def exercise_miller_arrays_as_cif_block():
from iotbx.cif import reader
cif_model = reader(input_string=cif_miller_array,
builder=cif.builders.cif_model_builder()).model()
ma_builder = cif.builders.miller_array_builder(cif_model['global'])
ma1 = ma_builder.arrays()['_refln_F_squared_meas']
mas_as_cif_block = cif.miller_arrays_as_cif_block(ma1,
array_type='meas',
format="corecif")
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.complex_double([1 - 1j] * ma1.size())),
array_type='calc')
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.complex_double([1 - 2j] * ma1.size())),
column_names=['_refln_A_calc', '_refln_B_calc'])
for key in ('_refln_F_squared_meas', '_refln_F_squared_sigma',
'_refln_F_calc', '_refln_phase_calc', '_refln_A_calc',
'_refln_A_calc'):
assert key in mas_as_cif_block.cif_block.keys(), key
#
mas_as_cif_block = cif.miller_arrays_as_cif_block(ma1,
array_type='meas',
format="mmcif")
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.complex_double([1 - 1j] * ma1.size())),
array_type='calc')
for key in ('_refln.F_squared_meas', '_refln.F_squared_sigma',
'_refln.F_calc', '_refln.phase_calc',
'_space_group_symop.operation_xyz', '_cell.length_a',
'_refln.index_h'):
assert key in mas_as_cif_block.cif_block.keys()
#
mas_as_cif_block = cif.miller_arrays_as_cif_block(
ma1,
column_names=[
'_diffrn_refln_intensity_net', '_diffrn_refln_intensity_sigma'
],
miller_index_prefix='_diffrn_refln')
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.std_string(ma1.size(), 'om')),
column_name='_diffrn_refln_intensity_u')
for key in ('_diffrn_refln_intensity_net', '_diffrn_refln_intensity_sigma',
'_diffrn_refln_intensity_u'):
assert key in mas_as_cif_block.cif_block.keys()
#
try:
reader(input_string=cif_global)
except CifParserError, e:
pass
def exercise_mmcif_structure_factors():
miller_arrays = cif.reader(input_string=r3adrsf).as_miller_arrays()
assert len(miller_arrays) == 16
hl_coeffs = find_miller_array_from_labels(
miller_arrays, ','.join([
'scale_group_code=1', 'crystal_id=2', 'wavelength_id=3',
'_refln.pdbx_HL_A_iso', '_refln.pdbx_HL_B_iso',
'_refln.pdbx_HL_C_iso', '_refln.pdbx_HL_D_iso']))
assert hl_coeffs.is_hendrickson_lattman_array()
assert hl_coeffs.size() == 2
mas_as_cif_block = cif.miller_arrays_as_cif_block(
hl_coeffs, column_names=('_refln.pdbx_HL_A_iso', '_refln.pdbx_HL_B_iso',
'_refln.pdbx_HL_C_iso', '_refln.pdbx_HL_D_iso'))
abcd = []
for key in ('_refln.pdbx_HL_A_iso', '_refln.pdbx_HL_B_iso',
'_refln.pdbx_HL_C_iso', '_refln.pdbx_HL_D_iso'):
assert key in mas_as_cif_block.cif_block.keys()
abcd.append(flex.double(mas_as_cif_block.cif_block[key]))
hl_coeffs_from_cif_block = flex.hendrickson_lattman(*abcd)
assert approx_equal(hl_coeffs.data(), hl_coeffs_from_cif_block)
f_meas_au = find_miller_array_from_labels(
miller_arrays, ','.join([
'scale_group_code=1', 'crystal_id=1', 'wavelength_id=1',
'_refln.F_meas_au', '_refln.F_meas_sigma_au']))
assert f_meas_au.is_xray_amplitude_array()
assert f_meas_au.size() == 5
assert f_meas_au.sigmas() is not None
assert f_meas_au.space_group_info().symbol_and_number() == 'C 1 2 1 (No. 5)'
