# -*- coding: utf-8 -*- from __future__ import absolute_import, division, print_function from libtbx import easy_run import iotbx.cif from libtbx.test_utils import approx_equal, show_diff from six.moves import cStringIO as StringIO import iotbx.mtz import os sf_5r82 = """\ data_r5r82sf # _audit.revision_id 1_0 _audit.creation_date 2020-03-11 _audit.update_record "Initial release" # _cell.entry_id 5r82 _cell.length_a 112.665 _cell.length_b 52.848 _cell.length_c 44.468 _cell.angle_alpha 90.000 _cell.angle_beta 102.966 _cell.angle_gamma 90.000 # _diffrn.id 1 _diffrn.details "data from final refinement with ligand, final.mtz" _diffrn.crystal_id 1 # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9126 # _entry.id 5r82 # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # _symmetry.entry_id 5r82 _symmetry.space_group_name_H-M "C 1 2 1" _symmetry.Int_Tables_number 5 # 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_au _refln.phase_calc _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.fom 1 1 1 -86 0 8 o ? ? 14.57 0.00 8.89 0.00 0.00 0.00 0.00 1 1 1 -85 1 3 o ? ? 74.69 159.82 45.89 159.75 0.00 0.00 0.00 1 1 1 -85 1 4 o ? ? 18.89 136.18 11.62 136.53 0.00 0.00 0.00 1 1 1 -85 1 5 o ? ? 40.54 44.81 24.89 44.97 0.00 0.00 0.00 1 1 1 -85 1 6 o ? ? 14.55 265.49 8.91 267.15 0.00 0.00 0.00 1 1 1 -85 1 7 o ? ? 38.21 15.80 23.59 15.42 0.00 0.00 0.00 1 1 1 -85 1 8 o ? ? 47.35 181.29 29.24 181.19 0.00 0.00 0.00 1 1 1 -85 1 9 o 56.21 26.85 38.50 89.75 41.26 89.77 17.50 89.77 0.58 1 1 1 -85 1 10 o 65.09 31.91 27.40 104.11 36.22 104.55 19.20 104.55 0.41 1 1 1 -85 1 11 o 54.28 26.34 24.33 27.77 29.23 27.86 14.13 27.86 0.41 1 1 1 -85 1 12 o 58.89 28.38 21.26 158.09 27.96 158.29 14.93 158.29 0.35 1 1 1 -85 3 4 o ? ? 16.70 93.70 10.28 93.61 0.00 0.00 0.00 1 1 1 -85 3 5 o ? ? 18.82 319.51 11.62 319.61 0.00 0.00 0.00 1 1 1 -85 3 6 o ? ? 9.64 143.57 6.02 143.97 0.00 0.00 0.00 1 1 1 -85 3 7 o ? ? 34.35 260.46 21.18 260.07 0.00 0.00 0.00 1 1 1 -85 3 8 o ? ? 30.57 8.43 18.77 8.70 0.00 0.00 0.00 1 1 1 -85 3 9 o 66.81 31.32 64.85 81.01 57.84 80.86 17.89 80.86 0.73 1 1 1 -85 3 10 o 59.74 28.33 64.04 132.52 49.17 132.36 9.69 132.36 0.74 1 1 1 -85 3 11 o 50.02 24.64 5.34 93.51 6.70 95.13 3.34 95.13 0.10 1 1 1 -85 5 5 o ? ? 29.69 339.80 18.22 340.06 0.00 0.00 0.00 1 1 1 -85 5 6 o ? ? 52.33 264.97 32.14 265.05 0.00 0.00 0.00 1 1 1 -85 5 7 o ? ? 63.54 232.41 39.02 232.26 0.00 0.00 0.00 1 1 1 -85 5 8 o ? ? 25.64 55.65 15.80 55.84 0.00 0.00 0.00 1 1 1 -85 5 9 o 44.64 22.72 27.71 201.58 23.51 202.12 6.57 202.12 0.45 1 1 1 -85 5 10 o ? ? 48.38 118.56 29.58 118.56 0.00 0.00 0.00 1 1 1 -84 0 1 o ? ? 3.94 180.00 2.34 180.00 0.00 0.00 0.00 1 1 1 -84 0 2 o ? ? 9.64 180.00 5.88 180.00 0.00 0.00 0.00 1 1 1 -84 0 3 o ? ? 57.42 180.00 35.50 180.00 0.00 0.00 0.00 1 1 1 -84 0 4 o ? ? 5.23 0.00 3.15 0.00 0.00 0.00 0.00 1 1 1 -84 0 5 o ? ? 3.86 180.00 2.39 180.00 0.00 0.00 0.00 1 1 1 -84 0 6 o ? ? 21.93 0.00 13.65 0.00 0.00 0.00 0.00 1 1 1 -84 0 7 o ? ? 7.45 0.00 4.61 0.00 0.00 0.00 0.00 1 1 1 -84 0 8 o 73.12 45.70 7.69 0.00 15.82 0.00 11.03 0.00 0.14 # data_r5r82Asf # _cell.entry_id 5r82 _cell.length_a 112.665 _cell.length_b 52.848 _cell.length_c 44.468 _cell.angle_alpha 90.000 _cell.angle_beta 102.966 _cell.angle_gamma 90.000 # _diffrn.id 1 _diffrn.details "data from original reflections, data.mtz" _diffrn.crystal_id 1 # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9126 # _entry.id 5r82 # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # _symmetry.entry_id 5r82 _symmetry.space_group_name_H-M "C 1 2 1" _symmetry.Int_Tables_number 5 # 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 1 1 1 -86 0 7 o ? ? 