def exercise_other_reflection_formats():
hkl_handler = reflections.reflections_handler(
allowed_param_names=phil_names)
# test other file formats (requires phenix_regression)
if (regression_dir is None):
print "phenix_regression not found, skipping exercise_other_reflection_formats()"
return
cns_file = os.path.join(regression_dir, "reflection_files", "enk.hkl")
hkl_handler.save_file(file_name=cns_file)
try:
hkl_handler.check_symmetry(file_name=cns_file)
except Sorry:
pass
else:
raise Exception_expected
sca_file = os.path.join(regression_dir, "reflection_files", "merge.sca")
hkl_handler.save_file(file_name=sca_file)
assert (hkl_handler.get_intensity_labels(file_name=sca_file) == [
'I(+),SIGI(+),I(-),SIGI(-)'
])
assert (hkl_handler.get_amplitude_labels(file_name=sca_file) == [])
# test handling of reconstructed (anomalous) amplitudes
dano_file = os.path.join(regression_dir, "reflection_files", "dano.mtz")
hkl_handler = reflections.reflections_handler(
allowed_param_names=["labin"])
hkl_handler.set_param_file(file_name=dano_file, file_param_name="labin")
labels = hkl_handler.get_anomalous_data_labels(file_param_name="labin")
assert (len(labels) == 3)
labels = hkl_handler.get_anomalous_data_labels(
file_param_name="labin", allow_reconstructed_amplitudes=False)
assert (len(labels) == 0)
def exercise_other_reflection_formats () :
hkl_handler = reflections.reflections_handler(allowed_param_names=phil_names)
# test other file formats (requires phenix_regression)
if (regression_dir is None) :
print "phenix_regression not found, skipping exercise_other_reflection_formats()"
return
cns_file = os.path.join(regression_dir, "reflection_files", "enk.hkl")
hkl_handler.save_file(file_name=cns_file)
try :
hkl_handler.check_symmetry(file_name=cns_file)
except Sorry :
pass
else :
raise Exception_expected
sca_file = os.path.join(regression_dir, "reflection_files", "merge.sca")
hkl_handler.save_file(file_name=sca_file)
assert (hkl_handler.get_intensity_labels(file_name=sca_file) ==
['I(+),SIGI(+),I(-),SIGI(-)'])
assert (hkl_handler.get_amplitude_labels(file_name=sca_file) == [])
# test handling of reconstructed (anomalous) amplitudes
dano_file = os.path.join(regression_dir, "reflection_files", "dano.mtz")
hkl_handler = reflections.reflections_handler(
allowed_param_names=["labin"])
hkl_handler.set_param_file(file_name=dano_file,
file_param_name="labin")
labels = hkl_handler.get_anomalous_data_labels(file_param_name="labin")
assert (len(labels) == 3)
labels = hkl_handler.get_anomalous_data_labels(file_param_name="labin",
allow_reconstructed_amplitudes=False)
assert (len(labels) == 0)
def exercise_reflections():
hkl_handler = reflections.reflections_handler(
allowed_param_names=phil_names)
from cctbx import miller
from cctbx import crystal
from cctbx.array_family import flex
symm = crystal.symmetry(unit_cell=(30, 30, 40, 90, 90, 120),
space_group_symbol="P 61 2 2")
miller_set = miller.build_set(crystal_symmetry=symm,
anomalous_flag=True,
d_min=1.5)
n_refl = miller_set.indices().size()
data = flex.random_double(n_refl)
sigmas = flex.random_double(n_refl)
f_obs = miller_set.array(data=data, sigmas=sigmas)
f_obs_merged = f_obs.average_bijvoet_mates()
