def exercise_automation_wrappers () :
from iotbx.reflection_file_utils import process_raw_data, \
change_space_group, load_f_obs_and_r_free
from cctbx import sgtbx
from libtbx.test_utils import approx_equal
mtz_file = "tmp_iotbx_reflection_file_utils.mtz"
crystal_symmetry = crystal.symmetry(
unit_cell=(10,11,12,90,95,90),
space_group_symbol="P 2")
miller_set = miller.build_set(
crystal_symmetry=crystal_symmetry,
anomalous_flag=True,
d_min=1.5)
n_obs = miller_set.indices().size()
i_obs = miller_set.array(
data=flex.random_double(size=n_obs)).set_observation_type_xray_intensity()
i_obs = i_obs.customized_copy(sigmas=flex.sqrt(i_obs.data()))
r_free_flags = miller_set.generate_r_free_flags()
r_free_flags_partial = r_free_flags.select(flex.random_bool(n_obs, 0.9))
out = StringIO()
processed = process_raw_data(
obs=i_obs,
r_free_flags=None,
test_flag_value=None,
log=out)
assert ("""WARNING: R-free flags not supplied.""" in out.getvalue())
assert (processed.data_labels() == "F(+),SIGF(+),F(-),SIGF(-)")
assert (processed.phase_labels() is None)
assert (processed.flags_are_new())
out2 = StringIO()
processed2 = process_raw_data(
obs=i_obs,
r_free_flags=r_free_flags_partial,
test_flag_value=True,
log=out2)
assert ("""WARNING: R-free flags are incomplete""" in out2.getvalue())
assert (not processed2.flags_are_new())
assert (processed.n_obs() == processed2.n_obs())
processed.write_mtz_file(mtz_file, title="tst_iotbx", wavelength=0.9792)
f_obs, r_free = load_f_obs_and_r_free(mtz_file)
change_space_group(mtz_file, sgtbx.space_group_info("P21"))
f_obs_new, r_free_new = load_f_obs_and_r_free(mtz_file)
assert (f_obs_new.size() == f_obs.size() - 4)
f_obs_new, r_free_new = load_f_obs_and_r_free(mtz_file,
anomalous_flag=True)
assert (str(f_obs_new.space_group_info()) == "P 1 21 1")
assert (approx_equal(f_obs_new.info().wavelength, 0.9792))
def exercise_automation_wrappers():
from iotbx.reflection_file_utils import process_raw_data, \
change_space_group, load_f_obs_and_r_free
from cctbx import sgtbx
from libtbx.test_utils import approx_equal
mtz_file = "tmp_iotbx_reflection_file_utils.mtz"
crystal_symmetry = crystal.symmetry(
unit_cell=(10,11,12,90,95,90),
space_group_symbol="P 2")
miller_set = miller.build_set(
crystal_symmetry=crystal_symmetry,
anomalous_flag=True,
d_min=1.5)
n_obs = miller_set.indices().size()
i_obs = miller_set.array(
data=flex.random_double(size=n_obs)).set_observation_type_xray_intensity()
i_obs = i_obs.customized_copy(sigmas=flex.sqrt(i_obs.data()))
r_free_flags = miller_set.generate_r_free_flags()
r_free_flags_partial = r_free_flags.select(flex.random_bool(n_obs, 0.9))
out = StringIO()
processed = process_raw_data(
obs=i_obs,
r_free_flags=None,
test_flag_value=None,
log=out)
assert ("""WARNING: R-free flags not supplied.""" in out.getvalue())
assert (processed.data_labels() == "F(+),SIGF(+),F(-),SIGF(-)")
assert (processed.phase_labels() is None)
assert (processed.flags_are_new())
out2 = StringIO()
processed2 = process_raw_data(
obs=i_obs,
r_free_flags=r_free_flags_partial,
test_flag_value=True,
log=out2)
assert ("""WARNING: R-free flags are incomplete""" in out2.getvalue())
assert (not processed2.flags_are_new())
assert (processed.n_obs() == processed2.n_obs())
processed.write_mtz_file(mtz_file, title="tst_iotbx", wavelength=0.9792)
f_obs, r_free = load_f_obs_and_r_free(mtz_file)
change_space_group(mtz_file, sgtbx.space_group_info("P21"))
f_obs_new, r_free_new = load_f_obs_and_r_free(mtz_file)
assert (f_obs_new.size() == f_obs.size() - 4)
f_obs_new, r_free_new = load_f_obs_and_r_free(mtz_file,
anomalous_flag=True)
assert (str(f_obs_new.space_group_info()) == "P 1 21 1")
assert (approx_equal(f_obs_new.info().wavelength, 0.9792))
def find_data_arrays(mtz_file,
log=None,
merge_anomalous=False,
preferred_labels=None,
crystal_symmetry=None):
"""
Guess an appropriate data array to use for refinement, plus optional
Hendrickson-Lattman coefficients and R-free flags if present.
