from __future__ import absolute_import, division, print_function import iotbx.ncs import iotbx.pdb import mmtbx.ncs.ncs_utils as nu from mmtbx.secondary_structure.build.ss_idealization import calculate_rmsd_smart test_pdb_1 = """\ CRYST1 272.680 272.680 272.680 90.00 90.00 90.00 F 2 3 96 ATOM 17 N LEU A 7 -3.960 -35.813 -28.701 1.00 59.07 N ATOM 18 CA LEU A 7 -2.543 -35.701 -29.071 1.00 52.98 C ATOM 19 C LEU A 7 -1.964 -34.379 -28.552 1.00 07.51 C ATOM 20 O LEU A 7 -2.502 -33.305 -28.832 1.00 95.11 O ATOM 21 CB LEU A 7 -2.337 -35.825 -30.589 1.00 93.68 C ATOM 22 CG LEU A 7 -2.092 -37.246 -31.147 1.00 36.57 C ATOM 23 CD1 LEU A 7 -3.388 -38.030 -31.314 1.00 45.19 C ATOM 24 CD2 LEU A 7 -1.342 -37.242 -32.482 1.00 52.49 C TER ATOM 17 N LEU B 7 1.133 -33.422 -31.479 1.00 59.07 N ATOM 18 CA LEU B 7 2.550 -33.310 -31.849 1.00 52.98 C ATOM 19 C LEU B 7 3.129 -31.988 -31.330 1.00 07.51 C ATOM 20 O LEU B 7 2.591 -30.914 -31.610 1.00 95.11 O ATOM 21 CB LEU B 7 2.756 -33.434 -33.367 1.00 93.68 C ATOM 22 CG LEU B 7 3.001 -34.855 -33.925 1.00 36.57 C ATOM 24 CD1 LEU B 7 3.751 -34.851 -35.260 1.00 52.49 C ATOM 23 CD2 LEU B 7 1.705 -35.639 -34.092 1.00 45.19 C END """ # same as test_pdb_1, but nothing is flipped test_pdb_1_1 = """\ CRYST1 272.680 272.680 272.680 90.00 90.00 90.00 F 2 3 96 ATOM 17 N LEU A 7 -3.960 -35.813 -28.701 1.00 59.07 N ATOM 18 CA LEU A 7 -2.543 -35.701 -29.071 1.00 52.98 C ATOM 19 C LEU A 7 -1.964 -34.379 -28.552 1.00 07.51 C ATOM 20 O LEU A 7 -2.502 -33.305 -28.832 1.00 95.11 O ATOM 21 CB LEU A 7 -2.337 -35.825 -30.589 1.00 93.68 C ATOM 22 CG LEU A 7 -2.092 -37.246 -31.147 1.00 36.57 C ATOM 23 CD1 LEU A 7 -3.388 -38.030 -31.314 1.00 45.19 C ATOM 24 CD2 LEU A 7 -1.342 -37.242 -32.482 1.00 52.49 C TER ATOM 17 N LEU B 7 1.133 -33.422 -31.479 1.00 59.07 N ATOM 18 CA LEU B 7 2.550 -33.310 -31.849 1.00 52.98 C ATOM 19 C LEU B 7 3.129 -31.988 -31.330 1.00 07.51 C ATOM 20 O LEU B 7 2.591 -30.914 -31.610 1.00 95.11 O ATOM 21 CB LEU B 7 2.756 -33.434 -33.367 1.00 93.68 C ATOM 22 CG LEU B 7 3.001 -34.855 -33.925 1.00 36.57 C ATOM 23 CD1 LEU B 7 1.705 -35.639 -34.092 1.00 45.19 C ATOM 24 CD2 LEU B 7 3.751 -34.851 -35.260 1.00 52.49 C END """ test_pdb_2 = """\ CRYST1 53.930 108.200 147.160 90.00 90.00 90.00 P 21 21 21 16 ATOM 1 N TYR A 1 30.440 8.711 1.306 1.00 64.98 N ATOM 2 CA TYR A 1 29.117 9.171 1.763 1.00 67.34 C ATOM 3 C TYR A 1 28.007 8.102 1.965 1.00 65.79 C ATOM 4 O TYR A 1 26.830 8.428 1.845 1.00 58.29 O ATOM 5 CB TYR A 1 29.262 10.057 3.008 1.00 67.25 C ATOM 6 CG TYR A 1 29.855 11.415 2.711 1.00 70.44 C ATOM 8 CD1 TYR A 1 31.185 11.716 3.026 1.00 71.73 C ATOM 7 CD2 TYR A 1 29.079 12.412 2.112 1.00 68.62 C ATOM 10 CE1 TYR A 1 31.716 12.971 2.753 1.00 72.09 C ATOM 9 CE2 TYR A 1 29.603 13.668 1.843 1.00 68.12 C ATOM 11 CZ TYR A 1 30.919 13.946 2.160 1.00 69.15 C ATOM 12 OH TYR A 1 31.432 15.200 1.886 1.00 61.93 O TER ATOM 1 N TYR B 1 30.440 8.711 6.306 1.00 64.98 N ATOM 2 CA TYR B 1 29.117 9.171 6.763 1.00 67.34 C ATOM 3 C TYR B 1 28.007 8.102 6.965 1.00 65.79 C ATOM 4 O TYR B 1 26.830 8.428 6.845 1.00 58.29 O ATOM 5 CB TYR B 1 29.262 10.057 8.008 1.00 67.25 C ATOM 6 CG TYR B 1 29.855 11.415 7.711 1.00 70.44 C ATOM 7 CD1 TYR B 1 29.079 12.412 7.112 1.00 68.62 C ATOM 8 CD2 TYR B 1 31.185 11.716 