flags = f_obs_merged.generate_r_free_flags()
# single dataset
mtz_dataset = f_obs_merged.as_mtz_dataset(column_root_label="F-obs",
wavelength=1.54)
mtz_dataset.add_miller_array(flags, column_root_label="R-free-flags")
file_name = "tst_iotbs_gui_tools.mtz"
mtz_dataset.mtz_object().write(file_name)
assert (hkl_handler.set_param_file(
file_name=file_name,
file_param_name="refinement.input.xray_data.file_name") == True)
assert (hkl_handler.set_param_file(
file_name=file_name,
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
False)
assert (hkl_handler.get_rfree_labels(
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
hkl_handler.get_rfree_labels(file_name=file_name) ==
['R-free-flags'])
assert (hkl_handler.get_rfree_labels(file_name=file_name, neutron=False) ==
hkl_handler.get_rfree_labels(file_name=file_name,
neutron=True) == ['R-free-flags'])
assert approx_equal(
1.54,
hkl_handler.get_wavelength(file_name=file_name,
labels="F-obs,SIGF-obs"))
# join X/N datasets
hkl_handler = reflections.reflections_handler(
allowed_param_names=phil_names)
data_neutron = flex.random_double(n_refl)
sigmas_neutron = flex.random_double(n_refl)
f_obs_neutron = miller_set.array(data=data_neutron, sigmas=sigmas_neutron)
mtz_dataset = f_obs_merged.as_mtz_dataset(column_root_label="F-obs-xray")
mtz_dataset.add_miller_array(f_obs_neutron,
column_root_label="F-obs-neutron")
mtz_dataset.add_miller_array(flags, column_root_label="R-free-flags-xray")
mtz_dataset.add_miller_array(flags.deep_copy(),
column_root_label="R-free-flags-neutron")
file_name = "tst_iotbs_gui_tools.mtz"
mtz_dataset.mtz_object().write(file_name)
assert (hkl_handler.set_param_file(
file_name=file_name,
file_param_name="refinement.input.xray_data.file_name") == True)
for i, phil_name in enumerate(phil_names[1:4]):
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name=phil_name) == False)
assert (hkl_handler.get_rfree_labels(
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
hkl_handler.get_rfree_labels(file_name=file_name) ==
['R-free-flags-xray', 'R-free-flags-neutron'])
assert (hkl_handler.get_rfree_labels(
file_name=file_name, neutron=False) == ['R-free-flags-xray'])
assert (hkl_handler.get_rfree_labels(
file_name=file_name, neutron=True) == ['R-free-flags-neutron'])
hkl_handler.check_symmetry(file_name=file_name)
assert (hkl_handler.get_data_labels(
file_param_name="refinement.input.xray_data.file_name") ==
hkl_handler.get_data_labels(file_name=file_name) ==
hkl_handler.get_amplitude_labels(file_name=file_name) == [
"F-obs-xray,SIGF-obs-xray",
"F-obs-neutron(+),SIGF-obs-neutron(+)," +
"F-obs-neutron(-),SIGF-obs-neutron(-)"
])
assert (hkl_handler.get_anomalous_data_labels(
file_param_name="refinement.input.xray_data.file_name") == [
"F-obs-neutron(+),SIGF-obs-neutron(+)," +
"F-obs-neutron(-),SIGF-obs-neutron(-)"
])
assert (hkl_handler.has_anomalous_data(
file_param_name="refinement.input.xray_data.file_name"))
assert (hkl_handler.get_rfree_flag_value(
array_name="F-obs-xray,SIGF-obs-xray",
file_param_name="refinement.input.xray_data.file_name") is None)
assert (hkl_handler.get_rfree_flag_value(
array_name='R-free-flags-xray',
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
1)
