from __future__ import absolute_import, division, print_function from cctbx.array_family import flex from cctbx import crystal, miller, sgtbx, uctbx from iotbx import cif from iotbx.cif import CifParserError from iotbx.cif.builders import CifBuilderError from iotbx import crystal_symmetry_from_any from iotbx.reflection_file_reader import any_reflection_file from libtbx.test_utils import \ approx_equal, show_diff, Exception_expected, open_tmp_file from six.moves import cStringIO as StringIO import sys from six.moves import zip 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.wavelength_id _refln.scale_group_code _refln.pdbx_I_plus _refln.pdbx_I_plus_sigma _refln.pdbx_I_minus _refln.pdbx_I_minus_sigma -87 5 46 1 3 1 40.2 40.4 6.7 63.9 -87 5 45 1 3 1 47.8 29.7 35.1 30.5 -87 5 44 1 3 1 18.1 33.2 0.5 34.6 -87 5 43 1 3 1 6.1 45.4 12.9 51.6 -87 5 42 1 3 1 -6.6 45.6 -15.5 55.8 -87 7 37 1 3 1 6.3 43.4 ? ? -87 7 36 1 3 1 -67.2 55.4 ? ? -88 2 44 1 3 1 0 -1 35 38.5 -88 2 43 1 3 1 0 -1 57.4 41.5 -88 4 45 1 3 1 -1 46.1 -9.1 45.6 -88 4 44 1 3 1 -19.8 49.2 0.3 34.7 -88 6 44 1 3 1 -1.8 34.8 ? ? """) def exercise_lex_parse_build(): exercise_parser(cif.reader, cif.builders.cif_model_builder) cm = cif.reader(input_string=cif_quoted_string).model() assert cm['global']['_a'] == 'a"b' assert cm['global']['_b'] == "a dog's life" stdout = sys.stdout s = StringIO() sys.stdout = s try: cif.reader(input_string=cif_invalid_missing_value) except CifParserError: pass else: raise Exception_expected r = cif.reader( input_string=cif_invalid_missing_value, raise_if_errors=False) assert r.error_count() == 1 try: cif.reader(input_string=cif_invalid_string) except CifParserError: pass else: raise Exception_expected a = cif.reader(input_string=cif_cod) assert a.error_count() == 0 try: cif.reader(input_string=cif_invalid_semicolon_text_field) except CifParserError: pass else: raise Exception_expected d = cif.reader(input_string=cif_valid_semicolon_text_field) assert d.error_count() == 0 assert d.model()['1']['_a'] == '\n1\n' e = cif.reader(input_string=cif_unquoted_string_semicolon) assert not show_diff(str(e.model()), """\ data_1 _a ;1 _b ; _c 2 """) cif_str_1 = """\ data_1 _a 1 """ cif_str_2 = """\ data_2 _b 2 """ cm = cif.reader(input_string=cif_str_1).model() assert list(cm.keys()) == ['1'] cif.reader(input_string=cif_str_2, cif_object=cm).model() assert list(cm.keys()) == ['1', '2'] try: cm = cif.reader(input_string=cif_invalid_loop).model() except CifParserError: pass else: raise Exception_expected try: cm = cif.reader(input_string=cif_invalid_loop_2).model() except CifParserError: pass else: raise Exception_expected sys.stdout = stdout arrays = miller.array.from_cif(file_object=StringIO( cif_miller_array_template %( '_refln_F_calc', '_refln_F_meas', '_refln_F_sigma')), data_block_name='global') assert sorted(arrays.keys()) == ['_refln_F_calc', '_refln_F_meas'] assert arrays['_refln_F_calc'].sigmas() is None assert isinstance(arrays['_refln_F_meas'].sigmas(), flex.double) arrays = miller.array.from_cif(file_object=StringIO( cif_miller_array_template %( '_refln_A_calc', '_refln_B_calc', '_refln_F_meas')), data_block_name='global') assert sorted(arrays.keys()) == ['_refln_A_calc', '_refln_F_meas'] assert arrays['_refln_A_calc'].is_complex_array() arrays = miller.array.from_cif(file_object=StringIO( cif_miller_array_template %( '_refln_A_meas', '_refln_B_meas', '_refln_F_meas')), data_block_name='global') assert sorted(arrays.keys()) == ['_refln_A_meas', '_refln_F_meas'] assert arrays['_refln_A_meas'].is_complex_array() arrays = miller.array.from_cif(file_object=StringIO( cif_miller_array_template %( '_refln_intensity_calc', '_refln_intensity_meas', '_refln_intensity_sigma')), data_block_name='global') assert sorted(arrays.keys()) == [ '_refln_intensity_calc', '_refln_intensity_meas'] arrays = miller.array.from_cif(file_object=StringIO( cif_miller_array_template %( '_refln_F_calc', '_refln_phase_calc', '_refln_F_sigma')), data_block_name='global') assert arrays['_refln_F_calc'].is_complex_array() for data_block_name in (None, "global"): miller_arrays = cif.reader(file_object=StringIO( cif_miller_array_template %( '_refln_F_calc', '_refln_F_meas', '_refln_F_sigma'))).as_miller_arrays(data_block_name=data_block_name) assert " ".join(sorted([str(ma.info()) for ma in miller_arrays])) \ == "cif:global,_refln_F_calc cif:global,_refln_F_meas,_refln_F_sigma" f = open_tmp_file(suffix="cif") f.write(cif_miller_array_template %( '_refln_F_calc', '_refln_F_meas', '_refln_F_sigma')) f.close() miller_arrays = any_reflection_file(file_name=f.name).as_miller_arrays() assert len(miller_arrays) == 2 cs = crystal.symmetry( space_group_info=sgtbx.space_group_info("P1") ) miller_arrays = any_reflection_file(file_name=f.name).as_miller_arrays( crystal_symmetry=cs, force_symmetry=True, anomalous=True) assert miller_arrays[0].anomalous_flag() is True assert miller_arrays[0].crystal_symmetry().space_group() == cs.space_group() def exercise_parser(reader, builder): cif_model = reader( input_string=cif_xray_structure, builder=builder()).model() xs_builder = cif.builders.crystal_structure_builder(cif_model['global']) xs1 = xs_builder.structure # also test construction of cif model from xray structure xs_cif_block = xs1.as_cif_block() xs2 = cif.builders.crystal_structure_builder(xs_cif_block).structure sio = StringIO() xs1.as_cif_simple(out=sio) xs3 = reader(input_string=sio.getvalue()).build_crystal_structures( data_block_name='global') xs_iso = xs1.deep_copy_scatterers() xs_iso.convert_to_isotropic() xs4 = cif.builders.crystal_structure_builder(xs_iso.as_cif_block()).structure for xs in (xs1, xs2, xs3): sc = xs.scatterers() assert list(sc.extract_labels()) == ['o','c'] assert list(sc.extract_scattering_types()) == ['O','C'] assert approx_equal(sc.extract_occupancies(), (0.8, 1)) assert approx_equal(sc.extract_sites(), ((0.5,0,0),(0,0,0))) assert approx_equal(sc.extract_u_star(), [(-1, -1, -1, -1, -1, -1), (1e-3, 5e-4, (1e-3)/3, 0, 0, 0)]) assert approx_equal(sc.extract_u_iso(), (0.1, -1)) assert approx_equal(xs.unit_cell().parameters(), (10,20,30,90,90,90)) assert str(xs.space_group_info()) == 'C 1 2/m 1' # cif_model = reader( input_string=cif_miller_array, builder=builder()).model() ma_builder = cif.builders.miller_array_builder(cif_model['global']) ma1 = ma_builder.arrays()['_refln_F_squared_meas'] if isinstance(cif_model, cif.model.cif): assert (ma_builder.arrays()['_refln_observed_status'].data() == flex.std_string(['o'] * ma1.size())) # also test construction of cif model from miller array ma2 = cif.builders.miller_array_builder( ma1.as_cif_block(array_type='meas')).arrays()['_refln.F_squared_meas'] for ma in (ma1, ma2): sio = StringIO() ma.show_array(sio) assert not show_diff(sio.getvalue(), """\ (1, 0, 0) 748.71 13.87 (2, 0, 0) 1318.51 24.29 (3, 0, 0) 1333.51 33.75 (4, 0, 0) 196.58 10.85 (5, 0, 0) 3019.71 55.29 (6, 0, 0) 1134.38 23.94 (7, 0, 0) 124.01 15.16 (8, 0, 0) -1.22 10.49 (9, 0, 0) 189.09 20.3 (10, 0, 0) 564.68 35.61 (-10, 1, 0) 170.23 22.26 """) sio = StringIO() ma1.show_summary(sio) # Miller array info: cif:_refln.F_squared_meas,_refln.F_squared_sigma assert not show_diff(sio.getvalue(), """\ Miller array info: cif:_refln_F_squared_meas,_refln_F_squared_sigma Observation type: xray.intensity Type of data: double, size=11 Type of sigmas: double, size=11 Number of Miller indices: 11 Anomalous flag: False Unit cell: (7.999, 9.372, 14.736, 82.625, 81.527, 81.726) Space group: P -1 (No. 2) """) sio = StringIO() ma2.show_summary(sio) # Miller array info: cif:_refln.F_squared_meas,_refln.F_squared_sigma assert not show_diff(sio.getvalue(), """\ Miller array info: cif:_refln.F_squared_meas,_refln.F_squared_sigma Observation type: xray.intensity Type of data: double, size=11 Type of sigmas: double, size=11 Number of Miller indices: 11 Anomalous flag: False Unit cell: (7.999, 9.372, 14.736, 82.625, 81.527, 81.726) Space group: P -1 (No. 2) """) cif_xray_structure = """\ data_global loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, y, -z' '-x, -y, -z' 'x, -y, z' 'x+1/2, y+1/2, z' '-x+1/2, y+1/2, -z' '-x+1/2, -y+1/2, -z' 'x+1/2, -y+1/2, z' _cell_length_a 10 _cell_length_b 20 _cell_length_c 30 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 loop_ # comment _atom_site_label # another comment _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_occupancy _atom_site_type_symbol 'o' 0.5 0 0 0.1 0.8 'O' 'c' 0 0 0 0.2 1 'C' loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 'c' 0.1 0.2 0.3 0 0 0 """ cif_miller_array = """\ data_global loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, -y, -z' _cell_length_a 7.999 _cell_length_b 9.372 _cell_length_c 14.736 _cell_angle_alpha 82.625 _cell_angle_beta 81.527 _cell_angle_gamma 81.726 loop_ _refln_index_h _refln_index_k _refln_index_l _refln_F_squared_calc _refln_F_squared_meas _refln_F_squared_sigma _refln_observed_status 1 0 0 756.07 748.71 13.87 o 2 0 0 1266.94 1318.51 24.29 o 3 0 0 1381.53 1333.51 33.75 o 4 0 0 194.77 196.58 10.85 o 5 0 0 3102.74 3019.71 55.29 o 6 0 0 1145.05 1134.38 23.94 o 7 0 0 103.98 124.01 15.16 o 8 0 0 16.94 -1.22 10.49 o 9 0 0 194.74 189.09 20.30 o 10 0 0 581.30 564.68 35.61 o -10 1 0 148.83 170.23 22.26 o """ cif_miller_array_template = """\ data_global loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, -y, -z' _cell_length_a 7.9999 _cell_length_b 9.3718 _cell_length_c 14.7362 _cell_angle_alpha 82.625 _cell_angle_beta 81.527 _cell_angle_gamma 81.726 loop_ _refln_index_h _refln_index_k _refln_index_l %s %s %s 1 0 0 1.2 1.3 0.1 2 0 0 2.3 2.4 0.2 3 0 0 3.4 3.5 0.3 4 0 0 4.5 6.7 0.4 # comment with WS before and after """ cif_cod = """\ data_global _a 1 _[b] 2 _c e43 _d # comment # another comment '1 2' _e ) """ cif_quoted_string = """\ data_global # both of these are legal apparently _a "a"b" _b 'a dog's life' """ cif_invalid_loop = """\ data_global loop_ _a _b _c 1 """ cif_invalid_loop_2 = """\ data_1 loop_ _a _b _c 1 2 3 4 5 """ cif_invalid_missing_value = """\ data_global _a 1 _b _c 3 """ cif_invalid_string = """\ data_global _a 'no closing quote _b 1 """ cif_invalid_semicolon_text_field = """\ data_1 _a ; 1 ; """ cif_valid_semicolon_text_field = """\ data_1 _a ; 1 ; """ cif_unquoted_string_semicolon = """\ data_1 _a ;1 _b ; _c 2 """ cif_global = """\ global_ _a 1 _b 2 data_1 _c 3 _d 4 """ def exercise_atom_type_loop(): from cctbx import xray cif_model = cif.reader(input_string=cif_xray_structure).model() xs = cif.builders.crystal_structure_builder(cif_model['global']).structure xs.set_inelastic_form_factors(photon=0.71073, table="henke") loop = cif.atom_type_cif_loop(xray_structure=xs, format="mmcif") s = StringIO() print(loop, file=s) assert not show_diff( "\n".join([li.rstrip() for li in s.getvalue().splitlines()]), """\ loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_a5 _atom_type.scat_Cromer_Mann_a6 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_b5 _atom_type.scat_Cromer_Mann_b6 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C 0.00347 0.00161 2.18189 1.77612 1.08772 0.64146 0.20789 0.10522 13.45337 32.57901 0.74729 0.25125 80.97993 0.05873 0.0 ; 6-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; 'Henke, Gullikson and Davis, At. Data and Nucl. Data Tables, 1993, 54, 2' O 0.01158 0.00611 2.91262 2.58808 0.98057 0.69663 0.68508 0.13677 14.48462 6.03818 0.42255 0.15446 35.53892 0.03841 0.0 ; 6-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; 'Henke, Gullikson and Davis, At. Data and Nucl. Data Tables, 1993, 54, 2' """) def exercise_partial_crystal_symmetry(): def get_inp(u, s): result = ["data_test"] if (u): result.append("_cell_length_a 12.605(3)") if (s): result.append("_symmetry_space_group_name_Hall '-P 2yn'") return "\n".join(result) def get_cs(input_string): cif_model = cif.reader(input_string=input_string).model() return cif.builders.crystal_symmetry_builder( cif_block=cif_model["test"]).crystal_symmetry cs = get_cs(get_inp(False, False)) assert cs.unit_cell() is None assert cs.space_group_info() is None cs = get_cs(get_inp(False, True)) assert cs.unit_cell() is None assert str(cs.space_group_info()) == "P 1 21/n 1" try: get_cs(get_inp(True, False)) except CifBuilderError as e: assert str(e) == "Not all unit cell parameters are given in the cif file" else: raise Exception_expected def exercise_crystal_symmetry(): cm = cif.reader(input_string=p1_sym_ops).model() cs_builder = cif.builders.crystal_symmetry_builder(cm["r1e5xsf"]) assert cs_builder.crystal_symmetry.space_group_info().symbol_and_number() \ == 'P 1 (No. 1)' file_object = open_tmp_file(suffix=".cif") file_object.write(p1_sym_ops) file_object.close() cs = crystal_symmetry_from_any.extract_from(file_name=file_object.name) assert cs.space_group_info().symbol_and_number() == 'P 1 (No. 1)' 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 find_miller_array_from_labels(miller_arrays, labels): for ma in miller_arrays: found = True for label in labels: if label not in ma.info().labels: found = False break if found: return ma raise RuntimeError("Could not find miller array with labels %s" %labels) r3adrsf = """ data_r3adrsf _cell.length_a 163.970 _cell.length_b 45.230 _cell.length_c 110.890 _cell.angle_alpha 90.000 _cell.angle_beta 131.640 _cell.angle_gamma 90.000 # _symmetry.entry_id 3adr _symmetry.space_group_name_H-M 'C 1 2 1' loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.status _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_HL_A_iso _refln.pdbx_HL_B_iso _refln.pdbx_HL_C_iso _refln.pdbx_HL_D_iso 1 1 1 o 0 2 2 484.70 11.74 -3.168 -3.662 3.247 3.261 1 1 1 o 0 2 3 337.40 4.60 2.287 -3.629 0.053 -0.597 1 1 1 o 0 2 4 735.40 8.43 0.476 -8.605 -4.861 0.921 1 1 1 o 0 2 5 433.70 4.76 2.453 -1.663 0.000 -9.540 1 1 1 o 0 2 6 435.20 4.96 -9.081 3.661 1.511 -2.736 2 3 1 o 0 2 7 427.50 4.56 8.677 -0.013 2.307 -4.220 2 3 1 o 0 2 8 661.00 7.26 -6.468 5.112 -5.411 -6.731 2 3 4 o 0 2 9 211.90 2.64 -2.279 0.914 0.455 -6.038 2 3 4 f 0 2 10 466.80 5.01 -0.005 6.330 -1.916 -0.598 2 3 4 o 0 2 11 424.20 4.66 -0.938 7.011 -1.603 1.724 #END data_r3adrAsf # # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.pdbx_I_plus _refln.pdbx_I_plus_sigma _refln.pdbx_I_minus _refln.pdbx_I_minus_sigma 1 3 1 87 5 -46 40.2 40.4 6.7 63.9 1 3 1 87 5 -45 47.8 29.7 35.1 30.5 1 3 1 87 5 -44 18.1 33.2 0.5 34.6 1 3 1 87 5 -43 6.1 45.4 12.9 51.6 1 3 1 87 5 -42 -6.6 45.6 -15.5 55.8 1 3 1 87 7 -37 6.3 43.4 ? ? 1 3 1 87 7 -36 -67.2 55.4 ? ? 1 3 1 88 2 -44 0 -1 35.0 38.5 1 3 1 88 2 -43 0 -1 57.4 41.5 1 3 1 88 4 -45 -1.0 46.1 -9.1 45.6 1 3 1 88 4 -44 -19.8 49.2 0.3 34.7 1 3 1 88 6 -44 -1.8 34.8 ? ? #END OF REFLECTIONS """ r3ad7sf = """ data_r3ad7sf _cell.length_a 198.9488 _cell.length_b 198.9488 _cell.length_c 196.7646 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 120.0000 loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 'X, Y, Z' 2 'X-Y, X, Z+5/6' 3 '-Y, X-Y, Z+2/3' 4 '-X, -Y, Z+1/2' 5 '-X+Y, -X, Z+1/3' 6 'Y, -X+Y, Z+1/6' 7 '-Y, -X, -Z+1/6' 8 'X-Y, -Y, -Z' 9 'X, X-Y, -Z+5/6' 10 'Y, X, -Z+2/3' 11 '-X+Y, Y, -Z+1/2' 12 '-X, -X+Y, -Z+1/3' loop_ _refln.wavelength_id _refln.crystal_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.F_meas_au _refln.F_meas_sigma_au _refln.F_calc _refln.phase_calc _refln.fom 1 1 1 0 0 6 o 267.2 12.1 353.2 180.0 0.04 1 1 1 0 0 12 o 4700.0 113.0 3962.4 360.0 1.00 1 1 1 0 0 18 o 10214.0 222.9 8775.9 360.0 1.00 1 1 1 0 0 24 o 8268.9 192.9 11557.1 180.0 1.00 1 2 1 0 0 30 o 3274.6 77.5 2214.5 0.0 1.00 1 2 1 0 0 36 o 317.8 30.4 1993.3 0.0 0.05 1 2 1 0 0 42 o 12026.4 286.2 6514.5 180.0 1.00 1 2 1 0 0 48 o 1972.6 51.4 1357.9 180.0 0.91 """ r3v56sf = """ data_r3v56sf _cell.length_a 121.6330 _cell.length_b 121.6330 _cell.length_c 157.2140 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 120.0000 loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 'X, Y, Z' 2 'X-Y, X, Z+5/6' 3 '-Y, X-Y, Z+2/3' 4 '-X, -Y, Z+1/2' 5 '-X+Y, -X, Z+1/3' 6 'Y, -X+Y, Z+1/6' loop_ _refln.index_h _refln.index_k _refln.index_l _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT 0 0 6 1793.541 297.538 758.340 297.538 0 0 12 926.361 8.616 79.780 8.616 0 0 18 2789.494 3.915 158.391 183.915 0 0 24 18.715 196.581 133.229 196.581 0 0 30 1040.906 174.397 370.046 174.397 0 0 36 2065.720 180.659 163.982 0.659 0 0 42 1850.858 199.047 1496.942 199.047 0 0 48 882.296 190.106 289.614 10.106 0 1 6 161.907 235.025 332.891 235.025 0 1 7 168.822 39.648 511.322 39.648 0 1 8 42.963 55.666 347.014 55.666 0 1 9 81.428 68.620 89.690 248.620 """ r6cxosf =""" data_r6cxosf # _audit.revision_id 1_0 _audit.creation_date 2018-09-05 _audit.update_record "Initial release" # _cell.entry_id 6cxo _cell.length_a 52.588 _cell.length_b 149.213 _cell.length_c 165.827 