def test_refine_bravais_settings_trypsin(dials_regression, tmpdir):
data_dir = os.path.join(dials_regression, "indexing_test_data", "trypsin")
pickle_path = os.path.join(data_dir, "indexed.pickle")
experiments_path = os.path.join(data_dir, "experiments.json")
with tmpdir.as_cwd():
refine_bravais_settings.run(
[pickle_path, experiments_path, "crystal_id=1"])
for i in range(1, 10):
assert tmpdir.join("bravais_setting_%i.expt" % i).check()
experiments_list = load.experiment_list(
tmpdir.join("bravais_setting_5.expt").strpath, check_format=False)
assert len(experiments_list) == 1
assert (experiments_list[0].crystal.get_unit_cell().is_similar_to(
uctbx.unit_cell((54.37, 58.29, 66.51, 90.00, 90.00, 90.00))))
assert (experiments_list[0].crystal.get_space_group().type().hall_symbol()
== " P 2 2")
assert tmpdir.join("bravais_summary.json").check()
with tmpdir.join("bravais_summary.json").open("rb") as fh:
bravais_summary = json.load(fh)
assert set(bravais_summary) == {
"1", "2", "3", "4", "5", "6", "7", "8", "9"
}
assert bravais_summary["5"]["unit_cell"] == pytest.approx(
[54.37, 58.29, 66.51, 90.00, 90.00, 90.00], abs=1e-1)
assert bravais_summary["5"]["bravais"] == "oP"
assert bravais_summary["5"]["rmsd"] == pytest.approx(0.1200, abs=1e-2)
assert bravais_summary["5"]["recommended"] is True
assert bravais_summary["9"]["recommended"] is False
def test_refine_bravais_settings_multi_sweep(dials_regression, tmpdir):
data_dir = os.path.join(dials_regression, "indexing_test_data",
"multi_sweep")
pickle_path = os.path.join(data_dir, "indexed.pickle")
experiments_path = os.path.join(data_dir, "experiments.json")
with tmpdir.as_cwd():
refine_bravais_settings.run([pickle_path, experiments_path])
for i in range(1, 10):
assert tmpdir.join("bravais_setting_%i.expt" % i).check()
experiments_list = load.experiment_list(
tmpdir.join("bravais_setting_9.expt").strpath, check_format=False)
assert len(experiments_list) == 4
assert len(experiments_list.crystals()) == 1
assert (experiments_list[0].crystal.get_unit_cell().is_similar_to(
uctbx.unit_cell((7.31, 7.31, 6.82, 90.00, 90.00, 90.00))))
assert experiments_list[0].crystal.get_space_group().type().hall_symbol(
) == " I 4"
assert tmpdir.join("bravais_summary.json").check()
with tmpdir.join("bravais_summary.json").open("rb") as fh:
bravais_summary = json.load(fh)
for i in range(1, 23):
assert str(i) in bravais_summary
assert bravais_summary["9"]["unit_cell"] == pytest.approx(
[7.31, 7.31, 6.82, 90.00, 90.00, 90.00], abs=1e-1)
assert bravais_summary["9"]["bravais"] == "tI"
assert bravais_summary["9"]["rmsd"] == pytest.approx(0.103, abs=1e-2)
assert bravais_summary["9"]["recommended"] is True
def test_setting_c2_vs_i2(
best_monoclinic_beta,
expected_space_group,
expected_unit_cell,
dials_data,
tmpdir,
capsys,
):
data_dir = dials_data("mpro_x0305_processed")
refl_path = data_dir.join("indexed.refl")
experiments_path = data_dir.join("indexed.expt")
with tmpdir.as_cwd():
refine_bravais_settings.run([
experiments_path.strpath,
refl_path.strpath,
f"best_monoclinic_beta={best_monoclinic_beta}",
])
expts_orig = load.experiment_list(experiments_path.strpath,
check_format=False)
expts = load.experiment_list(tmpdir.join("bravais_setting_2.expt").strpath,
check_format=False)
expected_bravais_lattice = str(
sgtbx.bravais_types.bravais_lattice(symbol=expected_space_group))
expts[0].crystal.get_space_group().type().lookup_symbol(
) == expected_space_group
assert expts[0].crystal.get_unit_cell().parameters() == pytest.approx(
expected_unit_cell, abs=1e-2)
with tmpdir.join("bravais_summary.json").open("rb") as fh:
bravais_summary = json.load(fh)
assert bravais_summary["2"]["bravais"] == expected_bravais_lattice
# Verify that the cb_op converts from the input setting to the refined setting
cb_op = sgtbx.change_of_basis_op(str(bravais_summary["2"]["cb_op"]))