(d_max, d_min) = hkl_handler.d_max_min()
assert approx_equal(d_max, 25.98, eps=0.01)
assert approx_equal(d_min, 1.5, eps=0.01)
assert hkl_handler.space_group_as_str() == "P 61 2 2"
assert (hkl_handler.unit_cell_as_str() == "30 30 40 90 90 120")
assert (hkl_handler.unit_cell_as_str(
separator=",") == "30,30,40,90,90,120")
n_refl_merged = len(f_obs_merged.indices())
phi_array = f_obs_merged.random_phases_compatible_with_phase_restrictions(
deg=True)
fom_array = phi_array.array(data=flex.random_double(n_refl_merged))
hl_data = flex.hendrickson_lattman(n_refl_merged, (0, 0, 0, 0))
hl_coeffs = phi_array.array(data=hl_data)
assert (hl_coeffs.is_hendrickson_lattman_array())
from iotbx.mtz import label_decorator
import iotbx.mtz
class resolve_label_decorator(label_decorator):
def phases(self, *args, **kwds):
return label_decorator.phases(self, *args, **kwds) + "M"
def hendrickson_lattman(self, *args, **kwds):
return label_decorator.hendrickson_lattman(self, *args, **
kwds) + "M"
mtz_dataset = f_obs_merged.as_mtz_dataset(column_root_label="FP")
mtz_dataset.add_miller_array(phi_array,
column_root_label="PHIM",
label_decorator=resolve_label_decorator(),
column_types="P")
mtz_dataset.add_miller_array(fom_array,
column_root_label="FOMM",
column_types="W")
mtz_dataset.add_miller_array(hl_coeffs,
column_root_label="HL",
label_decorator=resolve_label_decorator())
fwt_map = f_obs_merged.customized_copy(
sigmas=None).phase_transfer(phi_array)
mtz_dataset.add_miller_array(
fwt_map,
column_root_label="FWT",
label_decorator=iotbx.mtz.ccp4_label_decorator())
mtz_dataset.add_miller_array(flags, column_root_label="FreeR_flag")
resolve_file = "tst_iotbx_gui_tools_resolve.mtz"
mtz_dataset.mtz_object().write(resolve_file)
hkl_handler = reflections.reflections_handler(
allowed_param_names=["map_coeffs"])
hkl_handler.set_param_file(file_name=resolve_file,
file_param_name="map_coeffs")
assert hkl_handler.has_data(file_name=resolve_file)
l1 = hkl_handler.get_map_coeff_labels(file_name=resolve_file)
assert (l1 == ['FWT,PHWT', 'FP,PHIM,FOMM'])
l2 = hkl_handler.get_phase_deg_labels(file_name=resolve_file)
assert (l2 == [
'HLAM,HLBM,HLCM,HLDM',
'FWT,PHWT',
'PHIM',
]), l2
l3 = hkl_handler.get_experimental_phase_labels(file_name=resolve_file)
#print l3
l4 = hkl_handler.get_data_labels_for_wizard(file_name=resolve_file)
assert (l4 == ['FP SIGFP'])
l5 = hkl_handler.get_map_coeff_labels_for_build(file_name=resolve_file)
assert (l5 == ['FWT,PHWT', 'FP,PHIM,FOMM']), l5
hkl_in = hkl_handler.get_file(file_name=resolve_file)
assert (reflections.get_mtz_label_prefix(hkl_in) == "/crystal/dataset")
map_coeffs = reflections.map_coeffs_from_mtz_file(resolve_file,
f_label="FP,SIGFP")
assert map_coeffs.is_complex_array()
try:
map_coeffs = reflections.map_coeffs_from_mtz_file(resolve_file)
except Sorry:
pass
else:
raise Exception_expected
assert (hkl_handler.get_map_coeff_labels_for_fft(
file_name=resolve_file) == ['FWT,PHWT', 'FP,SIGFP PHIM FOMM'])
# miscellaneous utilities
file_name = resolve_file
hkl_in = file_reader.any_file(file_name)
hkl_server = hkl_in.file_server
assert approx_equal(reflections.get_high_resolution(hkl_server),
1.5,
eps=0.0001)
descriptions = []
for miller_array in hkl_server.miller_arrays:
