def test_symmetry_handler_c2_i2(crystal_symmetry):
cs_ref = crystal_symmetry.as_reference_setting()
cs_ref = cs_ref.change_basis(
cs_ref.change_of_basis_op_to_best_cell(best_monoclinic_beta=False)
)
cs_best = cs_ref.best_cell()
# best -> ref is different to cs_ref above
cs_best_ref = cs_best.as_reference_setting()
assert not cs_ref.is_similar_symmetry(cs_best_ref)
B = scitbx.matrix.sqr(
crystal_symmetry.unit_cell().fractionalization_matrix()
).transpose()
cryst = Crystal(B, sgtbx.space_group())
for cs in (crystal_symmetry, cs_ref, cs_best):
print(cs)
handler = symmetry.SymmetryHandler(space_group=cs.space_group())
new_cryst, cb_op = handler.apply_symmetry(cryst)
assert (
new_cryst.change_basis(cb_op).get_crystal_symmetry().is_similar_symmetry(cs)
)
for cs in (crystal_symmetry, cs_ref, cs_best, cs_best_ref):
print(cs)
handler = symmetry.SymmetryHandler(
unit_cell=cs.unit_cell(), space_group=cs.space_group()
)
new_cryst, cb_op = handler.apply_symmetry(cryst)
assert (
new_cryst.change_basis(cb_op).get_crystal_symmetry().is_similar_symmetry(cs)
)
def test_SymmetryHandler(space_group_symbol):
sgi = sgtbx.space_group_info(symbol=space_group_symbol)
sg = sgi.group()
cs = sgi.any_compatible_crystal_symmetry(volume=10000)
uc = cs.unit_cell()
handler = symmetry.SymmetryHandler(unit_cell=uc, space_group=sg)
assert (handler.target_symmetry_primitive.space_group() == sg.
build_derived_patterson_group().info().primitive_setting().group())
assert (handler.target_symmetry_reference_setting.space_group() == sg.
build_derived_patterson_group().info().reference_setting().group())
# test apply_symmetry on the primitive setting
cs_primitive = cs.primitive_setting()
B = scitbx.matrix.sqr(
cs_primitive.unit_cell().fractionalization_matrix()).transpose()
crystal = Crystal(B, sgtbx.space_group())
crystal_new, cb_op = handler.apply_symmetry(crystal)
crystal_new.get_crystal_symmetry(assert_is_compatible_unit_cell=True)
# test apply_symmetry on the minimum cell setting
cs_min_cell = cs.minimum_cell()
B = scitbx.matrix.sqr(
cs_min_cell.unit_cell().fractionalization_matrix()).transpose()
crystal = Crystal(B, sgtbx.space_group())
crystal_new, cb_op = handler.apply_symmetry(crystal)
crystal_new.get_crystal_symmetry(assert_is_compatible_unit_cell=True)
handler = symmetry.SymmetryHandler(space_group=sg)
assert handler.target_symmetry_primitive.unit_cell() is None
assert (handler.target_symmetry_primitive.space_group() == sg.
build_derived_patterson_group().info().primitive_setting().group())
assert handler.target_symmetry_reference_setting.unit_cell() is None
assert (handler.target_symmetry_reference_setting.space_group() == sg.
build_derived_patterson_group().info().reference_setting().group())
# test apply_symmetry on the primitive setting
cs_primitive = cs.primitive_setting()
B = scitbx.matrix.sqr(
cs_primitive.unit_cell().fractionalization_matrix()).transpose()
crystal = Crystal(B, sgtbx.space_group())
crystal_new, cb_op = handler.apply_symmetry(crystal)
crystal_new.get_crystal_symmetry(assert_is_compatible_unit_cell=True)
handler = symmetry.SymmetryHandler(
unit_cell=cs.minimum_cell().unit_cell(),
space_group=sgtbx.space_group(),
)
assert handler.target_symmetry_primitive.unit_cell().parameters(
) == pytest.approx(cs.minimum_cell().unit_cell().parameters())
assert handler.target_symmetry_primitive.space_group(
) == sgtbx.space_group("P-1")
assert (handler.target_symmetry_reference_setting.unit_cell().parameters()
== pytest.approx(cs.minimum_cell().unit_cell().parameters()))
assert handler.target_symmetry_reference_setting.space_group(
) == sgtbx.space_group("P-1")
def test_SymmetryHandler_no_match():
sgi = sgtbx.space_group_info(symbol="P422")
cs = sgi.any_compatible_crystal_symmetry(volume=10000)
B = scitbx.matrix.sqr(cs.unit_cell().fractionalization_matrix()).transpose()
crystal = Crystal(B, sgtbx.space_group())
handler = symmetry.SymmetryHandler(
unit_cell=None, space_group=sgtbx.space_group_info("I23").group()
)
assert handler.apply_symmetry(crystal) == (None, None)