def exercise_map_tools():
prefix = "tmp_iotbx_map_tools"
pdb_file = prefix + ".pdb"
mtz_file = prefix + ".mtz"
pdb_in = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1 N GLY P -1 -22.866 -2.627 15.217 1.00 0.00 N
ATOM 2 CA GLY P -1 -22.714 -3.068 16.621 1.00 0.00 C
ATOM 3 C GLY P -1 -21.276 -3.457 16.936 1.00 0.00 C
ATOM 4 O GLY P -1 -20.538 -3.887 16.047 1.00 0.00 O
ATOM 5 H1 GLY P -1 -22.583 -3.364 14.590 1.00 0.00 H
ATOM 6 H2 GLY P -1 -22.293 -1.817 15.040 1.00 0.00 H
ATOM 7 H3 GLY P -1 -23.828 -2.392 15.027 1.00 0.00 H
ATOM 8 HA2 GLY P -1 -23.016 -2.261 17.288 1.00 0.00 H
ATOM 9 HA3 GLY P -1 -23.352 -3.933 16.803 1.00 0.00 H
""")
xrs = pdb_in.input.xray_structure_simple()
with open(pdb_file, "w") as f:
f.write(pdb_in.hierarchy.as_pdb_string(xrs))
fc = xrs.structure_factors(d_min=1.5).f_calc()
dec = mtz.label_decorator(phases_prefix="PH")
# part 1: phenix.refine style
mtz_data = fc.as_mtz_dataset(column_root_label="2FOFCWT",
label_decorator=dec)
mtz_data.add_miller_array(fc,
column_root_label="2FOFCWT_no_fill",
label_decorator=dec)
mtz_data.add_miller_array(fc,
column_root_label="FOFCWT",
label_decorator=dec)
mtz_data.add_miller_array(fc,
column_root_label="ANOM",
label_decorator=dec)
mtz_data.mtz_object().write(mtz_file)
converted = map_tools.auto_convert_map_coefficients(mtz_file=mtz_file,
pdb_file=pdb_file)
assert (not None
in [converted.f_map, converted.diff_map, converted.anom_map])
assert (converted.f_map == "tmp_iotbx_map_tools_2mFo-DFc.ccp4")
assert (converted.f_map_type == "2mFo-DFc")
server = map_tools.server(mtz_file)
files = server.convert_phenix_maps(file_base=prefix)
files = [os.path.basename(file_name) for file_name in files]
assert (files == [
'tmp_iotbx_map_tools_anomalous.ccp4',
'tmp_iotbx_map_tools_mFo-DFc.ccp4',
'tmp_iotbx_map_tools_2mFo-DFc.ccp4',
'tmp_iotbx_map_tools_2mFo-DFc_no_fill.ccp4'
])
for fn in files:
assert os.path.isfile(fn)
os.remove(fn)
file_name = server.convert_any_map(f_label="2FOFCWT,PH2FOFCWT",
phi_label=None,
fom_label=None,
use_standard_map_names=True)
assert (file_name == "tmp_iotbx_map_tools_2mFo-DFc.ccp4")
assert os.path.isfile(file_name)
# part 2: Phaser/Refmac style
mtz_data = fc.as_mtz_dataset(column_root_label="FWT",
label_decorator=mtz.ccp4_label_decorator())
mtz_data.add_miller_array(fc,
column_root_label="DELFWT",
label_decorator=mtz.ccp4_label_decorator())
mtz_data.mtz_object().write(mtz_file)
converted = map_tools.auto_convert_map_coefficients(mtz_file=mtz_file,
pdb_file=pdb_file)
assert (not None in [converted.f_map, converted.diff_map])
assert (converted.f_map == 'tmp_iotbx_map_tools_FWT.ccp4')
assert (converted.f_map_type == "2mFo-DFc")
server = map_tools.server(mtz_file)
map_files = server.convert_ccp4_map(pdb_file=pdb_file)
map_files = [os.path.basename(file_name) for file_name in map_files]
assert (map_files == [
'tmp_iotbx_map_tools_FWT.ccp4', 'tmp_iotbx_map_tools_DELFWT.ccp4'
])
# part 3: Resolve style
mtz_data = fc.as_mtz_dataset(column_root_label="FWT",
label_decorator=mtz.ccp4_label_decorator())
ampl = abs(fc)
phases = fc.phases()
fom = fc.customized_copy(data=flex.double(fc.data().size(), 1),
observation_type=None)
mtz_data.add_miller_array(ampl, column_root_label="FP")
mtz_data.add_miller_array(phases, column_root_label="PHIM")
mtz_data.add_miller_array(fom, column_root_label="FOMM")
mtz_data.mtz_object().write(mtz_file)
server = map_tools.server(mtz_file)
map_file = server.convert_resolve_map(pdb_file=None, force=False)
assert (map_file == 'tmp_iotbx_map_tools.ccp4')
assert os.path.exists(map_file)
# write_map_coefficients_generic
map_tools.write_map_coefficients_generic(
