def is_alive(self):
from libtbx.development.timers import work_clock
return work_clock() < self.maxtime
def run(self):
# String describing the run that will be output to the specified file.
outString = 'reduce2 v.{}, run {}\n'.format(version, datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
for a in sys.argv:
outString += ' {}'.format(a)
outString += '\n'
make_sub_header('Loading Model', out=self.logger)
# Get our model.
self.model = self.data_manager.get_model()
# Fix up bogus unit cell when it occurs by checking crystal symmetry.
cs = self.model.crystal_symmetry()
if (cs is None) or (cs.unit_cell() is None):
self.model = shift_and_box_model(model = self.model)
if self.params.approach == 'add':
# Add Hydrogens to the model
make_sub_header('Adding Hydrogens', out=self.logger)
startAdd = work_clock()
reduce_add_h_obj = reduce_hydrogen.place_hydrogens(
model = self.model,
n_terminal_charge=self.params.n_terminal_charge,
stop_for_unknowns=True
)
reduce_add_h_obj.run()
self.model = reduce_add_h_obj.get_model()
doneAdd = work_clock()
# Interpret the model after shifting and adding Hydrogens to it so that
# all of the needed fields are filled in when we use them below.
# @todo Remove this once place_hydrogens() does all the interpretation we need.
make_sub_header('Interpreting Hydrogenated Model', out=self.logger)
startInt = work_clock()
self.model.get_hierarchy().sort_atoms_in_place()
self.model.get_hierarchy().atoms().reset_serial()
p = mmtbx.model.manager.get_default_pdb_interpretation_params()
p.pdb_interpretation.allow_polymer_cross_special_position=True
p.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
p.pdb_interpretation.use_neutron_distances = self.params.use_neutron_distances
p.pdb_interpretation.proceed_with_excessive_length_bonds=True
#p.pdb_interpretation.sort_atoms=True
self.model.process(make_restraints=True, pdb_interpretation_params=p) # make restraints
doneInt = work_clock()
make_sub_header('Optimizing', out=self.logger)
startOpt = work_clock()
Optimizers.probePhil = self.params.probe
opt = Optimizers.FastOptimizer(self.params.add_flip_movers, self.model, probeRadius=0.25,
altID=self.params.alt_id, preferenceMagnitude=self.params.preference_magnitude)
doneOpt = work_clock()
outString += opt.getInfo()
outString += 'Time to Add Hydrogen = '+str(doneAdd-startAdd)+'\n'
outString += 'Time to Interpret = '+str(doneInt-startInt)+'\n'
outString += 'Time to Optimize = '+str(doneOpt-startOpt)+'\n'
else: # Removing Hydrogens from the model rather than adding them.
make_sub_header('Removing Hydrogens', out=self.logger)
sel = self.model.selection("element H")
for a in self.model.get_atoms():
if sel[a.i_seq]:
a.parent().remove_atom(a)
# Re-process the model because we have removed some atoms that were previously
# bonded. Don't make restraints during the reprocessing.
# We had to do this to keep from crashing on a call to pair_proxies when generating
# mmCIF files, so we always do it for safety.
self.model.process(make_restraints=False, pdb_interpretation_params=p)
make_sub_header('Writing output', out=self.logger)
# Write the description output to the specified file.
of = open(self.params.output.description_file_name,"w")
of.write(outString)
of.close()
# Determine whether to write a PDB or CIF file and write the appropriate text output.
# Then determine the output file name and write it there.
if str(self.params.output.suffix).lower() == "pdb":
txt = self.model.model_as_pdb()
suffix = ".pdb"
else:
txt = self.model.model_as_mmcif()
suffix = ".cif"
if self.params.output.model_file_base_name is not None:
base = self.params.output.model_file_base_name
else:
file_name = self.data_manager.get_model_names()[0]
base = os.path.splitext(os.path.basename(file_name))[0] + "_reduced"
fullname = base+suffix
with open(fullname, 'w') as f:
f.write(txt)
print('Wrote',fullname,'and',self.params.output.description_file_name, file = self.logger)
# Report profiling info if we've been asked to in the Phil parameters
if self.params.profile:
print('Profile results:')
import pstats
profile_params = {'sort_by': 'time', 'num_entries': 20}
self._pr.disable()
ps = pstats.Stats(self._pr).sort_stats(profile_params['sort_by'])
ps.print_stats(profile_params['num_entries'])
def __init__(self, seconds):
from libtbx.development.timers import work_clock
self.maxtime = work_clock() + seconds