def _map_space_group_to_input_cell(intensities, space_group):
best_subgroup = find_matching_symmetry(intensities.unit_cell(),
space_group)
cb_op_inp_best = best_subgroup["cb_op_inp_best"]
best_subsym = best_subgroup["best_subsym"]
cb_op_best_ref = best_subsym.change_of_basis_op_to_reference_setting(
)
ref_subsym = best_subsym.change_basis(cb_op_best_ref)
cb_op_ref_primitive = (
ref_subsym.change_of_basis_op_to_primitive_setting())
sg_cb_op_inp_primitive = (space_group.info(
).change_of_basis_op_to_primitive_setting())
sg_primitive = space_group.change_basis(sg_cb_op_inp_primitive)
sg_best = sg_primitive.change_basis(
(cb_op_ref_primitive * cb_op_best_ref).inverse())
# best_subgroup above is the bravais type, so create thin copy here with the
# user-input space group instead
best_subgroup = {
"best_subsym":
best_subsym.customized_copy(
space_group_info=sg_best.info()),
"cb_op_inp_best":
cb_op_inp_best,
}
intensities = intensities.customized_copy(
space_group_info=sg_best.change_basis(
cb_op_inp_best.inverse()).info())
return intensities, best_subgroup
def _map_space_group_to_input_cell(intensities, space_group):
from cctbx.sgtbx.bravais_types import bravais_lattice
best_subgroup = find_matching_symmetry(
intensities.unit_cell(),
space_group,
best_monoclinic_beta=str(
bravais_lattice(group=space_group)) == "mI",
)
cb_op_inp_best = best_subgroup["cb_op_inp_best"]
best_subsym = best_subgroup["best_subsym"]
cb_op_best_primitive = (
best_subsym.change_of_basis_op_to_primitive_setting())
sg_cb_op_inp_primitive = (space_group.info(
).change_of_basis_op_to_primitive_setting())
sg_primitive = space_group.change_basis(sg_cb_op_inp_primitive)
sg_best = sg_primitive.change_basis(
cb_op_best_primitive.inverse())
# best_subgroup above is the bravais type, so create thin copy here with the
# user-input space group instead
best_subsym = best_subsym.customized_copy(
space_group_info=sg_best.info())
best_subgroup = {
"subsym":
best_subsym.change_basis(cb_op_inp_best.inverse()),
"best_subsym": best_subsym,
"cb_op_inp_best": cb_op_inp_best,
}
intensities = intensities.customized_copy(
space_group_info=sg_best.change_basis(
cb_op_inp_best.inverse()).info())
return intensities, best_subgroup
def test_combinations(setup_rlp):
max_cell = 1.3 * max(
setup_rlp["crystal_symmetry"].unit_cell().parameters()[:3])
strategy = FFT1D(max_cell)
basis_vectors, used = strategy.find_basis_vectors(setup_rlp["rlp"])
target_symmetry_primitive = (
setup_rlp["crystal_symmetry"].primitive_setting().customized_copy(
space_group_info=sgtbx.space_group().info()))
target_symmetry_sg_only = (
setup_rlp["crystal_symmetry"].primitive_setting().customized_copy(
unit_cell=None))
target_symmetry_ref = setup_rlp["crystal_symmetry"].as_reference_setting()
for target_symmetry in (
setup_rlp["crystal_symmetry"],
target_symmetry_primitive,
target_symmetry_sg_only,
target_symmetry_ref,
):
crystal_models = combinations.candidate_orientation_matrices(
basis_vectors, max_combinations=50)
crystal_models = list(crystal_models)
filtered_crystal_models = combinations.filter_known_symmetry(
crystal_models, target_symmetry=target_symmetry)
filtered_crystal_models = list(filtered_crystal_models)
assert filtered_crystal_models
for model in filtered_crystal_models:
best_subgroup = find_matching_symmetry(
model.get_unit_cell(), target_symmetry.space_group())
if target_symmetry.unit_cell() is not None:
assert best_subgroup["best_subsym"].unit_cell().is_similar_to(
setup_rlp["crystal_symmetry"].as_reference_setting().
best_cell().unit_cell(),
relative_length_tolerance=0.1,
absolute_angle_tolerance=5,
) or best_subgroup["best_subsym"].minimum_cell().unit_cell(
).is_similar_to(
setup_rlp["crystal_symmetry"].as_reference_setting().