(sg, uc) = reflections.get_miller_array_symmetry(miller_array)
assert (uc == "30 30 40 90 90 120")
assert (str(sg) == "P 61 2 2")
descriptions.append(reflections.get_array_description(miller_array))
assert (descriptions == [
'Amplitude', 'Phases', 'Weights', 'HL coeffs', 'Map coeffs',
'R-free flag'
]), descriptions
handler = reflections.reflections_handler()
handler.save_file(input_file=hkl_in)
assert (not handler.has_anomalous_data())
assert (handler.get_resolution_range(
file_name=file_name) == "(25.981 - 1.500)")
assert (handler.get_resolution_limits(file_name=file_name) == ('(25.981)',
'(1.500)'))
fmodel = phi_array.array(
data=flex.complex_double(n_refl_merged, complex(0.5, 0.8)))
m1 = phi_array.array(
data=flex.complex_double(n_refl_merged, complex(1, 0)))
m2 = phi_array.array(
data=flex.complex_double(n_refl_merged, complex(0.5, 0)))
m3 = phi_array.array(flex.complex_double(n_refl_merged, complex(1, 1)))
dec = label_decorator(phases_prefix="PH")
mtz_dataset = fmodel.as_mtz_dataset(column_root_label="F-model",
label_decorator=dec)
mtz_dataset.add_miller_array(m1,
column_root_label="2FOFCWT",
label_decorator=dec)
mtz_dataset.add_miller_array(m2,
column_root_label="FOFCWT",
label_decorator=dec)
mtz_dataset.add_miller_array(m3,
column_root_label="2FOFCWT_no_fill",
label_decorator=dec)
file_name = "tst_iotbx_gui_tools_map_coeffs.mtz"
mtz_dataset.mtz_object().write(file_name)
hkl_handler = reflections.reflections_handler(
allowed_param_names=["fmodel", "map_coeffs"])
hkl_handler.set_param_file(file_name=file_name, file_param_name="fmodel")
assert (hkl_handler.get_fmodel_labels(file_name=file_name) == [
'F-model,PHF-model'
])
assert (hkl_handler.get_amplitude_labels(file_name=file_name) == [])
phi_labels = hkl_handler.get_phase_deg_labels(file_name=file_name)
assert (len(phi_labels) == 4)
phi_cols = hkl_handler.get_phase_column_labels(file_name=file_name)
assert (phi_cols == [
'PHF-model', 'PH2FOFCWT', 'PHFOFCWT', 'PH2FOFCWT_no_fill'
])
assert (len(
hkl_handler.get_amplitude_column_labels(file_name=file_name,
allow_conversion=True)) == 0)
fc_cols = hkl_handler.get_fmodel_labels(file_name=file_name,
first_column_only=True)
assert (fc_cols == ['F-model'])
hkl_server = file_reader.any_file(file_name).file_server
map_labels = reflections.get_map_coeff_labels(hkl_server)
assert (map_labels == [
'2FOFCWT,PH2FOFCWT',
'FOFCWT,PHFOFCWT',
'2FOFCWT_no_fill,PH2FOFCWT_no_fill',
])
map_labels = reflections.get_map_coeffs_for_build(hkl_server)
assert map_labels == [
'2FOFCWT,PH2FOFCWT', '2FOFCWT_no_fill,PH2FOFCWT_no_fill'
]
map_coeffs = reflections.extract_phenix_refine_map_coeffs(file_name)
assert (len(map_coeffs) == 3)
hkl_file = file_reader.any_file(file_name)
assert reflections.get_mtz_label_prefix(hkl_file) == "/crystal/dataset"
# other stuff
(fp, fpp) = reflections.get_fp_fpp_from_sasaki("Se", 0.979)
assert fp is not None and fpp is not None
def exercise_reflections () :
hkl_handler = reflections.reflections_handler(allowed_param_names=phil_names)
from cctbx import miller
from cctbx import crystal
from cctbx.array_family import flex
symm = crystal.symmetry(
unit_cell=(30,30,40,90,90,120),
space_group_symbol="P 61 2 2")