8.026 1.00 71.73 C ATOM 9 CE1 TYR B 1 29.603 13.668 6.843 1.00 68.12 C ATOM 10 CE2 TYR B 1 31.716 12.971 7.753 1.00 72.09 C ATOM 11 CZ TYR B 1 30.919 13.946 7.160 1.00 69.15 C ATOM 12 OH TYR B 1 31.432 15.200 6.886 1.00 61.93 O """ test_pdb_3 = """\ CRYST1 53.930 108.200 147.160 90.00 90.00 90.00 P 21 21 21 16 ATOM 1 N TYR A 1 30.440 8.711 1.306 1.00 64.98 N ATOM 2 CA TYR A 1 29.117 9.171 1.763 1.00 67.34 C ATOM 3 C TYR A 1 28.007 8.102 1.965 1.00 65.79 C ATOM 4 O TYR A 1 26.830 8.428 1.845 1.00 58.29 O ATOM 5 CB TYR A 1 29.262 10.057 3.008 1.00 67.25 C ATOM 6 CG TYR A 1 29.855 11.415 2.711 1.00 70.44 C ATOM 8 CD1 TYR A 1 31.185 11.716 3.026 1.00 71.73 C ATOM 7 CD2 TYR A 1 29.079 12.412 2.112 1.00 68.62 C ATOM 9 CE1 TYR A 1 29.603 13.668 1.843 1.00 68.12 C ATOM 10 CE2 TYR A 1 31.716 12.971 2.753 1.00 72.09 C ATOM 11 CZ TYR A 1 30.919 13.946 2.160 1.00 69.15 C ATOM 12 OH TYR A 1 31.432 15.200 1.886 1.00 61.93 O TER ATOM 1 N TYR B 1 30.440 8.711 6.306 1.00 64.98 N ATOM 2 CA TYR B 1 29.117 9.171 6.763 1.00 67.34 C ATOM 3 C TYR B 1 28.007 8.102 6.965 1.00 65.79 C ATOM 4 O TYR B 1 26.830 8.428 6.845 1.00 58.29 O ATOM 5 CB TYR B 1 29.262 10.057 8.008 1.00 67.25 C ATOM 6 CG TYR B 1 29.855 11.415 7.711 1.00 70.44 C ATOM 7 CD1 TYR B 1 29.079 12.412 7.112 1.00 68.62 C ATOM 8 CD2 TYR B 1 31.185 11.716 8.026 1.00 71.73 C ATOM 9 CE1 TYR B 1 29.603 13.668 6.843 1.00 68.12 C ATOM 10 CE2 TYR B 1 31.716 12.971 7.753 1.00 72.09 C ATOM 11 CZ TYR B 1 30.919 13.946 7.160 1.00 69.15 C ATOM 12 OH TYR B 1 31.432 15.200 6.886 1.00 61.93 O """ test_pdb_4 = """\ ATOM 1 N HIS A 3 32.534 13.242 2.403 1.00 0.00 N ATOM 2 CA HIS A 3 33.724 12.970 3.202 1.00 0.00 C ATOM 3 C HIS A 3 34.993 13.295 2.422 1.00 0.00 C ATOM 4 O HIS A 3 35.327 12.618 1.450 1.00 0.00 O ATOM 5 CB HIS A 3 33.744 11.503 3.640 1.00 0.00 C ATOM 6 CG HIS A 3 32.618 11.130 4.554 1.00 0.00 C ATOM 7 ND1 HIS A 3 32.586 11.494 5.882 1.00 0.00 N ATOM 8 CD2 HIS A 3 31.485 10.424 4.330 1.00 0.00 C ATOM 9 CE1 HIS A 3 31.481 11.029 6.437 1.00 0.00 C ATOM 10 NE2 HIS A 3 30.795 10.375 5.517 1.00 0.00 N TER ATOM 1 N HIS B 3 34.434 0.922 2.403 1.00 0.00 N ATOM 2 CA HIS B 3 35.624 0.650 3.202 1.00 0.00 C ATOM 3 C HIS B 3 36.893 0.975 2.422 1.00 0.00 C ATOM 4 O HIS B 3 37.227 0.298 1.450 1.00 0.00 O ATOM 5 CB HIS B 3 35.644 -0.817 3.640 1.00 0.00 C ATOM 6 CG HIS B 3 34.518 -1.190 4.554 1.00 0.00 C ATOM 7 CD2 HIS B 3 34.486 -0.826 5.882 1.00 0.00 N ATOM 8 ND1 HIS B 3 33.385 -1.896 4.330 1.00 0.00 C ATOM 9 NE2 HIS B 3 33.381 -1.291 6.437 1.00 0.00 C ATOM 10 CE1 HIS B 3 32.695 -1.945 5.517 1.00 0.00 N """ test_pdb_5 = """\ ATOM 1 N ARG A 1 26.061 12.824 1.988 1.00 0.00 N ATOM 2 CA ARG A 1 27.253 12.525 2.773 1.00 0.00 C ATOM 3 C ARG A 1 28.520 12.882 2.003 1.00 0.00 C ATOM 4 O ARG A 1 28.853 12.243 1.005 1.00 0.00 O ATOM 5 CB ARG A 1 27.280 11.041 3.156 1.00 10.00 C ATOM 6 CG ARG A 1 26.107 10.591 4.022 1.00 10.00 C ATOM 7 CD ARG A 1 26.118 11.230 5.409 1.00 10.00 C ATOM 8 NE ARG A 1 27.283 10.828 6.201 1.00 10.00 N ATOM 9 CZ ARG A 1 27.735 11.441 7.298 1.00 10.00 C ATOM 10 NH1 ARG A 1 27.146 12.525 7.803 1.00 10.00 N ATOM 11 NH2 ARG A 1 28.808 10.956 7.908 1.00 10.00 N ATOM 1 N ALA A 2 29.223 13.907 2.474 1.00 0.00 N ATOM 2 CA ALA A 2 30.455 14.351 1.832 1.00 0.00 C ATOM 3 C