map_coeffs=[fc, fc.generate_bijvoet_mates(), fc, fc],
map_types=["2mFo-DFc", "mFo-DFc", "anom", "other"],
file_name="tmp_iotbx_map_tools2.mtz")
mtz_in = file_reader.any_file("tmp_iotbx_map_tools2.mtz")
labels = [
a.info().label_string() for a in mtz_in.file_server.miller_arrays
]
assert (labels == [
'2FOFCWT,PH2FOFCWT', 'FOFCWT,PHFOFCWT', 'ANOM,PHANOM', 'other,PHother'
])
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 recycle(miller_array, column_root_label, column_types=None, verbose=0):
original_dataset = to_mtz(miller_array, column_root_label, column_types)
label_decorator = mtz.label_decorator()
written = original_dataset.mtz_object()
if (0 or verbose):
written.show_summary()
original_dataset.mtz_object().write(file_name="tmp_iotbx_mtz.mtz")
restored = mtz.object(file_name="tmp_iotbx_mtz.mtz")
if (0 or verbose):
restored.show_summary()
assert restored.title() == written.title()
assert [line.rstrip() for line in restored.history()] \
== list(written.history())
assert restored.space_group_name() == written.space_group_name()
assert restored.space_group_number() == written.space_group_number()
assert restored.space_group() == written.space_group()
assert restored.point_group_name() == written.point_group_name()
assert restored.lattice_centring_type() == written.lattice_centring_type()
assert restored.n_batches() == written.n_batches()
assert restored.n_reflections() == written.n_reflections()
assert eps_eq(restored.max_min_resolution(),
written.max_min_resolution(),
eps=1.e-5)
assert restored.n_crystals() == written.n_crystals()
assert restored.n_active_crystals() == written.n_active_crystals()
assert restored.n_crystals() == 2
for rx, wx in zip(restored.crystals(), written.crystals()):
assert rx.name() == wx.name()
assert rx.project_name() == wx.project_name()
assert rx.unit_cell().is_similar_to(wx.unit_cell())
assert rx.n_datasets() == wx.n_datasets()
for rd, wd in zip(rx.datasets(), wx.datasets()):
assert rd.name() == wd.name()
assert rd.wavelength() == wd.wavelength()
assert rd.n_columns() == wd.n_columns()
miller_set = restored.crystals()[1].miller_set()
assert miller_set.indices().size() == restored.n_reflections()
crystal_symmetry = restored.crystals()[1].crystal_symmetry()
restored_dataset = restored.crystals()[1].datasets()[0]
if (not miller_array.anomalous_flag()):
if (miller_array.sigmas() is None):
if (miller_array.is_complex_array()):
assert restored_dataset.n_columns() == 3 + 2
group = restored.extract_complex(
column_label_ampl=column_root_label,
column_label_phi=label_decorator.phases(column_root_label))
elif (miller_array.is_hendrickson_lattman_array()):
assert restored_dataset.n_columns() == 3 + 4
deco = label_decorator.hendrickson_lattman
group = restored.extract_hendrickson_lattman(
column_label_a=deco(column_root_label, 0),
column_label_b=deco(column_root_label, 1),
column_label_c=deco(column_root_label, 2),
column_label_d=deco(column_root_label, 3))
else:
assert restored_dataset.n_columns() == 3 + 1
group = restored.extract_reals(column_label=column_root_label)
r = miller.array(miller_set=miller.set(
crystal_symmetry=crystal_symmetry,
indices=group.indices,
anomalous_flag=False),
data=group.data)
else:
assert restored_dataset.n_columns() == 3 + 2
group = restored.extract_observations(
column_label_data=column_root_label,
column_label_sigmas=label_decorator.sigmas(column_root_label))
r = miller.array(miller_set=miller.set(
crystal_symmetry=crystal_symmetry,
indices=group.indices,
anomalous_flag=False),
data=group.data,
sigmas=group.sigmas)
else:
if (miller_array.sigmas() is None):
if (miller_array.is_complex_array()):
assert restored_dataset.n_columns() == 3 + 4
group = restored.extract_complex_anomalous(
column_label_ampl_plus=label_decorator.anomalous(
column_root_label, "+"),
column_label_phi_plus=label_decorator.phases(
column_root_label, "+"),
column_label_ampl_minus=label_decorator.anomalous(
column_root_label, "-"),
column_label_phi_minus=label_decorator.phases(
column_root_label, "-"))
elif (miller_array.is_hendrickson_lattman_array()):
assert restored_dataset.n_columns() == 3 + 8
deco = label_decorator.hendrickson_lattman
group = restored.extract_hendrickson_lattman_anomalous(
column_label_a_plus=deco(column_root_label, 0, "+"),
column_label_b_plus=deco(column_root_label, 1, "+"),
column_label_c_plus=deco(column_root_label, 2, "+"),
column_label_d_plus=deco(column_root_label, 3, "+"),
column_label_a_minus=deco(column_root_label, 0, "-"),
column_label_b_minus=deco(column_root_label, 1, "-"),
column_label_c_minus=deco(column_root_label, 2, "-"),
column_label_d_minus=deco(column_root_label, 3, "-"))
else:
assert restored_dataset.n_columns() == 3 + 2
group = restored.extract_reals_anomalous(
column_label_plus=label_decorator.anomalous(
column_root_label, "+"),
column_label_minus=label_decorator.anomalous(
column_root_label, "-"))
r = miller.array(miller_set=miller.set(
crystal_symmetry=crystal_symmetry,
indices=group.indices,
anomalous_flag=True),
data=group.data)
else:
assert restored_dataset.n_columns() == 3 + 4
group = restored.extract_observations_anomalous(
column_label_data_plus=label_decorator.anomalous(
column_root_label, "+"),
column_label_sigmas_plus=label_decorator.sigmas(
column_root_label, "+"),
column_label_data_minus=label_decorator.anomalous(
column_root_label, "-"),
column_label_sigmas_minus=label_decorator.sigmas(
column_root_label, "-"))
r = miller.array(miller_set=miller.set(
crystal_symmetry=crystal_symmetry,
indices=group.indices,
anomalous_flag=True),
data=group.data,
sigmas=group.sigmas)
verify_miller_arrays(miller_array, r)
restored_miller_arrays = restored.as_miller_arrays()
assert len(restored_miller_arrays) == 1
thff = restored_miller_arrays[0].info().type_hints_from_file
assert thff is not None
assert miller_array.is_hendrickson_lattman_array() \
== (thff == "hendrickson_lattman")
verify_miller_arrays(miller_array, restored_miller_arrays[0])
mtz_object = miller_array.as_mtz_dataset(
column_root_label=column_root_label).mtz_object()
restored_miller_arrays = mtz_object.as_miller_arrays()
assert len(restored_miller_arrays) == 1
verify_miller_arrays(miller_array, restored_miller_arrays[0])
if (miller_array.is_bool_array() or miller_array.is_integer_array()
or miller_array.is_real_array()):
cb_op = miller_array.change_of_basis_op_to_niggli_cell()
mtz_object.change_basis_in_place(cb_op=cb_op)
cb_array = miller_array.change_basis(cb_op=cb_op)
assert mtz_object.space_group() == cb_array.space_group()
for mtz_crystal in mtz_object.crystals():
assert mtz_crystal.unit_cell().is_similar_to(cb_array.unit_cell())
restored_miller_arrays = mtz_object.as_miller_arrays()
assert len(restored_miller_arrays) == 1
verify_miller_arrays(cb_array, restored_miller_arrays[0])
mtz_object.change_basis_in_place(cb_op=cb_op.inverse())
assert mtz_object.space_group() == miller_array.space_group()
for mtz_crystal in mtz_object.crystals():
assert mtz_crystal.unit_cell().is_similar_to(
miller_array.unit_cell())
restored_miller_arrays = mtz_object.as_miller_arrays()
assert len(restored_miller_arrays) == 1
verify_miller_arrays(miller_array, restored_miller_arrays[0])