miller_set = miller.build_set(
crystal_symmetry=symm,
anomalous_flag=True,
d_min=1.5)
n_refl = miller_set.indices().size()
data = flex.random_double(n_refl)
sigmas = flex.random_double(n_refl)
f_obs = miller_set.array(data=data, sigmas=sigmas)
f_obs_merged = f_obs.average_bijvoet_mates()
flags = f_obs_merged.generate_r_free_flags()
# single dataset
mtz_dataset = f_obs_merged.as_mtz_dataset(
column_root_label="F-obs",
wavelength=1.54)
mtz_dataset.add_miller_array(flags,
column_root_label="R-free-flags")
file_name = "tst_iotbs_gui_tools.mtz"
mtz_dataset.mtz_object().write(file_name)
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name="refinement.input.xray_data.file_name") == True)
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name="refinement.input.xray_data.r_free_flags.file_name")
== False)
assert (hkl_handler.get_rfree_labels(
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
hkl_handler.get_rfree_labels(file_name=file_name) == ['R-free-flags'])
assert (hkl_handler.get_rfree_labels(file_name=file_name, neutron=False) ==
hkl_handler.get_rfree_labels(file_name=file_name, neutron=True) ==
['R-free-flags'])
assert approx_equal(1.54, hkl_handler.get_wavelength(file_name=file_name,
labels="F-obs,SIGF-obs"))
# join X/N datasets
hkl_handler = reflections.reflections_handler(allowed_param_names=phil_names)
data_neutron = flex.random_double(n_refl)
sigmas_neutron = flex.random_double(n_refl)
f_obs_neutron = miller_set.array(data=data_neutron, sigmas=sigmas_neutron)
mtz_dataset = f_obs_merged.as_mtz_dataset(
column_root_label="F-obs-xray")
mtz_dataset.add_miller_array(f_obs_neutron,
column_root_label="F-obs-neutron")
mtz_dataset.add_miller_array(flags,
column_root_label="R-free-flags-xray")
mtz_dataset.add_miller_array(flags.deep_copy(),
column_root_label="R-free-flags-neutron")
file_name = "tst_iotbs_gui_tools.mtz"
mtz_dataset.mtz_object().write(file_name)
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name="refinement.input.xray_data.file_name") == True)
for i, phil_name in enumerate(phil_names[1:4]) :
assert (hkl_handler.set_param_file(file_name=file_name,
file_param_name=phil_name) == False)
assert (hkl_handler.get_rfree_labels(
file_param_name="refinement.input.xray_data.r_free_flags.file_name") ==
hkl_handler.get_rfree_labels(file_name=file_name) ==
['R-free-flags-xray', 'R-free-flags-neutron'])
assert (hkl_handler.get_rfree_labels(file_name=file_name, neutron=False) ==
['R-free-flags-xray'])
assert (hkl_handler.get_rfree_labels(file_name=file_name, neutron=True) ==
['R-free-flags-neutron'])
hkl_handler.check_symmetry(file_name=file_name)
assert (hkl_handler.get_data_labels(
file_param_name="refinement.input.xray_data.file_name") ==
hkl_handler.get_data_labels(file_name=file_name) ==
hkl_handler.get_amplitude_labels(file_name=file_name) ==
["F-obs-xray,SIGF-obs-xray", "F-obs-neutron(+),SIGF-obs-neutron(+),"+
"F-obs-neutron(-),SIGF-obs-neutron(-)"])
assert (hkl_handler.get_anomalous_data_labels(
file_param_name="refinement.input.xray_data.file_name") ==
["F-obs-neutron(+),SIGF-obs-neutron(+)," +
"F-obs-neutron(-),SIGF-obs-neutron(-)"])
assert (hkl_handler.has_anomalous_data(
file_param_name="refinement.input.xray_data.file_name"))