best_cell().minimum_cell().unit_cell(),
relative_length_tolerance=0.1,
absolute_angle_tolerance=5,
)
else:
target_sg = (target_symmetry.space_group_info().
reference_setting().group())
from cctbx.sgtbx.lattice_symmetry import metric_subgroups
subgroups = metric_subgroups(model.get_crystal_symmetry(),
max_delta=5,
bravais_types_only=False)
if not target_sg.build_derived_patterson_group() in [
g["ref_subsym"].space_group()
for g in subgroups.result_groups
]:
assert 0
def filter_known_symmetry(
crystal_models,
target_symmetry,
relative_length_tolerance=0.1,
absolute_angle_tolerance=5,
max_delta=5,
):
"""Filter crystal models for known symmetry.
Args:
crystal_models (list): A list of :class:`dxtbx.model.Crystal` objects.
target_symmetry (cctbx.crystal.symmetry): The target symmetry for filtering.
relative_length_tolerance (float): Relative tolerance for unit cell lengths in
unit cell comparison (default value is 0.1).
absolute_angle_tolerance (float): Angular tolerance (in degrees) in unit cell
comparison (default value is 5).
max_delta (float): Maximum allowed Le Page delta used in searching for basis
vector combinations that are consistent with the given symmetry (default
value is 5).
"""
n_matched = 0
cb_op_ref_to_primitive = target_symmetry.change_of_basis_op_to_primitive_setting(
)
if target_symmetry.unit_cell() is not None:
target_symmetry_primitive = target_symmetry.change_basis(
cb_op_ref_to_primitive)
else:
target_symmetry_primitive = target_symmetry.customized_copy(
space_group_info=target_symmetry.space_group_info().change_basis(
cb_op_ref_to_primitive))
for model in crystal_models:
uc = model.get_unit_cell()
best_subgroup = find_matching_symmetry(
uc, target_symmetry_primitive.space_group(), max_delta=max_delta)
if best_subgroup is not None:
if target_symmetry.unit_cell() is not None and not (
best_subgroup["best_subsym"].unit_cell().is_similar_to(
target_symmetry.as_reference_setting().best_cell().
unit_cell(),
relative_length_tolerance=relative_length_tolerance,
absolute_angle_tolerance=absolute_angle_tolerance,
)):
logger.debug(
"Rejecting crystal model inconsistent with input symmetry:\n"
f" Unit cell: {str(model.get_unit_cell())}")
continue
n_matched += 1
yield model
if not n_matched:
logger.warning(
"No crystal models remaining after comparing with known symmetry")
def test_find_matching_symmetry(crystal_symmetry):
cs = crystal_symmetry
cs.show_summary()
for op in ("x,y,z", "z,x,y", "y,z,x", "-x,z,y", "y,x,-z", "z,-y,x")[:]:
cb_op = sgtbx.change_of_basis_op(op)
uc_inp = cs.unit_cell().change_basis(cb_op)
for ref_uc, ref_sg in [
(cs.unit_cell(), cs.space_group()),
(None, cs.space_group()),
][:]:
best_subgroup = symmetry.find_matching_symmetry(
uc_inp, target_space_group=ref_sg)
cb_op_inp_best = best_subgroup["cb_op_inp_best"]
assert uc_inp.change_basis(cb_op_inp_best).is_similar_to(
cs.as_reference_setting().best_cell().unit_cell())
def run_once(crystal_symmetry):
cs = crystal_symmetry
#print
cs.show_summary()
from cctbx.sgtbx import lattice_symmetry
subgroups = lattice_symmetry.metric_subgroups(cs, max_delta=5)
for op in ('x,y,z', 'z,x,y', 'y,z,x', '-x,z,y', 'y,x,-z', 'z,-y,x')[:]:
cb_op = sgtbx.change_of_basis_op(op)
uc_inp = cs.unit_cell().change_basis(cb_op)
for ref_uc, ref_sg in [(cs.unit_cell(), cs.space_group()),
(None, cs.space_group())][:]:
best_subgroup = symmetry.find_matching_symmetry(
uc_inp, target_space_group=ref_sg)
cb_op_inp_best = best_subgroup['cb_op_inp_best']
assert uc_inp.change_basis(cb_op_inp_best).is_similar_to(
cs.as_reference_setting().best_cell().unit_cell())
def run_once(crystal_symmetry):
cs = crystal_symmetry
#print
cs.show_summary()
from cctbx.sgtbx import lattice_symmetry
subgroups = lattice_symmetry.metric_subgroups(cs, max_delta=5)
for op in ('x,y,z', 'z,x,y', 'y,z,x', '-x,z,y', 'y,x,-z', 'z,-y,x')[:]:
cb_op = sgtbx.change_of_basis_op(op)
uc_inp = cs.unit_cell().change_basis(cb_op)
for ref_uc, ref_sg in [(cs.unit_cell(), cs.space_group()),
(None, cs.space_group())][:]:
best_subgroup = symmetry.find_matching_symmetry(
uc_inp,
target_space_group=ref_sg)
cb_op_inp_best = best_subgroup['cb_op_inp_best']
assert uc_inp.change_basis(cb_op_inp_best).is_similar_to(
cs.as_reference_setting().best_cell().unit_cell())
def filter_known_symmetry(
crystal_models,
target_symmetry,
relative_length_tolerance=0.1,
absolute_angle_tolerance=5,
max_delta=5,
):
"""Filter crystal models for known symmetry.
