def adp_volume_similarity_as_cif_loops(xray_structure, proxies):
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4e"
loop = model.loop(header=(
"_restr_U_volume_similar_atom_site_label_1",
"_restr_U_volume_similar_diff",
"_restr_U_volume_similar_class_id",
))
class_loop = model.loop(header=(
"_restr_U_volume_similar_class_class_id",
"_restr_U_volume_similar_class_target_weight_param",
"_restr_U_volume_similar_class_average",
"_restr_U_volume_similar_class_esd",
"_restr_U_volume_similar_class_diff_max",
))
unit_cell = xray_structure.unit_cell()
params = adp_restraints.adp_restraint_params(
u_cart=xray_structure.scatterers().extract_u_cart(unit_cell),
u_iso=xray_structure.scatterers().extract_u_iso(),
use_u_aniso=xray_structure.use_u_aniso())
class_id = 0
for proxy in proxies:
restraint = adp_restraints.adp_volume_similarity(params=params,
proxy=proxy)
class_id += 1
class_loop.add_row(
(class_id, fmt % math.sqrt(1 / proxy.weight),
fmt % restraint.mean_u_volume, fmt % restraint.rms_deltas(),
fmt % flex.max_absolute(restraint.deltas())))
for i, i_seq in enumerate(proxy.i_seqs):
loop.add_row(
(site_labels[i_seq], fmt % restraint.deltas()[i], class_id))
return class_loop, loop
def check_refinement_stability(self):
xs = self.xray_structure
xs0 = self.reference_xray_structure = xs.deep_copy_scatterers()
mi = xs0.build_miller_set(anomalous_flag=True, d_min=0.5)
fo_sq = mi.structure_factors_from_scatterers(
xs0, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
self.shake_selection = flex.bool([
True if sc.element_symbol() == 'O' else False
for sc in self.xray_structure.scatterers()
])
xs.shake_fps(selection=self.shake_selection)
xs.shake_fdps(selection=self.shake_selection)
self.reparametrisation = constraints.reparametrisation(
xs,
self.constraints,
self.connectivity_table,
temperature=self.t_celsius)
self.obs = fo_sq.as_xray_observations()
ls = least_squares.crystallographic_ls(
self.obs,
self.reparametrisation,
weighting_scheme=least_squares.mainstream_shelx_weighting())
self.cycles = self.normal_eqns_solving_method(ls)
print("%i %s iterations to recover from shaking" %
(self.cycles.n_iterations, self.cycles))
delta_fp = flex.double([
sc.fp - sc0.fp
for sc, sc0 in zip(xs.scatterers(), xs0.scatterers())
])
delta_fdp = flex.double([
sc.fdp - sc0.fdp
for sc, sc0 in zip(xs.scatterers(), xs0.scatterers())
])
assert flex.max_absolute(delta_fp) < self.fp_refinement_tolerance,\
self.__class__.__name__
assert flex.max_absolute(delta_fdp) < self.fdp_refinement_tolerance,\
self.__class__.__name__
def check_refinement_stability(self):
if not self.shall_refine_thermal_displacements:
for sc in self.xray_structure.scatterers():
sc.flags.set_grad_site(True)
if sc.flags.use_u_aniso(): sc.flags.set_grad_u_aniso(False)
if sc.flags.use_u_iso(): sc.flags.set_grad_u_iso(False)
xs = self.xray_structure
xs0 = self.reference_xray_structure = xs.deep_copy_scatterers()
mi = xs0.build_miller_set(anomalous_flag=False, d_min=0.5)
fo_sq = mi.structure_factors_from_scatterers(
xs0, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
xs.shake_sites_in_place(rms_difference=0.1)
if self.shall_refine_thermal_displacements:
# a spread of 10 for u_iso's would be enormous for our low temperature
# test structures if those u_iso's were not constrained
xs.shake_adp(
spread=10, # absolute
aniso_spread=0.2) # relative
