from __future__ import absolute_import, division, print_function from libtbx.test_utils import show_diff from libtbx import easy_run import sys def run_and_compare(commands, expected_output): def digest(lines): result = [] for line in lines: if (line.strip().startswith("Change of basis: ")): continue if (line.strip().startswith("Inverse: ")): continue result.append(line) result.sort() return "\n".join(result)+"\n" for command in commands: lines = easy_run.fully_buffered( command=command).raise_if_errors().stdout_lines assert not show_diff(digest(lines), digest(expected_output.splitlines())) def exercise(args): assert len(args) == 0 run_and_compare( ['iotbx.lattice_symmetry' ' --unit_cell="12.7923,12.8923,29.4356,102.846,103.846,22.7475"'], """\ Input ===== Unit cell: (12.7923, 12.8923, 29.4356, 102.846, 103.846, 22.7475) Space group: P 1 (No. 1) Angular tolerance: 3.000 degrees Similar symmetries ================== Symmetry in minimum-lengths cell: C 1 2/m 1 (z,x-y,2*y) (No. 12) Input minimum-lengths cell: (5.06616, 12.7923, 29.1526, 78.6285, 87.746, 79.7351) Symmetry-adapted cell: (5.06616, 12.7923, 29.2944, 77.3884, 87.7702, 79.7351) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (5.06616, 57.1752, 12.8923, 90, 102.483, 90) Change of basis: -x+1/2*z,-1/2*z,-x-y+1/2*z Inverse: -x-y,x-z,-2*y Maximal angular difference: 1.323 degrees Symmetry in minimum-lengths cell: P -1 (No. 2) Input minimum-lengths cell: (5.06616, 12.7923, 29.1526, 78.6285, 87.746, 79.7351) Symmetry-adapted cell: (5.06616, 12.7923, 29.1526, 78.6285, 87.746, 79.7351) Conventional setting: P -1 (No. 2) Unit cell: (5.06616, 12.7923, 29.1526, 78.6285, 87.746, 79.7351) Change of basis: -y,x+y-z,z Inverse: x+y+z,-x,z Maximal angular difference: 0.000 degrees """) # run_and_compare( ['iotbx.lattice_symmetry --unit_cell=12,12.2,12.1,89,90,92 F', 'cctbx.lattice_symmetry'], """\ Input ===== Unit cell: (12, 12.2, 12.1, 89, 90, 92) Space group: P 1 (-a+b+c,a-b+c,a+b-c) (No. 1) Angular tolerance: 3.000 degrees Similar symmetries ================== Symmetry in minimum-lengths cell: F m -3 m (-x+y+z,x-y+z,x+y-z) (No. 225) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.55619, 8.55619, 8.55619, 60, 60, 60) Conventional setting: F m -3 m (No. 225) Unit cell: (12.1003, 12.1003, 12.1003, 90, 90, 90) Change of basis: z,-x,-y Inverse: -y,-z,x Maximal angular difference: 2.236 degrees Symmetry in minimum-lengths cell: I 4/m m m (y-z,-x+z,x+z) (No. 139) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.55628, 8.55614, 8.55614, 60.0011, 59.9994, 59.9994) Conventional setting: I 4/m m m (No. 139) Unit cell: (8.55628, 8.55628, 12.1, 90, 90, 90) Change of basis: -x+y,-x-y,z Inverse: -1/2*x-1/2*y,1/2*x-1/2*y,z Maximal angular difference: 2.236 degrees Symmetry in minimum-lengths cell: I 4/m m m (-y+z,x-z,y+z) (No. 139) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.53852, 8.59142, 8.53852, 59.7948, 60.4103, 59.7948) Conventional setting: I 4/m m m (No. 139) Unit cell: (8.59142, 8.59142, 12, 90, 90, 90) Change of basis: -y+z,y+z,-x Inverse: -z,-1/2*x+1/2*y,1/2*x+1/2*y Maximal angular difference: 2.236 degrees Symmetry in minimum-lengths cell: I 4/m m m (y+z,-y+z,x-z) (No. 139) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.57387, 8.57387, 8.52071, 60.2049, 60.2049, 59.5902) Conventional setting: I 4/m m m (No. 139) Unit cell: (8.52071, 8.52071, 12.2, 90, 90, 90) Change of basis: -x+z,-x-z,-y Inverse: -1/2*x-1/2*y,-z,1/2*x-1/2*y Maximal angular difference: 2.236 degrees Symmetry in minimum-lengths cell: R -3 m :R (No. 166) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.481, 8.481, 8.481, 61.1714, 61.1714, 61.1714) Conventional