assert approx_equal(f_meas_au.unit_cell().parameters(),
(163.97, 45.23, 110.89, 90.0, 131.64, 90.0))
pdbx_I_plus_minus = find_miller_array_from_labels(
miller_arrays, ','.join(
['_refln.pdbx_I_plus', '_refln.pdbx_I_plus_sigma',
'_refln.pdbx_I_minus', '_refln.pdbx_I_minus_sigma']))
assert pdbx_I_plus_minus.is_xray_intensity_array()
assert pdbx_I_plus_minus.anomalous_flag()
assert pdbx_I_plus_minus.size() == 21
assert pdbx_I_plus_minus.unit_cell() is None # no symmetry information in
assert pdbx_I_plus_minus.space_group() is None # this CIF block
#
miller_arrays = cif.reader(input_string=r3ad7sf).as_miller_arrays()
assert len(miller_arrays) == 11
f_calc = find_miller_array_from_labels(
miller_arrays, ','.join([
'crystal_id=2', 'wavelength_id=1', '_refln.F_calc', '_refln.phase_calc']))
assert f_calc.is_complex_array()
assert f_calc.size() == 4
#
miller_arrays = cif.reader(input_string=integer_observations).as_miller_arrays()
assert len(miller_arrays) == 2
assert isinstance(miller_arrays[0].data(), flex.double)
assert isinstance(miller_arrays[0].sigmas(), flex.double)
#
miller_arrays = cif.reader(input_string=r3v56sf).as_miller_arrays()
assert len(miller_arrays) == 2
for ma in miller_arrays: assert ma.is_complex_array()
assert miller_arrays[0].info().labels == [
'r3v56sf', '_refln.pdbx_DELFWT', '_refln.pdbx_DELPHWT']
assert miller_arrays[1].info().labels == [
'r3v56sf', '_refln.pdbx_FWT', '_refln.pdbx_PHWT']
def exercise_mmcif_structure_factors():
miller_arrays = cif.reader(input_string=r3adrsf).as_miller_arrays()
assert len(miller_arrays) == 16
hl_coeffs = find_miller_array_from_labels(
miller_arrays, ','.join([
'scale_group_code=1', 'crystal_id=2', 'wavelength_id=3',
'_refln.pdbx_HL_A_iso', '_refln.pdbx_HL_B_iso',
'_refln.pdbx_HL_C_iso', '_refln.pdbx_HL_D_iso'
]))
assert hl_coeffs.is_hendrickson_lattman_array()
assert hl_coeffs.size() == 2
mas_as_cif_block = cif.miller_arrays_as_cif_block(
hl_coeffs,
column_names=('_refln.pdbx_HL_A_iso', '_refln.pdbx_HL_B_iso',
'_refln.pdbx_HL_C_iso', '_refln.pdbx_HL_D_iso'))
abcd = []
for key in ('_refln.pdbx_HL_A_iso', '_refln.pdbx_HL_B_iso',
'_refln.pdbx_HL_C_iso', '_refln.pdbx_HL_D_iso'):
assert key in list(mas_as_cif_block.cif_block.keys())
abcd.append(flex.double(mas_as_cif_block.cif_block[key]))
hl_coeffs_from_cif_block = flex.hendrickson_lattman(*abcd)
assert approx_equal(hl_coeffs.data(), hl_coeffs_from_cif_block)
f_meas_au = find_miller_array_from_labels(
miller_arrays, ','.join([
'scale_group_code=1', 'crystal_id=1', 'wavelength_id=1',
'_refln.F_meas_au', '_refln.F_meas_sigma_au'
]))
assert f_meas_au.is_xray_amplitude_array()
assert f_meas_au.size() == 5
assert f_meas_au.sigmas() is not None
assert f_meas_au.space_group_info().symbol_and_number(
) == 'C 1 2 1 (No. 5)'
assert approx_equal(f_meas_au.unit_cell().parameters(),
(163.97, 45.23, 110.89, 90.0, 131.64, 90.0))
pdbx_I_plus_minus = find_miller_array_from_labels(
miller_arrays, ','.join([
'_refln.pdbx_I_plus', '_refln.pdbx_I_plus_sigma',
'_refln.pdbx_I_minus', '_refln.pdbx_I_minus_sigma'
]))
assert pdbx_I_plus_minus.is_xray_intensity_array()
