def refine_window(self, window):
from mmtbx.building.alternate_conformations import real_space_annealing
processed_pdb_file = self.get_processed_pdb_file()
assert (processed_pdb_file is not None)
hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
#print window.residue_id_str
log = null_out()
if (self.debug):
log = sys.stdout
refinements = real_space_annealing.refine_into_difference_density(
fmodel=self.fmodel,
pdb_hierarchy=hierarchy.deep_copy(),
processed_pdb_file=processed_pdb_file,
selection=window.selection,
selection_score=window.residue_selection,
params=self.params,
nproc=self.nproc_2,
out=null_out()).get_filtered_trials(log=log)
result = ensemble(
window=window,
sites_trials=refinements)
n_keep = result.filter_trials(
sites_cart=self.sites_cart,
min_rmsd=self.params.min_rmsd,
min_dev=self.min_required_deviation)
if (n_keep > 0):
if (self.asynchronous_output):
print(result, file=self.out)
return result
return None
def refine_window (self, window) :
from mmtbx.building.alternate_conformations import real_space_annealing
processed_pdb_file = self.get_processed_pdb_file()
assert (processed_pdb_file is not None)
hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
#print window.residue_id_str
log = null_out()
if (self.debug) :
log = sys.stdout
refinements = real_space_annealing.refine_into_difference_density(
fmodel=self.fmodel,
pdb_hierarchy=hierarchy.deep_copy(),
processed_pdb_file=processed_pdb_file,
selection=window.selection,
selection_score=window.residue_selection,
params=self.params,
nproc=self.nproc_2,
out=null_out()).get_filtered_trials(log=log)
result = ensemble(
window=window,
sites_trials=refinements)
n_keep = result.filter_trials(
sites_cart=self.sites_cart,
min_rmsd=self.params.min_rmsd,
min_dev=self.min_required_deviation)
if (n_keep > 0) :
if (self.asynchronous_output) :
print >> self.out, result
return result
return None
def run(args, out=None):
if out is None:
out = sys.stdout
from mmtbx.building.alternate_conformations import real_space_annealing
import mmtbx.maps.utils
import mmtbx.utils
cmdline = mmtbx.utils.cmdline_load_pdb_and_data(
args=args, master_phil=master_phil, process_pdb_file=True, scattering_table="n_gaussian", out=out
)
params = cmdline.params
working_phil = master_phil.format(python_object=params)
master_phil.fetch_diff(source=working_phil).show(out=out)
fmodel = cmdline.fmodel
hierarchy = cmdline.pdb_hierarchy
sele_cache = hierarchy.atom_selection_cache()
if params.selection is None:
raise Sorry("Please specify the selection parameter.")
selection = sele_cache.selection(params.selection)
assert selection.count(True) > 0
t1 = time.time()
models = []
refined_hierarchy = real_space_annealing.refine_into_difference_density(
fmodel=fmodel,
pdb_hierarchy=hierarchy,
processed_pdb_file=cmdline.processed_pdb_file,
selection=selection,
params=params,
nproc=params.nproc,
out=out,
).as_pdb_ensemble(log=out)
t2 = time.time()
print >> out, "refinement time: %.3fs" % (t2 - t1)
if refined_hierarchy is not None:
refined_hierarchy.write_pdb_file(
file_name=params.output_file_name, crystal_symmetry=fmodel.xray_structure.crystal_symmetry()
)
print "wrote %s" % params.output_file_name
else:
raise Sorry("No conformations surviving filtering step!")
def run(args, out=None):
if (out is None) : out = sys.stdout
from mmtbx.building.alternate_conformations import real_space_annealing
import mmtbx.maps.utils
import mmtbx.utils
cmdline = mmtbx.utils.cmdline_load_pdb_and_data(
args=args,
master_phil=master_phil,
process_pdb_file=True,
scattering_table="n_gaussian",
out=out)
params = cmdline.params
working_phil = master_phil.format(python_object=params)
master_phil.fetch_diff(source=working_phil).show(out=out)
fmodel = cmdline.fmodel
hierarchy = cmdline.pdb_hierarchy
sele_cache = hierarchy.atom_selection_cache()
if (params.selection is None):
raise Sorry("Please specify the selection parameter.")
selection = sele_cache.selection(params.selection)
assert (selection.count(True) > 0)
t1 = time.time()
models = []
refined_hierarchy = real_space_annealing.refine_into_difference_density(
fmodel=fmodel,
pdb_hierarchy=hierarchy,
processed_pdb_file=cmdline.processed_pdb_file,
selection=selection,
params=params,
nproc=params.nproc,
out=out).as_pdb_ensemble(log=out)
t2 = time.time()
print >> out, "refinement time: %.3fs" % (t2-t1)
if (refined_hierarchy is not None):
refined_hierarchy.write_pdb_file(file_name=params.output_file_name,
crystal_symmetry = fmodel.xray_structure.crystal_symmetry())
print "wrote %s" % params.output_file_name
else :
raise Sorry("No conformations surviving filtering step!")
