def test_change_of_basis_ops_to_minimum_cell_mpro():
input_ucs = [
(46.023, 55.001, 64.452, 64.744, 78.659, 89.824),
(44.747, 53.916, 62.554, 114.985, 99.610, 90.736),
]
# Setup the input experiments and reflection tables
expts = ExperimentList()
for uc in input_ucs:
uc = uctbx.unit_cell(uc)
sg = sgtbx.space_group_info("P1").group()
B = scitbx.matrix.sqr(uc.fractionalization_matrix()).transpose()
expts.append(
Experiment(crystal=Crystal(B, space_group=sg, reciprocal=True)))
# Actually run the method we are testing
cb_ops = change_of_basis_ops_to_minimum_cell(
expts,
max_delta=5,
relative_length_tolerance=0.05,
absolute_angle_tolerance=2)
expts.change_basis(cb_ops, in_place=True)
assert symmetry.unit_cells_are_similar_to(
expts,
median_unit_cell(expts),
relative_length_tolerance=0.05,
absolute_angle_tolerance=2,
)
def test_experimentlist_change_basis(dials_data):
experiments = ExperimentList()
for i in range(4):
experiments.extend(
ExperimentList.from_file(
dials_data("vmxi_proteinase_k_sweeps") /
("experiments_%i.expt" % i),
check_format=False,
))
reindexed_uc = (68.368, 103.968, 68.368, 90.000, 90.000, 90.000)
reindexed_sg = sgtbx.space_group_info("P 4 2 2 (b,c,a)").group()
cb_op = sgtbx.change_of_basis_op("-a,-c,-b")
for cb_op in (cb_op, [cb_op] * len(experiments)):
expts_rdx = experiments.change_basis(cb_op)
for expt in expts_rdx:
assert expt.crystal.get_unit_cell().parameters() == pytest.approx(
reindexed_uc, abs=0.1)
assert expt.crystal.get_space_group() == reindexed_sg
experiments.change_basis(cb_op, in_place=True)
for expt in experiments:
assert expt.crystal.get_unit_cell().parameters() == pytest.approx(
reindexed_uc, abs=0.1)
assert expt.crystal.get_space_group() == reindexed_sg
with pytest.raises(AssertionError):
experiments.change_basis([cb_op, cb_op])
def test_change_of_basis_ops_to_minimum_cell_with_outlier():
symmetries = [
crystal.symmetry(unit_cell=uc, space_group="P1") for uc in (
(52.8868, 52.8868, 333.522, 90, 90, 120),
(52.6503, 53.0292, 333.783, 89.9872, 89.2247, 60.8078),
(52.9571, 53.0005, 334.255, 90.0493, 90.0042, 119.893),
(
54.4465,
56.5677,
355.775,
93.4376,
90.0999,
118.256,
), # This is an outlier
(52.9235, 52.9235, 335.296, 90, 90, 120),
(53.4531, 53.4531, 322.909, 90, 90, 120),
)
]
# Setup the input experiments and reflection tables
expts = ExperimentList()
for cs in symmetries:
B = scitbx.matrix.sqr(
cs.unit_cell().fractionalization_matrix()).transpose()
expts.append(
Experiment(crystal=Crystal(
B, space_group=cs.space_group(), reciprocal=True)))
# Actually run the method we are testing
cb_ops = change_of_basis_ops_to_minimum_cell(
expts,
max_delta=5,
relative_length_tolerance=0.05,
absolute_angle_tolerance=2)
assert cb_ops.count(None) == 1
assert cb_ops[3] is None
expts = ExperimentList(
[expt for expt, cb_op in zip(expts, cb_ops) if cb_op])
cb_ops = [cb_op for cb_op in cb_ops if cb_op]
expts.change_basis(cb_ops, in_place=True)
assert symmetry.unit_cells_are_similar_to(
expts,
median_unit_cell(expts),
relative_length_tolerance=0.05,
absolute_angle_tolerance=2,
)