ALA A 2 31.652 14.171 2.758 1.00 0.00 C ATOM 4 O ALA A 2 31.775 14.859 3.772 1.00 0.00 O ATOM 5 CB ALA A 2 30.331 15.807 1.408 1.00 0.00 C ATOM 1 N HIS A 3 32.534 13.242 2.403 1.00 0.00 N ATOM 2 CA HIS A 3 33.724 12.970 3.202 1.00 0.00 C ATOM 3 C HIS A 3 34.993 13.295 2.422 1.00 0.00 C ATOM 4 O HIS A 3 35.327 12.618 1.450 1.00 0.00 O ATOM 5 CB HIS A 3 33.744 11.503 3.640 1.00 0.00 C ATOM 6 CG HIS A 3 32.618 11.130 4.554 1.00 0.00 C ATOM 7 ND1 HIS A 3 32.586 11.494 5.882 1.00 0.00 N ATOM 8 CD2 HIS A 3 31.485 10.424 4.330 1.00 0.00 C ATOM 9 CE1 HIS A 3 31.481 11.029 6.437 1.00 0.00 C ATOM 10 NE2 HIS A 3 30.795 10.375 5.517 1.00 0.00 N ATOM 1 N ALA A 4 35.698 14.335 2.856 1.00 0.00 N ATOM 2 CA ALA A 4 36.932 14.752 2.201 1.00 0.00 C ATOM 3 C ALA A 4 38.127 14.604 3.136 1.00 0.00 C ATOM 4 O ALA A 4 38.248 15.329 4.124 1.00 0.00 O ATOM 5 CB ALA A 4 36.812 16.192 1.723 1.00 0.00 C ATOM 1 N ASP A 5 39.007 13.660 2.818 1.00 0.00 N ATOM 2 CA ASP A 5 40.194 13.415 3.630 1.00 0.00 C ATOM 3 C ASP A 5 41.467 13.708 2.841 1.00 0.00 C ATOM 4 O ASP A 5 41.801 12.995 1.896 1.00 0.00 O ATOM 5 CB ASP A 5 40.211 11.966 4.122 1.00 0.00 C ATOM 6 CG ASP A 5 41.346 11.691 5.089 1.00 0.00 C ATOM 7 OD1 ASP A 5 41.256 12.134 6.254 1.00 0.00 O ATOM 8 OD2 ASP A 5 42.327 11.032 4.685 1.00 0.00 O ATOM 1 N ALA A 6 42.172 14.763 3.238 1.00 0.00 N ATOM 2 CA ALA A 6 43.409 15.152 2.570 1.00 0.00 C ATOM 3 C ALA A 6 44.601 15.036 3.514 1.00 0.00 C ATOM 4 O ALA A 6 44.722 15.797 4.474 1.00 0.00 O ATOM 5 CB ALA A 6 43.294 16.573 2.039 1.00 0.00 C ATOM 1 N GLU A 7 45.480 14.079 3.234 1.00 0.00 N ATOM 2 CA GLU A 7 46.665 13.862 4.057 1.00 0.00 C ATOM 3 C GLU A 7 47.940 14.122 3.261 1.00 0.00 C ATOM 4 O GLU A 7 48.275 13.373 2.344 1.00 0.00 O ATOM 5 CB GLU A 7 46.677 12.432 4.604 1.00 0.00 C ATOM 6 CG GLU A 7 45.565 12.140 5.599 1.00 0.00 C ATOM 7 CD GLU A 7 45.595 10.711 6.103 1.00 0.00 C ATOM 8 OE1 GLU A 7 46.403 9.912 5.585 1.00 0.00 O ATOM 9 OE2 GLU A 7 44.809 10.384 7.019 1.00 0.00 O ATOM 1 N ALA A 8 48.647 15.189 3.620 1.00 0.00 N ATOM 2 CA ALA A 8 49.886 15.550 2.941 1.00 0.00 C ATOM 3 C ALA A 8 51.076 15.468 3.892 1.00 0.00 C ATOM 4 O ALA A 8 51.196 16.264 4.823 1.00 0.00 O ATOM 5 CB ALA A 8 49.776 16.951 2.356 1.00 0.00 C ATOM 1 N ALA A 10 55.122 15.615 4.002 1.00 0.00 N ATOM 2 CA ALA A 10 56.363 15.948 3.313 1.00 0.00 C ATOM 3 C ALA A 10 57.551 15.898 4.269 1.00 0.00 C ATOM 4 O ALA A 10 57.671 16.728 5.170 1.00 0.00 O ATOM 5 CB ALA A 10 56.258 17.326 2.676 1.00 0.00 C ATOM 1 N ASN A 11 58.427 14.919 4.065 1.00 0.00 N ATOM 2 CA ASN A 11 59.606 14.759 4.908 1.00 0.00 C ATOM 3 C ASN A 11 60.886 14.953 4.102 1.00 0.00 C ATOM 4 O ASN A 11 61.222 14.136 3.244 1.00 0.00 O ATOM 5 CB ASN A 11 59.609 13.379 5.562 1.00 0.00 C ATOM 6 CG ASN A 11 58.532 13.236 6.620 1.00 0.00 C ATOM 7 OD1 ASN A 11 58.296 14.149 7.410 1.00 0.00 O ATOM 8 ND2 ASN A 11 57.872 12.083 6.640 1.00 0.00 N ATOM 1 N ALA A 12 61.597 16.041 4.383 1.00 0.00 N ATOM 2 CA ALA A 12 62.841 16.345 3.686 1.00 0.00 C ATOM 3 C ALA A 12 64.025 16.328 4.646 1.00 0.00 C ATOM 4 O ALA A 12 64.145 17.191 5.515 1.00 0.00 O ATOM 5 CB ALA A 12 62.740 17.698 2.997 1.00 0.00 C ATOM 1 N GLN A 13 64.899 15.340 4.481 1.00 0.00 N ATOM 2 CA GLN A 13 66.076 15.209 5.332 1.00 0.00 C ATOM 3 C GLN A 