def recycle(miller_array, column_root_label, column_types=None, verbose=0):
original_dataset = to_mtz(miller_array, column_root_label, column_types)
label_decorator = mtz.label_decorator()
written = original_dataset.mtz_object()
if 0 or verbose:
written.show_summary()
original_dataset.mtz_object().write(file_name="tmp_iotbx_mtz.mtz")
restored = mtz.object(file_name="tmp_iotbx_mtz.mtz")
if 0 or verbose:
restored.show_summary()
assert restored.title() == written.title()
assert [line.rstrip() for line in restored.history()] == list(written.history())
assert restored.space_group_name() == written.space_group_name()
assert restored.space_group_number() == written.space_group_number()
assert restored.space_group() == written.space_group()
assert restored.point_group_name() == written.point_group_name()
assert restored.lattice_centring_type() == written.lattice_centring_type()
assert restored.n_batches() == written.n_batches()
assert restored.n_reflections() == written.n_reflections()
assert eps_eq(restored.max_min_resolution(), written.max_min_resolution(), eps=1.0e-5)
assert restored.n_crystals() == written.n_crystals()
assert restored.n_active_crystals() == written.n_active_crystals()
assert restored.n_crystals() == 2
for rx, wx in zip(restored.crystals(), written.crystals()):
assert rx.name() == wx.name()
assert rx.project_name() == wx.project_name()
assert rx.unit_cell().is_similar_to(wx.unit_cell())
assert rx.n_datasets() == wx.n_datasets()
for rd, wd in zip(rx.datasets(), wx.datasets()):
assert rd.name() == wd.name()
assert rd.wavelength() == wd.wavelength()
assert rd.n_columns() == wd.n_columns()
miller_set = restored.crystals()[1].miller_set()
assert miller_set.indices().size() == restored.n_reflections()
crystal_symmetry = restored.crystals()[1].crystal_symmetry()
restored_dataset = restored.crystals()[1].datasets()[0]
if not miller_array.anomalous_flag():
if miller_array.sigmas() is None:
if miller_array.is_complex_array():
assert restored_dataset.n_columns() == 3 + 2
group = restored.extract_complex(
column_label_ampl=column_root_label, column_label_phi=label_decorator.phases(column_root_label)
)
elif miller_array.is_hendrickson_lattman_array():
assert restored_dataset.n_columns() == 3 + 4
deco = label_decorator.hendrickson_lattman
group = restored.extract_hendrickson_lattman(
column_label_a=deco(column_root_label, 0),
column_label_b=deco(column_root_label, 1),
column_label_c=deco(column_root_label, 2),
column_label_d=deco(column_root_label, 3),
)
else:
assert restored_dataset.n_columns() == 3 + 1
group = restored.extract_reals(column_label=column_root_label)
r = miller.array(
miller_set=miller.set(crystal_symmetry=crystal_symmetry, indices=group.indices, anomalous_flag=False),
data=group.data,
)
else:
assert restored_dataset.n_columns() == 3 + 2
group = restored.extract_observations(
column_label_data=column_root_label, column_label_sigmas=label_decorator.sigmas(column_root_label)
)
r = miller.array(
miller_set=miller.set(crystal_symmetry=crystal_symmetry, indices=group.indices, anomalous_flag=False),
data=group.data,
sigmas=group.sigmas,
)
else:
if miller_array.sigmas() is None:
if miller_array.is_complex_array():
assert restored_dataset.n_columns() == 3 + 4
group = restored.extract_complex_anomalous(
column_label_ampl_plus=label_decorator.anomalous(column_root_label, "+"),
column_label_phi_plus=label_decorator.phases(column_root_label, "+"),
column_label_ampl_minus=label_decorator.anomalous(column_root_label, "-"),
column_label_phi_minus=label_decorator.phases(column_root_label, "-"),
)
