def run(args, out=sys.stdout):
from mmtbx.building import alternate_conformations
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
float_def="model_error_ml",
pdb_file_def="file_name")
params = cmdline.work.extract()
assert (params.file_name is not None)
pdb_in = cmdline.get_file(params.file_name)
hierarchy = pdb_in.file_object.construct_hierarchy()
xrs = pdb_in.file_object.xray_structure_simple()
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=hierarchy,
crystal_symmetry=xrs,
model_error_ml=params.model_error_ml,
params=params,
verbose=True,
log=out)
alternate_conformations.finalize_model(
pdb_hierarchy=hierarchy,
xray_structure=hierarchy.extract_xray_structure(
crystal_symmetry=pdb_in.file_object.xray_structure_simple()),
set_b_iso=True,
convert_to_isotropic=True)
if (n_modified == 0):
print >> out, "No residues modified."
else:
open("rejoined.pdb", "w").write(hierarchy.as_pdb_string())
print >> out, "wrote rejoined.pdb"
def rejoin(self):
make_sub_header("Re-joining identical conformers", out=self.out)
pdb_hierarchy = self.pdb_hierarchy.deep_copy()
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=pdb_hierarchy,
crystal_symmetry=self.fmodel.xray_structure,
model_error_ml=self.fmodel.model_error_ml(),
params=self.params.merging,
reset_occupancies=self.params.refinement.
constrain_correlated_occupancies,
verbose=self.verbose,
log=self.out)
if (n_modified > 0):
self.pdb_hierarchy = pdb_hierarchy
xray_structure = self.pdb_hierarchy.extract_xray_structure(
crystal_symmetry=self.fmodel.xray_structure)
self.fmodel.update_xray_structure(xray_structure)
self.map_file = None
alternate_conformations.finalize_model(
pdb_hierarchy=self.pdb_hierarchy,
xray_structure=self.pdb_hierarchy.extract_xray_structure(
crystal_symmetry=self.fmodel.xray_structure),
set_b_iso=None,
convert_to_isotropic=False)
return (n_modified > 0)
def run (args, out=sys.stdout) :
from mmtbx.building import alternate_conformations
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
float_def="model_error_ml",
pdb_file_def="file_name")
params = cmdline.work.extract()
assert (params.file_name is not None)
pdb_in = cmdline.get_file(params.file_name)
hierarchy = pdb_in.file_object.construct_hierarchy()
xrs = pdb_in.file_object.xray_structure_simple()
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=hierarchy,
crystal_symmetry=xrs,
model_error_ml=params.model_error_ml,
params=params,
verbose=True,
log=out)
alternate_conformations.finalize_model(
pdb_hierarchy=hierarchy,
xray_structure=hierarchy.extract_xray_structure(
crystal_symmetry=pdb_in.file_object.xray_structure_simple()),
set_b_iso=True,
convert_to_isotropic=True)
if (n_modified == 0) :
print >> out, "No residues modified."
else :
open("rejoined.pdb", "w").write(hierarchy.as_pdb_string())
print >> out, "wrote rejoined.pdb"
def rejoin (self) :
make_sub_header("Re-joining identical conformers", out=self.out)
pdb_hierarchy = self.pdb_hierarchy.deep_copy()
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=pdb_hierarchy,
crystal_symmetry=self.fmodel.xray_structure,
model_error_ml=self.fmodel.model_error_ml(),
params=self.params.merging,
reset_occupancies=self.params.refinement.constrain_correlated_occupancies,
verbose=self.verbose,
log=self.out)
if (n_modified > 0) :
self.pdb_hierarchy = pdb_hierarchy
xray_structure = self.pdb_hierarchy.extract_xray_structure(
crystal_symmetry=self.fmodel.xray_structure)
self.fmodel.update_xray_structure(xray_structure)
self.map_file = None
alternate_conformations.finalize_model(
pdb_hierarchy=self.pdb_hierarchy,
xray_structure=self.pdb_hierarchy.extract_xray_structure(
crystal_symmetry=self.fmodel.xray_structure),
set_b_iso=None,
convert_to_isotropic=False)
return (n_modified > 0)
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