def test_symmetry_basis_changes_for_C2(tmpdir):
"""Test the correctness of change of basis operations in dials.symmetry
Supply the unit cell of beta-lactamase, which triggers a change of
basis from input to minimum during symmetry analysis."""
os.chdir(tmpdir.strpath)
unit_cell = (53.173, 61.245, 69.292, 90.0, 93.04675, 90.0)
space_group = sgtbx.space_group_info("C 2").group()
experiments, reflections, _ = generate_experiments_reflections(
space_group=space_group,
unit_cell=unit_cell,
sample_size=1,
map_to_minimum=False,
)
experiments.as_json("tmp.expt")
expt_file = tmpdir.join("tmp.expt").strpath
joint_table = flex.reflection_table()
for r in reflections:
joint_table.extend(r)
joint_table.as_pickle("tmp.refl")
refl_file = tmpdir.join("tmp.refl").strpath
command = ["dials.symmetry", expt_file, refl_file]
result = procrunner.run(command, working_directory=tmpdir.strpath)
assert not result.returncode and not result.stderr
assert tmpdir.join("symmetrized.refl").check(file=1)
assert tmpdir.join("symmetrized.expt").check(file=1)
expts = load.experiment_list(tmpdir.join("symmetrized.expt").strpath,
check_format=False)
for v, expected in zip(expts[0].crystal.get_unit_cell().parameters(),
unit_cell):
assert v == pytest.approx(expected)
def test_synthetic(
space_group,
unit_cell,
dimensions,
sample_size,
use_known_space_group,
use_known_lattice_group,
tmpdir,
):
os.chdir(tmpdir.strpath)
space_group = sgtbx.space_group_info(space_group).group()
if unit_cell is not None:
unit_cell = uctbx.unit_cell(unit_cell)
experiments, reflections, reindexing_ops = generate_experiments_reflections(
space_group=space_group,
unit_cell=unit_cell,
unit_cell_volume=10000,
sample_size=sample_size,
map_to_p1=True,
d_min=1.5,
)
params = phil_scope.extract()
if use_known_space_group:
params.space_group = space_group.info()
if use_known_lattice_group:
params.lattice_group = space_group.info()
if dimensions is not None:
params.dimensions = dimensions
experiments, reflections = assign_unique_identifiers(
experiments, reflections)
cosym_instance = cosym(experiments, reflections, params=params)
register_default_cosym_observers(cosym_instance)
cosym_instance.run()
cosym_instance.export()
assert os.path.exists(params.output.experiments)
assert os.path.exists(params.output.reflections)
assert os.path.exists(params.output.html)
assert os.path.exists(params.output.json)
cosym_expts = load.experiment_list(params.output.experiments,
check_format=False)
assert len(cosym_expts) == len(experiments)
for expt in cosym_expts:
if unit_cell is not None:
assert expt.crystal.get_unit_cell().parameters() == pytest.approx(
unit_cell.parameters())
assert str(expt.crystal.get_space_group().info()) == str(
space_group.info())
assert expt.crystal.get_space_group() == space_group
def test_symmetry_basis_changes_for_C2(tmpdir):
"""Test the correctness of change of basis operations in dials.symmetry
Supply the unit cell of beta-lactamase, which triggers a change of
basis from input to minimum during symmetry analysis."""
os.chdir(tmpdir.strpath)
unit_cell = (53.173, 61.245, 69.292, 90.0, 93.04675, 90.0)
space_group = sgtbx.space_group_info("C 2").group()
experiments, reflections, _ = generate_experiments_reflections(
space_group=space_group,
unit_cell=unit_cell,
sample_size=1,
map_to_minimum=False,
)
experiments.as_json("tmp.expt")
expt_file = tmpdir.join("tmp.expt").strpath
joint_table = flex.reflection_table()
for r in reflections:
joint_table.extend(r)
joint_table.as_file("tmp.refl")
refl_file = tmpdir.join("tmp.refl").strpath
command = ["dials.symmetry", expt_file, refl_file, "json=symmetry.json"]
result = procrunner.run(command, working_directory=tmpdir.strpath)
assert not result.returncode and not result.stderr
assert tmpdir.join("symmetrized.refl").check(file=1)
assert tmpdir.join("symmetrized.expt").check(file=1)
expts = load.experiment_list(tmpdir.join("symmetrized.expt").strpath,
check_format=False)
for v, expected in zip(expts[0].crystal.get_unit_cell().parameters(),
unit_cell):
assert v == pytest.approx(expected)
# Using the change of basis ops from the json output we should be able to
# reindex the input experiments to match the output experiments
with tmpdir.join("symmetry.json").open() as f:
d = json.load(f)
cs = experiments[0].crystal.get_crystal_symmetry()
cb_op_inp_min = sgtbx.change_of_basis_op(str(d["cb_op_inp_min"][0]))