assert pdbx_I_plus_minus.anomalous_flag()
assert pdbx_I_plus_minus.size() == 21
assert pdbx_I_plus_minus.unit_cell() is None # no symmetry information in
assert pdbx_I_plus_minus.space_group() is None # this CIF block
#
miller_arrays = cif.reader(input_string=r3ad7sf).as_miller_arrays()
assert len(miller_arrays) == 11
f_calc = find_miller_array_from_labels(
miller_arrays, ','.join([
'crystal_id=2', 'wavelength_id=1', '_refln.F_calc',
'_refln.phase_calc'
]))
assert f_calc.is_complex_array()
assert f_calc.size() == 4
#
miller_arrays = cif.reader(
input_string=integer_observations).as_miller_arrays()
assert len(miller_arrays) == 2
assert isinstance(miller_arrays[0].data(), flex.double)
assert isinstance(miller_arrays[0].sigmas(), flex.double)
#
miller_arrays = cif.reader(input_string=r3v56sf).as_miller_arrays()
assert len(miller_arrays) == 2
for ma in miller_arrays:
assert ma.is_complex_array()
assert miller_arrays[0].info().labels == [
'r3v56sf', '_refln.pdbx_DELFWT', '_refln.pdbx_DELPHWT'
]
assert miller_arrays[1].info().labels == [
'r3v56sf', '_refln.pdbx_FWT', '_refln.pdbx_PHWT'
]
def exercise_miller_arrays_as_cif_block():
from iotbx.cif import reader
cif_model = reader(input_string=cif_miller_array,
builder=cif.builders.cif_model_builder()).model()
ma_builder = cif.builders.miller_array_builder(cif_model['global'])
ma1 = ma_builder.arrays()['_refln_F_squared_meas']
mas_as_cif_block = cif.miller_arrays_as_cif_block(ma1,
array_type='meas',
format="corecif")
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.complex_double([1 - 1j] * ma1.size())),
array_type='calc')
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.complex_double([1 - 2j] * ma1.size())),
column_names=['_refln_A_calc', '_refln_B_calc'])
for key in ('_refln_F_squared_meas', '_refln_F_squared_sigma',
'_refln_F_calc', '_refln_phase_calc', '_refln_A_calc',
'_refln_A_calc'):
assert (key in mas_as_cif_block.cif_block.keys()), key
#
mas_as_cif_block = cif.miller_arrays_as_cif_block(ma1,
array_type='meas',
format="mmcif")
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.complex_double([1 - 1j] * ma1.size())),
array_type='calc')
for key in ('_refln.F_squared_meas', '_refln.F_squared_sigma',
'_refln.F_calc', '_refln.phase_calc',
'_space_group_symop.operation_xyz', '_cell.length_a',
'_refln.index_h'):
assert key in mas_as_cif_block.cif_block.keys()
#
mas_as_cif_block = cif.miller_arrays_as_cif_block(
ma1,
column_names=[
'_diffrn_refln_intensity_net', '_diffrn_refln_intensity_sigma'
],
miller_index_prefix='_diffrn_refln')
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.std_string(ma1.size(), 'om')),
column_name='_diffrn_refln_intensity_u')
for key in ('_diffrn_refln_intensity_net', '_diffrn_refln_intensity_sigma',
'_diffrn_refln_intensity_u'):
assert key in list(mas_as_cif_block.cif_block.keys())
#
try:
reader(input_string=cif_global)
except CifParserError as e:
pass
else:
raise Exception_expected
cif_model = reader(input_string=cif_global, strict=False).model()
assert not show_diff(
str(cif_model), """\
data_1
_c 3
_d 4
""")
