# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function from libtbx.test_utils import contains_substring import os, subprocess os.environ['PYTHONIOENCODING'] = 'UTF-8' test1_cifstr = """ data_r4jglsf # _audit.revision_id 1_0 _audit.creation_date 2013-04-03 _audit.update_record ;The data loops contain the following: structure factors used in refinement, from crystal 185601 that is a Met-Inhibition crystal. unmerged original index intensities of data set used for refinement and phasing, this data set comes from crystal 185601 that is a Met-Inhibition crystal, wavelength 1. unmerged original index intensities of data set used for phasing, this data set comes from crystal 185601 that is a Met-Inhibition crystal, wavelength 2. unmerged original index intensities of data set used for phasing, this data set comes from crystal 185601 that is a Met-Inhibition crystal, wavelength 3. experimental phases from crystal 185601 that is a Met-Inhibition crystal. density modified experimental phases from crystal 185601 that is a Met-Inhibition crystal. ; # _cell.entry_id 4jgl _cell.length_a 79.322 _cell.length_b 79.322 _cell.length_c 50.113 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength 1 0.918401 2 0.979338 3 0.979108 # _entry.id 4jgl # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # _symmetry.entry_id 4jgl _symmetry.space_group_name_H-M 'P 61' # # loop_ _refln.crystal_id _refln.wavelength_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 1 1 1 0 0 3 o 1055.8 38.2 1482.3 7.0 1 1 1 0 0 12 x ? ? 1790.1 149.3 1 1 1 3 32 3 o 204.3 3.6 199.8 328.7 1 1 1 3 32 4 o 37.8 5.6 30.8 26.8 1 1 1 3 32 5 o 216.6 3.9 184.1 304.7 1 1 1 3 32 6 o 54.2 3.7 65.5 335.2 1 1 1 3 32 7 f 85.2 3.0 103.4 80.7 1 1 1 3 32 8 o 138.0 3.5 118.6 305.6 1 1 1 3 32 9 o 139.2 3.3 122.3 302.1 1 1 1 3 32 10 o 33.0 5.5 21.9 357.2 1 1 1 3 32 11 o 102.9 3.5 105.7 129.7 1 1 1 3 32 12 o 57.9 5.2 52.7 182.7 1 1 1 54 1 0 f 20.6 9.6 28.9 180.0 1 1 1 54 1 4 o 15.6 5.4 19.4 331.4 1 1 1 54 1 5 o 25.2 6.6 16.9 69.0 #END data_r4jglAsf # _cell.entry_id 4jgl _cell.length_a 79.3216 _cell.length_b 79.3216 _cell.length_c 50.1126 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 120.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ; unmerged original index intensities of data set used for refinement and phasing. ; # _entry.id 4jgl # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.intensity_meas _refln.intensity_sigma 1 1 1 0 0 2 o 5.3 11.4 1 1 1 0 0 -2 o 13.4 13.3 1 1 1 0 0 3 o -5.9 9.6 1 1 1 0 0 -3 o 14.8 14.3 1 1 1 2 -2 -36 o 1056.4 235.7 1 1 1 2 0 -36 o 1176.5 218.3 1 1 1 0 -2 36 o 788.1 195.6 1 1 1 2 -2 36 o 984.7 196.5 1 1 1 -1 55 5 o 285.9 179.5 1 1 1 1 -55 -5 o -105.2 188.9 1 1 1 -55 54 5 o 558.6 268.4 1 1 1 55 -54 -5 o 340.6 311.3 1 1 1 -54 -1 5 o 153.0 129.0 1 1 1 -54 -1 5 o -8.7 101.3 1 1 1 1 -55 5 o 52.0 249.1 1 1 1 -1 55 -5 o -80.1 130.8 1 1 1 55 -54 5 o 576.9 272.9 1 1 1 -55 54 -5 o 219.8 205.6 #END data_r4jglBsf # _cell.entry_id 4jgl _cell.length_a 79.3132 _cell.length_b 79.3132 _cell.length_c 50.1025 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 120.