Args:
crystal_models (list): A list of :class:`dxtbx.model.Crystal` objects.
target_symmetry (cctbx.crystal.symmetry): The target symmetry for filtering.
relative_length_tolerance (float): Relative tolerance for unit cell lengths in
unit cell comparision (default value is 0.1).
absolute_angle_tolerance (float): Angular tolerance (in degrees) in unit cell
comparison (default value is 5).
max_delta (float): Maximum allowed Le Page delta used in searching for basis
vector combinations that are consistent with the given symmetry (default
value is 5).
"""
cb_op_ref_to_primitive = target_symmetry.change_of_basis_op_to_primitive_setting(
)
if target_symmetry.unit_cell() is not None:
target_symmetry_primitive = target_symmetry.change_basis(
cb_op_ref_to_primitive)
target_min_cell = target_symmetry_primitive.minimum_cell().unit_cell()
else:
target_symmetry_primitive = target_symmetry.customized_copy(
space_group_info=target_symmetry.space_group_info().change_basis(
cb_op_ref_to_primitive))
target_min_cell = None
transformations = [sgtbx.change_of_basis_op()]
for model in crystal_models:
best_model = None
for T in transformations:
uc = model.get_unit_cell()
det = T.c().r().determinant()
if target_symmetry_primitive.unit_cell() is None:
if det > 1:
break
else:
primitive_volume = target_symmetry_primitive.unit_cell(
).volume()
if det > 1 and abs(uc.volume() / primitive_volume - det) < 1e-1:
uc = uc.change_basis(T)
best_subgroup = find_matching_symmetry(
uc,
target_symmetry_primitive.space_group(),
max_delta=max_delta)
cb_op_extra = None
if best_subgroup is None:
if not cb_op_ref_to_primitive.is_identity_op():
# if we have been told we have a centred unit cell check that
# indexing hasn't found the centred unit cell instead of the
# primitive cell
best_subgroup = find_matching_symmetry(
uc,
target_symmetry.space_group().
build_derived_point_group(),
max_delta=max_delta,
)
cb_op_extra = cb_op_ref_to_primitive
if best_subgroup is None:
continue
else:
continue
cb_op_inp_best = best_subgroup["cb_op_inp_best"]
best_subsym = best_subgroup["best_subsym"]
cb_op_best_ref = best_subsym.change_of_basis_op_to_reference_setting(
)
ref_subsym = best_subsym.change_basis(cb_op_best_ref)
cb_op_ref_primitive = ref_subsym.change_of_basis_op_to_primitive_setting(
)
cb_op_to_primitive = (cb_op_ref_primitive * cb_op_best_ref *
cb_op_inp_best * T)
if cb_op_extra is not None:
cb_op_to_primitive = cb_op_extra * cb_op_to_primitive
best_model = model.change_basis(cb_op_to_primitive)
if target_symmetry_primitive.unit_cell(
) is not None and not (best_model.get_unit_cell().is_similar_to(
target_symmetry_primitive.unit_cell(),
relative_length_tolerance=relative_length_tolerance,
absolute_angle_tolerance=absolute_angle_tolerance,
) or best_model.get_unit_cell().minimum_cell().is_similar_to(
target_min_cell,
relative_length_tolerance=relative_length_tolerance,
absolute_angle_tolerance=absolute_angle_tolerance,
)):
best_model = None
continue
else:
break
if best_model is not None:
yield best_model