setting: R -3 m :H (No. 166) Unit cell: (8.63072, 8.63072, 20.5883, 90, 90, 120) Change of basis: 4/3*x-2/3*y+2/3*z,2/3*x+2/3*y+4/3*z,-1/3*x-1/3*y+1/3*z Inverse: 1/2*x-z,-1/2*x+1/2*y-z,1/2*y+z Maximal angular difference: 1.474 degrees Symmetry in minimum-lengths cell: R -3 m :H (x+z,-y+z,-3*z) (No. 166) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.481, 8.481, 8.63072, 60.5722, 60.5722, 60) Conventional setting: R -3 m :H (No. 166) Unit cell: (8.481, 8.481, 21.3218, 90, 90, 120) Change of basis: -4/3*x-2/3*y-2/3*z,-2/3*x+2/3*y-4/3*z,1/3*x-1/3*y-1/3*z Inverse: -1/2*x+z,-1/2*x+1/2*y-z,-1/2*y-z Maximal angular difference: 1.498 degrees Symmetry in minimum-lengths cell: R -3 m :H (-y+z,-3*z,x+z) (No. 166) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.53148, 8.58082, 8.53148, 60.19, 60, 60.19) Conventional setting: R -3 m :H (No. 166) Unit cell: (8.53148, 8.53148, 21.0788, 90, 90, 120) Change of basis: -2/3*x+2/3*y+4/3*z,2/3*x+4/3*y+2/3*z,-1/3*x+1/3*y-1/3*z Inverse: -1/2*x+1/2*y-z,1/2*y+z,1/2*x-z Maximal angular difference: 2.177 degrees Symmetry in minimum-lengths cell: R -3 m :H (-3*z,x+z,-y+z) (No. 166) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.53148, 8.58082, 8.58082, 60, 59.8085, 59.8085) Conventional setting: R -3 m :H (No. 166) Unit cell: (8.58082, 8.58082, 20.8371, 90, 90, 120) Change of basis: 2/3*x-4/3*y+2/3*z,4/3*x-2/3*y-2/3*z,1/3*x+1/3*y+1/3*z Inverse: 1/2*y+z,-1/2*x+z,1/2*x-1/2*y+z Maximal angular difference: 2.177 degrees Symmetry in minimum-lengths cell: I m m m (y-z,-x+z,x+z) (No. 71) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.40567, 8.55614, 8.55614, 61.1489, 60.58, 60.58) Conventional setting: I m m m (No. 71) Unit cell: (8.40567, 8.70429, 12.1, 90, 90, 90) Change of basis: x+y,-x+y,z Inverse: 1/2*x-1/2*y,1/2*x+1/2*y,z Maximal angular difference: 1.187 degrees Symmetry in minimum-lengths cell: I m m m (-y+z,x-z,y+z) (No. 71) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.53852, 8.51612, 8.53852, 60.0867, 60.9908, 60.0867) Conventional setting: I m m m (No. 71) Unit cell: (8.51612, 8.66606, 12, 90, 90, 90) Change of basis: -y+z,y+z,-x Inverse: -z,-1/2*x+1/2*y,1/2*x+1/2*y Maximal angular difference: 2.000 degrees Symmetry in minimum-lengths cell: I m m m (y+z,-y+z,x-z) (No. 71) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.57387, 8.57387, 8.52071, 60.2049, 60.2049, 59.5902) Conventional setting: I m m m (No. 71) Unit cell: (8.52071, 8.52071, 12.2, 90, 90, 90) Change of basis: -x+z,-x-z,-y Inverse: -1/2*x-1/2*y,-z,1/2*x-1/2*y Maximal angular difference: 2.236 degrees Symmetry in minimum-lengths cell: F m m m (-x+y+z,x-y+z,x+y-z) (No. 69) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.55628, 8.59142, 8.52071, 60, 60.4101, 59.5899) Conventional setting: F m m m (No. 69) Unit cell: (12, 12.1, 12.2, 90, 90, 90) Change of basis: x,z,-y Inverse: x,-z,y Maximal angular difference: 2.236 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x+y,-x+y,x-y+z) (No. 12) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.55628, 8.59142, 8.52071, 60, 60.4101, 59.5899) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (8.52071, 12.2, 8.52071, 90, 90.4755, 90) Change of basis: x-z,y,x+z Inverse: 1/2*x+1/2*z,y,-1/2*x+1/2*z Maximal angular difference: 2.236 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x-y+z,x+y,-x+y) (No. 12) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.40567, 8.59142, 8.52071, 61.1478, 61.0005, 60.1608) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (8.40567, 12.1, 8.70429, 90, 90.9476, 90) Change of basis: x+y,z,x-y Inverse: 1/2*x+1/2*z,1/2*x-1/2*z,y Maximal angular difference: 1.001 