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ' unmerged original index intensities of data set used for phasing.' # _entry.id 4jgl # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.intensity_meas _refln.intensity_sigma 1 2 1 0 0 2 o 2.5 7.6 1 2 1 0 0 -2 o 0.5 11.0 1 2 1 0 0 3 o 20.5 17.2 1 2 1 -1 0 -12 o 22476.8 2327.6 1 2 1 0 -1 -12 o 22730.3 1962.0 1 2 1 1 -1 -12 o 23595.6 1782.0 1 2 1 -1 0 12 o 24913.4 1960.4 1 2 1 1 0 -12 o 23227.8 1777.6 1 2 1 -1 1 -12 o 22906.0 2033.0 1 2 1 0 -1 -14 o 10141.0 877.2 1 2 1 -1 1 14 o 8471.0 838.7 1 2 1 1 -1 -14 o 10248.7 748.4 1 2 1 -1 0 14 o 7835.0 786.6 1 2 1 1 -55 4 o -43.1 74.1 1 2 1 1 -55 5 o 105.6 60.3 1 2 1 55 -54 5 o 303.0 276.2 1 2 1 -55 54 -5 o -44.3 127.2 #END data_r4jglCsf # _cell.entry_id 4jgl _cell.length_a 79.4003 _cell.length_b 79.4003 _cell.length_c 50.1616 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 120.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ' unmerged original index intensities of data set used for phasing.' # _entry.id 4jgl # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.intensity_meas _refln.intensity_sigma 1 3 1 0 0 2 o 2.2 14.2 1 3 1 0 0 -2 o 12.7 14.3 1 3 1 0 0 3 o -9.5 3.8 1 3 1 0 0 -3 o -8.2 3.9 1 3 1 0 0 4 o 20.2 22.1 1 3 1 11 -11 20 o 7381.3 861.9 1 3 1 -11 11 -20 o 8143.7 797.9 1 3 1 11 0 20 o 7939.2 822.9 1 3 1 11 0 20 o 8401.4 889.9 1 3 1 -49 -2 5 o -682.5 697.3 1 3 1 50 1 1 o 164.3 164.9 1 3 1 -50 -1 -1 o 1390.9 464.9 1 3 1 -1 51 1 o -589.3 274.5 1 3 1 1 -51 -1 o 903.4 414.8 1 3 1 -51 50 1 o 63.5 67.2 1 3 1 -50 -1 1 o -1052.0 570.9 1 3 1 50 1 -1 o 174.0 158.8 1 3 1 1 -51 1 o 198.8 479.5 1 3 1 -1 51 -1 o -259.0 239.2 #END data_r4jglDsf # _cell.entry_id 4jgl _cell.length_a 79.3130 _cell.length_b 79.3130 _cell.length_c 50.1030 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 120.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ' experimental phases.' # _entry.id 4jgl # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.pdbx_HL_A_iso _refln.pdbx_HL_B_iso _refln.pdbx_HL_C_iso _refln.pdbx_HL_D_iso 1 1 1 0 0 3 o 0.28 -1.43 0.00 0.00 1 1 1 3 0 12 o 0.02 0.24 0.00 0.00 1 1 1 0 0 18 o 2.89 4.23 0.73 -1.26 1 1 1 0 0 24 o -0.08 -4.39 0.86 1.74 1 1 1 0 0 30 o 23.29 -37.82 13.58 1.94 1 1 1 0 0 36 o 3.35 3.12 0.29 -0.96 1 1 1 0 1 0 o ? ? ? ? 1 1 1 0 1 1 o ? ? ? ? 1 1 1 12 11 7 o -2.50 7.76 1.03 0.31 1 1 1 12 11 8 o -50.91 153.61 31.01 32.58 1 1 1 12 11 9 o 5.73 -8.35 0.09 2.76 1 1 1 12 11 10 o -27.65 30.85 -1.02 9.22 1 1 1 53 3 3 o -0.31 0.46 0.00 0.00 1 1 1 53 3 4 o 0.32 -0.06 0.00 0.00 1 1 1 54 1 0 o -0.27 0.00 0.00 0.00 1 1 1 54 1 1 o 0.47 -0.01 0.00 0.00 1 1 1 54 1 2 o -0.18 -0.34 -0.01 -0.02 1 1 1 54 1 3 o -0.02 -0.28 0.00 0.00 1 1 1 54 1 4 o 0.35 0.49 -0.01 -0.01 1 1 1 54 1 5 o 0.15 -0.48 0.00 0.00 #END data_r4jglEsf # _cell.entry_id 4jgl _cell.length_a 79.3130 _cell.length_b 79.3130 _cell.length_c 50.1030 _cell.angle_alpha 90.0000 _cell.angle_beta 90.0000 _cell.angle_gamma 