from __future__ import absolute_import, division, print_function from iotbx.pdb.atom_selection import selection_string_from_selection from iotbx.pdb.atom_selection import get_clean_selection_string from mmtbx.ncs.ncs_search import get_chains_info from scitbx.array_family import flex import iotbx.pdb from libtbx.test_utils import approx_equal from six.moves import range from six.moves import zip test_pdb_1 = '''\ CRYST1 577.812 448.715 468.790 90.00 90.00 90.00 P 1 SCALE1 0.001731 0.000000 0.000000 0.00000 SCALE2 0.000000 0.002229 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002133 0.00000 ATOM 1 CA LYS A 151 10.766 9.333 12.905 1.00 44.22 C ATOM 2 CA LYS A 152 10.117 9.159 11.610 1.00 49.42 C ATOM 3 CA LYS A 153 9.099 8.000 11.562 1.00 46.15 C ATOM 4 CA LYS A 154 8.000 8.202 11.065 1.00 52.97 C ATOM 5 CA LYS A 155 11.146 9.065 10.474 1.00 41.68 C ATOM 6 CA LYS A 156 10.547 9.007 9.084 1.00 55.55 C ATOM 7 CA LYS A 157 11.545 9.413 8.000 1.00 72.27 C ATOM 8 CA LYS A 158 12.277 10.718 8.343 1.00 75.78 C ATOM 9 CA LYS A 159 11.349 11.791 8.809 1.00 75.88 C TER ATOM 222 CA LEU X 40 94.618 -5.253 91.582 1.00 87.10 C ATOM 223 CA ARG X 41 62.395 51.344 80.786 1.00107.25 C ATOM 224 CA ARG X 42 62.395 41.344 80.786 1.00107.25 C TER ATOM 1 CA THR D 1 8.111 11.080 10.645 1.00 20.00 C ATOM 2 CA THR D 2 8.000 9.722 10.125 1.00 20.00 C ATOM 3 CA THR D 3 8.075 8.694 11.249 1.00 20.00 C ATOM 4 CA THR D 4 8.890 8.818 12.163 1.00 20.00 C ATOM 5 CA THR D 5 9.101 9.421 9.092 1.00 20.00 C ATOM 6 CA THR D 6 9.001 10.343 8.000 1.00 20.00 C ATOM 7 CA THR D 7 8.964 8.000 8.565 1.00 20.00 C END ''' test_pdb_2 = '''\ CRYST1 41.870 78.240 85.900 90.00 90.00 90.00 P 2 21 21 8 SCALE1 0.023883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011641 0.00000 ATOM 1 N LYS A 151 16.915 16.113 -32.818 1.00 44.22 N ATOM 2 CA LYS A 151 16.266 15.939 -34.113 1.00 49.42 C ATOM 3 C LYS A 151 15.248 14.780 -34.161 1.00 46.15 C ATOM 4 O LYS A 151 14.149 14.982 -34.658 1.00 52.97 O ATOM 5 CB LYS A 151 17.295 15.845 -35.249 1.00 41.68 C ATOM 6 CG LYS A 151 16.696 15.787 -36.639 1.00 55.55 C ATOM 7 CD LYS A 151 17.694 16.193 -37.723 1.00 72.27 C ATOM 8 CE LYS A 151 18.426 17.498 -37.380 1.00 75.78 C ATOM 9 NZ LYS A 151 17.498 18.571 -36.914 1.00 75.88 N ATOM 10 N ARG A 152 15.575 13.584 -33.658 1.00 41.11 N ATOM 11 CA ARG A 152 14.545 12.524 -33.623 1.00 39.90 C ATOM 12 C ARG A 152 14.775 11.251 -32.810 1.00 33.61 C ATOM 13 O ARG A 152 15.911 10.847 -32.533 1.00 34.25 O ATOM 14 CB ARG A 152 14.096 12.135 -35.040 1.00 41.02 C ATOM 15 CG ARG A 152 15.094 11.299 -35.813 1.00 45.33 C ATOM 16 CD ARG A 152 14.593 11.085 -37.231 1.00 44.56 C ATOM 17 NE ARG A 152 13.434 10.190 -37.278 1.00 44.10 N ATOM 18 CZ ARG A 152 12.734 9.937 -38.378 1.00 49.14 C ATOM 19 NH1 ARG A 152 13.064 10.532 -39.521 1.00 44.79 N ATOM 20 NH2 ARG A 152 11.700 9.097 -38.335 1.00 45.30 N ATOM 21 N ALA B 153 13.656 10.621 -32.456 1.00 30.81 N ATOM 22 CA ALA B 153 13.619 9.397 -31.651 1.00 29.91 C ATOM 23 C ALA B 153 14.208 8.219 -32.409 1.00 31.80 C ATOM 24 O ALA B 153 14.248 8.241 -33.644 1.00 31.66 O ATOM 25 CB ALA B 153 12.176 9.082 -31.250 1.00 29.44 C ATOM 26 N PRO B 154 14.636 7.168 -31.680 1.00 30.22 N ATOM 27 CA PRO B 154 15.163 5.989 -32.375 1.00 28.83 C ATOM 28 C PRO B 154 14.085 5.348 -33.254 1.00 33.21 C ATOM 29 O PRO B 154 12.885 5.472 -32.970 1.00 26.91 O ATOM 30 CB PRO B 154 15.534 5.028 -31.234 1.00 27.52 C ATOM 31 CG PRO B 154 15.512 5.870 -29.971 1.00 30.59 C ATOM 32 CD PRO B 154 14.507 6.943 -30.231 1.00 27.77 C ATOM 33 N TYR B 155 14.519 4.680 -34.318 1.00 28.01 N ATOM 34 CA TYR B 155 13.603 3.970 -35.194 1.00 26.28 C ATOM 35 C TYR B 155 14.387 2.846 -35.845 1.00 32.08 C ATOM 36 O TYR B 155 15.623 2.936 -35.993 1.00 29.48 O ATOM 37 CB TYR B 155 13.028 4.912 -36.264 1.00 29.02 C ATOM 38 CG TYR B 155 14.088 5.528 -37.164 1.00 36.38 C ATOM 39 CD1 TYR B 155 14.789 6.670 -36.769 1.00 29.69 C ATOM 40 CD2 TYR B 155 14.403 4.957 -38.401 1.00 38.19 C ATOM 41 CE1 TYR B 155 15.760 7.237 -37.584 1.00 37.04 C ATOM 42 CE2 TYR B 155 15.376 5.518 -39.226 1.00 43.21 C ATOM 43 CZ TYR B 155 16.051 6.654 -38.804 1.00 41.97 C END ''' test_pdb_3 = '''\ CRYST1 203.106 83.279 178.234 90.00 106.67 90.00 C 1 2 1 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.004924 0.000000 0.001474 0.00000 SCALE2 0.000000 0.012008 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005857 0.00000 ATOM 313 N CYS H 47 85.603 -27.032 6.791 1.00 42.51 N ATOM 314 CA CYS H 47 84.850 -28.275 6.785 1.00 44.04 C ATOM 315 C CYS H 47 83.442 -28.089 6.261 1.00 42.34 C ATOM 316 O CYS H 47 83.056 -26.989 5.881 1.00 42.28 O ATOM 317 CB CYS H 47 84.827 -28.861 8.204 1.00 47.91 C ATOM 318 SG CYS H 47 86.496 -29.154 8.879 1.00 51.94 S ATOM 319 N ARG H 48 82.680 -29.174 6.224 1.00 40.63 N ATOM 320 CA ARG H 48 81.318 -29.102 5.747 1.00 40.99 C ATOM 321 C ARG H 48 80.335 -28.971 6.890 1.00 41.07 C ATOM 322 O ARG H 48 80.596 -29.428 7.997 1.00 40.42 O ATOM 323 CB ARG H 48 80.994 -30.328 4.884 1.00 42.65 C ATOM 324 CG ARG H 48 81.469 -31.626 5.452 1.00 44.32 C ATOM 325 CD ARG H 48 81.043 -32.849 4.627 1.00 44.70 C ATOM 326 NE ARG H 48 81.529 -34.052 5.294 1.00 44.81 N ATOM 327 CZ ARG H 48 82.738 -34.580 5.140 1.00 45.11 C ATOM 328 NH1 ARG H 48 83.614 -34.042 4.313 1.00 43.19 N ATOM 329 NH2 ARG H 48 83.095 -35.620 5.877 1.00 47.83 N ATOM 330 N LEU H 49 79.221 -28.306 6.614 1.00 41.54 N ATOM 331 CA LEU H 49 78.167 -28.103 7.596 1.00 42.36 C ATOM 332 C LEU H 49 76.946 -28.837 7.064 1.00 41.91 C ATOM 333 O LEU H 49 76.756 -28.928 5.852 1.00 43.00 O ATOM 334 CB LEU H 49 77.839 -26.618 7.736 1.00 43.11 C ATOM 335 CG LEU H 49 78.845 -25.691 8.414 1.00 45.90 C ATOM 336 CD1 LEU H 49 78.506 -24.251 8.063 1.00 46.63 C ATOM 337 CD2 LEU H 49 78.809 -25.892 9.919 1.00 47.40 C ATOM 338 N GLY H 49A 76.120 -29.358 7.965 1.00 40.67 N ATOM 339 CA GLY H 49A 74.938 -30.081 7.530 1.00 39.48 C ATOM 340 C GLY H 49A 75.302 -31.190 6.558 1.00 39.18 C ATOM 341 O GLY H 49A 74.504 -31.580 5.700 1.00 38.72 O ATOM 342 N GLY H 50 76.527 -31.692 6.695 1.00 39.31 N ATOM 343 CA GLY H 50 77.002 -32.764 5.839 1.00 38.66 C ATOM 344 C GLY H 50 77.149 -32.388 4.377 1.00 38.02 C ATOM 345 O GLY H 50 77.152 -33.261 3.507 1.00 38.89 O ATOM 346 N ILE H 51 77.278 -31.095 4.097 1.00 36.09 N ATOM 347 CA ILE H 51 77.421 -30.635 2.725 1.00 33.47 C ATOM 348 C ILE H 51 78.689 -29.823 2.570 1.00 32.56 C ATOM 349 O ILE H 51 78.976 -28.949 3.378 1.00 31.71 O ATOM 350 CB ILE H 51 76.229 -29.776 2.323 1.00 32.60 C ATOM 351 CG1 ILE H 51 74.948 -30.588 2.503 1.00 33.26 C ATOM 352 CG2 ILE H 51 76.385 -29.303 0.880 1.00 31.47 C ATOM 353 CD1 ILE H 51 73.684 -29.786 2.351 1.00 33.83 C ATOM 354 N ALA H 52 79.443 -30.112 1.520 1.00 31.45 N ATOM 355 CA ALA H 52 80.688 -29.412 1.265 1.00 31.24 C ATOM 356 C ALA H 52 80.477 -27.950 0.892 1.00 32.00 C ATOM 357 O ALA H 52 79.410 -27.556 0.406 1.00 32.53 O ATOM 358 CB ALA H 52 81.455 -30.109 0.148 1.00 27.90 C ''' test_pdb_4 = '''\ CRYST1 577.812 448.715 468.790 90.00 90.00 90.00 P 1 SCALE1 0.001731 0.000000 0.000000 0.00000 SCALE2 0.000000 0.002229 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002133 0.00000 ATOM 1 CA LYS A 151 10.766 9.333 12.905 1.00 44.22 C ATOM 2 CA LYS A 152 10.117 9.159 11.610 1.00 49.42 C ATOM 3 CA LYS A 153 9.099 8.000 11.562 1.00 46.15 C ATOM 4 CA LYS A 154 8.000 8.202 11.065 1.00 52.97 C ATOM 5 CA LYS A 155 11.146 9.065 10.474 1.00 41.68 C ATOM 6 CA LYS A 156 10.547 9.007 9.084 1.00 55.55 C ATOM 7 CA LYS A 157 11.545 9.413 8.000 1.00 72.27 C HETATM 3512 O HOH A2001 -85.460 23.570 -79.414 1.00 34.05 O HETATM 3513 O HOH A2002 -81.492 18.186 -35.869 1.00 13.88 O HETATM 3514 O HOH A2003 -73.597 30.740 -72.170 1.00 33.13 O HETATM 3515 O HOH A2004 -74.933 23.929 -66.597 1.00 26.66 O HETATM 3516 O HOH A2005 -73.036 25.921 -66.605 1.00 23.41 END ''' test_pdb_5 = '''\ CRYST1 42.558 113.820 137.132 90.00 90.00 90.00 P 21 21 21 24 SCALE1 0.023497 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007292 0.00000 ATOM 2905 N ILE D 25 -21.903 62.095 51.650 1.00 19.95 N ATOM 2906 CA ILE D 25 -20.570 61.733 52.122 1.00 20.06 C ATOM 2907 C ILE D 25 -19.631 62.938 52.275 1.00 22.71 C ATOM 2908 O ILE D 25 -19.519 63.807 51.393 1.00 21.72 O ATOM 2909 CB ILE D 25 -19.887 60.655 51.241 1.00 15.34 C ATOM 2910 CG1 ILE D 25 -20.768 59.411 51.256 1.00 12.56 C ATOM 2911 CG2 ILE D 25 -18.438 60.365 51.831 1.00 14.73 C ATOM 2912 CD1 ILE D 25 -20.661 58.435 50.096 1.00 15.09 C ATOM 2913 N GLY D 26 -18.968 62.975 53.429 1.00 20.40 N ATOM 2914 CA GLY D 26 -17.920 63.914 53.711 1.00 22.40 C ATOM 2915 C GLY D 26 -18.420 65.290 54.086 1.00 23.10 C ATOM 2916 O GLY D 26 -18.155 65.781 55.197 1.00 24.70 O ATOM 2917 N VAL D 27 -19.117 65.935 53.151 1.00 23.71 N ATOM 2918 CA VAL D 27 -19.595 67.307 53.388 1.00 23.17 C ATOM 2919 C VAL D 27 -20.597 67.344 54.568 1.00 24.78 C ATOM 2920 O VAL D 27 -20.745 68.387 55.199 1.00 26.51 O ATOM 2921 CB VAL D 27 -20.183 67.930 52.109 1.00 25.99 C ATOM 2922 CG1 VAL D 27 -19.069 68.049 51.032 1.00 23.04 C ATOM 2923 CG2 VAL D 27 -21.399 67.121 51.609 1.00 21.43 C ATOM 2932 CB ASP D 28 -23.555 65.658 55.450 1.00 25.04 C ATOM 2933 CG ASP D 28 -24.173 66.689 54.514 1.00 28.36 C ATOM 2934 OD1 ASP D 28 -23.934 67.903 54.695 1.00 27.71 O ATOM 2935 OD2 ASP D 28 -24.948 66.267 53.632 1.00 24.68 O ATOM 2924 N