# exercise adding miller arrays with non-matching indices
cs = crystal.symmetry(unit_cell=uctbx.unit_cell((10, 10, 10, 90, 90, 90)),
space_group_info=sgtbx.space_group_info(symbol="P1"))
mi = flex.miller_index(((1, 0, 0), (1, 2, 3), (2, 3, 4)))
ms1 = miller.set(cs, mi)
ma1 = miller.array(ms1, data=flex.double((1, 2, 3)))
mas_as_cif_block = cif.miller_arrays_as_cif_block(
ma1, column_name="_refln.F_meas_au")
ms2 = miller.set(cs, mi[:2])
ma2 = miller.array(ms2, data=flex.complex_double([1 - 2j] * ms2.size()))
mas_as_cif_block.add_miller_array(ma2,
column_names=("_refln.F_calc_au",
"_refln.phase_calc")),
ms3 = miller.set(cs, flex.miller_index(((1, 0, 0), (5, 6, 7), (2, 3, 4))))
ma3 = miller.array(ms3, data=flex.double((4, 5, 6)))
mas_as_cif_block.add_miller_array(ma3, column_name="_refln.F_squared_meas")
ms4 = miller.set(
cs,
flex.miller_index(
((1, 2, 3), (5, 6, 7), (1, 1, 1), (1, 0, 0), (2, 3, 4))))
ma4 = ms4.d_spacings()
mas_as_cif_block.add_miller_array(ma4, column_name="_refln.d_spacing")
# extract arrays from cif block and make sure we get back what we started with
arrays = cif.builders.miller_array_builder(
mas_as_cif_block.cif_block).arrays()
recycled_arrays = (arrays['_refln.F_meas_au'], arrays['_refln.F_calc_au'],
arrays['_refln.F_squared_meas'],
arrays['_refln.d_spacing'])
for orig, recycled in zip((ma1, ma2, ma3, ma4), recycled_arrays):
assert orig.size() == recycled.size()
recycled = recycled.customized_copy(
anomalous_flag=orig.anomalous_flag())
orig, recycled = orig.common_sets(recycled)
assert orig.indices().all_eq(recycled.indices())
assert approx_equal(orig.data(), recycled.data(), eps=1e-5)
#
cif_model = reader(input_string=r3adrsf,
builder=cif.builders.cif_model_builder()).model()
cs = cif.builders.crystal_symmetry_builder(
cif_model["r3adrsf"]).crystal_symmetry
ma_builder = cif.builders.miller_array_builder(
cif_model['r3adrAsf'],
base_array_info=miller.array_info(crystal_symmetry_from_file=cs))
miller_arrays = list(ma_builder.arrays().values())
assert len(miller_arrays) == 4
mas_as_cif_block = cif.miller_arrays_as_cif_block(
miller_arrays[0].map_to_asu(),
column_names=miller_arrays[0].info().labels,
format="corecif")
for array in miller_arrays[1:]:
labels = array.info().labels
if len(labels) > 1:
for label in labels:
if label.startswith("wavelength_id"):
labels.remove(label)
mas_as_cif_block.add_miller_array(array=array.map_to_asu(),
column_names=array.info().labels)
s = StringIO()
print(mas_as_cif_block.refln_loop, file=s)
assert not show_diff(
s.getvalue(), """\
loop_
_refln_index_h
_refln_index_k
_refln_index_l
_refln.crystal_id
_refln.scale_group_code
_refln.wavelength_id
_refln.pdbx_I_plus
_refln.pdbx_I_plus_sigma
_refln.pdbx_I_minus
_refln.pdbx_I_minus_sigma
-87 5 46 1 1 3 40.2 40.4 6.7 63.9
-87 5 45 1 1 3 47.8 29.7 35.1 30.5
-87 5 44 1 1 3 18.1 33.2 0.5 34.6
-87 5 43 1 1 3 6.1 45.4 12.9 51.6
-87 5 42 1 1 3 -6.6 45.6 -15.5 55.8
-87 7 37 1 1 3 6.3 43.4 ? ?
-87 7 36 1 1 3 -67.2 55.4 ? ?
-88 2 44 1 1 3 0 -1 35 38.5
-88 2 43 1 1 3 0 -1 57.4 41.5
-88 4 45 1 1 3 -1 46.1 -9.1 45.6
-88 4 44 1 1 3 -19.8 49.2 0.3 34.7
-88 6 44 1 1 3 -1.8 34.8 ? ?