120.0000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ' density modified experimental phases.' # _entry.id 4jgl # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.phase_meas _refln.pdbx_FWT _refln.fom 1 1 1 0 0 3 o 41.29 1238.431 0.99 1 1 1 0 0 12 o 125.51 1995.770 1.00 1 1 1 0 0 18 o 99.07 807.187 0.98 1 1 1 0 0 24 o -122.68 491.014 0.97 1 1 1 0 0 30 o -25.97 161.558 0.99 1 1 1 0 0 36 o 31.40 56.578 0.81 1 1 1 53 2 1 o -126.70 22.452 0.60 1 1 1 53 2 2 o 92.10 17.818 0.61 1 1 1 53 2 3 o -93.89 7.406 0.27 1 1 1 53 2 4 o -168.56 10.492 0.43 1 1 1 53 3 3 o 127.04 10.290 0.35 1 1 1 53 3 4 o -0.28 4.982 0.18 1 1 1 54 1 0 o 180.00 7.752 0.33 1 1 1 54 1 1 o 13.94 5.584 0.21 1 1 1 54 1 2 o -111.70 4.379 0.16 1 1 1 54 1 3 o -79.85 4.164 0.15 1 1 1 54 1 4 o 56.34 8.051 0.32 1 1 1 54 1 5 o -69.69 7.166 0.29 #END OF REFLECTIONS """ phil1str = """ selected_info { labels = False description = True wavelength = True n_reflections = True span = False minmax_data = True minmax_sigmas = False d_minmax = True data_sigdata_max=True unit_cell = True space_group = True n_centrics = False is_anomalous = False is_symmetry_unique = False n_sys_abs = False data_completeness = True data_compl_infty = False ano_completeness = False ano_mean_diff = False n_bijvoet = False n_singletons = False } wrap_labels = -20 """ expected1str = """ Starting job =============================================================================== 33 Miller arrays in this dataset: Type | λ/Å | #HKLs | min,max data |MaxDatSigDat| d_min,d_max/Å | unit cell (a/Å, b/Å, c/Å, α%s, β%s, γ%s) | space group |Data compl.| Integer |0.918401 | 15 | 1.0, 1.0| nan | 1.25, 16.704| 79.322, 79.322, 50.113, 90, 90, 120 | P 61 (No. 169) |0.00029017 | Integer |0.918401 | 15 | 1.0, 1.0| nan | 1.25, 16.704| 79.322, 79.322, 50.113, 90, 90, 120 | P 61 (No. 169) |0.00029017 | Integer |0.918401 | 15 | 1.0, 1.0| nan | 1.25, 16.704| 79.322, 79.322, 50.113, 90, 90, 120 | P 61 (No. 169) |0.00029017 | String |0.918401 | 15 | nan, nan| nan | 1.25, 16.704| 79.322, 79.322, 50.113, 90, 90, 120 | P 61 (No. 169) |0.00029017 | Amplitude |0.918401 | 14 | 15.6, 1055.8| 56.75 | 1.25, 16.704| 79.322, 79.322, 50.113, 90, 90, 120 | P 61 (No. 169) |0.00034303 | Map coeffs |0.918401 | 15 | 16.9, 1790.1| nan | 1.25, 16.704| 79.322, 79.322, 50.113, 90, 90, 120 | P 61 (No. 169) |0.00029017 | Integer |0.918401 | 18 | 1.0, 1.0| nan | 1.25, 25.056| 79.322, 79.322, 50.113, 90, 90, 120 | ? | nan | Integer |0.918401 | 18 | 1.0, 1.0| nan | 1.25, 25.056| 79.322, 79.322, 50.113, 90, 90, 120 | ? | nan | Integer |0.918401 | 18 | 1.0, 1.0| nan | 1.25, 25.056| 79.322, 79.322, 50.113, 90, 90, 120 | ? | nan | String |0.918401 | 18 | nan, nan| nan | 1.25, 25.056| 79.322, 79.322, 50.113, 90, 90, 120 | ? | nan | Intensity |0.918401 | 18 | -105.2, 1176.5| 5.389 | 1.25, 25.056| 79.322, 79.322, 50.113, 90, 90, 120 | ? | nan | Integer |0.979338 | 17 | 1.0, 1.0| nan | 1.25, 25.051| 79.313, 79.313, 50.102, 90, 90, 120 | ? | nan | Integer |0.979338 | 17 | 2.0, 2.0| nan | 1.25, 25.051| 79.313, 