assert (hkl_handler.get_rfree_flag_value(
array_name="F-obs-xray,SIGF-obs-xray",
file_param_name="refinement.input.xray_data.file_name") is None)
assert (hkl_handler.get_rfree_flag_value(array_name='R-free-flags-xray',
file_param_name="refinement.input.xray_data.r_free_flags.file_name") == 1)
(d_max, d_min) = hkl_handler.d_max_min()
assert approx_equal(d_max, 25.98, eps=0.01)
assert approx_equal(d_min, 1.5, eps=0.01)
assert hkl_handler.space_group_as_str() == "P 61 2 2"
assert (hkl_handler.unit_cell_as_str() ==
"30 30 40 90 90 120")
assert (hkl_handler.unit_cell_as_str(separator=",") ==
"30,30,40,90,90,120")
n_refl_merged = len(f_obs_merged.indices())
phi_array = f_obs_merged.random_phases_compatible_with_phase_restrictions(
deg=True)
fom_array = phi_array.array(data=flex.random_double(n_refl_merged))
hl_data = flex.hendrickson_lattman(n_refl_merged, (0,0,0,0))
hl_coeffs = phi_array.array(data=hl_data)
assert (hl_coeffs.is_hendrickson_lattman_array())
from iotbx.mtz import label_decorator
import iotbx.mtz
class resolve_label_decorator (label_decorator) :
def phases (self, *args, **kwds) :
return label_decorator.phases(self, *args, **kwds) + "M"
def hendrickson_lattman (self, *args, **kwds) :
return label_decorator.hendrickson_lattman(self, *args, **kwds) + "M"
mtz_dataset = f_obs_merged.as_mtz_dataset(
column_root_label="FP")
mtz_dataset.add_miller_array(phi_array,
column_root_label="PHIM",
label_decorator=resolve_label_decorator(),
column_types="P")
mtz_dataset.add_miller_array(fom_array,
column_root_label="FOMM",
column_types="W")
mtz_dataset.add_miller_array(hl_coeffs,
column_root_label="HL",
label_decorator=resolve_label_decorator())
fwt_map = f_obs_merged.customized_copy(sigmas=None).phase_transfer(phi_array)
mtz_dataset.add_miller_array(fwt_map,
column_root_label="FWT",
label_decorator=iotbx.mtz.ccp4_label_decorator())
mtz_dataset.add_miller_array(flags,
column_root_label="FreeR_flag")
resolve_file = "tst_iotbx_gui_tools_resolve.mtz"
mtz_dataset.mtz_object().write(resolve_file)
hkl_handler = reflections.reflections_handler(
allowed_param_names=["map_coeffs"])
hkl_handler.set_param_file(
file_name=resolve_file,
file_param_name="map_coeffs")
assert hkl_handler.has_data(file_name=resolve_file)
l1 = hkl_handler.get_map_coeff_labels(file_name=resolve_file)
assert (l1 == ['FWT,PHWT', 'FP,PHIM,FOMM'])
l2 = hkl_handler.get_phase_deg_labels(file_name=resolve_file)
assert (l2 == ['HLAM,HLBM,HLCM,HLDM', 'FWT,PHWT', 'PHIM',]), l2
l3 = hkl_handler.get_experimental_phase_labels(file_name=resolve_file)
#print l3
l4 = hkl_handler.get_data_labels_for_wizard(file_name=resolve_file)
assert (l4 == ['FP SIGFP'])
l5 = hkl_handler.get_map_coeff_labels_for_build(file_name=resolve_file)
assert (l5 == ['FWT,PHWT', 'FP,PHIM,FOMM']), l5
hkl_in = hkl_handler.get_file(file_name=resolve_file)
assert (reflections.get_mtz_label_prefix(hkl_in) == "/crystal/dataset")
map_coeffs = reflections.map_coeffs_from_mtz_file(resolve_file,
f_label="FP,SIGFP")
assert map_coeffs.is_complex_array()
try :
map_coeffs = reflections.map_coeffs_from_mtz_file(resolve_file)
except Sorry :
pass
else :
raise Exception_expected
assert (hkl_handler.get_map_coeff_labels_for_fft(file_name=resolve_file) ==
