def make_box (self, selection, target_map) :
from mmtbx import building
box = building.box_build_refine_base(
pdb_hierarchy=self.pdb_hierarchy,
xray_structure=self.fmodel.xray_structure,
processed_pdb_file=self.processed_pdb_file,
target_map=target_map,
selection=selection,
d_min=self.fmodel.f_obs().d_min(),
out=null_out())
return box
def exercise_box_rebuild():
#
# UNSTABLE! 3x
#
pdb_in = get_1yjp_pdb()
xrs = pdb_in.input.xray_structure_simple()
fc = xrs.structure_factors(d_min=1.5).f_calc()
fc_fft = fc.fft_map(resolution_factor=0.25)
fc_map = fc_fft.apply_sigma_scaling().real_map_unpadded()
sel_cache = pdb_in.hierarchy.atom_selection_cache()
sel = sel_cache.selection("resseq 4:5")
sites_orig = xrs.sites_cart().deep_copy()
xrs.shake_sites_in_place(0.3, selection=sel)
pdb_in.hierarchy.atoms().set_xyz(xrs.sites_cart())
sites_shaken = xrs.sites_cart().deep_copy()
sites_new = building.run_real_space_annealing(
xray_structure=xrs,
pdb_hierarchy=pdb_in.hierarchy,
selection=sel,
target_map=fc_map,
rsr_after_anneal=False,
d_min=1.5,
out=null_out())
pdb_in.hierarchy.atoms().set_xyz(sites_new)
rmsd_start = sites_orig.rms_difference(sites_shaken)
assert (rmsd_start > 0.1)
#assert (sites_orig.rms_difference(sites_new) < rmsd_start), "%f < %f" % (
# sites_orig.rms_difference(sites_new), rmsd_start)
assert (sites_orig.select(sel).rms_difference(sites_new.select(sel)) > 0)
assert (sites_new.select(sel).rms_difference(sites_shaken.select(sel)) > 0)
assert approx_equal(
sites_orig.select(~sel).rms_difference(sites_new.select(~sel)), 0)
box_builder = building.box_build_refine_base(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
processed_pdb_file=None,
target_map=fc_map,
selection=sel,
d_min=1.5,
out=null_out())
box_builder.restrain_atoms(box_builder.others_in_box, 0.02)
box_builder.geometry_minimization()
box_builder.real_space_refine()
sites_new = box_builder.update_original_coordinates()
assert (sites_orig.rms_difference(sites_new) <
0.3), sites_orig.rms_difference(sites_new)
assert (box_builder.mean_density_at_sites() >
3), box_builder.mean_density_at_sites()
def exercise_box_rebuild () :
#
# UNSTABLE! 3x
#
pdb_in = get_1yjp_pdb()
xrs = pdb_in.input.xray_structure_simple()
fc = xrs.structure_factors(d_min=1.5).f_calc()
fc_fft = fc.fft_map(resolution_factor=0.25)
fc_map = fc_fft.apply_sigma_scaling().real_map_unpadded()
sel_cache = pdb_in.hierarchy.atom_selection_cache()
sel = sel_cache.selection("resseq 4:5")
sites_orig = xrs.sites_cart().deep_copy()
xrs.shake_sites_in_place(0.3, selection=sel)
pdb_in.hierarchy.atoms().set_xyz(xrs.sites_cart())
sites_shaken = xrs.sites_cart().deep_copy()
sites_new = building.run_real_space_annealing(
xray_structure=xrs,
pdb_hierarchy=pdb_in.hierarchy,
selection=sel,
target_map=fc_map,
rsr_after_anneal=False,
d_min=1.5,
out=null_out())
pdb_in.hierarchy.atoms().set_xyz(sites_new)
rmsd_start = sites_orig.rms_difference(sites_shaken)
assert (rmsd_start > 0.1)
#assert (sites_orig.rms_difference(sites_new) < rmsd_start), "%f < %f" % (
# sites_orig.rms_difference(sites_new), rmsd_start)
assert (sites_orig.select(sel).rms_difference(sites_new.select(sel)) > 0)
assert (sites_new.select(sel).rms_difference(sites_shaken.select(sel)) > 0)
assert (sites_orig.select(~sel).rms_difference(sites_new.select(~sel)) == 0)
box_builder = building.box_build_refine_base(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
processed_pdb_file=None,
target_map=fc_map,
selection=sel,
d_min=1.5,
out=null_out())
box_builder.restrain_atoms(box_builder.others_in_box, 0.02)
box_builder.geometry_minimization()
box_builder.real_space_refine()
sites_new = box_builder.update_original_coordinates()
assert (sites_orig.rms_difference(sites_new) < 0.3)
assert (box_builder.mean_density_at_sites() > 3)
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 __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)