cb_op_min_best = sgtbx.change_of_basis_op(
str(d["subgroup_scores"][0]["cb_op"]))
assert cs.change_basis(cb_op_min_best *
cb_op_inp_min).is_similar_symmetry(
expts[0].crystal.get_crystal_symmetry())
def test_synthetic(
space_group,
unit_cell,
dimensions,
sample_size,
use_known_space_group,
use_known_lattice_group,
tmpdir,
):
os.chdir(tmpdir.strpath)
space_group = sgtbx.space_group_info(space_group).group()
if unit_cell is not None:
unit_cell = uctbx.unit_cell(unit_cell)
experiments, reflections, _ = generate_experiments_reflections(
space_group=space_group,
unit_cell=unit_cell,
unit_cell_volume=10000,
sample_size=sample_size,
map_to_p1=True,
d_min=1.5,
)
experiments.as_json("tmp.expt")
expt_file = tmpdir.join("tmp.expt").strpath
joint_table = flex.reflection_table()
for r in reflections:
joint_table.extend(r)
joint_table.as_file("tmp.refl")
refl_file = tmpdir.join("tmp.refl").strpath
command = [
"dials.cosym",
expt_file,
refl_file,
"output.experiments=symmetrized.expt",
"output.reflections=symmetrized.refl",
"output.html=cosym.html",
"output.json=cosym.json",
]
if use_known_space_group:
command.append("space_group=%s" % space_group.info())
if use_known_lattice_group:
command.append("lattice_group=%s" % space_group.info())
if dimensions is not None:
command.append("dimensions=%s" % dimensions)
result = procrunner.run(command, working_directory=tmpdir.strpath)
assert not result.returncode and not result.stderr
assert tmpdir.join("symmetrized.refl").check(file=1)
assert tmpdir.join("symmetrized.expt").check(file=1)
assert tmpdir.join("cosym.html").check(file=1)
assert tmpdir.join("cosym.json").check(file=1)
"""experiments, reflections = assign_unique_identifiers(experiments, reflections)
cosym_instance = cosym(experiments, reflections, params=params)
register_default_cosym_observers(cosym_instance)
cosym_instance.run()
cosym_instance.export()
assert os.path.exists(params.output.experiments)
assert os.path.exists(params.output.reflections)
assert os.path.exists(params.output.html)
assert os.path.exists(params.output.json)"""
cosym_expts = load.experiment_list(tmpdir.join("symmetrized.expt").strpath,
check_format=False)
assert len(cosym_expts) == len(experiments)
for expt in cosym_expts:
if unit_cell is not None:
assert expt.crystal.get_unit_cell().parameters() == pytest.approx(
unit_cell.parameters())
if (str(expt.crystal.get_space_group().info()) == "P 6 2 2"
and str(space_group.info()) == "P 3 2 1"):
# This is fine
continue
assert str(expt.crystal.get_space_group().info()) == str(
space_group.info())
assert expt.crystal.get_space_group() == space_group
def test_synthetic(
space_group,
unit_cell,
dimensions,
sample_size,
use_known_space_group,
use_known_lattice_group,
run_in_tmpdir,
):
space_group = sgtbx.space_group_info(space_group).group()
if unit_cell is not None:
unit_cell = uctbx.unit_cell(unit_cell)
experiments, reflections, _ = generate_experiments_reflections(
space_group=space_group,
unit_cell=unit_cell,
unit_cell_volume=10000,
sample_size=sample_size,
map_to_p1=True,
d_min=1.5,
)
experiments.as_json("tmp.expt")
expt_file = "tmp.expt"
joint_table = flex.reflection_table()
for r in reflections:
joint_table.extend(r)
joint_table.as_file("tmp.refl")
refl_file = "tmp.refl"
args = [
expt_file,
refl_file,
"output.experiments=symmetrized.expt",
"output.reflections=symmetrized.refl",
"output.html=cosym.html",
"output.json=cosym.json",
]
if use_known_space_group:
args.append(f"space_group={space_group.info()}")
if use_known_lattice_group:
args.append(f"lattice_group={space_group.info()}")
if dimensions is not None:
args.append(f"dimensions={dimensions}")
dials_cosym.run(args=args)
assert os.path.isfile("symmetrized.refl")
assert os.path.isfile("symmetrized.expt")
assert os.path.isfile("cosym.html")
assert os.path.isfile("cosym.json")
cosym_expts = load.experiment_list("symmetrized.expt", check_format=False)
assert len(cosym_expts) == len(experiments)
for expt in cosym_expts:
if unit_cell is not None:
assert expt.crystal.get_unit_cell().parameters() == pytest.approx(
unit_cell.parameters()
)
if (
str(expt.crystal.get_space_group().info()) == "P 6 2 2"
and str(space_group.info()) == "P 3 2 1"
):
# This is fine
continue
assert str(expt.crystal.get_space_group().info()) == str(space_group.info())
assert expt.crystal.get_space_group() == space_group