13 67.359 15.370 4.522 1.00 0.00 C ATOM 4 O GLN A 13 67.695 14.521 3.697 1.00 0.00 O ATOM 5 CB GLN A 13 66.071 13.849 6.037 1.00 0.00 C ATOM 6 CG GLN A 13 67.212 13.651 7.023 1.00 0.00 C ATOM 7 CD GLN A 13 67.140 12.317 7.739 1.00 0.00 C ATOM 8 OE1 GLN A 13 66.251 11.506 7.477 1.00 0.00 O ATOM 9 NE2 GLN A 13 68.078 12.082 8.650 1.00 0.00 N ATOM 1 N ALA A 14 68.071 16.466 4.765 1.00 0.00 N ATOM 2 CA ALA A 14 69.318 16.740 4.059 1.00 0.00 C ATOM 3 C ALA A 14 70.500 16.757 5.022 1.00 0.00 C ATOM 4 O ALA A 14 70.620 17.652 5.859 1.00 0.00 O ATOM 5 CB ALA A 14 69.222 18.067 3.320 1.00 0.00 C ATOM 1 N LEU A 15 71.372 15.761 4.897 1.00 0.00 N ATOM 2 CA LEU A 15 72.547 15.660 5.755 1.00 0.00 C ATOM 3 C LEU A 15 73.832 15.788 4.943 1.00 0.00 C ATOM 4 O LEU A 15 74.168 14.907 4.151 1.00 0.00 O ATOM 5 CB LEU A 15 72.541 14.325 6.508 1.00 0.00 C ATOM 6 CG LEU A 15 71.415 14.114 7.526 1.00 0.00 C ATOM 7 CD1 LEU A 15 71.462 12.699 8.081 1.00 0.00 C ATOM 8 CD2 LEU A 15 71.487 15.136 8.654 1.00 0.00 C ATOM 1 N ALA A 16 74.546 16.890 5.146 1.00 0.00 N ATOM 2 CA ALA A 16 75.795 17.135 4.434 1.00 0.00 C ATOM 3 C ALA A 16 76.975 17.185 5.399 1.00 0.00 C ATOM 4 O ALA A 16 77.095 18.110 6.202 1.00 0.00 O ATOM 5 CB ALA A 16 75.704 18.434 3.646 1.00 0.00 C ATOM 1 N PHE A 17 77.845 16.184 5.313 1.00 0.00 N ATOM 2 CA PHE A 17 79.018 16.111 6.177 1.00 0.00 C ATOM 3 C PHE A 17 80.304 16.206 5.364 1.00 0.00 C ATOM 4 O PHE A 17 80.640 15.296 4.606 1.00 0.00 O ATOM 5 CB PHE A 17 79.005 14.807 6.980 1.00 0.00 C ATOM 6 CG PHE A 17 77.889 14.721 7.981 1.00 0.00 C ATOM 7 CD1 PHE A 17 77.992 15.351 9.210 1.00 0.00 C ATOM 8 CD2 PHE A 17 76.735 14.009 7.693 1.00 0.00 C ATOM 9 CE1 PHE A 17 76.966 15.272 10.133 1.00 0.00 C ATOM 10 CE2 PHE A 17 75.706 13.927 8.612 1.00 0.00 C ATOM 11 CZ PHE A 17 75.822 14.560 9.833 1.00 0.00 C ATOM 1 N ALA A 18 81.021 17.314 5.528 1.00 0.00 N ATOM 2 CA ALA A 18 82.272 17.529 4.810 1.00 0.00 C ATOM 3 C ALA A 18 83.450 17.613 5.775 1.00 0.00 C ATOM 4 O ALA A 18 83.570 18.567 6.543 1.00 0.00 O ATOM 5 CB ALA A 18 82.186 18.797 3.973 1.00 0.00 C ATOM 1 N TYR A 19 84.318 16.606 5.729 1.00 0.00 N ATOM 2 CA TYR A 19 85.488 16.564 6.598 1.00 0.00 C ATOM 3 C TYR A 19 86.777 16.625 5.785 1.00 0.00 C ATOM 4 O TYR A 19 87.113 15.687 5.063 1.00 0.00 O ATOM 5 CB TYR A 19 85.471 15.292 7.450 1.00 0.00 C ATOM 6 CG TYR A 19 84.363 15.258 8.479 1.00 0.00 C ATOM 7 CD1 TYR A 19 83.662 16.411 8.812 1.00 0.00 C ATOM 8 CD2 TYR A 19 84.016 14.074 9.116 1.00 0.00 C ATOM 9 CE1 TYR A 19 82.648 16.386 9.751 1.00 0.00 C ATOM 10 CE2 TYR A 19 83.002 14.039 10.057 1.00 0.00 C ATOM 11 CZ TYR A 19 82.323 15.197 10.369 1.00 0.00 C ATOM 12 OH TYR A 19 81.313 15.166 11.305 1.00 0.00 O ATOM 1 N ALA A 20 87.496 17.737 5.909 1.00 0.00 N ATOM 2 CA ALA A 20 88.749 17.922 5.187 1.00 0.00 C ATOM 3 C ALA A 20 89.925 18.039 6.151 1.00 0.00 C ATOM 4 O ALA A 20 90.046 19.021 6.883 1.00 0.00 O ATOM 5 CB ALA A 20 88.668 19.159 4.303 1.00 0.00 C ATOM 1 N VAL A 21 90.791 17.030 6.145 1.00 0.00 N ATOM 2 CA VAL A 21 91.959 17.017 7.018 1.00 0.00 C ATOM 3 C VAL A 21 93.250 17.045 6.207 1.00 0.00 C ATOM 4 O VAL A 21 93.585 16.079 5.521 1.00 0.00 O ATOM 5 CB VAL A 21 91.967 15.769 7.925 1.00 0.00 C ATOM 6 CG1 VAL A 21 93.241 15.722 8.760 1.00 0.00 C ATOM 7 CG2 