def data_target_and_grads(self, compute_gradients, x):
"""
Args:
compute_gradients: (bool) when True compute gradients
x: refined parameters
"""
g = None
tg = cctbx.maptbx.real_space_refinement_simple.target_and_gradients(
unit_cell=self.unit_cell,
density_map=self.map_data,
sites_cart=self.xray_structure.sites_cart(),
real_space_gradients_delta=self.real_space_gradients_delta,
selection=self.selection)
t = tg.target()
if compute_gradients:
if self.refine_sites:
g = tg.gradients()
elif self.refine_transformations:
grad_wrt_xyz = tg.gradients().as_double()
g = nu.compute_transform_grad(
grad_wrt_xyz=grad_wrt_xyz,
ncs_restraints_group_list=self.ncs_restraints_group_list,
xyz_asu=self.xray_structure.sites_cart(),
x=x)
return t, g
def data_target_and_grads(self, compute_gradients,x):
"""
Args:
compute_gradients: (bool) when True compute gradients
x: refined parameters
"""
g = None
tg = cctbx.maptbx.real_space_refinement_simple.target_and_gradients(
unit_cell = self.unit_cell,
density_map = self.map_data,
sites_cart = self.xray_structure.sites_cart(),
real_space_gradients_delta = self.real_space_gradients_delta,
selection = self.selection)
t = tg.target()
if compute_gradients:
if self.refine_sites:
g = tg.gradients()
elif self.refine_transformations:
grad_wrt_xyz = tg.gradients().as_double()
g = nu.compute_transform_grad(
grad_wrt_xyz = grad_wrt_xyz,
ncs_restraints_group_list = self.ncs_restraints_group_list,
xyz_asu = self.xray_structure.sites_cart(),
x = x)
return t, g
def data_target_and_grads(self, compute_gradients, sites_cart, x):
g = None
tgx = self.x_target_functor(compute_gradients=compute_gradients)
t = tgx.target_work()
if compute_gradients:
if self.refine_sites:
g = flex.vec3_double(
tgx.gradients_wrt_atomic_parameters(site=True).packed())
elif self.refine_u_iso:
g = tgx.gradients_wrt_atomic_parameters(u_iso=True)
elif self.refine_transformations:
grad_wrt_xyz = tgx.gradients_wrt_atomic_parameters(site=True).packed()
g = nu.compute_transform_grad(
grad_wrt_xyz = grad_wrt_xyz,
ncs_restraints_group_list = self.ncs_restraints_group_list,
xyz_asu = sites_cart,
x = x)
return t, g
def data_target_and_grads(self, compute_gradients, sites_cart, x):
g = None
tgx = self.x_target_functor(compute_gradients=compute_gradients)
t = tgx.target_work()
if compute_gradients:
if self.refine_sites:
g = flex.vec3_double(
tgx.gradients_wrt_atomic_parameters(site=True).packed())
elif self.refine_u_iso:
g = tgx.gradients_wrt_atomic_parameters(u_iso=True)
elif self.refine_transformations:
grad_wrt_xyz = tgx.gradients_wrt_atomic_parameters(
site=True).packed()
g = nu.compute_transform_grad(
grad_wrt_xyz=grad_wrt_xyz,
ncs_restraints_group_list=self.ncs_restraints_group_list,
xyz_asu=sites_cart,
x=x)
return t, g
def restraints_target_and_grads(ncs_restraints_group_list,
restraints_manager,
xray_structure,
grad,
x,
refine_sites=False,
refine_u_iso=False,
refine_transformations=False,
iso_restraints=None,
use_hd=None):
"""
Args:
ncs_restraints_group_list: NCS operator list
restraints_manager: (object)
xray_structure: (object)
grad: gradient without restraints
x: refined parameter
refine_sites: (bool) indicate refinement type
refine_u_iso: (bool) indicate refinement type
refine_transformations: (bool) indicate refinement type
iso_restraints: (object) iso restraints parameters
use_hd: (bool) Use hydrogen
Returns:
ef_target: (float) restraints target function value
ef_grad: (flex.double or flex.vec3_double) restraints gradient
"""
assert [refine_sites, refine_u_iso,
refine_transformations].count(True) == 1
ef_grad = None
ef = None
if (restraints_manager is not None):
if (refine_sites):
ef = restraints_manager.energies_sites(
sites_cart=xray_structure.sites_cart(), compute_gradients=True)
ef_grad = ef.gradients
elif (refine_u_iso):
ef = restraints_manager.energies_adp_iso(
xray_structure=xray_structure,
parameters=iso_restraints,
use_u_local_only=iso_restraints.use_u_local_only,
use_hd=use_hd,
compute_gradients=True)
ef_grad = ef.gradients
elif (refine_transformations):
ef = restraints_manager.energies_sites(
sites_cart=xray_structure.sites_cart(), compute_gradients=True)
ef_grad = nu.compute_transform_grad(
grad_wrt_xyz=ef.gradients.as_double(),
ncs_restraints_group_list=ncs_restraints_group_list,
xyz_asu=xray_structure.sites_cart(),
x=x)
if (ef is not None): return ef.target, ef_grad
elif not grad: return 0, 0
elif isinstance(grad, flex.vec3_double):
return 0, flex.vec3_double([
(0, 0, 0),
] * len(grad))
elif isinstance(grad, flex.double):
return 0, flex.double((0, 0, 0) * (len(grad) // 3))
else:
return None, None
def restraints_target_and_grads(
ncs_restraints_group_list,
restraints_manager,
xray_structure,
grad,
x,
refine_sites=False,
refine_u_iso=False,
refine_transformations=False,
iso_restraints=None,
use_hd=None):
"""
Args:
ncs_restraints_group_list: NCS operator list
restraints_manager: (object)
xray_structure: (object)
grad: gradient without restraints
x: refined parameter
refine_sites: (bool) indicate refinement type
refine_u_iso: (bool) indicate refinement type
refine_transformations: (bool) indicate refinement type
iso_restraints: (object) iso restraints parameters
use_hd: (bool) Use hydrogen
Returns:
ef_target: (float) restraints target function value
ef_grad: (flex.double or flex.vec3_double) restraints gradient
"""
assert [refine_sites, refine_u_iso, refine_transformations].count(True)==1
ef_grad = None
ef = None
if(restraints_manager is not None):
if(refine_sites):
ef = restraints_manager.energies_sites(
sites_cart = xray_structure.sites_cart(),
compute_gradients = True)
ef_grad = ef.gradients
elif(refine_u_iso):
ef = restraints_manager.energies_adp_iso(
xray_structure = xray_structure,
parameters = iso_restraints,
use_u_local_only = iso_restraints.use_u_local_only,
use_hd = use_hd,
compute_gradients = True)
ef_grad = ef.gradients
elif(refine_transformations):
ef = restraints_manager.energies_sites(
sites_cart = xray_structure.sites_cart(),
compute_gradients = True)
ef_grad = nu.compute_transform_grad(
grad_wrt_xyz = ef.gradients.as_double(),
ncs_restraints_group_list = ncs_restraints_group_list,
xyz_asu = xray_structure.sites_cart(),
x = x)
if(ef is not None): return ef.target, ef_grad
elif not grad: return 0, 0
elif isinstance(grad,flex.vec3_double):
return 0, flex.vec3_double([(0,0,0),]*len(grad))
elif isinstance(grad,flex.double):
return 0, flex.double((0,0,0)*(len(grad)//3))
else: return None,None