AASP D 28 -21.219 66.203 54.890 0.50 22.16 N ATOM 2926 CA AASP D 28 -22.200 66.120 55.994 0.50 24.54 C ATOM 2928 C AASP D 28 -21.780 65.239 57.184 0.50 21.81 C ATOM 2930 O AASP D 28 -22.627 64.713 57.901 0.50 22.07 O ATOM 2925 N BASP D 28 -21.261 66.213 54.799 0.50 23.07 N ATOM 2927 CA BASP D 28 -22.155 66.024 55.923 0.50 25.72 C ATOM 2929 C BASP D 28 -21.575 64.885 56.777 0.50 24.87 C ATOM 2931 O BASP D 28 -21.997 63.731 56.681 0.50 28.18 O ATOM 2936 N SER D 29 -20.479 65.193 57.444 1.00 26.01 N ATOM 2937 CA SER D 29 -19.892 64.371 58.495 1.00 24.17 C ATOM 2938 C SER D 29 -19.715 65.264 59.716 1.00 23.31 C ATOM 2939 O SER D 29 -19.972 66.479 59.622 1.00 23.57 O ATOM 2940 CB SER D 29 -18.538 63.871 58.037 1.00 21.39 C ATOM 2941 OG SER D 29 -17.658 64.927 57.738 1.00 20.49 O ATOM 2942 N ALA D 30 -19.259 64.708 60.836 1.00 19.54 N ATOM 2943 CA ALA D 30 -18.937 65.524 61.993 1.00 21.15 C ATOM 2944 C ALA D 30 -17.875 66.586 61.555 1.00 20.92 C ATOM 2945 O ALA D 30 -18.026 67.767 61.866 1.00 18.58 O ATOM 2946 CB ALA D 30 -18.461 64.657 63.163 1.00 17.17 C ''' test_pdb_6 = '''\ CRYST1 203.106 83.279 178.234 90.00 106.67 90.00 C 1 2 1 12 ATOM 1 N ARG H 48 82.680 -29.174 6.224 1.00 40.63 N ATOM 2 CA ARG H 48 81.318 -29.102 5.747 1.00 40.99 C ATOM 3 C ARG H 48 80.335 -28.971 6.890 1.00 41.07 C ATOM 4 O ARG H 48 80.596 -29.428 7.997 1.00 40.42 O ATOM 5 N LEU H 49 79.221 -28.306 6.614 1.00 41.54 N ATOM 6 CA LEU H 49 78.167 -28.103 7.596 1.00 42.36 C ATOM 7 C LEU H 49 76.946 -28.837 7.064 1.00 41.91 C ATOM 8 O LEU H 49 76.756 -28.928 5.852 1.00 43.00 O ATOM 9 CB LEU H 49 77.839 -26.618 7.736 1.00 43.11 C ATOM 10 CG LEU H 49 78.845 -25.691 8.414 1.00 45.90 C ATOM 11 CD1 LEU H 49 78.506 -24.251 8.063 1.00 46.63 C ATOM 12 CD2 LEU H 49 78.809 -25.892 9.919 1.00 47.40 C ATOM 13 N GLY H 49A 76.120 -29.358 7.965 1.00 40.67 N ATOM 14 CA GLY H 49A 74.938 -30.081 7.530 1.00 39.48 C ATOM 15 C GLY H 49A 75.302 -31.190 6.558 1.00 39.18 C ATOM 16 O GLY H 49A 74.504 -31.580 5.700 1.00 38.72 O ATOM 17 N GLY H 50 76.527 -31.692 6.695 1.00 39.31 N ATOM 18 CA GLY H 50 77.002 -32.764 5.839 1.00 38.66 C ATOM 19 C GLY H 50 77.149 -32.388 4.377 1.00 38.02 C ATOM 20 O GLY H 50 77.152 -33.261 3.507 1.00 38.89 O ''' test_pdb_7 = """\ ATOM 1 N ILE A 14 -14.366 134.691 190.492 1.00 65.50 N ATOM 2 CA ILE A 14 -13.578 133.563 190.974 1.00 63.49 C ATOM 3 C ILE A 14 -12.354 134.128 191.678 1.00 62.68 C ATOM 4 O ILE A 14 -11.609 134.922 191.093 1.00 63.22 O ATOM 5 CB ILE A 14 -13.151 132.610 189.839 1.00 63.05 C ATOM 6 CG1 ILE A 14 -14.374 131.920 189.230 1.00 63.83 C ATOM 7 CG2 ILE A 14 -12.167 131.562 190.366 1.00 61.34 C ATOM 8 CD1 ILE A 14 -14.061 131.063 188.013 1.00 63.78 C ATOM 9 N ALA A 15 -12.147 133.721 192.927 1.00 60.93 N ATOM 10 CA ALA A 15 -11.017 134.168 193.727 1.00 60.26 C ATOM 11 C ALA A 15 -10.262 132.961 194.262 1.00 58.80 C ATOM 12 O ALA A 15 -10.871 131.958 194.644 1.00 58.33 O ATOM 13 CB ALA A 15 -11.474 135.043 194.893 1.00 60.84 C ATOM 14 N GLY A 16 -8.937 133.066 194.291 1.00 59.81 N ATOM 15 CA GLY A 16 -8.107 131.990 194.797 1.00 58.83 C ATOM 16 C GLY A 16 -6.893 132.537 195.514 1.00 58.70 C ATOM 17 O GLY A 16 -6.463 133.670 195.277 1.00 59.33 O ATOM 18 N ASP A 17 -6.340 131.714 196.401 1.00 58.04 N ATOM 19 CA ASP A 17 -5.148 132.100 197.141 1.00 58.08 C ATOM 20 C ASP A 17 -3.917 131.803 196.282 1.00 58.37 C ATOM 21 O ASP A 17 -4.024 131.476 195.097 1.00 58.58 O ATOM 22 CB ASP A 17 -5.110 131.397 198.496 1.00 57.69 C ATOM 23 CG ASP A 17 -4.577 129.986 198.405 1.00 57.48 C ATOM 24 OD1 ASP A 17 -4.995 129.243 197.491 1.00 57.38 O ATOM 25 OD2 ASP A 17 -3.733 129.619 199.249 1.00 57.63 O1- """ test_pdb_8 = """\ ATOM 1 N ALA A 125 -29.026 54.443 -42.502 1.00 32.57 N ATOM 2 CA ALA A 125 -27.931 53.547 -42.137 1.00 31.14 C ATOM 3 C ALA A 125 -28.182 52.145 -42.679 1.00 31.38 C ATOM 4 O ALA A 125 -27.272 51.499 -43.215 1.00 39.47 O ATOM 5 CB ALA A 125 -27.774 53.497 -40.615 1.00 27.41 C ATOM 6 N SER A 126 -29.423 51.670 -42.564 1.00 30.06 N ATOM 7 CA SER A 126 -29.767 50.337 -43.032 1.00 32.18 C ATOM 8 C SER A 126 -29.602 50.216 -44.538 1.00 38.36 C ATOM 9 O SER A 126 -29.386 49.109 -45.039 1.00 45.79 O ATOM 10 CB SER A 126 -31.190 49.988 -42.605 1.00 29.70 C ATOM 11 OG SER A 126 -31.370 48.579 -42.545 1.00 40.98 O ATOM 12 N ALA A 127 -29.671 51.312 -45.252 1.00 45.06 N ATOM 13 CA ALA A 127 -29.521 51.369 -46.685 1.00 48.16 C ATOM 14 C ALA A 127 -28.142 51.136 -47.248 1.00 53.02 C ATOM 15 O ALA A 127 -28.024 50.717 -48.363 1.00 58.10 O ATOM 16 CB ALA A 127 -30.098 52.647 -47.231 1.00 47.36 C ATOM 17 N LYS A 128 -27.105 51.433 -46.492 1.00 54.75 N ATOM 18 CA LYS A 128 -25.742 51.247 -46.964 1.00 57.26 C ATOM 19 C LYS A 128 -25.482 49.795 -47.340 1.00 52.16 C ATOM 20 O LYS A 128 -25.996 48.893 -46.720 1.00 45.54 O ATOM 21 CB LYS A 128 -24.759 51.535 -45.843 1.00 30.00 C ATOM 22 CG LYS A 128 -24.496 52.960 -45.461 1.00 30.00 C ATOM 23 CD LYS A 128 -22.989 53.226 -45.366 1.00 30.00 C ATOM 24 CE LYS A 128 -22.248 52.508 -44.239 1.00 30.00 C ATOM 25 NZ LYS A 128 -20.903 53.077 -43.987 1.00 30.00 N """ test_pdb_9 = """\ ATOM 1 N ARG A 124 -31.625 55.204 -43.320 1.00 36.06 N ATOM 2 CA ARG A 124 -30.475 55.601 -44.092 1.00 34.32 C ATOM 3 C ARG A 124 -29.278 54.709 -43.767 1.00 36.61 C ATOM 4 O ARG A 124 -28.616 54.266 -44.645 1.00 40.69 O ATOM 5 CB ARG A 124 -30.122 57.063 -43.899 1.00 30.00 C ATOM 6 CG ARG A 124 -28.740 57.425 -44.418 1.00 30.00 C ATOM 7 CD ARG A 124 -28.283 58.842 -44.132 1.00 30.00 C ATOM 8 NE ARG A 124 -28.977 59.388 -42.992 1.00 30.00 N ATOM 9 CZ ARG A 124 -28.813 60.609 -42.544 1.00 30.00 C ATOM 10 NH1 ARG A 124 -27.970 61.414 -43.148 1.00 30.00 N ATOM 11 NH2 ARG A 124 -29.492 61.020 -41.504 1.00 30.00 N ATOM 12 N ALA A 125 -29.026 54.443 -42.502 1.00 32.57 N ATOM 13 CA ALA A 125 -27.931 53.547 -42.137 1.00 31.14 C ATOM 14 C ALA A 125 -28.182 52.145 -42.679 1.00 31.38 C ATOM 15 O ALA A 125 -27.272 51.499 -43.215 1.00 39.47 O ATOM 16 CB ALA A 125 -27.774 53.497 -40.615 1.00 27.41 C ATOM 17 N SER A 126 -29.423 51.670 -42.564 1.00 30.06 N ATOM 18 CA SER A 126 -29.767 50.337 -43.032 1.00 32.18 C ATOM 19 C SER A 126 -29.602 50.216 -44.538 1.00 38.36 C ATOM 20 O SER A 126 -29.386 49.109 -45.039 1.00 45.79 O ATOM 21 CB SER A 126 -31.190 49.988 -42.605 1.00 29.70 C ATOM 22 OG SER A 126 -31.370 48.579 -42.545 1.00 40.98 O ATOM 23 N ALA A 127 -29.671 51.312 -45.252 1.00 45.06 N ATOM 24 CA ALA A 127 -29.521 51.369 -46.685 1.00 48.16 C ATOM 25 C ALA A 127 -28.142 51.136 -47.248 1.00 53.02 C ATOM 26 O ALA A 127 -28.024 50.717 -48.363 1.00 58.10 O ATOM 27 CB ALA A 127 -30.098 52.647 -47.231 1.00 47.36 C """ test_pdb_10 = """\ ATOM 885 N ASP A 117 -38.120 61.598 -35.985 1.00 24.56 N ATOM 886 CA ASP A 117 -37.446 61.205 -37.186 1.00 24.60 C ATOM 887 C ASP A 117 -36.374 60.119 -37.011 1.00 26.59 C ATOM 888 O ASP A 117 -35.562 59.977 -37.870 1.00 19.99 O ATOM 889 CB ASP A 117 -36.851 62.414 -37.878 1.00 33.00 C ATOM 890 CG ASP A 117 -37.507 62.725 -39.182 1.00 46.28 C ATOM 891 OD1 ASP A 117 -38.553 62.190 -39.479 1.00 53.20 O ATOM 892 OD2 ASP A 117 -36.964 63.519 -39.921 1.00 54.16 O ATOM 1 N ARG A 124 -31.625 55.204 -43.320 1.00 36.06 N ATOM 2 CA ARG A 124 -30.475 55.601 -44.092 1.00 34.32 C ATOM 3 C ARG A 124 -29.278 54.709 -43.767 1.00 36.61 C ATOM 4 O ARG A 124 -28.616 54.266 -44.645 1.00 40.69 O ATOM 5 CB ARG A 124 -30.122 57.063 -43.899 1.00 30.00 C ATOM 6 CG ARG A 124 -28.740 57.425 -44.418 1.00 30.00 C ATOM 7 CD ARG A 124 -28.283 58.842 -44.132 1.00 30.00 C ATOM 8 NE ARG A 124 -28.977 59.388 -42.992 1.00 30.00 N ATOM 9 CZ ARG A 124 -28.813 60.609 -42.544 1.00 30.00 C ATOM 10 NH1 ARG A 124 -27.970 61.414 -43.148 1.00 30.00 N ATOM 11 NH2 ARG A 124 -29.492 61.020 -41.504 1.00 30.00 N ATOM 12 N ALA A 125 -29.026 54.443 -42.502 1.00 32.57 N ATOM 13 CA ALA A 125 -27.931 53.547 -42.137 1.00 31.14 C ATOM 14 C ALA A 125 -28.182 52.145 -42.679 1.00 31.38 C ATOM 15 O ALA A 125 -27.272 51.499 -43.215 1.00 39.47 O ATOM 16 CB ALA A 125 -27.774 53.497 -40.615 1.00 27.41 C ATOM 17 N SER A 126 -29.423 51.670 -42.564 1.00 30.06 N ATOM 18 CA SER A 126 -29.767 50.337 -43.032 1.00 32.18 C ATOM 19 C SER A 126 -29.602 50.216 -44.538 1.00 38.36 C ATOM 20 O SER A 126 -29.386 49.109 -45.039 1.00 45.79 O ATOM 21 CB SER A 126 -31.190 49.988 -42.605 1.00 29.70 C ATOM 22 OG SER A 126 -31.370 48.579 -42.545 1.00 40.98 O ATOM 23 N ALA A 127 -29.671 51.312 -45.252 1.00 45.06 N ATOM 24 CA ALA A 127 -29.521 51.369 -46.685 1.00 48.16 C ATOM 25 C ALA A 127 -28.142 51.136 -47.248 1.00 53.02 C ATOM 26 O ALA A 127 -28.024 50.717 -48.363 1.00 58.10 O ATOM 27 CB ALA A 127 -30.098 52.647 -47.231 1.00 47.36 C """ test_pdb_11 = """\ ATOM 1 CA MET A 480 -10.152 -1.677 37.457 1.00 28.90 AA- C ATOM 2 CG MET A 480 -9.517 0.607 38.489 1.00 49.21 AA- C ATOM 3 CA VAL A 481 -11.857 -5.041 37.936 1.00 23.15 AA- C ATOM 4 CA VAL A 482 -13.580 -5.715 41.251 1.00 34.23 AA- C ATOM 5 CA ARG A 483 -14.378 -9.189 42.566 1.00 30.50 AA- C ATOM 6 CG ARG A 483 -12.194 -10.275 42.051 1.00 28.52 AA- C ATOM 7 CA ARG A 484 -17.677 -9.381 44.419 1.00 41.14 AA- C ATOM 8 CA MET B 480 -16.603 9.979 4.769 1.00 32.68 BA- C ATOM 9 CG MET B 480 -16.554 7.723 3.530 1.00 54.69 BA- C ATOM 10 CA VAL B 481 -17.675 13.614 4.970 1.00 34.88 BA- C ATOM 11 CA VAL B 482 -20.607 14.715 2.834 1.00 35.95 BA- C ATOM 12 CA