VAL A 21 90.735 15.749 8.820 1.00 0.00 C ATOM 1 N ALA A 22 93.971 18.159 6.291 1.00 0.00 N ATOM 2 CA ALA A 22 95.226 18.315 5.565 1.00 0.00 C ATOM 3 C ALA A 22 96.400 18.465 6.527 1.00 0.00 C ATOM 4 O ALA A 22 96.521 19.473 7.222 1.00 0.00 O ATOM 5 CB ALA A 22 95.150 19.517 4.636 1.00 0.00 C TER 156 ALA A 22 ATOM 1 N ARG B 1 27.961 0.504 1.988 1.00 0.00 N ATOM 2 CA ARG B 1 29.153 0.205 2.773 1.00 0.00 C ATOM 3 C ARG B 1 30.420 0.562 2.003 1.00 0.00 C ATOM 4 O ARG B 1 30.753 -0.077 1.005 1.00 0.00 O ATOM 5 CB ARG B 1 29.180 -1.279 3.156 1.00 10.00 C ATOM 6 CG ARG B 1 28.007 -1.729 4.022 1.00 10.00 C ATOM 7 CD ARG B 1 28.018 -1.090 5.409 1.00 10.00 C ATOM 8 NE ARG B 1 29.183 -1.492 6.201 1.00 10.00 N ATOM 9 CZ ARG B 1 29.635 -0.879 7.298 1.00 10.00 C ATOM 10 NH2 ARG B 1 29.046 0.205 7.803 1.00 10.00 N ATOM 11 NH1 ARG B 1 30.708 -1.364 7.908 1.00 10.00 N ATOM 1 N ALA B 2 31.123 1.587 2.474 1.00 0.00 N ATOM 2 CA ALA B 2 32.355 2.031 1.832 1.00 0.00 C ATOM 3 C ALA B 2 33.552 1.851 2.758 1.00 0.00 C ATOM 4 O ALA B 2 33.675 2.539 3.772 1.00 0.00 O ATOM 5 CB ALA B 2 32.231 3.487 1.408 1.00 0.00 C ATOM 1 N HIS B 3 34.434 0.922 2.403 1.00 0.00 N ATOM 2 CA HIS B 3 35.624 0.650 3.202 1.00 0.00 C ATOM 3 C HIS B 3 36.893 0.975 2.422 1.00 0.00 C ATOM 4 O HIS B 3 37.227 0.298 1.450 1.00 0.00 O ATOM 5 CB HIS B 3 35.644 -0.817 3.640 1.00 0.00 C ATOM 6 CG HIS B 3 34.518 -1.190 4.554 1.00 0.00 C ATOM 7 CD2 HIS B 3 34.486 -0.826 5.882 1.00 0.00 N ATOM 8 ND1 HIS B 3 33.385 -1.896 4.330 1.00 0.00 C ATOM 9 NE2 HIS B 3 33.381 -1.291 6.437 1.00 0.00 C ATOM 10 CE1 HIS B 3 32.695 -1.945 5.517 1.00 0.00 N ATOM 1 N ALA B 4 37.598 2.015 2.856 1.00 0.00 N ATOM 2 CA ALA B 4 38.832 2.432 2.201 1.00 0.00 C ATOM 3 C ALA B 4 40.027 2.284 3.136 1.00 0.00 C ATOM 4 O ALA B 4 40.148 3.009 4.124 1.00 0.00 O ATOM 5 CB ALA B 4 38.712 3.872 1.723 1.00 0.00 C ATOM 1 N ASP B 5 40.907 1.340 2.818 1.00 0.00 N ATOM 2 CA ASP B 5 42.094 1.095 3.630 1.00 0.00 C ATOM 3 C ASP B 5 43.367 1.388 2.841 1.00 0.00 C ATOM 4 O ASP B 5 43.701 0.675 1.896 1.00 0.00 O ATOM 5 CB ASP B 5 42.111 -0.354 4.122 1.00 0.00 C ATOM 6 CG ASP B 5 43.246 -0.629 5.089 1.00 0.00 C ATOM 7 OD2 ASP B 5 43.156 -0.186 6.254 1.00 0.00 O ATOM 8 OD1 ASP B 5 44.227 -1.288 4.685 1.00 0.00 O ATOM 1 N ALA B 6 44.072 2.443 3.238 1.00 0.00 N ATOM 2 CA ALA B 6 45.309 2.832 2.570 1.00 0.00 C ATOM 3 C ALA B 6 46.501 2.716 3.514 1.00 0.00 C ATOM 4 O ALA B 6 46.622 3.477 4.474 1.00 0.00 O ATOM 5 CB ALA B 6 45.194 4.253 2.039 1.00 0.00 C ATOM 1 N GLU B 7 47.380 1.759 3.234 1.00 0.00 N ATOM 2 CA GLU B 7 48.565 1.542 4.057 1.00 0.00 C ATOM 3 C GLU B 7 49.840 1.802 3.261 1.00 0.00 C ATOM 4 O GLU B 7 50.175 1.053 2.344 1.00 0.00 O ATOM 5 CB GLU B 7 48.577 0.112 4.604 1.00 0.00 C ATOM 6 CG GLU B 7 47.465 -0.180 5.599 1.00 0.00 C ATOM 7 CD GLU B 7 47.495 -1.609 6.103 1.00 0.00 C ATOM 8 OE2 GLU B 7 48.303 -2.408 5.585 1.00 0.00 O ATOM 9 OE1 GLU B 7 46.709 -1.936 7.019 1.00 0.00 O ATOM 1 N ALA B 8 50.547 2.869 3.620 1.00 0.00 N ATOM 2 CA ALA B 8 51.786 3.230 2.941 1.00 0.00 C ATOM 3 C ALA B 8 52.976 3.148 3.892 1.00 0.00 C ATOM 4 O ALA B 8 53.096 3.944 4.823 1.00 0.00 O ATOM 5 CB ALA B 8 51.676 4.631 2.356 1.00 0.00 C ATOM 1 N ALA B 10 57.022 3.295 4.002 1.00 0.00 N ATOM 2 CA ALA B 10 58.263 3.628 3.313 