def try_den_weight_torsion(self, grid_pair):
#backup_k_rep = self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep
local_seed = int(self.random_seed+grid_pair[1])
flex.set_random_seed(value=local_seed)
random.seed(local_seed)
self.fmodels.fmodel_xray().xray_structure.replace_scatterers(
self.save_scatterers_local.deep_copy())
self.fmodels.update_xray_structure(
xray_structure = self.fmodels.fmodel_xray().xray_structure,
update_f_calc = True)
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.xray_structure)
gamma_local = grid_pair[0]
weight_local = grid_pair[1]
self.model.restraints_manager.geometry.\
den_manager.gamma = gamma_local
self.model.restraints_manager.geometry.\
den_manager.weight = weight_local
cycle = 0
self.model.restraints_manager.geometry.\
den_manager.current_cycle = cycle+1
num_den_cycles = self.model.restraints_manager.geometry.\
den_manager.num_cycles
if self.params.den.optimize and \
self.nproc != Auto and \
self.nproc > 1:
local_log = sys.stdout
elif self.params.den.optimize and \
self.nproc == 1:
if self.verbose:
local_log = self.log
else:
local_log = StringIO()
else:
local_log = self.log
print >> self.log, " ...trying gamma %.1f, weight %.1f" % (
gamma_local, weight_local)
while cycle < num_den_cycles:
#if self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.current_cycle == \
# self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.torsion_mid_point+1:
# self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep = 1.0
print >> local_log, "DEN cycle %d" % (cycle+1)
#print >> local_log, "Random seed: %d" % flex.get_random_seed()
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at start of SA cycle: %.4f" % r_free
print >> local_log, "k_rep = %.2f" % \
self.params.tardy.\
prolsq_repulsion_function_changes.k_rep
tardy.run(
fmodels=self.fmodels,
model=self.model,
target_weights=self.target_weights,
params=self.params.tardy,
log=local_log,
format_for_phenix_refine=True,
call_back_after_step=False)
if self.params.den.bulk_solvent_and_scale:
self.bulk_solvent_and_scale(log=local_log)
self.fmodels.fmodel_xray().xray_structure = self.model.xray_structure
if self.params.den.refine_adp:
self.adp_refinement(log=local_log)
self.model.restraints_manager.geometry.update_dihedral_ncs_restraints(
sites_cart=self.model.xray_structure.sites_cart(),
pdb_hierarchy=self.model.pdb_hierarchy(sync_with_xray_structure=True),
log=local_log)
cycle += 1
self.model.restraints_manager.geometry.\
den_manager.current_cycle += 1
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at end of SA cycle: %f" % r_free
r_free = self.fmodels.fmodel_xray().r_free()
step_xray_structure = self.fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
step_eq_distances = self.model.restraints_manager.geometry.\
den_manager.get_current_eq_distances()
return (gamma_local,
weight_local,
r_free,
step_xray_structure,
step_eq_distances)
def try_den_weight_torsion(self, grid_pair):
#backup_k_rep = self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep
local_seed = int(self.random_seed+grid_pair[1])
flex.set_random_seed(value=local_seed)
random.seed(local_seed)
self.fmodels.fmodel_xray().xray_structure.replace_scatterers(
self.save_scatterers_local.deep_copy())
self.fmodels.update_xray_structure(
xray_structure = self.fmodels.fmodel_xray().xray_structure,
update_f_calc = True)
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.get_xray_structure())
gamma_local = grid_pair[0]
weight_local = grid_pair[1]
self.model.restraints_manager.geometry.\
den_manager.gamma = gamma_local
self.model.restraints_manager.geometry.\
den_manager.weight = weight_local
cycle = 0
self.model.restraints_manager.geometry.\
den_manager.current_cycle = cycle+1
num_den_cycles = self.model.restraints_manager.geometry.\
den_manager.num_cycles
if self.params.den.optimize and \
self.nproc != Auto and \
self.nproc > 1:
local_log = sys.stdout
elif self.params.den.optimize and \
self.nproc == 1:
if self.verbose:
local_log = self.log
else:
local_log = StringIO()
else:
local_log = self.log
print >> self.log, " ...trying gamma %.1f, weight %.1f" % (
gamma_local, weight_local)
while cycle < num_den_cycles:
#if self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.current_cycle == \
# self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.torsion_mid_point+1:
# self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep = 1.0
print >> local_log, "DEN cycle %d" % (cycle+1)
#print >> local_log, "Random seed: %d" % flex.get_random_seed()
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at start of SA cycle: %.4f" % r_free
print >> local_log, "k_rep = %.2f" % \
self.params.tardy.\
prolsq_repulsion_function_changes.k_rep
tardy.run(
fmodels=self.fmodels,
model=self.model,
target_weights=self.target_weights,
params=self.params.tardy,
log=local_log,
format_for_phenix_refine=True,
call_back_after_step=False)
if self.params.den.bulk_solvent_and_scale:
self.bulk_solvent_and_scale(log=local_log)
self.fmodels.fmodel_xray().xray_structure = self.model.get_xray_structure()
if self.params.den.refine_adp:
self.adp_refinement(log=local_log)
self.model.torsion_ncs_restraints_update(log=local_log)
cycle += 1
self.model.restraints_manager.geometry.\
den_manager.current_cycle += 1
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at end of SA cycle: %f" % r_free
r_free = self.fmodels.fmodel_xray().r_free()
step_xray_structure = self.fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
step_eq_distances = self.model.restraints_manager.geometry.\
den_manager.get_current_eq_distances()
return (gamma_local,
weight_local,
r_free,
step_xray_structure,
step_eq_distances)