def build_cycle(pdb_hierarchy,
fmodel,
geometry_restraints_manager,
params,
selection=None,
cif_objects=(),
nproc=Auto,
out=sys.stdout,
verbose=False,
debug=None,
i_cycle=0):
from mmtbx import restraints
from scitbx.array_family import flex
t_start = time.time()
hd_sel = fmodel.xray_structure.hd_selection()
n_hydrogen = hd_sel.count(True)
if (n_hydrogen > 0) and (True): #params.building.delete_hydrogens):
print("WARNING: %d hydrogen atoms will be removed!" % n_hydrogen,
file=out)
non_hd_sel = ~hd_sel
# XXX it's better to do this in-place for the hierarchy, because calling
# pdb_hierarchy.select(non_hd_sel) will not remove parent-child
# relationships involving hydrogens, which causes problems when running
# the MolProbity validation.
pdb_hierarchy.remove_hd(reset_i_seq=True)
xray_structure = fmodel.xray_structure.select(non_hd_sel)
assert (
pdb_hierarchy.atoms_size() == xray_structure.scatterers().size())
fmodel.update_xray_structure(xray_structure)
geometry_restraints_manager = geometry_restraints_manager.select(
non_hd_sel)
pdb_atoms = pdb_hierarchy.atoms()
segids = pdb_atoms.extract_segid().strip()
if (not segids.all_eq("")):
print("WARNING: resetting segids to blank", file=out)
for i_seq, atom in enumerate(pdb_atoms):
atom.segid = ""
sc = fmodel.xray_structure.scatterers()[i_seq]
sc.label = atom.id_str()
if isinstance(selection, str):
sele_cache = pdb_hierarchy.atom_selection_cache()
selection = sele_cache.selection(selection)
make_header("Build cycle %d" % (i_cycle + 1), out=out)
fmodel.info().show_rfactors_targets_scales_overall(out=out)
if (debug > 0):
from mmtbx.maps.utils import get_maps_from_fmodel
from iotbx.map_tools import write_map_coeffs
two_fofc, fofc = get_maps_from_fmodel(fmodel,
exclude_free_r_reflections=True)
write_map_coeffs(fwt_coeffs=two_fofc,
delfwt_coeffs=fofc,
file_name="cycle_%d_start.mtz" % (i_cycle + 1))
candidate_residues = alt_confs.filter_before_build(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
geometry_restraints_manager=geometry_restraints_manager,
selection=selection,
params=params.prefilter,
verbose=verbose,
log=out)
t1 = time.time()
print("filtering: %.3fs" % (t1 - t_start), file=out)
restraints_manager = restraints.manager(
geometry=geometry_restraints_manager, normalization=True)
make_sub_header("Finding alternate conformations", out=out)
building_trials = find_all_alternates(
residues=candidate_residues,
pdb_hierarchy=pdb_hierarchy,
restraints_manager=restraints_manager,
fmodel=fmodel,
params=params.residue_fitting,
nproc=params.nproc,
verbose=verbose,
debug=debug,
log=out).results
t2 = time.time()
print(" building: %.3fs" % (t2 - t1), file=out)
make_sub_header("Scoring and assembling alternates", out=out)
n_alternates = process_results(pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
residues_in=candidate_residues,
building_trials=building_trials,
params=params.residue_fitting,
verbose=verbose,
log=out)
if (n_alternates > 0):
print("", file=out)
print(" %d disordered residues built" % n_alternates, file=out)
n_split = alt_confs.spread_alternates(
pdb_hierarchy,
new_occupancy=params.residue_fitting.expected_occupancy,
split_all_adjacent=True,
log=out)
assert (n_split > 0)
print(" %d adjacent residues split" % n_split, file=out)
else:
print("No alternates built this round.", file=out)
t3 = time.time()
print(" assembly: %.3fs" % (t3 - t2), file=out)
if (not params.cleanup.rsr_after_build):
if (n_alternates > 0):
print("Skipping final RSR step (rsr_after_build=False).", file=out)
else:
print("No refinement needs to be performed.", file=out)
else:
make_sub_header("Real-space refinement", out=out)
print("", file=out)
pdb_hierarchy = real_space_refine(pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
cif_objects=cif_objects,
params=params,
nproc=params.nproc,
remediate=True,
out=out)
t4 = time.time()