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (-x+y,x-y+z,x+y) (No. 12) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.55628, 8.51612, 8.52071, 60.2943, 60.9905, 59.8794) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (8.51612, 12, 8.66606, 90, 90.4716, 90) Change of basis: y-z,x,-y-z Inverse: y,1/2*x-1/2*z,-1/2*x-1/2*z Maximal angular difference: 2.000 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (z,x-y,x+y) (No. 12) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.40567, 8.51842, 8.51842, 61.4489, 61.0277, 61.0277) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (8.40567, 8.70429, 12.1, 90, 90.7257, 90) Change of basis: x+y,x-y,-z Inverse: 1/2*x+1/2*y,1/2*x-1/2*y,-z Maximal angular difference: 1.172 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x+y,z,x-y) (No. 12) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.46339, 8.51612, 8.46339, 60.9617, 61.5908, 60.9617) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (8.51612, 8.66606, 12, 90, 91.4324, 90) Change of basis: y-z,y+z,x Inverse: z,1/2*x+1/2*y,-1/2*x+1/2*y Maximal angular difference: 1.474 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x-y,x+y,z) (No. 12) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.46108, 8.46108, 8.52071, 61.5187, 61.5187, 60.4668) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (8.52071, 8.52071, 12.2, 90, 92.1185, 90) Change of basis: x-z,-x-z,y Inverse: 1/2*x-1/2*y,z,-1/2*x-1/2*y Maximal angular difference: 0.860 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (-z,-2*x+z,x+y) (No. 12) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.53686, 8.61072, 8.52071, 60.3452, 60.0626, 59.589) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (8.52071, 8.52071, 12.2, 90, 90.6981, 90) Change of basis: x+z,x-z,y Inverse: 1/2*x+1/2*y,z,1/2*x-1/2*y Maximal angular difference: 2.177 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (-z,-x+y,2*x+z) (No. 12) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.46339, 8.51612, 8.61299, 60.3713, 60.9859, 59.7937) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (8.66606, 8.51612, 12, 90, 91.4076, 90) Change of basis: -y-z,-y+z,-x Inverse: -z,-1/2*x-1/2*y,-1/2*x+1/2*y Maximal angular difference: 1.498 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (-x+y,z,2*x-z) (No. 12) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.40567, 8.51842, 8.59369, 61.1477, 60.7211, 60.4369) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (8.70429, 8.40567, 12.1, 90, 90.7008, 90) Change of basis: x-y,x+y,z Inverse: 1/2*x+1/2*y,-1/2*x+1/2*y,z Maximal angular difference: 1.187 degrees Symmetry in minimum-lengths cell: P -1 (No. 2) Input minimum-lengths cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Symmetry-adapted cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Conventional setting: P -1 (No. 2) Unit cell: (8.40567, 8.51612, 8.52071, 61.4489, 61.5879, 60.4641) Change of basis: -x-y-z,x-y+z,-x+y+z Inverse: -1/2*x-1/2*z,-1/2*x-1/2*y,1/2*y+1/2*z Maximal angular difference: 0.000 degrees """) # run_and_compare( ['iotbx.lattice_symmetry --unit_cell="22.54 22.64 6.35 90.1 89.9 90.3" I', 'cctbx.lattice_symmetry 1'], """\ Input ===== Unit cell: (22.54, 22.64, 6.35, 90.1, 89.9, 90.3) Space group: P 1 (b+c,a+c,a+b) (No. 1) Angular tolerance: 3.000 degrees Similar symmetries ================== Symmetry in minimum-lengths cell: I 4/m m m (-y+z,x+y,-x+y) (No. 139) Input minimum-lengths cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Symmetry-adapted cell: (6.35, 16.2861, 16.2861, 87.8219, 78.7581, 78.7581) Conventional setting: I 4/m m m (No. 139) Unit cell: (22.5901, 22.5901, 6.35, 90, 90, 90) Change of basis: x,y,z