['FWT,PHWT', 'FP,SIGFP PHIM FOMM'])
# miscellaneous utilities
file_name = resolve_file
hkl_in = file_reader.any_file(file_name)
hkl_server = hkl_in.file_server
assert approx_equal(reflections.get_high_resolution(hkl_server), 1.5,
eps=0.0001)
descriptions = []
for miller_array in hkl_server.miller_arrays :
(sg, uc) = reflections.get_miller_array_symmetry(miller_array)
assert (uc == "30 30 40 90 90 120")
assert (str(sg) == "P 61 2 2")
descriptions.append(reflections.get_array_description(miller_array))
assert (descriptions == [
'Amplitude', 'Phases', 'Weights', 'HL coeffs', 'Map coeffs',
'R-free flag']), descriptions
handler = reflections.reflections_handler()
handler.save_file(input_file=hkl_in)
assert (not handler.has_anomalous_data())
assert (handler.get_resolution_range(file_name=file_name)=="(25.981 - 1.500)")
assert (handler.get_resolution_limits(file_name=file_name) ==
('(25.981)', '(1.500)'))
fmodel = phi_array.array(data=flex.complex_double(n_refl_merged,
complex(0.5,0.8)))
m1 = phi_array.array(data=flex.complex_double(n_refl_merged, complex(1,0)))
m2 = phi_array.array(data=flex.complex_double(n_refl_merged, complex(0.5,0)))
m3 = phi_array.array(flex.complex_double(n_refl_merged, complex(1,1)))
dec = label_decorator(phases_prefix="PH")
mtz_dataset = fmodel.as_mtz_dataset(
column_root_label="F-model",
label_decorator=dec)
mtz_dataset.add_miller_array(m1,
column_root_label="2FOFCWT",
label_decorator=dec)
mtz_dataset.add_miller_array(m2,
column_root_label="FOFCWT",
label_decorator=dec)
mtz_dataset.add_miller_array(m3,
column_root_label="2FOFCWT_no_fill",
label_decorator=dec)
file_name = "tst_iotbx_gui_tools_map_coeffs.mtz"
mtz_dataset.mtz_object().write(file_name)
hkl_handler = reflections.reflections_handler(
allowed_param_names=["fmodel", "map_coeffs"])
hkl_handler.set_param_file(
file_name=file_name,
file_param_name="fmodel")
assert (hkl_handler.get_fmodel_labels(file_name=file_name) ==
['F-model,PHF-model'])
assert (hkl_handler.get_amplitude_labels(file_name=file_name) == [])
phi_labels = hkl_handler.get_phase_deg_labels(file_name=file_name)
assert (len(phi_labels) == 4)
phi_cols = hkl_handler.get_phase_column_labels(file_name=file_name)
assert (phi_cols == ['PHF-model','PH2FOFCWT','PHFOFCWT','PH2FOFCWT_no_fill'])
assert (len(hkl_handler.get_amplitude_column_labels(file_name=file_name,
allow_conversion=True)) == 0)
fc_cols = hkl_handler.get_fmodel_labels(file_name=file_name,
first_column_only=True)
assert (fc_cols == ['F-model'])
hkl_server = file_reader.any_file(file_name).file_server
map_labels = reflections.get_map_coeff_labels(hkl_server)
assert (map_labels == ['2FOFCWT,PH2FOFCWT', 'FOFCWT,PHFOFCWT',
'2FOFCWT_no_fill,PH2FOFCWT_no_fill',])
map_labels = reflections.get_map_coeffs_for_build(hkl_server)
assert map_labels == ['2FOFCWT,PH2FOFCWT','2FOFCWT_no_fill,PH2FOFCWT_no_fill']
map_coeffs = reflections.extract_phenix_refine_map_coeffs(file_name)
assert (len(map_coeffs) == 3)
hkl_file = file_reader.any_file(file_name)
assert reflections.get_mtz_label_prefix(hkl_file) == "/crystal/dataset"
# other stuff
(fp, fpp) = reflections.get_fp_fpp_from_sasaki("Se", 0.979)
assert fp is not None and fpp is not None
