoms().extract_i_seq())
assert (len(selection) > 0) and (not selection.all_eq(0))
occupancies = []
if (params.expected_occupancy is not None):
assert (0.0 <= params.expected_occupancy <= 1.0)
occupancies = [params.expected_occupancy]
else:
occupancies = [0.2, 0.3, 0.4, 0.5]
trials = []
sites_start_1d = pdb_hierarchy.atoms().extract_xyz().as_double()
from mmtbx.rotamer import rotamer_eval
rotamer_manager = rotamer_eval.RotamerEval(data_version="8000")
id_str = residue.id_str()
delete_selection = None
if (params.omit_waters):
delete_selection = building.get_nearby_water_selection(
pdb_hierarchy=pdb_hierarchy,
xray_structure=fmodel.xray_structure,
selection=selection)
for occupancy in occupancies:
prefix = "%s_%.2f" % (id_str.replace(" ", "_"), occupancy)
map_file_name = None
if (debug > 1):
map_file_name = prefix + ".mtz"
two_fofc_map, fofc_map = alt_confs.get_partial_omit_map(
fmodel=fmodel.deep_copy(),
selection=selection,
selection_delete=delete_selection,
negate_surrounding=True,
map_file_name=map_file_name,
partial_occupancy=1.0 - occupancy)
rebuild = rebuild_residue(
target_map=fofc_map,
pdb_hierarchy=pdb_hierarchy,
xray_structure=fmodel.xray_structure,
geometry_restraints_manager=restraints_manager,
rotamer_eval=rotamer_manager,
d_min=fmodel.f_obs().d_min())
new_hierarchy = rebuild(
atom_group=residue,
window_size=params.window_size,
backbone_sample_angle=params.backbone_sample_angle,
anneal=params.anneal,
annealing_temperature=params.annealing_temperature,
use_chi1_sampling=params.simple_chi1_sampling,
log=log)
trial = residue_trial(residue=residue,
new_hierarchy=new_hierarchy,
occupancy=occupancy,
rotamer_eval=rotamer_manager,
fmodel=fmodel,
two_fofc_map=two_fofc_map,
fofc_map=fofc_map)
trials.append(trial)
if (debug > 1):
open("%s.pdb" % prefix,
"w").write(trial.new_hierarchy.as_pdb_string())
sites_end_1d = pdb_hierarchy.atoms().extract_xyz().as_double()
assert sites_start_1d.all_eq(sites_end_1d)
t2 = time.time()
if (debug > 1):
print(" %d build trials (%s): %.3fs" %
(len(occupancies), residue.id_str(), t2 - t1),
file=log)
return trials
def __call__ (self,
atom_group,
log,
window_size=2,
backbone_sample_angle=10,
anneal=False,
annealing_temperature=1000,
use_chi1_sampling=False) :
import iotbx.pdb.hierarchy
from scitbx.array_family import flex
assert (atom_group is not None)
pdb_hierarchy = self.pdb_hierarchy.deep_copy()
xray_structure = self.xray_structure.deep_copy_scatterers()
geometry_restraints_manager = self.geometry_restraints_manager
# FIXME this doesn't work - can't recover the atom_group afterwards!
#hd_sel = xray_structure.hd_selection()
#n_hydrogen = hd_sel.count(True)
#if (n_hydrogen > 0) :
# non_hd_sel = ~hd_sel
# pdb_hierarchy = pdb_hierarchy.select(non_hd_sel)
# xray_structure = xray_structure.select(non_hd_sel)
# geometry_restraints_manager = geometry_restraints_manager.select(
# non_hd_sel)
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
isel = building.extract_iselection([atom_group])
atom_group = pdb_atoms[isel[0]].parent()
atom_group_start = atom_group.detached_copy()
needs_rebuild = not building.is_stub_residue(atom_group)
residue_group = atom_group.parent()
assert (len(residue_group.atom_groups()) == 1)
sel_residues = building.get_window_around_residue(
residue=atom_group,
window_size=window_size)
# get rid of sidechains for surrounding residues only
adjacent_residues = []
for other_rg in sel_residues :
if (other_rg != residue_group) :
adjacent_residues.append(other_rg)
building.remove_sidechain_atoms(adjacent_residues)
pdb_atoms = pdb_hierarchy.atoms()
adjacent_trimmed_atom_names = pdb_atoms.extract_name()
adjacent_trimmed_sel = pdb_atoms.extract_i_seq()
xrs_adjacent_trimmed = xray_structure.select(adjacent_trimmed_sel)
grm_adjacent_trimmed = geometry_restraints_manager.select(
adjacent_trimmed_sel)
pdb_atoms.reset_i_seq()
# get rid of central sidechain and refine mainchain for entire window
truncate = (not atom_group.resname in ["GLY","ALA"]) # XXX PRO?