elif miller_array.is_hendrickson_lattman_array():
assert restored_dataset.n_columns() == 3 + 8
deco = label_decorator.hendrickson_lattman
group = restored.extract_hendrickson_lattman_anomalous(
column_label_a_plus=deco(column_root_label, 0, "+"),
column_label_b_plus=deco(column_root_label, 1, "+"),
column_label_c_plus=deco(column_root_label, 2, "+"),
column_label_d_plus=deco(column_root_label, 3, "+"),
column_label_a_minus=deco(column_root_label, 0, "-"),
column_label_b_minus=deco(column_root_label, 1, "-"),
column_label_c_minus=deco(column_root_label, 2, "-"),
column_label_d_minus=deco(column_root_label, 3, "-"),
)
else:
assert restored_dataset.n_columns() == 3 + 2
group = restored.extract_reals_anomalous(
column_label_plus=label_decorator.anomalous(column_root_label, "+"),
column_label_minus=label_decorator.anomalous(column_root_label, "-"),
)
r = miller.array(
miller_set=miller.set(crystal_symmetry=crystal_symmetry, indices=group.indices, anomalous_flag=True),
data=group.data,
)
else:
assert restored_dataset.n_columns() == 3 + 4
group = restored.extract_observations_anomalous(
column_label_data_plus=label_decorator.anomalous(column_root_label, "+"),
column_label_sigmas_plus=label_decorator.sigmas(column_root_label, "+"),
column_label_data_minus=label_decorator.anomalous(column_root_label, "-"),
column_label_sigmas_minus=label_decorator.sigmas(column_root_label, "-"),
)
r = miller.array(
miller_set=miller.set(crystal_symmetry=crystal_symmetry, indices=group.indices, anomalous_flag=True),
data=group.data,
sigmas=group.sigmas,
)
verify_miller_arrays(miller_array, r)
restored_miller_arrays = restored.as_miller_arrays()
assert len(restored_miller_arrays) == 1
thff = restored_miller_arrays[0].info().type_hints_from_file
assert thff is not None
assert miller_array.is_hendrickson_lattman_array() == (thff == "hendrickson_lattman")
verify_miller_arrays(miller_array, restored_miller_arrays[0])
mtz_object = miller_array.as_mtz_dataset(column_root_label=column_root_label).mtz_object()
restored_miller_arrays = mtz_object.as_miller_arrays()
assert len(restored_miller_arrays) == 1
verify_miller_arrays(miller_array, restored_miller_arrays[0])
if miller_array.is_bool_array() or miller_array.is_integer_array() or miller_array.is_real_array():
cb_op = miller_array.change_of_basis_op_to_niggli_cell()
mtz_object.change_basis_in_place(cb_op=cb_op)
cb_array = miller_array.change_basis(cb_op=cb_op)
assert mtz_object.space_group() == cb_array.space_group()
for mtz_crystal in mtz_object.crystals():
assert mtz_crystal.unit_cell().is_similar_to(cb_array.unit_cell())
restored_miller_arrays = mtz_object.as_miller_arrays()
assert len(restored_miller_arrays) == 1
verify_miller_arrays(cb_array, restored_miller_arrays[0])
mtz_object.change_basis_in_place(cb_op=cb_op.inverse())
assert mtz_object.space_group() == miller_array.space_group()
for mtz_crystal in mtz_object.crystals():
assert mtz_crystal.unit_cell().is_similar_to(miller_array.unit_cell())
restored_miller_arrays = mtz_object.as_miller_arrays()
assert len(restored_miller_arrays) == 1
verify_miller_arrays(miller_array, restored_miller_arrays[0])
def exercise_map_tools () :
prefix = "tmp_iotbx_map_tools"
pdb_file = prefix + ".pdb"
mtz_file = prefix + ".mtz"
pdb_in = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1 N GLY P -1 -22.866 -2.627 15.217 1.00 0.00 N
ATOM 2 CA GLY P -1 -22.714 -3.068 16.621 1.00 0.00 C
ATOM 3 C GLY P -1 -21.276 -3.457 16.936 1.00 0.00 C
ATOM 4 O GLY P -1 -20.538 -3.887 16.047 1.00 0.00 O
ATOM 5 H1 GLY P -1 -22.583 -3.364 14.590 1.00 0.00 H