79.313, 50.102, 90, 90, 120 | ? | nan | Integer |0.979338 | 17 | 1.0, 1.0| nan | 1.25, 25.051| 79.313, 79.313, 50.102, 90, 90, 120 | ? | nan | String |0.979338 | 17 | nan, nan| nan | 1.25, 25.051| 79.313, 79.313, 50.102, 90, 90, 120 | ? | nan | Intensity |0.979338 | 17 | -44.3, 2.4913e+04| 13.69 | 1.25, 25.051| 79.313, 79.313, 50.102, 90, 90, 120 | ? | nan | Integer |0.979108 | 19 | 1.0, 1.0| nan | 1.361, 25.081| 79.4, 79.4, 50.162, 90, 90, 120 | ? | nan | Integer |0.979108 | 19 | 3.0, 3.0| nan | 1.361, 25.081| 79.4, 79.4, 50.162, 90, 90, 120 | ? | nan | Integer |0.979108 | 19 | 1.0, 1.0| nan | 1.361, 25.081| 79.4, 79.4, 50.162, 90, 90, 120 | ? | nan | String |0.979108 | 19 | nan, nan| nan | 1.361, 25.081| 79.4, 79.4, 50.162, 90, 90, 120 | ? | nan | Intensity |0.979108 | 19 | -1052.0, 8401.4| 10.21 | 1.361, 25.081| 79.4, 79.4, 50.162, 90, 90, 120 | ? | nan | Integer |0.918401 | 20 | 1.0, 1.0| nan | 1.25, 68.687| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | Integer |0.918401 | 20 | 1.0, 1.0| nan | 1.25, 68.687| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | Integer |0.918401 | 20 | 1.0, 1.0| nan | 1.25, 68.687| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | String |0.918401 | 20 | nan, nan| nan | 1.25, 68.687| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | HL coeffs |0.918401 | 18 | -1.87, 166.29| nan | 1.25, 16.701| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | Integer |0.918401 | 18 | 1.0, 1.0| nan | 1.25, 16.701| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | Integer |0.918401 | 18 | 1.0, 1.0| nan | 1.25, 16.701| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | Integer |0.918401 | 18 | 1.0, 1.0| nan | 1.25, 16.701| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | String |0.918401 | 18 | nan, nan| nan | 1.25, 16.701| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | Floating-point |0.918401 | 18 | -168.56, 180.0| nan | 1.25, 16.701| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | Floating-point |0.918401 | 18 | 4.164, 1995.8| nan | 1.25, 16.701| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | Floating-point |0.918401 | 18 | 0.15, 1.0| nan | 1.25, 16.701| 79.313, 79.313, 50.103, 90, 90, 120 | ? | nan | =============================================================================== Job complete """ %("\u00b0", "\u00b0", "\u00b0") test2_cifstr = """ data_mytest # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x-y,z+1/3 3 -x+y,-x,z+2/3 # _diffrn.id 1 _diffrn.crystal_id 1 # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.997432 # _reflns_scale.group_code 1 # _space_group.crystal_system trigonal _space_group.IT_number 144 _space_group.name_H-M_alt 'P 31' _space_group.name_Hall ' P 31' _symmetry.space_group_name_H-M 'P 31' _symmetry.space_group_name_Hall ' P 31' _symmetry.Int_Tables_number 144 _cell.length_a 50.000 _cell.length_b 50.000 _cell.length_c 40.000 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.volume 86602.540 loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.I _refln.SIGI _refln.MyMap _refln.PHIMyMap _refln.Oink _refln.bleep _refln.FOM _refln.A_calc _refln.B_calc 1 1 1 1 -2 3 11.205 13.695 1 180 24.9 12.429 0 2.3 -3.2 1 1 1 0 0 -4 6.353 6.353 3 120 14.521 ? 