1.00 0.00 C ATOM 3 C ALA B 10 59.451 3.578 4.269 1.00 0.00 C ATOM 4 O ALA B 10 59.571 4.408 5.170 1.00 0.00 O ATOM 5 CB ALA B 10 58.158 5.006 2.676 1.00 0.00 C ATOM 1 N ASN B 11 60.327 2.599 4.065 1.00 0.00 N ATOM 2 CA ASN B 11 61.506 2.439 4.908 1.00 0.00 C ATOM 3 C ASN B 11 62.786 2.633 4.102 1.00 0.00 C ATOM 4 O ASN B 11 63.122 1.816 3.244 1.00 0.00 O ATOM 5 CB ASN B 11 61.509 1.059 5.562 1.00 0.00 C ATOM 6 CG ASN B 11 60.432 0.916 6.620 1.00 0.00 C ATOM 7 ND2 ASN B 11 60.196 1.829 7.410 1.00 0.00 O ATOM 8 OD1 ASN B 11 59.772 -0.237 6.640 1.00 0.00 N ATOM 1 N ALA B 12 63.497 3.721 4.383 1.00 0.00 N ATOM 2 CA ALA B 12 64.741 4.025 3.686 1.00 0.00 C ATOM 3 C ALA B 12 65.925 4.008 4.646 1.00 0.00 C ATOM 4 O ALA B 12 66.045 4.871 5.515 1.00 0.00 O ATOM 5 CB ALA B 12 64.640 5.378 2.997 1.00 0.00 C ATOM 1 N GLN B 13 66.799 3.020 4.481 1.00 0.00 N ATOM 2 CA GLN B 13 67.976 2.889 5.332 1.00 0.00 C ATOM 3 C GLN B 13 69.259 3.050 4.522 1.00 0.00 C ATOM 4 O GLN B 13 69.595 2.201 3.697 1.00 0.00 O ATOM 5 CB GLN B 13 67.971 1.529 6.037 1.00 0.00 C ATOM 6 CG GLN B 13 69.112 1.331 7.023 1.00 0.00 C ATOM 7 CD GLN B 13 69.040 -0.003 7.739 1.00 0.00 C ATOM 8 NE2 GLN B 13 68.151 -0.814 7.477 1.00 0.00 O ATOM 9 OE1 GLN B 13 69.978 -0.238 8.650 1.00 0.00 N ATOM 1 N ALA B 14 69.971 4.146 4.765 1.00 0.00 N ATOM 2 CA ALA B 14 71.218 4.420 4.059 1.00 0.00 C ATOM 3 C ALA B 14 72.400 4.437 5.022 1.00 0.00 C ATOM 4 O ALA B 14 72.520 5.332 5.859 1.00 0.00 O ATOM 5 CB ALA B 14 71.122 5.747 3.320 1.00 0.00 C ATOM 1 N LEU B 15 73.272 3.441 4.897 1.00 0.00 N ATOM 2 CA LEU B 15 74.447 3.340 5.755 1.00 0.00 C ATOM 3 C LEU B 15 75.732 3.468 4.943 1.00 0.00 C ATOM 4 O LEU B 15 76.068 2.587 4.151 1.00 0.00 O ATOM 5 CB LEU B 15 74.441 2.005 6.508 1.00 0.00 C ATOM 6 CG LEU B 15 73.315 1.794 7.526 1.00 0.00 C ATOM 7 CD2 LEU B 15 73.362 0.379 8.081 1.00 0.00 C ATOM 8 CD1 LEU B 15 73.387 2.816 8.654 1.00 0.00 C ATOM 1 N ALA B 16 76.446 4.570 5.146 1.00 0.00 N ATOM 2 CA ALA B 16 77.695 4.815 4.434 1.00 0.00 C ATOM 3 C ALA B 16 78.875 4.865 5.399 1.00 0.00 C ATOM 4 O ALA B 16 78.995 5.790 6.202 1.00 0.00 O ATOM 5 CB ALA B 16 77.604 6.114 3.646 1.00 0.00 C ATOM 1 N PHE B 17 79.745 3.864 5.313 1.00 0.00 N ATOM 2 CA PHE B 17 80.918 3.791 6.177 1.00 0.00 C ATOM 3 C PHE B 17 82.204 3.886 5.364 1.00 0.00 C ATOM 4 O PHE B 17 82.540 2.976 4.606 1.00 0.00 O ATOM 5 CB PHE B 17 80.905 2.487 6.980 1.00 0.00 C ATOM 6 CG PHE B 17 79.789 2.401 7.981 1.00 0.00 C ATOM 7 CD2 PHE B 17 79.892 3.031 9.210 1.00 0.00 C ATOM 8 CD1 PHE B 17 78.635 1.689 7.693 1.00 0.00 C ATOM 9 CE2 PHE B 17 78.866 2.952 10.133 1.00 0.00 C ATOM 10 CE1 PHE B 17 77.606 1.607 8.612 1.00 0.00 C ATOM 11 CZ PHE B 17 77.722 2.240 9.833 1.00 0.00 C ATOM 1 N ALA B 18 82.921 4.994 5.528 1.00 0.00 N ATOM 2 CA ALA B 18 84.172 5.209 4.810 1.00 0.00 C ATOM 3 C ALA B 18 85.350 5.293 5.775 1.00 0.00 C ATOM 4 O ALA B 18 85.470 6.247 6.543 1.00 0.00 O ATOM 5 CB ALA B 18 84.086 6.477 3.973 1.00 0.00 C ATOM 1 N TYR B 19 86.218 4.286 5.729 1.00 0.00 N ATOM 2 CA TYR B 19 87.388 4.244 6.598 1.00 0.00 C ATOM 3 C TYR B 19 88.677 4.305 5.785 1.00 0.00 C ATOM 4 O TYR B 19 89.013 3.367 5.063 1.00 0.00 O ATOM 5 CB TYR B 19 87.371 2.972 7.450 1.00 0.00 C ATOM 6 CG TYR B 19 86.263 2.938 8.479 1.00 0.00 C ATOM 