ARG B 483 -21.481 18.297 1.835 1.00 23.95 BA- C ATOM 13 CA ARG B 484 -25.162 19.109 1.469 1.00 47.03 BA- C ATOM 14 CG ARG B 484 -25.746 17.004 2.827 1.00 47.49 BA- C """ test_pdb_12 = """\ ATOM 1 N ASP A 279 148.294 135.256 14.514 1.00361.90 N ATOM 2 CA ASP A 279 148.944 135.688 13.244 1.00363.91 C ATOM 3 C ASP A 279 150.116 136.660 13.498 1.00311.37 C ATOM 4 O ASP A 279 150.890 136.977 12.584 1.00265.25 O ATOM 5 CB ASP A 279 147.909 136.283 12.247 1.00340.39 C ATOM 6 CG ASP A 279 148.544 136.866 10.940 1.00317.09 C ATOM 7 OD1 ASP A 279 149.462 136.253 10.337 1.00271.02 O ATOM 8 OD2 ASP A 279 148.085 137.945 10.494 1.00309.85 O ATOM 9 N ARG A 280 150.240 137.122 14.743 1.00282.66 N ATOM 10 CA ARG A 280 151.405 137.889 15.191 1.00243.53 C ATOM 11 C ARG A 280 152.420 136.982 15.887 1.00239.61 C ATOM 12 O ARG A 280 153.345 137.464 16.539 1.00231.28 O ATOM 13 CB ARG A 280 150.976 139.011 16.137 1.00252.04 C ATOM 14 N LEU A 281 152.236 135.669 15.740 1.00271.48 N ATOM 15 CA LEU A 281 153.120 134.676 16.348 1.00298.95 C ATOM 16 C LEU A 281 153.688 133.669 15.334 1.00293.08 C ATOM 17 O LEU A 281 154.558 132.864 15.675 1.00325.01 O ATOM 18 CB LEU A 281 152.411 133.959 17.495 1.00294.06 C ATOM 19 CG LEU A 281 153.236 133.921 18.776 1.00316.57 C ATOM 20 CD1 LEU A 281 153.263 135.296 19.436 1.00243.06 C ATOM 21 CD2 LEU A 281 152.663 132.873 19.709 1.00298.46 C ATOM 22 N GLU A 282 153.167 133.706 14.106 1.00247.81 N ATOM 23 CA GLU A 282 153.827 133.132 12.921 1.00294.79 C ATOM 24 C GLU A 282 154.887 134.153 12.467 1.00320.33 C ATOM 25 O GLU A 282 155.953 133.788 11.917 1.00233.13 O ATOM 26 CB GLU A 282 152.782 132.842 11.808 1.00321.01 C ATOM 27 CG GLU A 282 153.279 132.850 10.343 1.00432.99 C ATOM 28 CD GLU A 282 152.275 133.402 9.306 1.00369.39 C ATOM 29 OE1 GLU A 282 151.087 133.604 9.642 1.00323.25 O ATOM 30 OE2 GLU A 282 152.674 133.646 8.135 1.00284.42 O ATOM 31 N ARG A 283 154.572 135.429 12.728 1.00357.16 N ATOM 32 CA ARG A 283 155.454 136.572 12.483 1.00384.53 C ATOM 33 C ARG A 283 156.436 136.825 13.640 1.00275.79 C ATOM 34 O ARG A 283 157.288 137.710 13.545 1.00265.14 O ATOM 35 CB ARG A 283 154.626 137.840 12.208 1.00316.05 C ATOM 36 N ARG A 284 156.321 136.051 14.722 1.00266.18 N ATOM 37 CA ARG A 284 157.243 136.156 15.872 1.00255.82 C ATOM 38 C ARG A 284 158.154 134.935 16.094 1.00314.62 C ATOM 39 O ARG A 284 159.154 135.024 16.825 1.00253.48 O ATOM 40 CB ARG A 284 156.469 136.452 17.153 1.00230.14 C ATOM 41 N SER A 285 157.800 133.808 15.471 1.00393.24 N ATOM 42 CA SER A 285 158.572 132.562 15.569 1.00358.40 C ATOM 43 C SER A 285 159.419 132.307 14.317 1.00418.23 C ATOM 44 O SER A 285 158.898 132.157 13.204 1.00380.17 O ATOM 45 CB SER A 285 157.651 131.363 15.841 1.00264.20 C """ test_pdb_13 = """\ ATOM 1 N GLU A 260 74.225 41.166 25.753 1.00 58.41 N ATOM 2 CA GLU A 260 75.147 41.741 24.757 1.00 58.93 C ATOM 3 C GLU A 260 75.096 41.010 23.404 1.00 59.55 C ATOM 4 O GLU A 260 75.896 41.322 22.519 1.00 59.69 O ATOM 5 CB GLU A 260 76.587 41.677 25.279 1.00 59.13 C ATOM 6 CG GLU A 260 76.899 42.547 26.490 1.00 59.98 C ATOM 7 CD GLU A 260 78.326 42.347 27.001 1.00 61.43 C ATOM 8 OE1 GLU A 260 78.859 41.213 26.938 1.00 61.60 O ATOM 9 OE2 GLU A 260 78.934 43.331 27.468 1.00 64.79 O ATOM 10 N CYS A 261 74.177 40.043 23.246 1.00 60.12 N ATOM 11 CA CYS A 261 74.105 39.192 22.050 1.00 60.18 C ATOM 12 C CYS A 261 72.733 39.239 21.359 1.00 61.64 C ATOM 13 O CYS A 261 72.355 38.276 20.698 1.00 61.42 O ATOM 14 CB CYS A 261 74.439 37.718 22.407 1.00 59.87 C ATOM 15 SG CYS A 261 76.011 37.403 23.356 1.00 57.71 S ATOM 16 N GLY A 262 72.018 40.364 21.494 1.00 63.62 N ATOM 17 CA GLY A 262 70.666 40.587 20.921 1.00 65.14 C ATOM 18 C GLY A 262 69.546 40.080 21.841 1.00 66.01 C ATOM 19 O GLY A 262 68.528 39.491 21.408 1.00 66.75 O ATOM 20 OXT GLY A 262 69.622 40.268 23.068 1.00 66.78 O TER ATOM 21 N CYS B 261 74.710 74.423 33.026 1.00 51.47 N ATOM 22 CA CYS B 261 74.050 74.094 31.771 1.00 51.64 C ATOM 23 C CYS B 261 73.663 75.409 31.099 1.00 53.38 C ATOM 24 O CYS B 261 72.609 75.498 30.502 1.00 53.30 O ATOM 25 CB CYS B 261 72.820 73.215 32.017 1.00 50.99 C ATOM 26 SG CYS B 261 73.155 71.752 33.046 1.00 46.82 S ATOM 27 N GLY B 262 74.546 76.413 31.226 1.00 55.76 N ATOM 28 CA GLY B 262 74.424 77.787 30.642 1.00 57.82 C ATOM 29 C GLY B 262 73.715 78.804 31.551 1.00 58.64 C ATOM 30 O GLY B 262 73.579 78.604 32.783 1.00 58.58 O ATOM 31 OXT GLY B 262 73.311 79.889 31.060 1.00 59.70 O TER HETATM 32 N GLU A 301 75.002 26.783 43.217 1.00 28.86 N HETATM 33 CA GLU A 301 76.076 25.770 43.503 1.00 29.91 C HETATM 34 C GLU A 301 76.194 25.508 45.002 1.00 30.65 C HETATM 35 O GLU A 301 77.025 