0.1 12.4 4.7 1 1 1 1 2 3 26.167 24.921 0.8 90 ? -3.328 0.25 -1.5 -4.8 1 1 1 0 1 2 14.94 6.225 2 60 3.738 3.738 0.35 7.9 10.2 1 1 1 1 0 2 2.42 11.193 4 0 22.429 4.9 0.4 8.3 22.5 1 1 1 -1 1 -2 24.921 26.167 1 -60 28.635 ? 0.5 ? ? 1 1 1 2 -2 -2 16.185 8.715 1 -90 ? -5.521 0.6 -9.4 8.6 1 1 1 -2 1 0 11.798 4.538 5 -120 3.328 10.738 0.75 -1.4 6.3 1 1 1 1 0 -2 21.183 27.413 ? ? 3.738 ? ? 9.1 7.7 1 1 1 0 0 2 4.98 21.165 6 135 19.92 19.92 1 3.9 -2.1 1 1 1 -1 -2 3 456.5 36.3 ? ? ? ? ? -3.1 5.9 1 1 1 0 0 4 654.36 9.123 ? ? ? ? ? 6.9 13.8 1 1 1 1 2 -3 -78.234 76.37 ? ? ? ? ? ? ? 1 1 1 0 -1 2 369.78 11.29 ? ? ? ? ? 0.7 -3.2 1 1 1 -1 0 2 672.899 56.14 ? ? ? ? ? 7.8 0.2 1 1 1 -1 1 2 90.316 78.9 ? ? ? ? ? 2.8 11.5 1 1 1 0 0 -3 ? ? ? ? ? 38.635 ? 7.1 3.8 """ phil2str = """ selected_info { labels = True description = True wavelength = False n_reflections = True span = True minmax_data = True minmax_sigmas = False data_sigdata_max = False d_minmax = True unit_cell = False space_group = True n_centrics = False is_anomalous = True is_symmetry_unique = False n_sys_abs = False data_completeness = True data_compl_infty = False ano_completeness = False ano_mean_diff = False n_bijvoet = False n_singletons = False } wrap_labels = -20 """ expected2str =""" Starting job =============================================================================== 9 Miller arrays in this dataset: Labels | Type | #HKLs | Span | min,max data | d_min,d_max/Å | space group |Anomalous|Data compl.| mytest,_refln.crystal_id | Integer | 17 | (-2, -2, -4), (2, 2, 4) | 1.0, 1.0| 10.0, 25.0| P 31 (No. 144) | True | nan | mytest,_refln.wavelength_id | Integer | 17 | (-2, -2, -4), (2, 2, 4) | 1.0, 1.0| 10.0, 25.0| P 31 (No. 144) | True | nan | mytest,_refln.scale_group_code | Integer | 17 | (-2, -2, -4), (2, 2, 4) | 1.0, 1.0| 10.0, 25.0| P 31 (No. 144) | True | nan | mytest,_refln.I,_refln.SIGI | Floating-point | 16 | (-2, -2, -4), (2, 2, 4) | -78.234, 672.9| 10.0, 25.0| P 31 (No. 144) | True | nan | mytest,_refln.MyMap,_refln.PHIMyMap | Map coeffs | 9 | (-2, -2, -4), (2, 2, 3) | 0.8, 6.0| 10.0, 25.0| P 31 (No. 144) | True | 0.067308 | mytest,_refln.Oink | Floating-point | 8 | (-2, -2, -4), (1, 1, 3) | 3.328, 28.635| 10.0, 25.0| P 31 (No. 144) | True | nan | mytest,_refln.bleep | Floating-point | 8 | (-2, -2, -3), (2, 2, 3) | -5.521, 38.635| 10.337, 25.0| P 31 (No. 144) | False | 0.13462 | mytest,_refln.FOM | Floating-point | 9 | (-2, -2, -4), (2, 2, 3) | 0.0, 1.0| 10.0, 25.0| P 31 (No. 144) | True | 0.067308 | mytest,_refln.A_calc,_refln.B_calc | Map coeffs | 15 | (-2, -2, -4), (2, 2, 4) | 3.2757, 23.982| 10.0, 25.0| P 31 (No. 144) | True | nan | =============================================================================== Job complete """ testhklstr = """!FORMAT=XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=TRUE !OUTPUT_FILE=XDS_ASCII.HKL