print("", file=out)
print("RSR: %.3fs" % (t4 - t3), file=out)
fmodel.info().show_targets(out=out, text="Rebuilt model")
t_end = time.time()
alt_confs.finalize_model(
pdb_hierarchy=pdb_hierarchy,
xray_structure=pdb_hierarchy.extract_xray_structure(
crystal_symmetry=fmodel.xray_structure),
set_b_iso=params.cleanup.set_b_iso,
convert_to_isotropic=params.cleanup.convert_to_isotropic,
selection="altloc A or altloc B")
t_end = time.time()
print("Total runtime for cycle: %.3fs" % (t_end - t_start), file=out)
return pdb_hierarchy, n_alternates
def build_cycle (pdb_hierarchy,
fmodel,
geometry_restraints_manager,
params,
selection=None,
cif_objects=(),
nproc=Auto,
out=sys.stdout,
verbose=False,
debug=None,
i_cycle=0) :
from mmtbx import restraints
from scitbx.array_family import flex
t_start = time.time()
hd_sel = fmodel.xray_structure.hd_selection()
n_hydrogen = hd_sel.count(True)
if (n_hydrogen > 0) and (True) : #params.building.delete_hydrogens) :
print >> out, "WARNING: %d hydrogen atoms will be removed!" % n_hydrogen
non_hd_sel = ~hd_sel
# XXX it's better to do this in-place for the hierarchy, because calling
# pdb_hierarchy.select(non_hd_sel) will not remove parent-child
# relationships involving hydrogens, which causes problems when running
# the MolProbity validation.
pdb_hierarchy.remove_hd(reset_i_seq=True)
xray_structure = fmodel.xray_structure.select(non_hd_sel)
assert (pdb_hierarchy.atoms_size() == xray_structure.scatterers().size())
fmodel.update_xray_structure(xray_structure)
geometry_restraints_manager = geometry_restraints_manager.select(non_hd_sel)
pdb_atoms = pdb_hierarchy.atoms()
segids = pdb_atoms.extract_segid().strip()
if (not segids.all_eq("")) :
print >> out, "WARNING: resetting segids to blank"
for i_seq, atom in enumerate(pdb_atoms) :
atom.segid = ""
sc = fmodel.xray_structure.scatterers()[i_seq]
sc.label = atom.id_str()
if isinstance(selection, str) :
sele_cache = pdb_hierarchy.atom_selection_cache()
selection = sele_cache.selection(selection)
make_header("Build cycle %d" % (i_cycle+1), out=out)
fmodel.info().show_rfactors_targets_scales_overall(out=out)
if (debug > 0) :
from mmtbx.maps.utils import get_maps_from_fmodel
from iotbx.map_tools import write_map_coeffs
two_fofc, fofc = get_maps_from_fmodel(fmodel,
exclude_free_r_reflections=True)
write_map_coeffs(
fwt_coeffs=two_fofc,
delfwt_coeffs=fofc,
file_name="cycle_%d_start.mtz" % (i_cycle+1))
candidate_residues = alt_confs.filter_before_build(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
geometry_restraints_manager=geometry_restraints_manager,
selection=selection,
params=params.prefilter,
verbose=verbose,
log=out)
t1 = time.time()
print >> out, "filtering: %.3fs" % (t1-t_start)
restraints_manager = restraints.manager(
geometry=geometry_restraints_manager,
normalization=True)
make_sub_header("Finding alternate conformations", out=out)
building_trials = find_all_alternates(
residues=candidate_residues,
pdb_hierarchy=pdb_hierarchy,
restraints_manager=restraints_manager,
fmodel=fmodel,
params=params.residue_fitting,
nproc=params.nproc,
verbose=verbose,
debug=debug,
log=out).results
t2 = time.time()
print >> out, " building: %.3fs" % (t2-t1)
make_sub_header("Scoring and assembling alternates", out=out)
n_alternates = process_results(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
residues_in=candidate_residues,
building_trials=building_trials,
params=params.residue_fitting,
verbose=verbose,
log=out)
if (n_alternates > 0) :
print >> out, ""
print >> out, " %d disordered residues built" % n_alternates
n_split = alt_confs.spread_alternates(pdb_hierarchy,
new_occupancy=params.residue_fitting.expected_occupancy,
split_all_adjacent=True,
log=out)
assert (n_split > 0)
print >> out, " %d adjacent residues split" % n_split
else :
print >> out, "No alternates built this round."
