def minimize(self):
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.xray_structure)
self.model.set_refine_individual_adp()
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = self.individual_adp_params.iso.max_number_of_iterations)
is_neutron_scat_table = False
if(self.all_params.main.scattering_table == "neutron"):
is_neutron_scat_table = True
minimized = minimization.lbfgs(
restraints_manager = self.model.restraints_manager,
fmodels = self.fmodels,
model = self.model,
refine_adp = True,
is_neutron_scat_table = is_neutron_scat_table,
lbfgs_termination_params = lbfgs_termination_params,
iso_restraints = self.adp_restraints_params.iso,
verbose = 0,
target_weights = self.target_weights,
h_params = self.h_params)
self.model.xray_structure = self.fmodels.fmodel_xray().xray_structure
assert minimized.xray_structure is self.model.xray_structure
utils.assert_xray_structures_equal(
x1 = minimized.xray_structure,
x2 = self.model.xray_structure)
return minimized
def minimize(self):
utils.assert_xray_structures_equal(
x1=self.fmodels.fmodel_xray().xray_structure,
x2=self.model.xray_structure)
self.model.set_refine_individual_adp()
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=self.individual_adp_params.iso.
max_number_of_iterations)
is_neutron_scat_table = False
if (self.all_params.main.scattering_table == "neutron"):
is_neutron_scat_table = True
minimized = minimization.lbfgs(
restraints_manager=self.model.restraints_manager,
fmodels=self.fmodels,
model=self.model,
refine_adp=True,
is_neutron_scat_table=is_neutron_scat_table,
lbfgs_termination_params=lbfgs_termination_params,
iso_restraints=self.adp_restraints_params.iso,
verbose=0,
target_weights=self.target_weights,
h_params=self.h_params)
self.model.xray_structure = self.fmodels.fmodel_xray().xray_structure
assert minimized.xray_structure is self.model.xray_structure
utils.assert_xray_structures_equal(x1=minimized.xray_structure,
x2=self.model.xray_structure)
return minimized
def refine_adp(self):
if (not self.filter_only and self.params.refine_adp
and self.model.refinement_flags.individual_adp
and self.model.solvent_selection().count(True) > 0):
self.fmodels.update_xray_structure(
xray_structure=self.model.get_xray_structure(),
update_f_calc=True,
update_f_mask=True)
print(
"ADP refinement (water only), start r_work=%6.4f r_free=%6.4f"
% (self.fmodel.r_work(), self.fmodel.r_free()),
file=self.log)
# set refinement flags (not exercised!)
hd_sel = self.model.get_hd_selection()
not_hd_sel = ~hd_sel
sol_sel = self.model.solvent_selection()
not_sol_sel = ~sol_sel
selection_aniso = self.model.get_xray_structure().use_u_aniso(
).deep_copy()
if (self.params.new_solvent == "anisotropic"):
selection_aniso.set_selected(sol_sel, True)
selection_iso = self.model.get_xray_structure().use_u_iso(
).deep_copy()
selection_aniso.set_selected(not_sol_sel, False)
selection_iso.set_selected(not_sol_sel, False)
if (not self.is_neutron_scat_table):
selection_aniso.set_selected(hd_sel, False)
selection_iso.set_selected(hd_sel, False)
selection_aniso.set_selected(selection_iso, False)
selection_iso.set_selected(selection_aniso, False)
self.model.set_refine_individual_adp(
selection_aniso=selection_aniso, selection_iso=selection_iso)
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=25)
minimized = minimization.lbfgs(
restraints_manager=None,
fmodels=self.fmodels,
model=self.model,
is_neutron_scat_table=self.is_neutron_scat_table,
refine_adp=True,
lbfgs_termination_params=lbfgs_termination_params)
print(
"ADP refinement (water only), final r_work=%6.4f r_free=%6.4f"
% (self.fmodel.r_work(), self.fmodel.r_free()),
file=self.log)
def refine_adp(self):
if(not self.filter_only and self.params.refine_adp and
self.model.refinement_flags.individual_adp and
self.model.solvent_selection().count(True) > 0):
self.fmodels.update_xray_structure(
xray_structure = self.model.xray_structure,
update_f_calc = True,
update_f_mask = True)
print >> self.log, \
"ADP refinement (water only), start r_work=%6.4f r_free=%6.4f"%(
self.fmodel.r_work(), self.fmodel.r_free())
