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from __future__ import annotations
import os
import pytest
from cctbx import crystal
from mmtbx.command_line import cif_as_mtz
from dials.util.reference import (
intensities_from_reference_data_file,
intensities_from_reference_file,
intensities_from_reference_model_file,
)
def test_intensities_from_reference_model(dials_data):
"Test importing from a pdb/cif model"
pdb_file = os.fspath(dials_data("cunir_serial", pathlib=True) / "2BW4.pdb")
intensities = intensities_from_reference_file(pdb_file)
assert intensities.data()
assert not intensities.anomalous_flag()
i2 = intensities_from_reference_model_file(pdb_file, wavelength=1.0)
assert i2.data()
assert i2.anomalous_flag()
bad_input = "bad.pdbb"
with pytest.raises(ValueError):
_ = intensities_from_reference_file(bad_input)
with pytest.raises(ValueError):
_ = intensities_from_reference_model_file(bad_input)
# Now try with the cif model
cif_file = os.fspath(dials_data("cunir_serial", pathlib=True) / "2bw4.cif")
i3 = intensities_from_reference_file(cif_file, wavelength=1.0)
assert i3.data()
assert i3.anomalous_flag()
def test_intensities_from_reference_data_file(dials_data, tmp_path):
"Test importing from an mtz/cif datafile"
mtz_file = os.fspath(
dials_data("x4wide_processed", pathlib=True) / "AUTOMATIC_DEFAULT_scaled.mtz"
)
intensities = intensities_from_reference_file(mtz_file)
assert intensities.data()
assert intensities.anomalous_flag()
i2 = intensities_from_reference_data_file(mtz_file)
assert i2.data() == intensities.data()
bad_input = "bad.mtzz"
with pytest.raises(ValueError):
_ = intensities_from_reference_data_file(bad_input)
# Now try with the cif data file from PDB entry 2BW4
cif_file = os.fspath(dials_data("cunir_serial", pathlib=True) / "2bw4-sf.cif")
i3 = intensities_from_reference_file(cif_file)
assert i3.data()
# In this file, the data is not anomalous
assert not i3.anomalous_flag()
mtz_file = os.fspath(tmp_path / "2bw4.mtz")
cif_as_mtz.process_files(
file_name=cif_file,
crystal_symmetry=crystal.symmetry(unit_cell=None, space_group=None),
output_file_name=os.fspath(mtz_file),
wavelength_id=None,
crystal_id=None,
show_details_if_error=False,
output_r_free_label="FREERFLAG",
)
i4 = intensities_from_reference_file(mtz_file)
assert i4.data()
# In this file, the data is not anomalous
assert not i4.anomalous_flag()
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