DATE=10-Aug-2012 !Generated by CORRECT (VERSION March 15, 2012) !PROFILE_FITTING= TRUE !NAME_TEMPLATE_OF_DATA_FRAMES=../../img/x4_1_?????.cbf CBF !DATA_RANGE= 1 360 !ROTATION_AXIS= 0.999993 -0.000046 -0.003827 !OSCILLATION_RANGE= 1.000000 !STARTING_ANGLE= 0.000 !STARTING_FRAME= 1 !INCLUDE_RESOLUTION_RANGE= 50.000 0.798 !SPACE_GROUP_NUMBER= 1 !UNIT_CELL_CONSTANTS= 7.484 13.661 21.131 94.941 96.598 99.633 !UNIT_CELL_A-AXIS= 4.886 -4.416 3.556 !UNIT_CELL_B-AXIS= -8.390 -9.505 -5.088 !UNIT_CELL_C-AXIS= 11.220 2.222 -17.768 !REFLECTING_RANGE_E.S.D.= 0.837 !BEAM_DIVERGENCE_E.S.D.= 0.136 !X-RAY_WAVELENGTH= 0.700010 !INCIDENT_BEAM_DIRECTION= 0.003855 0.003610 1.428541 !FRACTION_OF_POLARIZATION= 0.990 !POLARIZATION_PLANE_NORMAL= 0.000000 1.000000 0.000000 !AIR= 0.000107 !SILICON= 1.347949 !SENSOR_THICKNESS= 0.320000 !DETECTOR=PILATUS !OVERLOAD= 1048500 !DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000 !DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000 !DETECTOR_DISTANCE= 170.465 !ORGX= 1248.63 ORGY= 1252.18 !NX= 2463 NY= 2527 QX= 0.172000 QY= 0.172000 !VARIANCE_MODEL= 1.494E+00 1.180E-03 !NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD=12 !ITEM_H=1 !ITEM_K=2 !ITEM_L=3 !ITEM_IOBS=4 !ITEM_SIGMA(IOBS)=5 !ITEM_XD=6 !ITEM_YD=7 !ITEM_ZD=8 !ITEM_RLP=9 !ITEM_PEAK=10 !ITEM_CORR=11 !ITEM_PSI=12 !END_OF_HEADER 0 0 -1 4.691E+02 2.124E+01 1232.6 1282.1 271.8 0.02777 100 30 16.89 0 0 -1 4.685E+02 2.084E+01 1232.7 1226.9 94.1 0.02777 100 27 -164.84 0 0 1 4.884E+02 2.164E+01 1270.1 1281.9 91.8 0.02777 99 22 163.53 0 0 1 5.193E+02 2.330E+01 1270.0 1227.1 274.1 0.02777 100 25 -15.58 0 0 -2 4.858E+04 2.040E+03 1213.9 1199.3 95.3 0.05557 100 20 -165.49 0 0 -2 4.852E+04 2.038E+03 1213.8 1309.6 270.6 0.05553 100 16 17.54 0 0 2 4.915E+04 2.064E+03 1288.9 1309.5 90.7 0.05557 100 16 162.88 0 0 2 4.800E+04 2.017E+03 1288.7 1199.6 275.3 0.05558 100 17 -14.92 0 0 -3 2.103E+04 8.846E+02 1195.0 1171.6 96.5 0.08343 100 24 -166.14 0 0 -3 2.041E+04 8.589E+02 1194.8 1337.3 269.4 0.08328 100 27 18.20 """ phil3str = """ selected_info { labels = True description = True wavelength = False n_reflections = True span = False minmax_data = True minmax_sigmas = False d_minmax = True unit_cell = False space_group = True n_centrics = False is_anomalous = True is_symmetry_unique = False n_sys_abs = False data_completeness = True data_compl_infty = True ano_completeness = True ano_mean_diff = False n_bijvoet = True n_singletons = True } merge_equivalents = True wrap_labels = -20 """ expected3str = """ Starting job =============================================================================== 1 Miller arrays in this dataset: Labels | Type | #HKLs | min,max data | d_min,d_max/Å | space group |Anomalous|Data compl.|Compl.inf.