""")
def exercise_mmcif_structure_factors():
miller_arrays = cif.reader(input_string=r3adrsf).as_miller_arrays()
assert len(miller_arrays) == 16
hl_coeffs = find_miller_array_from_labels(miller_arrays, [
'_refln.pdbx_HL_A_iso', '_refln.pdbx_HL_B_iso', '_refln.pdbx_HL_C_iso',
'_refln.pdbx_HL_D_iso', 'scale_group_code=1', 'crystal_id=2',
'wavelength_id=3'
])
assert hl_coeffs.is_hendrickson_lattman_array()
assert hl_coeffs.size() == 2
mas_as_cif_block = cif.miller_arrays_as_cif_block(
hl_coeffs,
column_names=('_refln.pdbx_HL_A_iso', '_refln.pdbx_HL_B_iso',
'_refln.pdbx_HL_C_iso', '_refln.pdbx_HL_D_iso'))
abcd = []
for key in ('_refln.pdbx_HL_A_iso', '_refln.pdbx_HL_B_iso',
'_refln.pdbx_HL_C_iso', '_refln.pdbx_HL_D_iso'):
assert key in list(mas_as_cif_block.cif_block.keys())
abcd.append(flex.double(mas_as_cif_block.cif_block[key]))
hl_coeffs_from_cif_block = flex.hendrickson_lattman(*abcd)
assert approx_equal(hl_coeffs.data(), hl_coeffs_from_cif_block)
f_meas_au = find_miller_array_from_labels(miller_arrays, [
'_refln.F_meas_au', '_refln.F_meas_sigma_au', 'scale_group_code=1',
'crystal_id=1', 'wavelength_id=1'
])
assert f_meas_au.is_xray_amplitude_array()
assert f_meas_au.size() == 5
assert f_meas_au.sigmas() is not None
assert f_meas_au.space_group_info().symbol_and_number(
) == 'C 1 2 1 (No. 5)'
assert approx_equal(f_meas_au.unit_cell().parameters(),
(163.97, 45.23, 110.89, 90.0, 131.64, 90.0))
pdbx_I_plus_minus = find_miller_array_from_labels(miller_arrays, [
'_refln.pdbx_I_plus', '_refln.pdbx_I_plus_sigma',
'_refln.pdbx_I_minus', '_refln.pdbx_I_minus_sigma'
])
assert pdbx_I_plus_minus.is_xray_intensity_array()
assert pdbx_I_plus_minus.anomalous_flag()
assert pdbx_I_plus_minus.size() == 21
assert pdbx_I_plus_minus.unit_cell() is None # no symmetry information in
assert pdbx_I_plus_minus.space_group() is None # this CIF block
#
miller_arrays = cif.reader(input_string=r3ad7sf).as_miller_arrays()
assert len(miller_arrays) == 11
f_calc = find_miller_array_from_labels(
miller_arrays,
['r3ad7sf', '_refln.F_calc', '_refln.phase_calc', 'crystal_id=2'
]) #, 'wavelength_id=1']))
assert f_calc.is_complex_array()
assert f_calc.size() == 4
#
miller_arrays = cif.reader(
input_string=integer_observations).as_miller_arrays()
assert len(miller_arrays) == 2
fmeas_sigmeas = find_miller_array_from_labels(miller_arrays,
['_refln.F_meas_au'])
assert isinstance(fmeas_sigmeas.data(), flex.double)
assert isinstance(fmeas_sigmeas.sigmas(), flex.double)
#
miller_arrays = cif.reader(input_string=r3v56sf).as_miller_arrays()
assert len(miller_arrays) == 2
for ma in miller_arrays:
assert ma.is_complex_array()
find_miller_array_from_labels(
miller_arrays,
['r3v56sf', '_refln.pdbx_DELFWT', '_refln.pdbx_DELPHWT'])
find_miller_array_from_labels(
miller_arrays, ['r3v56sf', '_refln.pdbx_FWT', '_refln.pdbx_PHWT'])
# verify _refln.pdbx_FWT', '_refln.pdbx_PHWT' are parsed as complex arrays in the presence of other columns
miller_arrays = cif.reader(input_string=r6cxosf).as_miller_arrays()
assert len(miller_arrays) == 11
ma = find_miller_array_from_labels(
miller_arrays, ['r6cxosf', '_refln.pdbx_FWT', '_refln.pdbx_PHWT'])
assert ma.is_complex_array()
ma = find_miller_array_from_labels(
miller_arrays,
['r6cxosf', '_refln.pdbx_DELFWT', '_refln.pdbx_DELPHWT'])
assert ma.is_complex_array()
# accept unconventional cif column labels resembling mtz column labels
miller_arrays = cif.reader(input_string=r6c5f_phases).as_miller_arrays()
