def _run(self):
try:
run(self.cmd)
except Exception as e:
self.logger.error(
'Dials estimate resolution execution found an exception: {}'.
format(e))
def test_mismatched_experiments_reflections(dials_data, run_in_tmpdir):
location = dials_data("l_cysteine_dials_output")
filenames = [
location.join("11_integrated.expt"),
location.join("11_integrated.refl"),
location.join("23_integrated.refl"),
]
with pytest.raises(SystemExit):
cmdline.run([f.strpath for f in filenames])
def test_multi_sequence_with_batch_range(dials_data, run_in_tmpdir, capsys):
location = dials_data("l_cysteine_4_sweeps_scaled")
refls = location.join("scaled_20_25.refl")
expts = location.join("scaled_20_25.expt")
cmdline.run(["batch_range=1900,3600", refls.strpath, expts.strpath], )
captured = capsys.readouterr()
expected_output = "Resolution cc_half: 0.61"
for line in expected_output:
assert line in captured.out
assert run_in_tmpdir.join("dials.estimate_resolution.html").check(file=1)
def test_handle_fit_failure(dials_data, run_in_tmpdir, capsys):
location = dials_data("l_cysteine_dials_output")
filenames = [
location.join("11_integrated.expt"),
location.join("11_integrated.refl"),
location.join("23_integrated.expt"),
location.join("23_integrated.refl"),
]
cmdline.run(["misigma=1"] + [f.strpath for f in filenames])
captured = capsys.readouterr()
expected_output = (
"Resolution fit against cc_half failed: No reflections left for fitting",
"Resolution Mn(I/sig): 0.62",
)
for line in expected_output:
assert line in captured.out
assert run_in_tmpdir.join("dials.estimate_resolution.html").check(file=1)
def test_x4wide(input_files, dials_data, run_in_tmpdir, capsys):
paths = [dials_data("x4wide_processed").join(p).strpath for p in input_files]
reference_mtz = dials_data("x4wide_processed").join("AUTOMATIC_DEFAULT_scaled.mtz")
result = cmdline.run(
[
"cc_half=0.9",
"isigma=2",
"misigma=3",
"rmerge=0.5",
"completeness=1.0",
"i_mean_over_sigma_mean=3",
"batch_range=1,20",
"batch_range=70,90",
"space_group=P43212",
f"reference={reference_mtz}",
"cc_ref=0.9",
"labels=IMEAN,SIGIMEAN",
"html=resolutionizer.html",
"json=resolutionizer.json",
]
+ paths,
)
captured = capsys.readouterr()
expected_output = (
"Resolution rmerge: 1.34",
"Resolution cc_half: 1.56",
"Resolution cc_ref: 1.3",
"Resolution I/sig: 1.53",
"Resolution Mn(I/sig): 1.51",
"Resolution Mn(I)/Mn(sig): 1.50",
)
for line in expected_output:
assert line in captured.out
assert run_in_tmpdir.join("resolutionizer.html").check(file=1)
expected_keys = {
"cc_half",
"cc_ref",
"isigma",
"misigma",
"i_mean_over_sigma_mean",
"rmerge",
"completeness",
}
assert set(result.keys()) == expected_keys
assert run_in_tmpdir.join("resolutionizer.json").check(file=1)
with run_in_tmpdir.join("resolutionizer.json").open("r") as fh:
d = json.load(fh)
assert set(d.keys()) == expected_keys