from __future__ import division 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 cStringIO import StringIO import sys 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 ? ? """) 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 cm.keys() == ['1'] cif.reader(input_string=cif_str_2, cif_object=cm).model() assert 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 sorted(arrays.keys()) == ['_refln_F_calc'] 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 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() ma.show_summary(sio) 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 >> s, loop 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, 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, ','.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 find_miller_array_from_labels(miller_arrays, labels): for ma in miller_arrays: if labels in str(ma.info()): 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 """ 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, 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, 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, e: pass else: raise Exception_expected def exercise(): 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() if __name__ == '__main__': exercise() print "OK"