if (truncate) :
building.remove_sidechain_atoms([ atom_group ])
pdb_atoms = pdb_hierarchy.atoms()
all_mc_sel = pdb_atoms.extract_i_seq()
xrs_mc = xrs_adjacent_trimmed.select(all_mc_sel)
pdb_atoms.reset_i_seq()
window_mc_sel = building.extract_iselection(sel_residues)
selection = flex.bool(pdb_atoms.size(), False).set_selected(window_mc_sel,
True)
restraints_manager = grm_adjacent_trimmed.select(all_mc_sel)
box = building.box_build_refine_base(
xray_structure=xrs_mc,
pdb_hierarchy=pdb_hierarchy,
selection=selection,
processed_pdb_file=None,
target_map=self.target_map,
geometry_restraints_manager=restraints_manager.geometry,
d_min=self.d_min,
out=null_out(),
debug=True)
box.restrain_atoms(
selection=box.others_in_box,
reference_sigma=0.1)
box.real_space_refine(selection=box.selection_in_box)
sites_new = box.update_original_coordinates()
pdb_atoms.set_xyz(sites_new)
# extend and replace existing residue. this is done in such a way that
# the original atom ordering for the central residue is preserved, which
# allows us to use the pre-existing geometry restraints instead of
# re-calculating them every time this function is called.
new_atom_group_base = extend_sidechains.extend_residue(
residue=atom_group,
ideal_dict=self.ideal_dict,
hydrogens=False,
mon_lib_srv=self.mon_lib_srv,
match_conformation=True)
new_atom_group = iotbx.pdb.hierarchy.atom_group(resname=atom_group.resname)
for atom in atom_group_start.atoms() :
for new_atom in new_atom_group_base.atoms() :
if (new_atom.name == atom.name) :
new_atom_group.append_atom(new_atom.detached_copy())
n_atoms_new = len(new_atom_group.atoms())
n_atoms_start = len(atom_group_start.atoms())
if (n_atoms_new != n_atoms_start) :
raise RuntimeError(("Inconsistent atom counts for residue %s after "+
"building (%d versus %d).") % (atom_group.id_str(), n_atoms_start,
n_atoms_new))
rg = atom_group.parent()
rg.remove_atom_group(atom_group)
rg.append_atom_group(new_atom_group)
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
new_names = pdb_atoms.extract_name()
assert new_names.all_eq(adjacent_trimmed_atom_names)
# get new box around this residue
residue_sel = building.extract_iselection([ new_atom_group ])
selection = flex.bool(pdb_atoms.size(), False).set_selected(residue_sel,
True)
xrs_adjacent_trimmed.set_sites_cart(pdb_atoms.extract_xyz())
box = building.box_build_refine_base(
xray_structure=xrs_adjacent_trimmed,
pdb_hierarchy=pdb_hierarchy,
selection=selection,
processed_pdb_file=None,
target_map=self.target_map,
geometry_restraints_manager=grm_adjacent_trimmed.geometry,
d_min=self.d_min,
out=null_out(),
debug=True)
# place sidechain using mmtbx.refinement.real_space.fit_residue
if ((atom_group.resname in rotatable_sidechain_atoms) and
(use_chi1_sampling)) :
fit_chi1_simple(
residue=box.only_residue(),
unit_cell=box.unit_cell_box,
target_map=box.target_map_box,
rotamer_eval=self.rotamer_eval)
box.update_sites_from_pdb_atoms()
else :
box.fit_residue_in_box(backbone_sample_angle=backbone_sample_angle)
if (anneal) :
box.anneal(start_temperature=annealing_temperature)
#box.real_space_refine()
sites_new = box.update_original_coordinates()
pdb_hierarchy.atoms().set_xyz(sites_new)
return building.atom_group_as_hierarchy(new_atom_group)