Inverse: x,y,z Maximal angular difference: 0.316 degrees Symmetry in minimum-lengths cell: I m m m (y-z,-x+z,x+z) (No. 71) Input minimum-lengths cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Symmetry-adapted cell: (6.35, 16.2861, 16.2861, 87.5777, 78.7581, 78.7581) Conventional setting: I m m m (No. 71) Unit cell: (6.35, 22.54, 22.64, 90, 90, 90) Change of basis: -z,-x,y Inverse: -y,z,-x Maximal angular difference: 0.316 degrees Symmetry in minimum-lengths cell: F m m m (x-y+z,-2*z,2*y) (No. 69) Input minimum-lengths cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Symmetry-adapted cell: (6.35, 16.245, 16.327, 87.8218, 78.7867, 78.7293) Conventional setting: F m m m (No. 69) Unit cell: (6.35, 31.8634, 32.0307, 90, 90, 90) Change of basis: -z,-1/2*x-1/2*y,-1/2*x+1/2*y Inverse: -y-z,-y+z,-x Maximal angular difference: 0.290 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (-x+y,z,2*x-z) (No. 12) Input minimum-lengths cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Symmetry-adapted cell: (6.35, 16.245, 16.327, 87.5777, 78.7867, 78.7293) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (22.54, 6.35, 22.64, 90, 90.3, 90) Change of basis: x,-z,y Inverse: x,z,-y Maximal angular difference: 0.141 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x-y,2*y,z) (No. 12) Input minimum-lengths cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Symmetry-adapted cell: (6.35, 16.245, 16.3194, 87.8479, 78.9224, 78.7293) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (6.35, 31.8634, 16.3194, 90, 101.078, 90) Change of basis: -1/2*x+1/2*y-z,-1/2*x-1/2*y,-x+y Inverse: -y-1/2*z,-y+1/2*z,-x+1/2*z Maximal angular difference: 0.254 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x+y,z,-2*y) (No. 12) Input minimum-lengths cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Symmetry-adapted cell: (6.35, 16.245, 16.327, 87.8219, 78.7867, 78.7296) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (6.35, 32.0307, 16.245, 90, 101.27, 90) Change of basis: 1/2*x+1/2*y-z,-1/2*x+1/2*y,x+y Inverse: -y+1/2*z,y+1/2*z,-x+1/2*z Maximal angular difference: 0.290 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (z,x-y,x+y) (No. 12) Input minimum-lengths cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Symmetry-adapted cell: (6.35, 16.2822, 16.2822, 87.6037, 78.8263, 78.8263) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (6.35, 22.54, 22.64, 90, 90.1, 90) Change of basis: -z,x,-y Inverse: y,-z,-x Maximal angular difference: 0.316 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x-y+z,x+y,-x+y) (No. 12) Input minimum-lengths cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Symmetry-adapted cell: (6.35, 16.2899, 16.2822, 87.5777, 78.826, 78.6902) Conventional setting: I 1 2/m 1 (No. 12) Unit cell: (6.35, 22.64, 22.54, 90, 90.1, 90) Change of basis: -z,y,x Inverse: z,y,-x Maximal angular difference: 0.316 degrees Symmetry in minimum-lengths cell: P -1 (No. 2) Input minimum-lengths cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Symmetry-adapted cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Conventional setting: P -1 (No. 2) Unit cell: (6.35, 16.245, 16.3194, 87.6037, 78.9224, 78.7296) Change of basis: -y+z,x+y,-x+y Inverse: 1/2*y-1/2*z,1/2*y+1/2*z,x+1/2*y+1/2*z Maximal angular difference: 0.000 degrees """) # run_and_compare( ['iotbx.lattice_symmetry' ' --unit_cell="78.9 82.3 57.0 90 93.4 90.1" C --delta=1.4'], """\ Input ===== Unit cell: (78.9, 82.3, 57, 90, 93.4, 90.1) Space group: P 1 (a+b,a-b,-c) (No. 1) Angular tolerance: 1.400 degrees Similar symmetries ================== Symmetry in minimum-lengths cell: R -3 m :R (No. 166) Input minimum-lengths