"""
from iotbx import reflection_file_utils
from iotbx.file_reader import any_file
if (log is None): log = sys.stdout
phases = data = flags = flag_value = None
hkl_in = any_file(mtz_file, force_type="hkl")
hkl_server = hkl_in.file_server
# always use anomalous data if available! also, prefer amplitudes over
# intensities if possible, as they may already be on an absolute scale
data_arrays = hkl_server.get_xray_data(file_name=None,
labels=None,
ignore_all_zeros=False,
parameter_scope="",
return_all_valid_arrays=True,
minimum_score=4,
prefer_amplitudes=True,
prefer_anomalous=True)
if (len(data_arrays) == 0):
raise Sorry("No data arrays found in %s." % mtz_file)
data = data_arrays[0]
if (preferred_labels is not None):
for array in data_arrays:
array_labels = array.info().label_string()
if (array_label == preferred_labels):
data = array
break
else:
raise Sorry("Can't find label string '%s'!" % preferred_labels)
else:
print("Defaulting to using %s" % data.info().label_string(), file=log)
hl_arrays = hkl_server.get_experimental_phases(
file_name=None,
labels=None,
ignore_all_zeros=True,
parameter_scope="",
return_all_valid_arrays=True,
minimum_score=1)
if (len(hl_arrays) > 0):
phases = hl_arrays[0]
flags_and_values = hkl_server.get_r_free_flags(
file_name=None,
label=None,
test_flag_value=None,
disable_suitability_test=False,
parameter_scope="",
return_all_valid_arrays=True,
minimum_score=1)
if (len(flags_and_values) > 0):
flags, flag_value = flags_and_values[0]
if (crystal_symmetry is not None):
data = data.customized_copy(crystal_symmetry=crystal_symmetry)
if (flags is not None):
flags = flags.customized_copy(crystal_symmetry=crystal_symmetry)
if (phases is not None):
phases = phases.customized_copy(crystal_symmetry=crystal_symmetry)
return reflection_file_utils.process_raw_data(
obs=data,
r_free_flags=flags,
test_flag_value=flag_value,
phases=phases,
log=log,
merge_anomalous=merge_anomalous)
def find_data_arrays (mtz_file, log=None, merge_anomalous=False,
preferred_labels=None, crystal_symmetry=None) :
"""
Guess an appropriate data array to use for refinement, plus optional
Hendrickson-Lattman coefficients and R-free flags if present.
"""
from iotbx import reflection_file_utils
from iotbx.file_reader import any_file
if (log is None) : log = sys.stdout
phases = data = flags = flag_value = None
hkl_in = any_file(mtz_file, force_type="hkl")
hkl_server = hkl_in.file_server
# always use anomalous data if available! also, prefer amplitudes over
# intensities if possible, as they may already be on an absolute scale
data_arrays = hkl_server.get_xray_data(
file_name = None,
labels = None,
ignore_all_zeros = False,
parameter_scope = "",
return_all_valid_arrays = True,
minimum_score = 4,
prefer_amplitudes = True,
prefer_anomalous = True)
if (len(data_arrays) == 0) :
raise Sorry("No data arrays found in %s." % mtz_file)
data = data_arrays[0]
if (preferred_labels is not None) :
for array in data_arrays :
array_labels = array.info().label_string()
if (array_label== preferred_labels) :
data = array
break
else :
raise Sorry("Can't find label string '%s'!" % preferred_labels)
else :
print >> log, "Defaulting to using %s" % data.info().label_string()
hl_arrays = hkl_server.get_experimental_phases(
file_name = None,
labels = None,
ignore_all_zeros = True,
parameter_scope = "",
return_all_valid_arrays = True,
minimum_score = 1)
if (len(hl_arrays) > 0) :
phases = hl_arrays[0]
flags_and_values = hkl_server.get_r_free_flags(
file_name=None,
label=None,
test_flag_value=None,
disable_suitability_test=False,
parameter_scope="",
return_all_valid_arrays=True,
minimum_score=1)
if (len(flags_and_values) > 0) :
flags, flag_value = flags_and_values[0]
if (crystal_symmetry is not None) :
data = data.customized_copy(crystal_symmetry=crystal_symmetry)
if (flags is not None) :
flags = flags.customized_copy(crystal_symmetry=crystal_symmetry)
if (phases is not None) :
phases = phases.customized_copy(crystal_symmetry=crystal_symmetry)
return reflection_file_utils.process_raw_data(
obs=data,
r_free_flags=flags,
test_flag_value=flag_value,
phases=phases,
log=log,
merge_anomalous=merge_anomalous)