ATOM 6 H2 GLY P -1 -22.293 -1.817 15.040 1.00 0.00 H
ATOM 7 H3 GLY P -1 -23.828 -2.392 15.027 1.00 0.00 H
ATOM 8 HA2 GLY P -1 -23.016 -2.261 17.288 1.00 0.00 H
ATOM 9 HA3 GLY P -1 -23.352 -3.933 16.803 1.00 0.00 H
""")
xrs = pdb_in.input.xray_structure_simple()
open(pdb_file, "w").write(pdb_in.hierarchy.as_pdb_string(xrs))
fc = xrs.structure_factors(d_min=1.5).f_calc()
dec = mtz.label_decorator(phases_prefix="PH")
# part 1: phenix.refine style
mtz_data = fc.as_mtz_dataset(
column_root_label="2FOFCWT",
label_decorator=dec)
mtz_data.add_miller_array(fc,
column_root_label="2FOFCWT_no_fill",
label_decorator=dec)
mtz_data.add_miller_array(fc,
column_root_label="FOFCWT",
label_decorator=dec)
mtz_data.add_miller_array(fc,
column_root_label="ANOM",
label_decorator=dec)
mtz_data.mtz_object().write(mtz_file)
converted = map_tools.auto_convert_map_coefficients(
mtz_file=mtz_file,
pdb_file=pdb_file)
assert (not None in [converted.f_map,converted.diff_map,converted.anom_map])
assert (converted.f_map == "tmp_iotbx_map_tools_2mFo-DFc.ccp4")
assert (converted.f_map_type == "2mFo-DFc")
server = map_tools.server(mtz_file)
files = server.convert_phenix_maps(file_base=prefix)
files = [ os.path.basename(file_name) for file_name in files ]
assert (files == ['tmp_iotbx_map_tools_anomalous.ccp4',
'tmp_iotbx_map_tools_mFo-DFc.ccp4', 'tmp_iotbx_map_tools_2mFo-DFc.ccp4',
'tmp_iotbx_map_tools_2mFo-DFc_no_fill.ccp4'])
for fn in files :
assert os.path.isfile(fn)
os.remove(fn)
file_name = server.convert_any_map(
f_label="2FOFCWT,PH2FOFCWT",
phi_label=None,
fom_label=None,
use_standard_map_names=True)
assert (file_name == "tmp_iotbx_map_tools_2mFo-DFc.ccp4")
assert os.path.isfile(file_name)
# part 2: Phaser/Refmac style
mtz_data = fc.as_mtz_dataset(
column_root_label="FWT",
label_decorator=mtz.ccp4_label_decorator())
mtz_data.add_miller_array(fc,
column_root_label="DELFWT",
label_decorator=mtz.ccp4_label_decorator())
mtz_data.mtz_object().write(mtz_file)
converted = map_tools.auto_convert_map_coefficients(
mtz_file=mtz_file,
pdb_file=pdb_file)
assert (not None in [converted.f_map, converted.diff_map])
assert (converted.f_map == 'tmp_iotbx_map_tools_FWT.ccp4')
assert (converted.f_map_type == "2mFo-DFc")
server = map_tools.server(mtz_file)
map_files = server.convert_ccp4_map(pdb_file=pdb_file)
map_files = [ os.path.basename(file_name) for file_name in map_files ]
assert (map_files == ['tmp_iotbx_map_tools_FWT.ccp4',
'tmp_iotbx_map_tools_DELFWT.ccp4'])
# part 3: Resolve style
mtz_data = fc.as_mtz_dataset(
column_root_label="FWT",
label_decorator=mtz.ccp4_label_decorator())
ampl = abs(fc)
phases = fc.phases()
fom = fc.customized_copy(
data=flex.double(fc.data().size(), 1),
observation_type=None)
mtz_data.add_miller_array(ampl, column_root_label="FP")
mtz_data.add_miller_array(phases, column_root_label="PHIM")
mtz_data.add_miller_array(fom, column_root_label="FOMM")
mtz_data.mtz_object().write(mtz_file)
server = map_tools.server(mtz_file)
map_file = server.convert_resolve_map(pdb_file=None,
force=False)
assert (map_file == 'tmp_iotbx_map_tools.ccp4')
assert os.path.exists(map_file)
# write_map_coefficients_generic
map_tools.write_map_coefficients_generic(
map_coeffs=[fc, fc.generate_bijvoet_mates(), fc, fc],
map_types=["2mFo-DFc", "mFo-DFc", "anom", "other"],
file_name="tmp_iotbx_map_tools2.mtz")
mtz_in = file_reader.any_file("tmp_iotbx_map_tools2.mtz")
labels = [a.info().label_string() for a in mtz_in.file_server.miller_arrays]
assert (labels == ['2FOFCWT,PH2FOFCWT', 'FOFCWT,PHFOFCWT', 'ANOM,PHANOM',
'other,PHother'])
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