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.2036 # _entry.id 6cxo # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # _symmetry.entry_id 6cxo _symmetry.space_group_name_H-M "P 21 2 21" _symmetry.Int_Tables_number 2018 # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.pdbx_r_free_flag _refln.F_meas_au _refln.F_meas_sigma_au _refln.F_calc_au _refln.phase_calc _refln.pdbx_HL_A_iso _refln.pdbx_HL_B_iso _refln.pdbx_HL_C_iso _refln.pdbx_HL_D_iso _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.fom 1 1 1 0 0 6 o 10 2637.91 60.30 80.15 180.00 -0.30 0.00 0.00 0.00 975.82 180.00 895.68 180.00 0.29 1 1 1 0 0 8 o 12 976.72 17.78 1455.08 180.00 -3.75 0.00 0.00 0.00 120.17 0.00 1575.25 0.00 1.00 1 1 1 0 0 10 o 17 473.14 11.64 474.88 0.00 0.84 0.00 0.00 0.00 33.10 180.00 507.98 180.00 0.69 1 1 1 0 0 18 f 0 2590.99 42.02 1898.47 180.00 -32.04 0.00 0.00 0.00 1546.52 180.00 351.95 0.00 1.00 1 1 1 0 1 4 o 16 1300.19 15.72 28.41 180.00 -0.06 0.00 0.00 0.00 71.53 180.00 43.12 180.00 0.06 1 1 1 0 1 5 o 11 106.11 7.63 367.11 90.00 0.00 0.04 0.00 0.00 361.40 270.00 728.52 270.00 0.04 1 1 1 0 1 6 o 14 946.07 10.00 504.84 180.00 -1.32 0.00 0.00 0.00 620.26 180.00 115.42 180.00 0.87 1 1 1 0 1 12 o 4 640.34 9.55 59.40 0.00 0.30 0.00 0.00 0.00 191.03 0.00 131.62 0.00 0.29 1 1 1 0 1 13 o 4 56.14 9.21 53.87 90.00 0.00 0.02 0.00 0.00 52.30 270.00 106.18 270.00 0.02 """ r6c5f_phases =""" data_6c5f_phases # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x-y,z 3 -x+y,-x,z _space_group.crystal_system trigonal _space_group.IT_number 143 _space_group.name_H-M_alt 'P 3' _space_group.name_Hall ' P 3' _symmetry.space_group_name_H-M 'P 3' _symmetry.space_group_name_Hall ' P 3' _symmetry.Int_Tables_number 143 _cell.length_a 83.936 _cell.length_b 83.936 _cell.length_c 40.479 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.volume 246977.230 loop_ _refln.index_h _refln.index_k _refln.index_l _refln.FREE _refln.FP _refln.SIGFP _refln.FC _refln.PHIC _refln.FC_ALL _refln.PHIC_ALL _refln.FWT _refln.PHWT _refln.DELFWT _refln.PHDELWT _refln.FOM _refln.FC_ALL_LS _refln.PHIC_ALL_LS 0 0 2 1 676.187 6.17276 2809.82 -154.6 452.62 -175.696 839.275 -175.696 386.655 -175.696 0.955279 390.291 176.785 0 0 3 1 563.624 5.12057 1839.65 75.6562 786.515 93.5793 309.766 93.5793 476.749 -86.4207 0.972529 862.338 93.9542 0 0 4 1 344.711 2.51519 677.686 -13.7128 617.668 -3.12039 36.3321 -3.12039 581.336 176.88 0.948621 693.021 -3.41476 0 0 5 1 669.529 4.32892 1158.44 -95.7759 701.642 -69.0476 610.651 -69.0476 90.9919 110.952 0.980012 815.552 -71.438 0 0 6 1 208.118 1.47303 348.769 38.3981 150.027 -1.98773 138.218 -1.98773 11.8089 178.012 0.692503 184.095 5.08278 0 0 7 1 834.241 7.56552 361.555 58.3196 639.886 67.9106 1003.72 67.9106 363.837 67.9106 0.985092 655.782 66.9071 0 0 8 1 268.459 2.64541 328.863 -136.983 259.118 -124.253 211.27 -124.253 47.8489 55.7467 0.876088 296.701 -128.016 0 0 9 1 265.482 2.68548 552.45 -169.384 359.081 -166.58 138.292 -166.58 220.789 13.42 0.936738 437.08 -167.718 0 0 10 1 183.754 1.99406 195.673 33.4295 219.826 58.527 87.9439 58.527 131.882 -121.473 0.837452 210.823 50.7412 """ integer_observations = """ data_r3ad7sf _cell.length_a 198.9488 _cell.length_b 198.9488 _cell.length_c 196.7646 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 120.0000 loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 