t3 = time.time()
print >> out, " assembly: %.3fs" % (t3-t2)
if (not params.cleanup.rsr_after_build) :
if (n_alternates > 0) :
print >> out, "Skipping final RSR step (rsr_after_build=False)."
else :
print >> out, "No refinement needs to be performed."
else :
make_sub_header("Real-space refinement", out=out)
print >> out, ""
pdb_hierarchy = real_space_refine(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
cif_objects=cif_objects,
params=params,
nproc=params.nproc,
remediate=True,
out=out)
t4 = time.time()
print >> out, ""
print >> out, "RSR: %.3fs" % (t4-t3)
fmodel.info().show_targets(out=out, text="Rebuilt model")
t_end = time.time()
alt_confs.finalize_model(
pdb_hierarchy=pdb_hierarchy,
xray_structure=pdb_hierarchy.extract_xray_structure(
crystal_symmetry=fmodel.xray_structure),
set_b_iso=params.cleanup.set_b_iso,
convert_to_isotropic=params.cleanup.convert_to_isotropic,
selection="altloc A or altloc B")
t_end = time.time()
print >> out, "Total runtime for cycle: %.3fs" % (t_end-t_start)
return pdb_hierarchy, n_alternates
def real_space_refine(
pdb_hierarchy,
fmodel,
cif_objects,
params,
out,
nproc=None,
max_cycles=100, # arbitrarily large
remediate=False):
from scitbx.array_family import flex
i_cycle = 0
while (i_cycle < max_cycles):
print(" Cycle %d:" % (i_cycle + 1), file=out)
# this keeps track of which residues were split in the previous cycle -
# we only refine segments that have had residues added
rebuilt_flags = pdb_hierarchy.atoms().extract_tmp_as_size_t()
processed_pdb_file = building.reprocess_pdb(
pdb_hierarchy=pdb_hierarchy,
cif_objects=cif_objects,
crystal_symmetry=fmodel.xray_structure,
out=null_out())
# get the 2mFo-DFc map without new alternates!
#two_fofc_map = fmodel.two_fofc_map(exclude_free_r_reflections=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_atoms = pdb_hierarchy.atoms()
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints_manager = \
processed_pdb_file.geometry_restraints_manager(show_energies=False)
fmodel.update_xray_structure(xray_structure)
sele_cache = pdb_hierarchy.atom_selection_cache()
# FIXME very inefficient when looping!
# this will include both the newly built residues and the original atoms,
# including residues split to allow for backbone flexibility.
sele_split = sele_cache.selection(alt_confs.SELECTION_MODIFIED)
sele_main_conf = sele_cache.selection(alt_confs.SELECTION_OLD)
assert (len(sele_split) > 0)
k = 0
fragments = []
while (k < len(sele_split)):
if (sele_split[k]):
current_fragment = flex.size_t()
while (sele_split[k]):
current_fragment.append(k)
k += 1
atom_start = pdb_atoms[current_fragment[0]].fetch_labels()
atom_end = pdb_atoms[current_fragment[-1]].fetch_labels()
frag_selection = flex.bool(sele_split.size(), current_fragment)
if (i_cycle > 0):
flags = rebuilt_flags.select(frag_selection)
if flags.all_eq(0):
continue
fragments.append(current_fragment)
else:
k += 1
if (len(fragments) == 0):
pass
refine_fragments = rsr_fragments_parallel(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
processed_pdb_file=processed_pdb_file,
sele_main_conf=sele_main_conf,
rsr_fofc_map_target=(i_cycle == 0
and params.cleanup.rsr_fofc_map_target))
refined = easy_mp.pool_map(fixed_func=refine_fragments,
iterable=fragments,
processes=nproc)
sites_refined = pdb_atoms.extract_xyz()
for result in refined:
assert (result is not None)
result.show(out=out, prefix=" ")
sites_refined.set_selected(result.selection, result.sites_cart)
pdb_atoms.set_xyz(sites_refined)
xray_structure.set_sites_cart(sites_refined)
fmodel.update_xray_structure(xray_structure)
if (not remediate) or (max_cycles == 1):
break
else:
for atom in pdb_hierarchy.atoms():
if (atom.segid == alt_confs.SEGID_NEW_SPLIT):
atom.segid = alt_confs.SEGID_NEW_REBUILT
print(" checking for conformational strain...", file=out)
n_split = alt_confs.spread_alternates(
pdb_hierarchy=pdb_hierarchy,
new_occupancy=params.residue_fitting.expected_occupancy,
split_all_adjacent=False,
selection=alt_confs.SELECTION_NEW_REBUILT)
if (n_split > 0):
print(" split another %d residue(s) - will re-run RSR" % \
n_split, file=out)
else:
break
i_cycle += 1
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=fmodel.xray_structure)
fmodel.update_xray_structure(xray_structure,
update_f_mask=True,
update_f_calc=True)
#fmodel.info().show_targets(out=out, text="After real-space refinement")
t2 = time.time()
return pdb_hierarchy
def real_space_refine (
pdb_hierarchy,
fmodel,
cif_objects,
params,
out,
nproc=None,
max_cycles=100, # arbitrarily large
remediate=False) :
from scitbx.array_family import flex
i_cycle = 0
while (i_cycle < max_cycles) :
print >> out, " Cycle %d:" % (i_cycle+1)
# this keeps track of which residues were split in the previous cycle -
# we only refine segments that have had residues added
rebuilt_flags = pdb_hierarchy.atoms().extract_tmp_as_size_t()
processed_pdb_file = building.reprocess_pdb(
pdb_hierarchy=pdb_hierarchy,
cif_objects=cif_objects,
crystal_symmetry=fmodel.xray_structure,
out=null_out())