7 CD2 TYR B 19 85.562 4.091 8.812 1.00 0.00 C ATOM 8 CD1 TYR B 19 85.916 1.754 9.116 1.00 0.00 C ATOM 9 CE2 TYR B 19 84.548 4.066 9.751 1.00 0.00 C ATOM 10 CE1 TYR B 19 84.902 1.719 10.057 1.00 0.00 C ATOM 11 CZ TYR B 19 84.223 2.877 10.369 1.00 0.00 C ATOM 12 OH TYR B 19 83.213 2.846 11.305 1.00 0.00 O ATOM 1 N ALA B 20 89.396 5.417 5.909 1.00 0.00 N ATOM 2 CA ALA B 20 90.649 5.602 5.187 1.00 0.00 C ATOM 3 C ALA B 20 91.825 5.719 6.151 1.00 0.00 C ATOM 4 O ALA B 20 91.946 6.701 6.883 1.00 0.00 O ATOM 5 CB ALA B 20 90.568 6.839 4.303 1.00 0.00 C ATOM 1 N VAL B 21 92.691 4.710 6.145 1.00 0.00 N ATOM 2 CA VAL B 21 93.859 4.697 7.018 1.00 0.00 C ATOM 3 C VAL B 21 95.150 4.725 6.207 1.00 0.00 C ATOM 4 O VAL B 21 95.485 3.759 5.521 1.00 0.00 O ATOM 5 CB VAL B 21 93.867 3.449 7.925 1.00 0.00 C ATOM 6 CG2 VAL B 21 95.141 3.402 8.760 1.00 0.00 C ATOM 7 CG1 VAL B 21 92.635 3.429 8.820 1.00 0.00 C ATOM 1 N ALA B 22 95.871 5.839 6.291 1.00 0.00 N ATOM 2 CA ALA B 22 97.126 5.995 5.565 1.00 0.00 C ATOM 3 C ALA B 22 98.300 6.145 6.527 1.00 0.00 C ATOM 4 O ALA B 22 98.421 7.153 7.222 1.00 0.00 O ATOM 5 CB ALA B 22 97.050 7.197 4.636 1.00 0.00 C TER 312 ALA B 22 END """ ncs_pars = iotbx.ncs.input.get_default_params() ncs_pars.ncs_search.chain_max_rmsd=0.1 def test_1(): h = iotbx.pdb.input(source_info=None, lines=test_pdb_1).construct_hierarchy() asc = h.atom_selection_cache() ncs_inp = iotbx.ncs.input( hierarchy=h, params=ncs_pars.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 # group 1 assert ncs_groups[0].master_iselection.all_eq( asc.selection(string = "chain A").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain B").iselection()) def test_2(): """ Testing TYR both CD and CE flips""" h = iotbx.pdb.input(source_info=None, lines=test_pdb_2).construct_hierarchy() asc = h.atom_selection_cache() ncs_inp = iotbx.ncs.input( hierarchy=h, params=ncs_pars.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 # group 1 assert ncs_groups[0].master_iselection.all_eq( asc.selection(string = "chain A").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain B").iselection()) def test_3(): """ Testing TYR only CD and flip. Not sure if such flip is valid. This test is not working when we use torsion angles because in this procedure we don't flip only one atom out of two like in this case""" h = iotbx.pdb.input(source_info=None, lines=test_pdb_3).construct_hierarchy() asc = h.atom_selection_cache() ncs_inp = iotbx.ncs.input( hierarchy=h, params=ncs_pars.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 # group 1 assert ncs_groups[0].master_iselection.all_eq( asc.selection(string = "chain A").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain B").iselection()) def test_4(): """ HIS is interesting because of different atoms can be flipped """ h = iotbx.pdb.input(source_info=None, lines=test_pdb_4).construct_hierarchy() asc = h.atom_selection_cache() ncs_inp = iotbx.ncs.input( hierarchy=h, params=ncs_pars.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 # group 1 assert ncs_groups[0].master_iselection.all_eq( asc.selection(string = "chain A").