'X, Y, Z' 2 'X-Y, X, Z+5/6' 3 '-Y, X-Y, Z+2/3' 4 '-X, -Y, Z+1/2' 5 '-X+Y, -X, Z+1/3' 6 'Y, -X+Y, Z+1/6' 7 '-Y, -X, -Z+1/6' 8 'X-Y, -Y, -Z' 9 'X, X-Y, -Z+5/6' 10 'Y, X, -Z+2/3' 11 '-X+Y, Y, -Z+1/2' 12 '-X, -X+Y, -Z+1/3' loop_ _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.F_meas_au _refln.F_meas_sigma_au 0 0 6 o 267 12 0 0 12 o 4700 113 0 0 18 o 10214 222 0 0 24 o 8268 192 0 0 30 o 3274 77 0 0 36 o 317 30 0 0 42 o 12026 286 0 0 48 o 1972 51 """ p1_sym_ops = """\ data_r1e5xsf _cell.entry_id 1E5X _cell.length_a 57.760 _cell.length_b 62.140 _cell.length_c 76.590 _cell.angle_alpha 109.48 _cell.angle_beta 97.61 _cell.angle_gamma 112.74 _cell.formula_units_Z 2 _symmetry_equiv.id 1 _symmetry_equiv.pos_as_xyz X,Y,Z """ def exercise_detect_binary(): binary_string = '\xff\xf8\x00\x00\x00\x00\x00\x00' from iotbx.cif import reader try: reader(input_string=binary_string) except CifParserError as e: pass else: raise Exception_expected def exercise_syntax_errors(): empty_loop_str = """\ data_fred loop_ loop_ _a _b 1 2 3 4 """ try: cif.reader(input_string=empty_loop_str) except CifParserError as e: pass else: raise Exception_expected bad_semicolon_text_field = """\ data_sucrose _a 1 _exptl_absorpt_process_details ; Final HKLF 4 output contains 64446 reflections, Rint = 0.0650 (47528 with I > 3sig(I), Rint = 0.0624); """ try: cif.reader(input_string=bad_semicolon_text_field) except CifParserError as e: pass else: raise Exception_expected def exercise_missing_atom_site_type_symbol(): m = cif.reader(input_string=cif_with_atom_site_type_symbol).model() xs = cif.builders.crystal_structure_builder(m['9000000']).structure sc = xs.scatterers() assert len(sc) == 18 assert sc[0].label == 'Fe1' assert sc[0].scattering_type == 'Fe' assert sc[-1].label == 'O7' assert sc[-1].scattering_type == 'O' cif_with_atom_site_type_symbol = """\ #------------------------------------------------------------------------------ #$Date$ #$Revision$ #$URL: svn://www.crystallography.net/cod/cif/9/00/00/9000000.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/. The original data for this entry # were provided the American Mineralogist Crystal Structure Database, # http://rruff.geo.arizona.edu/AMS/amcsd.php # # The file may be used within the scientific community so long as # proper attribution is given to the journal article from which the # data were obtained. # data_9000000 loop_ _publ_author_name 'Finger, L. W.' _publ_section_title ; The crystal structure and cation distribution of a grunerite Locality: Wabush iron formation, Labrador, Canada ; _journal_name_full 'Mineralogical Society of America Special Paper' _journal_page_first 95 _journal_page_last 100 _journal_volume 2 _journal_year 1969 _chemical_formula_sum 'F0.5 Fe6.1 H1.5 Mg0.9 O23.5 Si8' _chemical_name_mineral Grunerite _space_group_IT_number 12 _symmetry_space_group_name_Hall '-C 2y' _symmetry_space_group_name_H-M 'C 1 2/m 1' _cell_angle_alpha 90 _cell_angle_beta 101.892 _cell_angle_gamma 90 _cell_length_a 9.5642 _cell_length_b 18.393 _cell_length_c 5.3388 _cell_volume 919.015 _exptl_crystal_density_diffrn 3.521 _[local]_cod_chemical_formula_sum_orig '(Fe6.1 Mg.9) Si8 O23.5 (F.5 H1.5)' _cod_database_code 9000000 loop_ _symmetry_equiv_pos_as_xyz x,y,z 1/2+x,1/2+y,z x,-y,z 1/2+x,1/2-y,z -x,y,-z 1/2-x,1/2+y,-z -x,-y,-z 1/2-x,1/2-y,-z loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 Fe1 0.00532 0.00943 0.00498 0.00000 0.00198 0.00000 Mg1 0.00532 0.00943 0.00498 0.00000 0.00198 0.00000 Fe2 0.00532 0.00823 0.00622 0.00000 0.00198 0.00000 Mg2 0.00532 0.00823 0.00622 0.00000 0.00198 0.00000 Fe3 0.00621 0.00857 0.00622 0.00000 0.00074 0.00000 Mg3 0.00621 0.00857 0.00622 0.00000 0.00074 0.00000 Fe4 0.00843 0.01645 0.01106 0.00000 0.00421 0.00000 Mg4 0.00843 0.01645 0.01106 0.00000 0.00421 0.00000 Si1 0.00399 0.00703 0.00553 -0.00026 0.00050 0.00000 Si2 0.00444 0.00651 0.00747 -0.00166 0.00074 0.00000 O1 0.00577 0.01028 0.00899 0.00000 0.00173 0.00146 O2 0.00399 0.01028 0.00940 -0.00087 0.00272 -0.00146 OH3 0.01864 0.01200 0.01272 0.00000 0.00570 0.00000 F3 0.01864 0.01200 0.01272 0.00000 0.00570 0.00000 O4 0.00887 0.00686 0.00567 -0.00087 -0.00050 0.00097 O5 0.00355 0.01371 0.01244 -0.00262 0.00223 0.00730 O6 0.00399 0.02057 0.00760 0.00349 -0.00025 -0.00438 O7 0.00843 0.00000 0.02019 0.00000 0.00520 0.00000 loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy _atom_site_U_iso_or_equiv Fe1 0.00000 0.08781 0.50000 0.84800 0.00646 Mg1 0.00000 0.08781 0.50000 0.15200 0.00646 Fe2 0.00000 0.17936 0.00000 0.77300 0.00646 Mg2 0.00000 0.17936 0.00000 0.22700 0.00646 Fe3 0.00000 0.00000 0.00000 0.88800 0.00709 Mg3 0.00000 0.00000 0.00000 0.11200 0.00709 Fe4 0.00000 0.25741 0.50000 0.98500 0.01165 Mg4 0.00000 0.25741 0.50000 0.01500 0.01165 Si1 0.28670 0.08360 0.27070 1.00000 0.00557 Si2 0.29930 0.16670 0.77800 1.00000 0.00621 O1 0.11200 0.08820 0.20440 1.00000 0.00849 O2 0.12530 0.17350 0.71420 1.00000 0.00747 O-H3 0.11470 0.00000 0.70350 0.75000 0.01381 F3 0.11470 0.00000 0.70350 0.25000 0.01381 O4 0.38390 0.24160 0.76890 1.00000 0.00735 O5 0.34830 0.12750 0.05190 1.00000 0.00975 O6 0.34780 0.11820 0.55300 1.00000 0.01089 O7 0.33760 0.00000 0.27000 1.00000 0.00937 """ def exercise_build_with_wavelength(): m = cif.reader(input_string=cif_xray_structure_with_wavelength).model() xs = cif.builders.crystal_structure_builder(m['global']).structure assert approx_equal(xs.wavelength, 1.54184) cif_xray_structure_missing_wavelength = \ cif_xray_structure_with_wavelength.replace('1.54184', '?') m = cif.reader(input_string=cif_xray_structure_missing_wavelength).model() xs = cif.builders.crystal_structure_builder(m['global']).structure assert xs.wavelength == None cif_xray_structure_with_wavelength = """\ data_global loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, y, -z' '-x, -y, -z' 'x, -y, z' 'x+1/2, y+1/2, z' '-x+1/2, y+1/2, -z' '-x+1/2, -y+1/2, -z' 'x+1/2, -y+1/2, z' _cell_length_a 10 _cell_length_b 20 _cell_length_c 30 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _diffrn_radiation_wavelength 1.54184 loop_ # comment _atom_site_label # another comment _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_occupancy _atom_site_type_symbol 'o' 0.5 0 0 0.1 0.8 'O' 'c' 0 0 0 0.2 1 'C' loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 'c' 0.1 0.2 0.3 0 0 0 """ def exercise(): exercise_missing_atom_site_type_symbol() exercise_syntax_errors() exercise_detect_binary() exercise_crystal_symmetry() exercise_miller_arrays_as_cif_block() exercise_lex_parse_build() exercise_partial_crystal_symmetry() exercise_mmcif_structure_factors() exercise_atom_type_loop() exercise_build_with_wavelength() if __name__ == '__main__': exercise() print("OK")