# get the 2mFo-DFc map without new alternates!
#two_fofc_map = fmodel.two_fofc_map(exclude_free_r_reflections=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_atoms = pdb_hierarchy.atoms()
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints_manager = \
processed_pdb_file.geometry_restraints_manager(show_energies=False)
fmodel.update_xray_structure(xray_structure)
sele_cache = pdb_hierarchy.atom_selection_cache()
# FIXME very inefficient when looping!
# this will include both the newly built residues and the original atoms,
# including residues split to allow for backbone flexibility.
sele_split = sele_cache.selection(alt_confs.SELECTION_MODIFIED)
sele_main_conf = sele_cache.selection(alt_confs.SELECTION_OLD)
assert (len(sele_split) > 0)
k = 0
fragments = []
while (k < len(sele_split)) :
if (sele_split[k]) :
current_fragment = flex.size_t()
while (sele_split[k]) :
current_fragment.append(k)
k += 1
atom_start = pdb_atoms[current_fragment[0]].fetch_labels()
atom_end = pdb_atoms[current_fragment[-1]].fetch_labels()
frag_selection = flex.bool(sele_split.size(), current_fragment)
if (i_cycle > 0) :
flags = rebuilt_flags.select(frag_selection)
if flags.all_eq(0) :
continue
fragments.append(current_fragment)
else :
k += 1
if (len(fragments) == 0) :
pass
refine_fragments = rsr_fragments_parallel(
pdb_hierarchy=pdb_hierarchy,
fmodel=fmodel,
processed_pdb_file=processed_pdb_file,
sele_main_conf=sele_main_conf,
rsr_fofc_map_target=(i_cycle==0 and params.cleanup.rsr_fofc_map_target))
refined = easy_mp.pool_map(
fixed_func=refine_fragments,
iterable=fragments,
processes=nproc)
sites_refined = pdb_atoms.extract_xyz()
for result in refined :
assert (result is not None)
result.show(out=out, prefix=" ")
sites_refined.set_selected(result.selection, result.sites_cart)
pdb_atoms.set_xyz(sites_refined)
xray_structure.set_sites_cart(sites_refined)
fmodel.update_xray_structure(xray_structure)
if (not remediate) or (max_cycles == 1) :
break
else :
for atom in pdb_hierarchy.atoms() :
if (atom.segid == alt_confs.SEGID_NEW_SPLIT) :
atom.segid = alt_confs.SEGID_NEW_REBUILT
print >> out, " checking for conformational strain..."
n_split = alt_confs.spread_alternates(
pdb_hierarchy=pdb_hierarchy,
new_occupancy=params.residue_fitting.expected_occupancy,
split_all_adjacent=False,
selection=alt_confs.SELECTION_NEW_REBUILT)
if (n_split > 0) :
print >> out, " split another %d residue(s) - will re-run RSR" % \
n_split
else :
break
i_cycle += 1
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=fmodel.xray_structure)
fmodel.update_xray_structure(xray_structure,
update_f_mask=True,
update_f_calc=True)
#fmodel.info().show_targets(out=out, text="After real-space refinement")
t2 = time.time()
return pdb_hierarchy