assert len(miller_arrays) == 8
ma = find_miller_array_from_labels(
miller_arrays, ['6c5f_phases', '_refln.FP', '_refln.SIGFP'])
assert ma.is_xray_amplitude_array()
ma = find_miller_array_from_labels(
miller_arrays, ['6c5f_phases', '_refln.FC', '_refln.PHIC'])
assert ma.is_complex_array()
ma = find_miller_array_from_labels(
miller_arrays, ['6c5f_phases', '_refln.FC_ALL', '_refln.PHIC_ALL'])
assert ma.is_complex_array()
ma = find_miller_array_from_labels(
miller_arrays, ['6c5f_phases', '_refln.DELFWT', '_refln.PHDELWT'])
assert ma.is_complex_array()
def exercise_miller_arrays_as_cif_block():
from iotbx.cif import reader
cif_model = reader(input_string=cif_miller_array,
builder=cif.builders.cif_model_builder()).model()
ma_builder = cif.builders.miller_array_builder(cif_model['global'])
ma1 = ma_builder.arrays()['_refln_F_squared_meas']
mas_as_cif_block = cif.miller_arrays_as_cif_block(
ma1, array_type='meas')
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.complex_double([1-1j]*ma1.size())), array_type='calc')
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.complex_double([1-2j]*ma1.size())), column_names=[
'_refln_A_calc', '_refln_B_calc'])
for key in ('_refln_F_squared_meas', '_refln_F_squared_sigma',
'_refln_F_calc', '_refln_phase_calc',
'_refln_A_calc', '_refln_A_calc'):
assert key in mas_as_cif_block.cif_block.keys()
#
mas_as_cif_block = cif.miller_arrays_as_cif_block(
ma1, array_type='meas', format="mmcif")
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.complex_double([1-1j]*ma1.size())), array_type='calc')
for key in ('_refln.F_squared_meas', '_refln.F_squared_sigma',
'_refln.F_calc', '_refln.phase_calc',
'_space_group_symop.operation_xyz',
'_cell.length_a', '_refln.index_h'):
assert key in mas_as_cif_block.cif_block.keys()
#
mas_as_cif_block = cif.miller_arrays_as_cif_block(
ma1, column_names=['_diffrn_refln_intensity_net',
'_diffrn_refln_intensity_sigma'],
miller_index_prefix='_diffrn_refln')
mas_as_cif_block.add_miller_array(
ma1.array(data=flex.std_string(ma1.size(), 'om')),
column_name='_diffrn_refln_intensity_u')
for key in ('_diffrn_refln_intensity_net', '_diffrn_refln_intensity_sigma',
'_diffrn_refln_intensity_u'):
assert key in mas_as_cif_block.cif_block.keys()
#
try: reader(input_string=cif_global)
except CifParserError, e: pass
else: raise Exception_expected
cif_model = reader(input_string=cif_global, strict=False).model()
assert not show_diff(str(cif_model), """\
data_1
_c 3
_d 4
""")
# exercise adding miller arrays with non-matching indices
cs = crystal.symmetry(unit_cell=uctbx.unit_cell((10, 10, 10, 90, 90, 90)),
space_group_info=sgtbx.space_group_info(symbol="P1"))
mi = flex.miller_index(((1,0,0), (1,2,3), (2,3,4)))
ms1 = miller.set(cs, mi)
ma1 = miller.array(ms1, data=flex.double((1,2,3)))
mas_as_cif_block = cif.miller_arrays_as_cif_block(
ma1, column_name="_refln.F_meas_au")
ms2 = miller.set(cs, mi[:2])
ma2 = miller.array(ms2, data=flex.complex_double([1-2j]*ms2.size()))
mas_as_cif_block.add_miller_array(
ma2, column_names=("_refln.F_calc_au", "_refln.phase_calc")),
ms3 = miller.set(cs, flex.miller_index(((1,0,0), (5,6,7), (2,3,4))))
ma3 = miller.array(ms3, data=flex.double((4,5,6)))
mas_as_cif_block.add_miller_array(ma3, column_name="_refln.F_squared_meas")
ms4 = miller.set(cs, flex.miller_index(((1,2,3), (5,6,7), (1,1,1), (1,0,0), (2,3,4))))
ma4 = ms4.d_spacings()
