def compute_target(self, compute_gradients, u_iso_refinable_params):
self.stereochemistry_residuals = None
self.fmodels.update_xray_structure(
xray_structure = self.xray_structure,
update_f_calc = True)
fmodels_target_and_gradients = self.fmodels.target_and_gradients(
weights = self.weights,
compute_gradients = compute_gradients,
u_iso_refinable_params = u_iso_refinable_params)
self.f = fmodels_target_and_gradients.target()
self.g = fmodels_target_and_gradients.gradients()
if(self.refine_xyz and self.restraints_manager is not None and
self.weights.w > 0.0):
self.stereochemistry_residuals = \
self.model.restraints_manager_energies_sites(
compute_gradients = compute_gradients)
# QBLIB INSERT
if(self.qblib_params is not None and self.qblib_params.qblib):
from qbpy import qb_refinement
self.qblib_cycle_count +=1
if(self.tmp_XYZ is not None):
diff,max_diff,max_elem = qb_refinement.array_difference(
self.tmp_XYZ,
self.model.xray_structure.sites_cart(),
)
if(self.XYZ_diff_curr is not None):
self.XYZ_diff_curr=max_elem
else:
self.XYZ_diff_curr=max_elem
if(max_elem>=self.qblib_params.skip_divcon_threshold):
self.tmp_XYZ = self.model.xray_structure.sites_cart()
else:
self.tmp_XYZ = self.model.xray_structure.sites_cart()
if (self.macro_cycle != self.qblib_params.macro_cycle_to_skip):
qblib_call = qb_refinement.QBblib_call_manager(
hierarchy = self.model.pdb_hierarchy(),
xray_structure=self.model.xray_structure,
geometry_residuals = self.stereochemistry_residuals,
qblib_params=self.qblib_params,
diff_curr=self.XYZ_diff_curr,
macro=self.macro_cycle,
micro=self.qblib_cycle_count,
)
try:
qblib_call.run()
except Exception, e:
if e.__class__.__name__=="QB_none_fatal_error":
raise Sorry(e.message)
else:
raise e
if(qblib_call.QBStatus):
qblib_g=qblib_call.result_QBlib.gradients
qblib_f=qblib_call.result_QBlib.target
self.stereochemistry_residuals.gradients=qblib_g
self.stereochemistry_residuals.target=qblib_f
# QBLIB END
er = self.stereochemistry_residuals.target
self.f += er * self.weights.w
if(compute_gradients):
sgc = self.stereochemistry_residuals.gradients
# ias do not participate in geometry restraints
if(self.model is not None and self.model.ias_selection is not None and
self.model.ias_selection.count(True) > 0):
sgc.extend(flex.vec3_double(
self.model.ias_selection.count(True),[0,0,0]))
xray.minimization.add_gradients(
scatterers = self.xray_structure.scatterers(),
xray_gradients = self.g,
site_gradients = sgc*self.weights.w)
def compute_target(self, compute_gradients, u_iso_refinable_params):
self.stereochemistry_residuals = None
self.fmodels.update_xray_structure(
xray_structure = self.xray_structure,
update_f_calc = True)
fmodels_target_and_gradients = self.fmodels.target_and_gradients(
weights = self.weights,
compute_gradients = compute_gradients,
u_iso_refinable_params = u_iso_refinable_params)
self.f = fmodels_target_and_gradients.target()
self.g = fmodels_target_and_gradients.gradients()
if(self.refine_xyz and self.restraints_manager is not None and
self.weights.w > 0.0):
self.stereochemistry_residuals = \
self.model.restraints_manager_energies_sites(
compute_gradients = compute_gradients)
# QBLIB INSERT
if(self.qblib_params is not None and self.qblib_params.qblib):
from qbpy import qb_refinement
self.qblib_cycle_count +=1
if(self.tmp_XYZ is not None):
diff,max_diff,max_elem = qb_refinement.array_difference(
self.tmp_XYZ,
self.model.get_sites_cart(),
)
if(self.XYZ_diff_curr is not None):
self.XYZ_diff_curr=max_elem
else:
self.XYZ_diff_curr=max_elem
if(max_elem>=self.qblib_params.skip_divcon_threshold):
self.tmp_XYZ = self.model.get_sites_cart()
else:
self.tmp_XYZ = self.model.get_sites_cart()
if (self.macro_cycle != self.qblib_params.macro_cycle_to_skip):
qblib_call = qb_refinement.QBblib_call_manager(
hierarchy = self.model.get_hierarchy(),
xray_structure=self.model.get_xray_structure(),
geometry_residuals = self.stereochemistry_residuals,
qblib_params=self.qblib_params,
diff_curr=self.XYZ_diff_curr,
macro=self.macro_cycle,
micro=self.qblib_cycle_count,
)
try:
qblib_call.run()
except Exception as e:
if e.__class__.__name__=="QB_none_fatal_error":
raise Sorry(e.message)
else:
raise e
if(qblib_call.QBStatus):
qblib_g=qblib_call.result_QBlib.gradients
qblib_f=qblib_call.result_QBlib.target
self.stereochemistry_residuals.gradients=qblib_g
self.stereochemistry_residuals.target=qblib_f
# QBLIB END
er = self.stereochemistry_residuals.target
self.f += er * self.weights.w
if(compute_gradients):
sgc = self.stereochemistry_residuals.gradients
# ias do not participate in geometry restraints
if self.model is not None and self.model.ias_manager is not None:
ias_selection = self.model.ias_manager.get_ias_selection()
if ias_selection is not None and ias_selection.count(True) > 0:
sgc.extend(flex.vec3_double(ias_selection.count(True),[0,0,0]))
xray.minimization.add_gradients(
scatterers = self.xray_structure.scatterers(),
xray_gradients = self.g,
site_gradients = sgc*self.weights.w)
if(self.refine_adp and self.restraints_manager is not None and
self.restraints_manager.geometry is not None
and self.weights.w > 0.0 and self.iso_restraints is not None):
use_hd = False
if(self.fmodels.fmodel_n is not None or
(self.is_neutron_scat_table is not None and
self.is_neutron_scat_table == "neutron") or
self.h_params.refine == "individual"):
use_hd = True
energies_adp = self.model.energies_adp(
iso_restraints = self.iso_restraints,
use_hd = use_hd,
compute_gradients = compute_gradients)
self.f += energies_adp.target * self.weights.w
if(compute_gradients):
if(energies_adp.u_aniso_gradients is None):
xray.minimization.add_gradients(
scatterers = self.xray_structure.scatterers(),
xray_gradients = self.g,
u_iso_gradients = energies_adp.u_iso_gradients * self.weights.w)
else:
energies_adp.u_aniso_gradients *= self.weights.w
if(energies_adp.u_iso_gradients is not None):
energies_adp.u_iso_gradients *= self.weights.w
xray.minimization.add_gradients(
scatterers = self.xray_structure.scatterers(),
xray_gradients = self.g,
u_aniso_gradients = energies_adp.u_aniso_gradients,
u_iso_gradients = energies_adp.u_iso_gradients)
energies_adp.u_aniso_gradients = None # just for safety
energies_adp.u_iso_gradients = None