1 1 1 -86 0 8 o ? ? 1 1 1 -85 1 3 o ? ? 1 1 1 -85 1 4 o ? ? 1 1 1 -85 1 5 o ? ? 1 1 1 -85 1 6 o ? ? 1 1 1 -85 1 7 o ? ? 1 1 1 -85 1 8 o ? ? 1 1 1 -85 1 9 o 1.28 0.61 1 1 1 -85 1 10 o 1.47 0.72 1 1 1 -85 1 11 o 1.21 0.59 1 1 1 -85 1 12 o 1.30 0.63 1 1 1 -85 3 4 o ? ? 1 1 1 -85 3 5 o ? ? 1 1 1 -85 3 6 o ? ? 1 1 1 -85 3 7 o ? ? 1 1 1 -85 3 8 o ? ? 1 1 1 -85 3 9 o 1.53 0.72 1 1 1 -85 3 10 o 1.35 0.64 1 1 1 -85 3 11 o 1.12 0.55 1 1 1 -85 3 12 o ? ? 1 1 1 -85 5 5 o ? ? 1 1 1 -85 5 6 o ? ? 1 1 1 -85 5 7 o ? ? 1 1 1 -85 5 8 o ? ? 1 1 1 -85 5 9 o 1.02 0.52 1 1 1 -85 5 10 o ? ? 1 1 1 -84 0 1 o ? ? 1 1 1 -84 0 2 o ? ? 1 1 1 -84 0 3 o ? ? 1 1 1 -84 0 4 o ? ? 1 1 1 -84 0 5 o ? ? 1 1 1 -84 0 6 o ? ? 1 1 1 -84 0 7 o ? ? 1 1 1 -84 0 8 o 1.71 1.07 # data_r5r82Bsf # _cell.entry_id 5r82 _cell.length_a 112.665 _cell.length_b 52.848 _cell.length_c 44.468 _cell.angle_alpha 90.000 _cell.angle_beta 102.970 _cell.angle_gamma 90.000 # _diffrn.id 1 _diffrn.details "data for ligand evidence map (PanDDA event map), event_map_1.mtz" _diffrn.crystal_id 1 # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9126 # _entry.id 5r82 # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # _symmetry.entry_id 5r82 _symmetry.space_group_name_H-M "P 1" _symmetry.Int_Tables_number 1 # 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.pdbx_PHWT 1 1 1 -85 -6 7 o 183.35 1.00 42.48 1 1 1 -85 -6 8 o 204.28 1.00 118.73 1 1 1 -85 -5 5 o 408.51 1.00 26.47 1 1 1 -85 -5 6 o 368.34 1.00 -17.28 1 1 1 -85 -5 7 o 105.28 1.00 -108.00 1 1 1 -85 -5 8 o 447.04 1.00 49.71 1 1 1 -85 -5 9 o 151.27 1.00 76.05 1 1 1 -85 -5 10 o 177.73 1.00 -11.88 1 1 1 -85 -4 4 o 176.60 1.00 137.96 1 1 1 -85 -4 5 o 94.48 1.00 45.34 1 1 1 -85 -4 6 o 269.47 1.00 3.56 1 1 1 -85 -4 7 o 146.26 1.00 103.92 1 1 1 -85 -4 8 o 251.33 1.00 152.35 1 1 1 -85 -4 9 o 189.51 1.00 -158.44 1 1 1 -85 -4 10 o 340.08 1.00 50.25 1 1 1 -85 -4 11 o 85.03 1.00 42.71 1 1 1 -85 -3 4 o 458.44 1.00 -148.81 1 1 1 -85 -3 5 o 928.82 1.00 25.99 1 1 1 -85 -3 6 o 266.68 1.00 -145.70 1 1 1 -85 -3 7 o 524.04 1.00 20.59 1 1 1 -85 -3 8 o 824.38 1.00 126.20 1 1 1 -85 -3 9 o 334.69 1.00 -9.45 1 1 1 -85 -3 10 o 367.92 1.00 -34.78 1 1 1 -85 -3 11 o 622.58 1.00 74.86 1 1 1 -85 -2 3 o 197.98 1.00 -127.10 1 1 1 -85 -2 4 o 140.13 1.00 -111.56 # #END OF REFLECTIONS """ sf_5r82_mtz_results = {'r5r82sf': """\ Title: phenix.cif_as_mtz Space group symbol from file: C2 Space group number from file: 5 Space group from matrices: C 1 2 1 (No. 5) Point group symbol from file: 2 Number of crystals: 2 Number of Miller indices: 33 Resolution range: 1.34113 1.30997 History: Crystal 1: Name: HKL_base Project: HKL_base Id: 0 Unit cell: (112.665, 52.848, 44.468, 90, 102.966, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 0 Crystal 2: Name: crystal_0 Project: project_0 Id: 2 Unit cell: (112.665, 52.848, 44.468, 90, 102.966, 90) Number of datasets: 1 Dataset 1: Name: dataset Id: 1 Wavelength: 0.9126 Number of columns: 13 label #valid %valid min max type H 33 100.00% -86.00 -84.00 H: index h,k,l K 33 100.00% 0.00 5.00 H: index h,k,l L 33 100.00% 1.00 12.00 