def adp_refinement(self, log):
if log is None:
log = sys.stdout
save_xray_structure = self.fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
###> Make ADP of H/D sites equal
self.model.reset_adp_of_hd_sites_to_be_equal()
self.fmodels.update_xray_structure(
xray_structure = self.model.get_xray_structure(),
update_f_calc = True)
self.adp_refinement_manager = adp_refinement.manager(
fmodels = self.fmodels,
model = self.model,
group_adp_selections = self.model.refinement_flags.adp_group,
group_adp_selections_h = self.model.refinement_flags.group_h,
group_adp_params = self.params.group_b_iso,
tls_selections = self.model.refinement_flags.adp_tls,
all_params = self.params,
tls_params = self.params.tls,
individual_adp_params = self.params.adp,
adp_restraints_params = self.params.adp_restraints,
refine_adp_individual = self.model.refinement_flags.individual_adp,
refine_adp_group = self.model.refinement_flags.group_adp,
refine_tls = self.model.refinement_flags.tls,
tan_b_iso_max = self.tan_b_iso_max,
restraints_manager = self.model.restraints_manager,
macro_cycle = self.macro_cycle,
target_weights = self.target_weights,
log = log,
h_params = self.params.hydrogens,
nproc = 1)
def adp_refinement(self, log):
if log is None:
log = sys.stdout
save_xray_structure = self.fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
###> Make ADP of H/D sites equal
self.model.reset_adp_of_hd_sites_to_be_equal()
self.fmodels.update_xray_structure(
xray_structure = self.model.xray_structure,
update_f_calc = True)
self.adp_refinement_manager = adp_refinement.manager(
fmodels = self.fmodels,
model = self.model,
group_adp_selections = self.model.refinement_flags.adp_group,
group_adp_selections_h = self.model.refinement_flags.group_h,
group_adp_params = self.params.group_b_iso,
tls_selections = self.model.refinement_flags.adp_tls,
all_params = self.params,
tls_params = self.params.tls,
individual_adp_params = self.params.adp,
adp_restraints_params = self.params.adp_restraints,
refine_adp_individual = self.model.refinement_flags.individual_adp,
refine_adp_group = self.model.refinement_flags.group_adp,
refine_tls = self.model.refinement_flags.tls,
tan_b_iso_max = self.tan_b_iso_max,
restraints_manager = self.model.restraints_manager,
macro_cycle = self.macro_cycle,
target_weights = self.target_weights,
log = log,
h_params = self.params.hydrogens,
nproc = 1)
def run(
model,
params,
fmodels,
save_optimize_adp_weight,
log,
macro_cycle,
prefix,
target_weights):
target_weights_params = params.target_weights
h_params = params.hydrogens
print_statistics.make_header(prefix, out = log)
if(save_optimize_adp_weight):
r_work = fmodels.fmodel_xray().r_work()
r_free = fmodels.fmodel_xray().r_free()
if ((r_free < r_work or (r_free-r_work)<0.01) and
(not target_weights_params.force_optimize_weights)) :
target_weights_params.optimize_adp_weight = False
else:
target_weights_params.optimize_adp_weight=save_optimize_adp_weight
fmodels.fmodel_xray().xray_structure.scatterers().flags_set_grads(
state = False)
# Exclude H from ADP refinement
if ((params.hydrogens.refine == "riding") or
(params.hydrogens.force_riding_adp)) :
excl_h = model.xray_structure.hd_selection().count(True) > 0
if(excl_h and model.refinement_flags.adp_individual_iso is not None):
model.refinement_flags.adp_individual_iso.set_selected(
model.xray_structure.hd_selection(), False)
if(excl_h and model.refinement_flags.adp_individual_aniso is not None):
model.refinement_flags.adp_individual_aniso.set_selected(
model.xray_structure.hd_selection(), False)
#
save_xray_structure = \
fmodels.fmodel_xray().xray_structure.deep_copy_scatterers() # XXX ?
###> Make ADP of H/D sites equal
model.reset_adp_of_hd_sites_to_be_equal()
fmodels.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc = True)
tidy_us(params=params, fmodels=fmodels, model=model, log=log)
adp_refinement_manager = adp_refinement.manager(
fmodels = fmodels,
model = model,
group_adp_selections = model.refinement_flags.adp_group,
group_adp_selections_h = model.refinement_flags.group_h,
group_adp_params = params.group_b_iso,
tls_selections = model.refinement_flags.adp_tls,
nm_selections = model.refinement_flags.adp_nm,
all_params = params,
tls_params = params.tls,
nm_params = params.nm,
individual_adp_params = params.adp,
adp_restraints_params = params.adp_restraints,
refine_adp_individual = model.refinement_flags.individual_adp,
refine_adp_group = model.refinement_flags.group_adp,
refine_tls = model.refinement_flags.tls,
refine_nm = model.refinement_flags.nm,
tan_b_iso_max = 0,
restraints_manager = model.restraints_manager,
macro_cycle = macro_cycle,
target_weights = target_weights,
log = log,
h_params = h_params)
assert fmodels.fmodel_xray().xray_structure.min_u_cart_eigenvalue()>=0
print >> log
model.show_adp_statistics(padded = True)
print >> log
fmodels.update_xray_structure(update_f_calc = True)
###> Make ADP of H/D sites equal
model.reset_adp_of_hd_sites_to_be_equal()
fmodels.update_xray_structure(xray_structure = model.xray_structure,
update_f_calc = True)
assert fmodels.fmodel_xray().xray_structure.min_u_cart_eigenvalue()>=0