self.reparametrisation = constraints.reparametrisation(
xs,
self.constraints,
self.connectivity_table,
temperature=self.t_celsius)
obs = fo_sq.as_xray_observations()
ls = least_squares.crystallographic_ls(
obs,
self.reparametrisation,
weighting_scheme=least_squares.mainstream_shelx_weighting())
self.cycles = self.normal_eqns_solving_method(ls)
print("%i %s iterations to recover from shaking" %
(self.cycles.n_iterations, self.cycles))
if 0:
from crys3d.qttbx.xray_structure_viewer import display
display(xray_structure=xs)
diff = xray.meaningful_site_cart_differences(xs0, xs)
assert diff.max_absolute() < self.site_refinement_tolerance,\
self.__class__.__name__
if self.shall_refine_thermal_displacements:
delta_u = []
for sc, sc0 in itertools.izip(xs.scatterers(), xs0.scatterers()):
if not sc.flags.use_u_aniso() or not sc0.flags.use_u_aniso():
continue
delta_u.extend(matrix.col(sc.u_star) - matrix.col(sc0.u_star))
delta_u = flex.double(delta_u)
assert flex.max_absolute(delta_u) < self.u_star_refinement_tolerance,\
self.__class__.__name__
def check_refinement_stability(self):
if not self.shall_refine_thermal_displacements:
for sc in self.xray_structure.scatterers():
sc.flags.set_grad_site(True)
if sc.flags.use_u_aniso(): sc.flags.set_grad_u_aniso(False)
if sc.flags.use_u_iso(): sc.flags.set_grad_u_iso(False)
xs = self.xray_structure
xs0 = self.reference_xray_structure = xs.deep_copy_scatterers()
mi = xs0.build_miller_set(anomalous_flag=False, d_min=0.5)
fo_sq = mi.structure_factors_from_scatterers(
xs0, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
xs.shake_sites_in_place(rms_difference=0.1)
if self.shall_refine_thermal_displacements:
# a spread of 10 for u_iso's would be enormous for our low temperature
# test structures if those u_iso's were not constrained
xs.shake_adp(spread=10, # absolute
aniso_spread=0.2) # relative
self.reparametrisation = constraints.reparametrisation(
xs, self.constraints, self.connectivity_table,
temperature=self.t_celsius)
obs = fo_sq.as_xray_observations()
ls = least_squares.crystallographic_ls(
obs,
self.reparametrisation,
weighting_scheme=least_squares.mainstream_shelx_weighting())
self.cycles = self.normal_eqns_solving_method(ls)
print ("%i %s iterations to recover from shaking"
% (self.cycles.n_iterations,
self.cycles))
if 0:
from crys3d.qttbx.xray_structure_viewer import display
display(xray_structure=xs)
diff = xray.meaningful_site_cart_differences(xs0, xs)
assert diff.max_absolute() < self.site_refinement_tolerance,\
self.__class__.__name__
if self.shall_refine_thermal_displacements:
delta_u = []
for sc, sc0 in itertools.izip(xs.scatterers(), xs0.scatterers()):
if not sc.flags.use_u_aniso() or not sc0.flags.use_u_aniso(): continue
delta_u.extend(matrix.col(sc.u_star) - matrix.col(sc0.u_star))
delta_u = flex.double(delta_u)
assert flex.max_absolute(delta_u) < self.u_star_refinement_tolerance,\
self.__class__.__name__
def bond_similarity_as_cif_loops(xray_structure, proxies):
space_group_info = sgtbx.space_group_info(
group=xray_structure.space_group())
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_equal_distance_atom_site_label_1",
"_restr_equal_distance_atom_site_label_2",
"_restr_equal_distance_site_symmetry_2",
"_restr_equal_distance_class_id",
))
class_loop = model.loop(header=(
"_restr_equal_distance_class_class_id",
