def find_candidate_orientation_matrices(self, candidate_basis_vectors):
candidate_crystal_models = combinations.candidate_orientation_matrices(
candidate_basis_vectors,
max_combinations=self.params.basis_vector_combinations.max_combinations,
)
if self._symmetry_handler.target_symmetry_reference_setting is not None:
target_symmetry = self._symmetry_handler.target_symmetry_reference_setting
elif self._symmetry_handler.target_symmetry_primitive is not None:
target_symmetry = self._symmetry_handler.target_symmetry_primitive
else:
target_symmetry = None
if target_symmetry is not None:
candidate_crystal_models = combinations.filter_known_symmetry(
candidate_crystal_models,
target_symmetry,
relative_length_tolerance=self.params.known_symmetry.relative_length_tolerance,
absolute_angle_tolerance=self.params.known_symmetry.absolute_angle_tolerance,
max_delta=self.params.known_symmetry.max_delta,
)
if self.refined_experiments is not None and len(self.refined_experiments) > 0:
candidate_crystal_models = combinations.filter_similar_orientations(
candidate_crystal_models,
self.refined_experiments.crystals(),
minimum_angular_separation=self.params.multiple_lattice_search.minimum_angular_separation,
)
return candidate_crystal_models
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())
subgroups = metric_subgroups(model.get_crystal_symmetry(),
max_delta=5,
bravais_types_only=False)
assert target_sg.build_derived_patterson_group() in [
g["ref_subsym"].space_group()
for g in subgroups.result_groups
]
def test_filter_known_symmetry_no_matches(caplog):
caplog.set_level(logging.DEBUG)
unit_cell = uctbx.unit_cell((10, 10, 10, 90, 90, 90))
crystal_models = []
# the reciprocal matrix
B = scitbx.matrix.sqr(unit_cell.fractionalization_matrix()).transpose()
for _ in range(10):
crystal_models.append(
Crystal(B, space_group=sgtbx.space_group(), reciprocal=True))
target_symmetry = crystal.symmetry(unit_cell=(15, 15, 15, 85, 85, 85),
space_group=sgtbx.space_group())
list(
combinations.filter_known_symmetry(crystal_models,
target_symmetry=target_symmetry))
assert "Rejecting crystal model inconsistent with input symmetry" in caplog.text
assert ("No crystal models remaining after comparing with known symmetry"
in caplog.text)