assert (expts_orig[0].crystal.change_basis(
cb_op).get_unit_cell().is_similar_to(
expts[0].crystal.get_unit_cell(),
relative_length_tolerance=0.1,
absolute_angle_tolerance=1,
))
captured = capsys.readouterr()
assert bravais_summary["2"]["cb_op"] in captured.out
assert f"| {expected_bravais_lattice} |" in captured.out
expected_short_name = refine_bravais_settings.short_space_group_name(
sgtbx.space_group_info(expected_space_group).group())
assert f"{expected_bravais_lattice}: {expected_short_name}" in captured.out
def test_refine_bravais_settings_i04_weak_data(dials_regression, tmpdir):
data_dir = os.path.join(dials_regression, "indexing_test_data", "i04_weak_data")
pickle_path = os.path.join(data_dir, "indexed.pickle")
experiments_path = os.path.join(data_dir, "experiments.json")
with tmpdir.as_cwd():
refine_bravais_settings.run(
[
pickle_path,
experiments_path,
"reflections_per_degree=5",
"minimum_sample_size=500",
"beam.fix=all",
"detector.fix=all",
"prefix=tst_",
]
)
for i in range(1, 10):
assert tmpdir.join("tst_bravais_setting_%i.expt" % i).check()
experiments_list = load.experiment_list(
tmpdir.join("tst_bravais_setting_9.expt").strpath, check_format=False
)
assert len(experiments_list) == 1
assert (
experiments_list[0]
.crystal.get_unit_cell()
.is_similar_to(uctbx.unit_cell((57.782, 57.782, 150.011, 90, 90, 90)))
)
assert experiments_list[0].crystal.get_space_group().type().hall_symbol() == " P 4"
assert tmpdir.join("tst_bravais_summary.json").check()
with tmpdir.join("tst_bravais_summary.json").open("rb") as fh:
bravais_summary = json.load(fh)
assert set(bravais_summary) == {"1", "2", "3", "4", "5", "6", "7", "8", "9"}
assert set(bravais_summary["9"]).issuperset(
{"bravais", "max_angular_difference", "unit_cell", "rmsd", "nspots"}
)
assert bravais_summary["9"]["unit_cell"] == pytest.approx(
[57.78, 57.78, 150.0, 90.0, 90.0, 90.0], abs=1e-1
)
assert bravais_summary["9"]["bravais"] == "tP"
assert bravais_summary["9"]["recommended"] is True
assert bravais_summary["9"]["rmsd"] == pytest.approx(0.047, abs=1e-2)
def test_refine_bravais_settings_554(dials_regression, tmpdir):
data_dir = os.path.join(dials_regression, "dials-554")
pickle_path = os.path.join(data_dir, "indexed.pickle")
experiments_path = os.path.join(data_dir, "experiments.json")
with tmpdir.as_cwd():
refine_bravais_settings.run([pickle_path, experiments_path])
for i in range(1, 5):
assert tmpdir.join("bravais_setting_%i.expt" % i).check()
experiments_list = load.experiment_list(
tmpdir.join("bravais_setting_5.expt").strpath, check_format=False
)
assert len(experiments_list) == 7
assert len(experiments_list.crystals()) == 1
crystal = experiments_list.crystals()[0]
assert crystal.get_unit_cell().is_similar_to(
uctbx.unit_cell((4.75863, 4.75863, 12.9885, 90, 90, 120))
)
assert crystal.get_space_group().type().hall_symbol() == " R 3"
# assert all of the detectors are different
for expt in experiments_list[1:]:
assert expt.detector != experiments_list[0].detector
for i in (0, 1, 6):
assert experiments_list[i].detector[0].get_origin() == pytest.approx(
(-41, 5.5, -135), abs=1
)
for i in (2, 3, 4, 5):
assert experiments_list[i].detector[0].get_origin() == pytest.approx(
(-41, 91, -99), abs=1
)
assert tmpdir.join("bravais_summary.json").check()
with tmpdir.join("bravais_summary.json").open("rb") as fh:
bravais_summary = json.load(fh)
for i in range(1, 5):
assert str(i) in bravais_summary
assert bravais_summary["5"]["unit_cell"] == pytest.approx(
[4.75863, 4.75863, 12.9885, 90, 90, 120], abs=1e-1
)
assert bravais_summary["5"]["bravais"] == "hR"
assert bravais_summary["5"]["rmsd"] == pytest.approx(0.104, abs=1e-2)
assert bravais_summary["5"]["recommended"] is True