"_restr_equal_distance_class_target_weight_param",
"_restr_equal_distance_class_average",
"_restr_equal_distance_class_esd",
"_restr_equal_distance_class_diff_max",
))
class_id = 0
for proxy in proxies:
restraint = geometry_restraints.bond_similarity(unit_cell=unit_cell,
sites_cart=sites_cart,
proxy=proxy)
class_id += 1
esd = math.sqrt(
flex.sum(flex.pow2(restraint.deltas())) *
(1. / proxy.i_seqs.size()))
class_loop.add_row((
class_id,
fmt % math.sqrt(1 / proxy.weights[0]), # assume equal weights
fmt % restraint.mean_distance(),
fmt % esd,
fmt % flex.max_absolute(restraint.deltas())))
for i in range(proxy.i_seqs.size()):
i_seq, j_seq = proxy.i_seqs[i]
if proxy.sym_ops is None:
sym_op = sgtbx.rt_mx()
else:
sym_op = proxy.sym_ops[i]
loop.add_row(
(site_labels[i_seq], site_labels[j_seq],
space_group_info.cif_symmetry_code(sym_op), class_id))
return class_loop, loop
def bond_similarity_as_cif_loops(xray_structure, proxies):
space_group_info = sgtbx.space_group_info(group=xray_structure.space_group())
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_equal_distance_atom_site_label_1",
"_restr_equal_distance_atom_site_label_2",
"_restr_equal_distance_site_symmetry_2",
"_restr_equal_distance_class_id",
))
class_loop = model.loop(header=(
"_restr_equal_distance_class_class_id",
"_restr_equal_distance_class_target_weight_param",
"_restr_equal_distance_class_average",
"_restr_equal_distance_class_esd",
"_restr_equal_distance_class_diff_max",
))
class_id = 0
for proxy in proxies:
restraint = geometry_restraints.bond_similarity(
unit_cell=unit_cell,
sites_cart=sites_cart,
proxy=proxy)
class_id += 1
esd = math.sqrt(flex.sum(flex.pow2(restraint.deltas())) *
(1./proxy.i_seqs.size()))
class_loop.add_row((class_id,
fmt % math.sqrt(1/proxy.weights[0]),# assume equal weights
fmt % restraint.mean_distance(),
fmt % esd,
fmt % flex.max_absolute(restraint.deltas())))
for i in range(proxy.i_seqs.size()):
i_seq, j_seq = proxy.i_seqs[i]
if proxy.sym_ops is None:
sym_op = sgtbx.rt_mx()
else:
sym_op = proxy.sym_ops[i]
loop.add_row((site_labels[i_seq],
site_labels[j_seq],
space_group_info.cif_symmetry_code(sym_op),
class_id))
return class_loop, loop
def adp_volume_similarity_as_cif_loops(xray_structure, proxies):
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4e"
loop = model.loop(header=(
"_restr_U_volume_similar_atom_site_label_1",
"_restr_U_volume_similar_diff",
"_restr_U_volume_similar_class_id",
))
class_loop = model.loop(header=(
"_restr_U_volume_similar_class_class_id",
"_restr_U_volume_similar_class_target_weight_param",
"_restr_U_volume_similar_class_average",
"_restr_U_volume_similar_class_esd",
"_restr_U_volume_similar_class_diff_max",
))
unit_cell = xray_structure.unit_cell()
params = adp_restraints.adp_restraint_params(
u_cart=xray_structure.scatterers().extract_u_cart(unit_cell),
u_iso=xray_structure.scatterers().extract_u_iso(),
use_u_aniso=xray_structure.use_u_aniso()
)
class_id = 0
for proxy in proxies:
restraint = adp_restraints.adp_volume_similarity(
params=params,
proxy=proxy)
class_id += 1
class_loop.add_row((class_id,
fmt % math.sqrt(1/proxy.weight),
fmt % restraint.mean_u_volume,
fmt % restraint.rms_deltas(),
fmt % flex.max_absolute(restraint.deltas())))
for i, i_seq in enumerate(proxy.i_seqs):
loop.add_row((site_labels[i_seq],
fmt % restraint.deltas()[i],
class_id))
return class_loop, loop