# set refinement flags (not exercised!)
hd_sel = self.model.xray_structure.hd_selection()
not_hd_sel = ~hd_sel
sol_sel = self.model.solvent_selection()
not_sol_sel= ~sol_sel
selection_aniso = self.model.xray_structure.use_u_aniso().deep_copy()
if(self.params.new_solvent == "anisotropic"):
selection_aniso.set_selected(sol_sel, True)
selection_iso = self.model.xray_structure.use_u_iso().deep_copy()
selection_aniso.set_selected(not_sol_sel, False)
selection_iso .set_selected(not_sol_sel, False)
if(not self.is_neutron_scat_table):
selection_aniso.set_selected(hd_sel, False)
selection_iso.set_selected(hd_sel, False)
selection_aniso.set_selected(selection_iso, False)
selection_iso.set_selected(selection_aniso, False)
self.model.set_refine_individual_adp(
selection_aniso = selection_aniso, selection_iso = selection_iso)
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = 25)
minimized = minimization.lbfgs(
restraints_manager = None,
fmodels = self.fmodels,
model = self.model,
is_neutron_scat_table = self.is_neutron_scat_table,
refine_adp = True,
lbfgs_termination_params = lbfgs_termination_params)
print >> self.log,\
"ADP refinement (water only), final r_work=%6.4f r_free=%6.4f"%(
self.fmodel.r_work(), self.fmodel.r_free())
def run_lbfgs(self):
if (self.model.get_ncs_groups() is None
or not self.all_params.ncs.constraints.apply_to_adp):
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=self.individual_adp_params.iso.
max_number_of_iterations)
is_neutron_scat_table = False
if (self.all_params.main.scattering_table == "neutron"):
is_neutron_scat_table = True
minimized = minimization.lbfgs(
restraints_manager=self.model.restraints_manager,
fmodels=self.fmodels,
model=self.model,
refine_adp=True,
is_neutron_scat_table=is_neutron_scat_table,
lbfgs_termination_params=lbfgs_termination_params,
iso_restraints=self.adp_restraints_params.iso,
verbose=0,
target_weights=self.target_weights,
h_params=self.h_params)
elif (self.all_params.ncs.constraints.apply_to_coordinates):
fmodel = self.fmodels.fmodel_xray()
# update NCS groups
import mmtbx.ncs.ncs_utils as nu
nu.get_list_of_best_ncs_copy_map_correlation(
ncs_groups=self.model.get_ncs_groups(), fmodel=fmodel)
assert "individual_adp" in self.all_params.refine.strategy
minimized = minimization.run_constrained(
model=self.model,
fmodel=fmodel,
target_weight=self.target_weights.xyz_weights_result.wx,
log=self.log,
params=self.all_params,
refine_u_iso=True,
prefix="NCS constrained ADP refinement").minimized
self.model.set_xray_structure(fmodel.xray_structure)
else:
raise RuntimeError("Bad ncs options.")
def run_lbfgs(self):
if(self.model.ncs_groups is None or
not self.all_params.ncs.constraints.apply_to_adp):
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = self.individual_adp_params.iso.max_number_of_iterations)
is_neutron_scat_table = False
if(self.all_params.main.scattering_table == "neutron"):
is_neutron_scat_table = True
minimized = minimization.lbfgs(
restraints_manager = self.model.restraints_manager,
fmodels = self.fmodels,
model = self.model,
refine_adp = True,
is_neutron_scat_table = is_neutron_scat_table,
lbfgs_termination_params = lbfgs_termination_params,
iso_restraints = self.adp_restraints_params.iso,
verbose = 0,
target_weights = self.target_weights,
h_params = self.h_params)
elif(self.all_params.ncs.constraints.apply_to_coordinates):
fmodel = self.fmodels.fmodel_xray()
# update NCS groups
import mmtbx.ncs.ncs_utils as nu
nu.get_list_of_best_ncs_copy_map_correlation(
ncs_groups = self.model.ncs_groups,
fmodel = fmodel)
assert "individual_adp" in self.all_params.refine.strategy
minimized = minimization.run_constrained(
model = self.model,
fmodel = fmodel,
target_weight = self.target_weights.xyz_weights_result.wx,
log = self.log,
params = self.all_params,
refine_u_iso = True,
prefix = "NCS constrained ADP refinement").minimized
self.model.xray_structure = fmodel.xray_structure
else: raise RuntimeError("Bad ncs options.")