|Ano.complete|#Bijvoets|#Singletons| iobs,sigma_iobs | Intensity | 5 | 468.79, 4.8562e+04| 6.956, 20.869| P 1 (No. 1) | True | 0.22727 | 0.22727 | 0.18182 | 2 | 1 | =============================================================================== Job complete """ testscastr = """ 1 -987 44.151 44.151 44.151 80.000 80.000 80.000 h3 1 0 0 -0.2 0.4 2 -1 0 0.2 0.6 2 -1 2 2471.3 119.7 2 0 1 3166.3 237.6 2602.5 113.7 3 0 1 10052.2 496.7 10107.3 504.2 3 0 2 15486.2 469.7 15548.0 590.2 3 0 3 4730.2 167.5 4454.7 188.8 3 0 4 9840.6 543.6 8136.2 375.4 4 -3 1 23731.2 553.5 20271.4 584.9 4 -3 2 1311.5 57.1 1342.2 49.4 4 -3 3 556.5 22.2 1231.4 56.0 4 -3 4 17415.2 642.7 21023.1 1031.7 4 -3 5 27394.1 1103.3 29405.3 2926.8 4 -3 6 1462.1 75.0 1507.1 170.9 4 -2 0 3763.1 166.4 4 -2 1 15626.8 900.8 15210.5 706.0 4 -2 2 5633.4 164.3 6092.0 186.0 4 -2 3 236.7 12.3 428.2 17.7 4 -2 4 837.0 40.5 762.2 45.4 5 -3 2 6569.5 193.7 7542.3 254.6 5 -3 3 6283.6 190.9 7280.4 241.6 5 -3 4 567.3 36.4 949.3 46.8 5 -3 5 77.0 43.2 26.9 58.7 5 -3 6 3170.0 185.7 3134.1 175.3 5 -3 7 1859.2 124.2 1936.3 158.1 5 -3 8 3124.1 253.3 3047.0 216.0 5 -3 9 2296.7 138.1 5 -3 18 -11.8 53.3 5 -2 0 10279.5 312.4 6 -5 1 7179.4 200.2 7433.3 194.9 6 -5 2 8662.2 388.1 10568.4 365.1 6 -5 3 15441.5 598.0 14331.0 551.3 """ phil4str = """ selected_info { labels = True description = True wavelength = False n_reflections = True span = False minmax_data = True minmax_sigmas = True d_minmax = True unit_cell = False space_group = True data_sigdata=True n_centrics = False is_anomalous = True is_symmetry_unique = False n_sys_abs = False data_completeness = True data_compl_infty = False ano_completeness = True ano_mean_diff = False n_bijvoet = True n_singletons = True } wrap_labels = -10 """ expected4str = """ Starting job =============================================================================== 1 Miller arrays in this dataset: Labels | Type | #HKLs | min,max data | min,max sigmas | DatSigDat| d_min,d_max/Å | space group |Anomalous|Data compl.|Ano.complete|#Bijvoets|#Singletons| I(+),SIGI(+),I(-),SIGI(-) | Intensity | 57 | -11.8, 2.9405e+04| 0.4, 2926.8| 21.45 | 2.293, 43.002| R 3 :R (No. 146) | True | 0.0059511 | 0.0052203 | 25 | 7 | =============================================================================== Job complete """ def test_hklinfo_run(cifstr, filename, philstr, expectedstr): with open(filename, "w") as fh: fh.write(cifstr) with open("philinput.txt", "w") as fh: fh.write(philstr) obj = subprocess.Popen("cctbx.HKLinfo %s philinput.txt" %filename, shell=True, stdin = subprocess.PIPE, stdout = subprocess.PIPE, stderr = subprocess.STDOUT) out,err = obj.communicate() fullstdout = out.decode().replace("\r\n", "\n") # omit \r\n line endings on Windows #import code, traceback; code.interact(local=locals(), banner="".join( traceback.format_stack(limit=10) ) ) assert (contains_substring( fullstdout, expectedstr ) ) # ============================================================================= if (__name__ == '__main__'): test_hklinfo_run(test1_cifstr, "test-sf.cif", phil1str, expected1str) test_hklinfo_run(test2_cifstr, "test-sf.cif", phil2str, expected2str) test_hklinfo_run(testhklstr, "test.hkl", phil3str, expected3str) test_hklinfo_run(testscastr, "test.sca", phil4str, expected4str) print('OK')