def exercise_rejoin():
from mmtbx.building.alternate_conformations.tst_build_simple import pdb_raw
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
hierarchy = pdb_in.hierarchy
params = alternate_conformations.rejoin_phil.extract()
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=hierarchy,
params=params,
model_error_ml=0.5,
log=null_out())
assert (n_modified == 3), n_modified # Gln5
# split residue 6 without changing coordinates, set occupancy very low
chain = hierarchy.only_model().chains()[0]
rg6 = chain.residue_groups()[5]
ag = rg6.only_atom_group().detached_copy()
for atom in ag.atoms():
atom.occ = 0.05
for atom in rg6.atoms():
atom.occ = 0.95
rg6.only_atom_group().altloc = 'A'
ag.altloc = 'B'
rg6.append_atom_group(ag)
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=hierarchy.deep_copy(),
params=params,
model_error_ml=0.5,
log=null_out())
assert (n_modified == 1), n_modified
# now with higher B-factors for all atoms
for atom in hierarchy.atoms():
atom.b = atom.b * 10
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=hierarchy, params=params, log=null_out())
assert (n_modified == 1), n_modified
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 exercise_rejoin () :
from mmtbx.building.alternate_conformations.tst_build_simple import pdb_raw
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
hierarchy = pdb_in.hierarchy
params = alternate_conformations.rejoin_phil.extract()
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=hierarchy,
params=params,
model_error_ml=0.5,
log=null_out())
assert (n_modified == 3), n_modified # Gln5
# split residue 6 without changing coordinates, set occupancy very low
chain = hierarchy.only_model().chains()[0]
rg6 = chain.residue_groups()[5]
ag = rg6.only_atom_group().detached_copy()
for atom in ag.atoms() :
atom.occ = 0.05
for atom in rg6.atoms() :
atom.occ = 0.95
rg6.only_atom_group().altloc = 'A'
ag.altloc = 'B'
rg6.append_atom_group(ag)
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=hierarchy.deep_copy(),
params=params,
model_error_ml=0.5,
log=null_out())
assert (n_modified == 1), n_modified
# now with higher B-factors for all atoms
for atom in hierarchy.atoms() :
atom.b = atom.b * 10
n_modified = alternate_conformations.rejoin_split_single_conformers(
pdb_hierarchy=hierarchy,
params=params,
log=null_out())
assert (n_modified == 1), n_modified
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)