mas_as_cif_block.add_miller_array(ma4, column_name="_refln.d_spacing")
# extract arrays from cif block and make sure we get back what we started with
arrays = cif.builders.miller_array_builder(mas_as_cif_block.cif_block).arrays()
recycled_arrays = (arrays['_refln.F_meas_au'],
arrays['_refln.F_calc_au'],
arrays['_refln.F_squared_meas'],
arrays['_refln.d_spacing'])
for orig, recycled in zip((ma1, ma2, ma3, ma4), recycled_arrays):
assert orig.size() == recycled.size()
recycled = recycled.customized_copy(anomalous_flag=orig.anomalous_flag())
orig, recycled = orig.common_sets(recycled)
assert orig.indices().all_eq(recycled.indices())
assert approx_equal(orig.data(), recycled.data(), eps=1e-5)
#
cif_model = reader(input_string=r3adrsf,
builder=cif.builders.cif_model_builder()).model()
cs = cif.builders.crystal_symmetry_builder(cif_model["r3adrsf"]).crystal_symmetry
ma_builder = cif.builders.miller_array_builder(
cif_model['r3adrAsf'],
base_array_info=miller.array_info(crystal_symmetry_from_file=cs))
miller_arrays = ma_builder.arrays().values()
assert len(miller_arrays) == 4
mas_as_cif_block = cif.miller_arrays_as_cif_block(
miller_arrays[0].map_to_asu(), column_names=miller_arrays[0].info().labels)
for array in miller_arrays[1:]:
labels = array.info().labels
if len(labels) > 1 :
for label in labels :
if label.startswith("wavelength_id") :
labels.remove(label)
mas_as_cif_block.add_miller_array(
array=array.map_to_asu(), column_names=array.info().labels)
s = StringIO()
print >> s, mas_as_cif_block.refln_loop
assert not show_diff(s.getvalue(), """\
loop_
_refln_index_h
_refln_index_k
_refln_index_l
_refln.crystal_id
_refln.scale_group_code
_refln.wavelength_id
_refln.pdbx_I_plus
_refln.pdbx_I_plus_sigma
_refln.pdbx_I_minus
_refln.pdbx_I_minus_sigma
-87 5 46 1 1 3 40.2 40.4 6.7 63.9
-87 5 45 1 1 3 47.8 29.7 35.1 30.5
-87 5 44 1 1 3 18.1 33.2 0.5 34.6
-87 5 43 1 1 3 6.1 45.4 12.9 51.6
-87 5 42 1 1 3 -6.6 45.6 -15.5 55.8
-87 7 37 1 1 3 6.3 43.4 ? ?
-87 7 36 1 1 3 -67.2 55.4 ? ?
-88 2 44 1 1 3 0 -1 35 38.5
-88 2 43 1 1 3 0 -1 57.4 41.5
-88 4 45 1 1 3 -1 46.1 -9.1 45.6
-88 4 44 1 1 3 -19.8 49.2 0.3 34.7
-88 6 44 1 1 3 -1.8 34.8 ? ?
""")
else:
raise Exception_expected
cif_model = reader(input_string=cif_global, strict=False).model()
assert not show_diff(
str(cif_model), """\
data_1
_c 3
_d 4
""")
# exercise adding miller arrays with non-matching indices
cs = crystal.symmetry(unit_cell=uctbx.unit_cell((10, 10, 10, 90, 90, 90)),
space_group_info=sgtbx.space_group_info(symbol="P1"))
mi = flex.miller_index(((1, 0, 0), (1, 2, 3), (2, 3, 4)))
ms1 = miller.set(cs, mi)
ma1 = miller.array(ms1, data=flex.double((1, 2, 3)))
mas_as_cif_block = cif.miller_arrays_as_cif_block(
ma1, column_name="_refln.F_meas_au")
ms2 = miller.set(cs, mi[:2])
ma2 = miller.array(ms2, data=flex.complex_double([1 - 2j] * ms2.size()))
mas_as_cif_block.add_miller_array(ma2,
column_names=("_refln.F_calc_au",
"_refln.phase_calc")),
ms3 = miller.set(cs, flex.miller_index(((1, 0, 0), (5, 6, 7), (2, 3, 4))))
ma3 = miller.array(ms3, data=flex.double((4, 5, 6)))
mas_as_cif_block.add_miller_array(ma3, column_name="_refln.F_squared_meas")
ms4 = miller.set(
cs,
flex.miller_index(
((1, 2, 3), (5, 6, 7), (1, 1, 1), (1, 0, 0), (2, 3, 4))))
ma4 = ms4.d_spacings()
mas_as_cif_block.add_miller_array(ma4, column_name="_refln.d_spacing")
# extract arrays from cif block and make sure we get back what we started with