24.681 45.464 1.00 30.01 O HETATM 36 CB GLU A 301 77.422 26.205 42.939 1.00 30.22 C HETATM 37 CG GLU A 301 77.563 26.074 41.392 1.00 29.97 C HETATM 38 CD GLU A 301 77.627 24.641 40.897 1.00 30.03 C HETATM 39 OE1 GLU A 301 77.884 23.761 41.746 1.00 26.02 O HETATM 40 OE2 GLU A 301 77.475 24.404 39.651 1.00 30.03 O HETATM 41 OXT GLU A 301 75.416 26.080 45.793 1.00 30.21 O """ def test_get_clean_selection_string(): """ Check get_clean_selection_string """ # print sys._getframe().f_code.co_name ch_sel = 'chain A' res_selection1 = ['resid 1:10'] res_id = '27c' s = '(resid ' + res_id + ' and (name ' atom_name = [x for x in [' CA',' N']] atom_str = ' or name '.join(atom_name) s = s + atom_str + ')' res_selection2 = ['resid 1:10',s] result1 = get_clean_selection_string(ch_sel,[]) result2 = get_clean_selection_string(ch_sel,res_selection1) result3 = get_clean_selection_string(ch_sel,res_selection2) assert result1 == 'chain A', result1 assert result2 == 'chain A and resid 1:10', result2 expt = 'chain A and (resid 1:10 or (resid 27c and (name CA or name N))' assert result3 == expt, result3 def test_selection_string_from_selection(): """ Test selection_string_from_selection """ pdb_h = iotbx.pdb.input(source_info=None, lines=test_pdb_1).construct_hierarchy() isel1 = flex.size_t([12, 13, 14, 15, 16, 17, 18]) isel2 = flex.size_t([12, 13, 14, 16, 17, 18]) isel3 = flex.size_t([12, 13, 14, 15, 16, 17]) sel_str1 = selection_string_from_selection(pdb_h,isel1) sel_str2 = selection_string_from_selection(pdb_h,isel2) sel_str3 = selection_string_from_selection(pdb_h,isel3) assert sel_str1 == "chain 'D'", sel_str1 assert sel_str2 == "(chain 'D' and (resid 1 through 3 or resid 5 through 7))", sel_str2 assert sel_str3 == "(chain 'D' and resid 1 through 6)", sel_str3 # asc = pdb_h.atom_selection_cache() sel1 = list(asc.iselection(sel_str1)) sel2 = list(asc.iselection(sel_str2)) sel3 = list(asc.iselection(sel_str3)) # assert sel1 == list(isel1), sel1 assert sel2 == list(isel2), sel2 assert sel3 == list(isel3), sel3 def test_selection_string_from_selection2(): """ Test selection_string_from_selection """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_2).construct_hierarchy() l1 = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25, 26,27,28,29,30,31] l2 = [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17 ,20,21,22,23,24,25, 26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42] isel1 = flex.size_t(l1) isel2 = flex.size_t(l2) # sel_str1 = selection_string_from_selection(pdb_h,isel1) sel_str2 = selection_string_from_selection(pdb_h,isel2) assert sel_str1 == "chain 'A' or (chain 'B' and resid 153 through 154)", sel_str1 s = "(chain 'A' and (resid 151 or (resid 152 and (name N or name CA or " s += "name C or name O or name CB or name CG or name CD or name NE or " s += "name CZ )))) or chain 'B'" assert sel_str2 == s, sel_str2 # asc = pdb_h.atom_selection_cache() sel1 = list(asc.iselection(sel_str1)) sel2 = list(asc.iselection(sel_str2)) # assert sel1 == list(isel1), sel1 assert sel2 == list(isel2), sel2 def test_avoid_chain_selection(): pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_2).construct_hierarchy() isel1 = flex.size_t([0,1,2,3,4,5,6,7,8]) sel_str1 = selection_string_from_selection(pdb_h,isel1) s = "(chain 'A' and resid 151)" assert sel_str1 == s, sel_str1 def test_avoid_chain_selection2(): pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_3).construct_hierarchy() isel1 = flex.size_t(range(6,46)) sel_str1 = selection_string_from_selection(pdb_h,isel1) # s = '(chain H and (resid 48 or resid 49 or resid 49A or resid 50:52))' # better way: s = "(chain 'H' and resid 48 through 52)" assert sel_str1 == s, sel_str1 # l1 = list(range(6,25)) + list(range(29,46)) isel1 = flex.size_t(l1) # s = '(chain H and (resid 48 or resid 49 or resid 50:52))' # better way: s = "(chain 'H' and (resid 48 through 49 or resid 50 through 52))" sel_str1 = selection_string_from_selection(pdb_h,isel1) assert sel_str1 == s, sel_str1 def test_avoid_hoh(): pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_4).construct_hierarchy() isel1 = flex.size_t(range(7)) sel_str1 = selection_string_from_selection(pdb_h,isel1) s = "(chain 'A' and resid 151 through 157)" assert sel_str1 == s, sel_str1 # asc = pdb_h.atom_selection_cache() sel = asc.iselection(s) assert sel.size() == 7, sel.size() def test_include_hoh(): pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_4).construct_hierarchy() isel1 = flex.size_t(range(7)) sel_str1 = selection_string_from_selection( pdb_h,isel1) s = "(chain 'A' and resid 151 through 157)" assert sel_str1 == s, sel_str1 # asc = pdb_h.atom_selection_cache() sel = asc.iselection(s) assert sel.size() == 7, sel.size() # isel1 = flex.size_t(range(12)) sel_str1 = selection_string_from_selection( pdb_h,isel1) assert sel_str1 == "chain 'A'", sel_str def test_selection_with_alternative_conformers(): pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_5).construct_hierarchy(sort_atoms=True) asc = pdb_h.atom_selection_cache() chains_info = get_chains_info(pdb_h) ch_D = chains_info['D'] # test conditions verification assert ch_D.no_altloc == [True, True, True, False, True, True] select_all = sorted([x for xi in ch_D.atom_selection for x in xi]) test_list = list(asc.iselection("not altloc B")) assert select_all == test_list, "%s" % select_all def test_insertions(): pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_6).construct_hierarchy() isel = flex.size_t(range(15)) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'H' and (resid 48 through 49 or (resid 49A and (name N or name CA or name C ))))", tsel isel = flex.size_t(range(16)) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'H' and resid 48 through 49A)", tsel def test_2(): """ behavior with GLY: don't stop selection string: if a user wants only N, CA, C, O atoms, there is no reason to break the selection range just because there is GLY and it doesn't need names. And we even skip the residue range here, tested extensively in test_5 """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_7).construct_hierarchy() isel = flex.size_t([0,1,2,3,8,9,10,11,13,14,15,16,17,18,19,20]) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'A' and (name N or name CA or name C or name O ))" , tsel def test_3(): """ single atom selections """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_6).construct_hierarchy() for i, answ in zip(range(20), [ "(chain 'H' and (resid 48 and (name N )))", "(chain 'H' and (resid 48 and (name CA )))", "(chain 'H' and (resid 48 and (name C )))", "(chain 'H' and (resid 48 and (name O )))", "(chain 'H' and (resid 49 and (name N )))", "(chain 'H' and (resid 49 and (name CA )))", "(chain 'H' and (resid 49 and (name C )))", "(chain 'H' and (resid 49 and (name O )))", "(chain 'H' and (resid 49 and (name CB )))", "(chain 'H' and (resid 49 and (name CG )))", "(chain 'H' and (resid 49 and (name CD1)))", "(chain 'H' and (resid 49 and (name CD2)))", "(chain 'H' and (resid 49A and (name N )))", "(chain 'H' and (resid 49A and (name CA )))", "(chain 'H' and (resid 49A and (name C )))", "(chain 'H' and (resid 49A and (name O )))", "(chain 'H' and (resid 50 and (name N )))", "(chain 'H' and (resid 50 and (name CA )))", "(chain 'H' and (resid 50 and (name C )))", "(chain 'H' and (resid 50 and (name O )))"]): isel = flex.size_t([i]) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == answ, "%s != %s" % (tsel, answ) def test_4(): """ double atoms selections """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_6).construct_hierarchy() for i, answ in zip(range(0,20,2), [ "(chain 'H' and (resid 48 and (name N or name CA )))", "(chain 'H' and (resid 48 and (name C or name O )))", "(chain 'H' and (resid 49 and (name N or name CA )))", "(chain 'H' and (resid 49 and (name C or name O )))", "(chain 'H' and (resid 49 and (name CB or name CG )))", "(chain 'H' and (resid 49 and (name CD1 or name CD2)))", "(chain 'H' and (resid 49A and (name N or name CA )))", "(chain 'H' and (resid 49A and (name C or name O )))", "(chain 'H' and (resid 50 and (name N or name CA )))", "(chain 'H' and (resid 50 and (name C or name O )))"]): isel = flex.size_t([i,i+1]) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == answ, "%s != %s" % (tsel, answ) # and now odd: for i, answ in zip(range(1,19,2), [ "(chain 'H' and (resid 48 and (name CA or name C )))", "(chain 'H' and ((resid 48 and (name O )) or (resid 49 and (name N ))))", "(chain 'H' and (resid 49 and (name CA or name C )))", "(chain 'H' and (resid 49 and (name O or name CB )))", "(chain 'H' and (resid 49 and (name CG or name CD1)))", "(chain 'H' and ((resid 49 and (name CD2)) or (resid 49A and (name N ))))", "(chain 'H' and (resid 49A and (name CA or name C )))", "(chain 'H' and ((resid 49A and (name O )) or (resid 50 and (name N ))))", "(chain 'H' and (resid 50 and (name CA or name C )))"]): isel = flex.size_t([i,i+1]) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == answ, "%s != %s" % (tsel, answ) def test_5(): """ Don't output the residue range if it covers whole chain, even if there is atom name selection """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_7).construct_hierarchy() isel = flex.size_t(range(25)) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "chain 'A'", tsel isel = flex.size_t([0,8,13,17]) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'A' and (name N ))", tsel isel = flex.size_t([0,1,8,9,13,14,17,18]) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'A' and (name N or name CA ))", tsel isel = flex.size_t([0,1,2,8,9,13,14,17,18]) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'A' and ((resid 14 and (name N or name CA or name C )) or (resid 15 through 17 and (name N or name CA ))))", tsel def test_6(): """ previous range is all atoms selected, next residue is not, but selected atoms are the same as for the last residue. In this case the range with all atoms should be dumped. """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_8).construct_hierarchy() isel = flex.size_t(range(21)) tsel = selection_string_from_selection(pdb_h, isel) # print "tsel", tsel assert tsel == "(chain 'A' and (resid 125 through 127 or (resid 128 and (name N or name CA or name C or name O or name CB ))))" , tsel def test_7(): """ """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_9).construct_hierarchy() isel = flex.size_t([0,1,2,3,4]+list(range(11,27))) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'A' and ((resid 124 through 125 and (name N or name CA or name C or name O or name CB )) or resid 126 through 127))", tsel # print "tsel", tsel def test_8(): pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_10).construct_hierarchy() isel = flex.size_t(list(range(8))+[8,9,10,11,12]+list(range(19,35))) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'A' and (resid 117 or (resid 124 through 125 and (name N or name CA or name C or name O or name CB )) or resid 126 through 127))", tsel def test_11(): """ outputting name selection at the end of hierarchy?.. """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_11).construct_hierarchy() isel = flex.size_t(list(range(5))+[6]) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'A' and (resid 480 through 482 or (resid 483 through 484 and (name CA ))))", tsel def test_12(): """ Not the first range in hierarchy, some atoms are absent for the first residue in the range, but atoms of the several next residues are coniside with present atoms of the first residue. And hierarchy ends. Make sure list of atoms is outputted for the last range. """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_12).construct_hierarchy() isel = flex.size_t(list(range(26))+list(range(30,45))) tsel = selection_string_from_selection(pdb_h, isel) assert tsel == "(chain 'A' and (resid 279 through 281 or (resid 282 through 285 and (name N or name CA or name C or name O or name CB ))))", tsel def test_13(): """ Test correct handling of portion of a chain at the end of the pdb file. """ pdb_h = iotbx.pdb.input( source_info=None, lines=test_pdb_13).construct_hierarchy() isel = flex.size_t(list(range(20))+list(range(31,41))) tsel = selection_string_from_selection(pdb_h, isel) # print tsel assert tsel == "chain 'A'" isel = flex.size_t(list(range(19))+list(range(31,41))) tsel = selection_string_from_selection(pdb_h, isel) # print tsel assert tsel == "(chain 'A' and (resid 260 through 261 or (resid 262 and (name N or name CA or name C or name O )) or resid 301))" def test_14(): """ Test correct handling of altloc upper and lower cases. """ lines = """ CRYST1 45.640 40.754 30.275 90.00 90.00 90.00 P 21 21 21 ATOM 2 CA AVAL A 1 -4.890 1.653 12.849 0.50 13.49 C ATOM 9 CA aVAL A 1 -4.195 1.706 13.326 0.50 16.74 C """ h = iotbx.pdb.input(source_info=None, lines=lines).construct_hierarchy() asc = h.atom_selection_cache() # case 1 isel = asc.selection("chain A resseq 1 and altloc a").iselection() assert isel.size()==1 h0 = h.select(isel) assert approx_equal(h0.atoms().extract_xyz()[0][0], -4.195) # case 2 isel = asc.selection("chain A resseq 1 and altloc A").iselection() assert isel.size()==1 h0 = h.select(isel) assert approx_equal(h0.atoms().extract_xyz()[0][0], -4.890) ### # case 1 isel = asc.selection("chain A resseq 1 and altid a").iselection() assert isel.size()==1 h0 = h.select(isel) assert approx_equal(h0.atoms().extract_xyz()[0][0], -4.195) # case 2 isel = asc.selection("chain A resseq 1 and altid A").iselection() assert isel.size()==1 h0 = h.select(isel) assert approx_equal(h0.atoms().extract_xyz()[0][0], -4.890) if __name__=='__main__': test_get_clean_selection_string() test_selection_string_from_selection() test_selection_string_from_selection2() test_avoid_chain_selection() test_avoid_chain_selection2() test_avoid_hoh() test_include_hoh() test_selection_with_alternative_conformers() test_insertions() test_2() test_3() test_4() test_5() test_6() test_7() test_8() test_11() test_12() test_13() test_14() print("OK")