cell: (56.9558, 57, 57.0552, 92.3502, 92.4166, 92.3543) Symmetry-adapted cell: (57.0037, 57.0037, 57.0037, 92.3737, 92.3737, 92.3737) Conventional setting: R -3 m :H (No. 166) Unit cell: (82.2678, 82.2678, 94.5557, 90, 90, 120) Change of basis: -2/3*x+2/3*z,-1/3*x-y+1/3*z,2/3*x+1/3*z Inverse: -1/2*x+z,1/2*x-y,x+z Maximal angular difference: 0.100 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x-y,x+y,z) (No. 12) Input minimum-lengths cell: (56.9558, 57, 57.0552, 92.3502, 92.4166, 92.3543) Symmetry-adapted cell: (56.9779, 56.9779, 57.0552, 92.3834, 92.3834, 92.3543) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (78.9065, 82.2173, 57.0552, 90, 93.4431, 90) Change of basis: 1/2*x+1/2*y+1/2*z,-1/2*x-1/2*y+1/2*z,x-y Inverse: 1/2*x-1/2*y+1/2*z,1/2*x-1/2*y-1/2*z,x+y Maximal angular difference: 0.065 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x+y,z,x-y) (No. 12) Input minimum-lengths cell: (56.9558, 57, 57.0552, 92.3502, 92.4166, 92.3543) Symmetry-adapted cell: (57.0055, 57, 57.0055, 92.3522, 92.4166, 92.3522) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (78.9, 82.3, 57, 90, 93.4, 90) Change of basis: x,y,z Inverse: x,y,z Maximal angular difference: 0.100 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (z,x-y,x+y) (No. 12) Input minimum-lengths cell: (56.9558, 57, 57.0552, 92.3502, 92.4166, 92.3543) Symmetry-adapted cell: (56.9558, 57.0276, 57.0276, 92.3502, 92.3854, 92.3854) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (78.9783, 82.2861, 56.9558, 90, 93.446, 90) Change of basis: 1/2*x-1/2*y+1/2*z,1/2*x-1/2*y-1/2*z,x+y Inverse: 1/2*x+1/2*y+1/2*z,-1/2*x-1/2*y+1/2*z,x-y Maximal angular difference: 0.069 degrees Symmetry in minimum-lengths cell: P -1 (No. 2) Input minimum-lengths cell: (56.9558, 57, 57.0552, 92.3502, 92.4166, 92.3543) Symmetry-adapted cell: (56.9558, 57, 57.0552, 92.3502, 92.4166, 92.3543) Conventional setting: P -1 (No. 2) Unit cell: (56.9558, 57, 57.0552, 92.3502, 92.4166, 92.3543) Change of basis: x+y,z,x-y Inverse: 1/2*x+1/2*z,1/2*x-1/2*z,y Maximal angular difference: 0.000 degrees """) assert tst_instability_on_the_lepage_tolerance() print("OK") def tst_instability_on_the_lepage_tolerance(): """Basic idea: we introduced the Lepage tolerance to solve the problem that numerically-determined or experimentally-determined twofolds do not fall at exact positions. However, when the input is exact, we expect to be able to reduce the tolerance to zero.""" def give_cases(): from cctbx import crystal from cctbx.uctbx import unit_cell from cctbx.sgtbx import space_group_info pdb =["1vjg/P 32 2 1/(56.192, 56.192, 129.318, 90, 90, 120)/16", "1vjz/P 43 21 2/(64.684, 64.684, 202.189, 90, 90, 90)/10", "1vl6/P 65/(143.963, 143.963, 163.428, 90, 90, 120)/16", "1vlc/P 3 2 1/(118.78, 118.78, 56.699, 90, 90, 120)/16", "2ash/C 1 2 1/(169.467, 99.422, 124.163, 90, 123.8, 90)/2", "2etj/P 31/(51.821, 51.821, 76.293, 90, 90, 120)/16", "2qyv/P 21 21 2/(173.922, 84.293, 123.204, 90, 90, 90)/5"] for header in pdb: tokens=header.split("/") case = {"pdb_code":tokens[0],"centring_type":tokens[1][0], "unit_cell":unit_cell(eval(tokens[2])), "expected_centrosymmetric_subgroups_of_metric":int(tokens[3])} case["symmetry"]=crystal.symmetry(space_group_info= space_group_info(tokens[1]), unit_cell=case["unit_cell"]) yield case from cctbx.sgtbx.lattice_symmetry import metric_subgroups for small_max_delta in [1.E-6, 0.0]: for case in give_cases(): G = metric_subgroups(case["symmetry"], max_delta=small_max_delta,bravais_types_only=False) assert len(G.result_groups)==case["expected_centrosymmetric_subgroups_of_metric"] return True if (__name__ == "__main__"): exercise(sys.argv[1:])