H: index h,k,l R-free-flags 33 100.00% 1.00 1.00 I: integer FOBS 9 27.27% 44.64 73.12 F: amplitude SIGFOBS 9 27.27% 22.72 45.70 Q: standard deviation FC 33 100.00% 3.86 74.69 F: amplitude PHIFC 33 100.00% -178.71 180.00 P: phase angle in degrees FWT 33 100.00% 2.34 57.84 F: amplitude PHWT 33 100.00% -178.81 180.00 P: phase angle in degrees DELFWT 33 100.00% 0.00 19.20 F: amplitude PHDELWT 33 100.00% -157.88 158.29 P: phase angle in degrees FOM 33 100.00% 0.00 0.74 F: amplitude """, 'r5r82Asf': """Title: phenix.cif_as_mtz Space group symbol from file: C2 Space group number from file: 5 Space group from matrices: C 1 2 1 (No. 5) Point group symbol from file: 2 Number of crystals: 2 Number of Miller indices: 35 Resolution range: 1.34113 1.3096 History: Crystal 1: Name: HKL_base Project: HKL_base Id: 0 Unit cell: (112.665, 52.848, 44.468, 90, 102.966, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 0 Crystal 2: Name: crystal_0 Project: project_0 Id: 2 Unit cell: (112.665, 52.848, 44.468, 90, 102.966, 90) Number of datasets: 1 Dataset 1: Name: dataset Id: 1 Wavelength: 0.9126 Number of columns: 6 label #valid %valid min max type H 35 100.00% -86.00 -84.00 H: index h,k,l K 35 100.00% 0.00 5.00 H: index h,k,l L 35 100.00% 1.00 12.00 H: index h,k,l R-free-flags 35 100.00% 1.00 1.00 I: integer FOBS 9 25.71% 1.02 1.71 F: amplitude SIGFOBS 9 25.71% 0.52 1.07 Q: standard deviation """, 'r5r82Bsf': """\ Title: phenix.cif_as_mtz Space group symbol from file: P1 Space group number from file: 1 Space group from matrices: P 1 (No. 1) Point group symbol from file: 1 Number of crystals: 2 Number of Miller indices: 26 Resolution range: 1.3216 1.31054 History: Crystal 1: Name: HKL_base Project: HKL_base Id: 0 Unit cell: (112.665, 52.848, 44.468, 90, 102.97, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 0 Crystal 2: Name: crystal_0 Project: project_0 Id: 2 Unit cell: (112.665, 52.848, 44.468, 90, 102.97, 90) Number of datasets: 1 Dataset 1: Name: dataset Id: 1 Wavelength: 0.9126 Number of columns: 7 label #valid %valid min max type H 26 100.00% -85.00 -85.00 H: index h,k,l K 26 100.00% -6.00 -2.00 H: index h,k,l L 26 100.00% 3.00 11.00 H: index h,k,l R-free-flags 26 100.00% 1.00 1.00 I: integer FOBS 26 100.00% 85.03 928.82 F: amplitude SIGFOBS 26 100.00% 1.00 1.00 Q: standard deviation PHWT 26 100.00% -158.44 152.35 P: phase angle in degrees """} def tst_1(prefix="tst_split_data_cif_1"): with open(prefix+'.cif', 'w') as f: f.write(sf_5r82) easy_run.fully_buffered('iotbx.split_data_cif %s.cif' % prefix) original_model = iotbx.cif.reader(input_string=sf_5r82).model() block_names = original_model.keys() for bn in block_names: assert os.path.isfile('%s.cif_%s_000.mtz' % (prefix, bn)) assert os.path.isfile('%s.cif_%s_000.cif' % (prefix, bn)) # testing output cif for bn in block_names: m = iotbx.cif.reader(file_path='%s.cif_%s_000.cif' % (prefix, bn)).model() for k in original_model[bn].keys(): assert approx_equal(m[bn][k], original_model[bn][k]) # testing output mtz for bn in block_names: mtz_obj = iotbx.mtz.object('%s.cif_%s_000.mtz' % (prefix, bn)) # print('working with', '%s.cif_%s_000.mtz' % (prefix, bn)) strio = StringIO() mtz_obj.show_summary(out=strio) # mtz_obj.show_column_data(out=strio) val = strio.getvalue() assert not show_diff(val, sf_5r82_mtz_results[bn]) if __name__ == '__main__': tst_1() print("OK")