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain B").iselection()) def test_5(): """ Testing all possible residues at once. All flipped wherever possible in chain B """ h = iotbx.pdb.input(source_info=None, lines=test_pdb_5).construct_hierarchy() asc = h.atom_selection_cache() ncs_inp = iotbx.ncs.input( hierarchy=h, params=ncs_pars.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 # group 1 assert ncs_groups[0].master_iselection.all_eq( asc.selection(string = "chain A").iselection()) g1_c = ncs_groups[0].copies assert len(g1_c)==1 assert g1_c[0].iselection.all_eq( asc.selection(string = "chain B").iselection()) def test_6(): "Actually making flips for test_pdb_1" h = iotbx.pdb.input(source_info=None, lines=test_pdb_1_1).construct_hierarchy() asc = h.atom_selection_cache() ncs_inp = iotbx.ncs.input( hierarchy=h, params=ncs_pars.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() nu.flip_atoms_in_ncs_groups(h, ncs_groups) h.write_pdb_file("test_6_result.pdb") def test_7(): "Actually making flips for test_pdb_2" answer_pdb_str = """ ATOM 1 N TYR A 1 30.440 8.711 1.306 1.00 64.98 N ATOM 2 CA TYR A 1 29.117 9.171 1.763 1.00 67.34 C ATOM 3 C TYR A 1 28.007 8.102 1.965 1.00 65.79 C ATOM 4 O TYR A 1 26.830 8.428 1.845 1.00 58.29 O ATOM 5 CB TYR A 1 29.262 10.057 3.008 1.00 67.25 C ATOM 6 CG TYR A 1 29.855 11.415 2.711 1.00 70.44 C ATOM 7 CD1 TYR A 1 31.185 11.716 3.026 1.00 71.73 C ATOM 8 CD2 TYR A 1 29.079 12.412 2.112 1.00 68.62 C ATOM 9 CE1 TYR A 1 31.716 12.971 2.753 1.00 72.09 C ATOM 10 CE2 TYR A 1 29.603 13.668 1.843 1.00 68.12 C ATOM 11 CZ TYR A 1 30.919 13.946 2.160 1.00 69.15 C ATOM 12 OH TYR A 1 31.432 15.200 1.886 1.00 61.93 O TER ATOM 13 N TYR B 1 30.440 8.711 6.306 1.00 64.98 N ATOM 14 CA TYR B 1 29.117 9.171 6.763 1.00 67.34 C ATOM 15 C TYR B 1 28.007 8.102 6.965 1.00 65.79 C ATOM 16 O TYR B 1 26.830 8.428 6.845 1.00 58.29 O ATOM 17 CB TYR B 1 29.262 10.057 8.008 1.00 67.25 C ATOM 18 CG TYR B 1 29.855 11.415 7.711 1.00 70.44 C ATOM 19 CD1 TYR B 1 31.187 11.692 8.031 1.00 68.62 C ATOM 20 CD2 TYR B 1 29.098 12.427 7.109 1.00 71.73 C ATOM 21 CE1 TYR B 1 31.752 12.929 7.755 1.00 68.12 C ATOM 22 CE2 TYR B 1 29.658 13.669 6.836 1.00 72.09 C ATOM 23 CZ TYR B 1 30.988 13.916 7.161 1.00 69.15 C ATOM 24 OH TYR B 1 31.560 15.146 6.892 1.00 61.93 O TER """ h = iotbx.pdb.input(source_info=None, lines=test_pdb_2).construct_hierarchy() anwer_h = iotbx.pdb.input(source_info=None, lines=answer_pdb_str).construct_hierarchy() h.write_pdb_file("test_7_before.pdb") ncs_inp = iotbx.ncs.input( hierarchy=h, params=ncs_pars.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() nu.flip_atoms_in_ncs_groups(h, ncs_groups) h.write_pdb_file("test_7_result.pdb") rmsd_smart = calculate_rmsd_smart(anwer_h, h) print(rmsd_smart) assert rmsd_smart < 0.01 def test_8(): """ Actually making flips for test_pdb_5""" answer_pdb_str = """ ATOM 1 N ARG A 1 26.061 12.824 1.988 1.00 0.00 N ATOM 2 CA ARG A 1 27.253 12.525 2.773 1.00 0.00 C ATOM 3 C ARG A 1 28.520 12.882 2.003 1.00 0.00 C ATOM 4 O ARG A 1 28.853 12.243 1.005 1.00 0.00 O ATOM 5 CB ARG A 1 27.280 11.041 3.156 1.00 10.00 C ATOM 6 CG ARG A 1 26.107 10.591 4.022 1.00 10.00 C ATOM 7 CD ARG A 1 26.118 11.230 5.409 1.00 10.00 C ATOM 8 NE ARG A 1 27.283 10.828 6.201 1.00 10.00 N ATOM 9 CZ ARG A 1 27.735 11.441 7.298 1.00 10.00 C ATOM 10 NH1 ARG A 1 27.146 12.525 7.803 1.00 10.00 N ATOM 11 NH2 ARG A 1 28.808 10.956 7.908 1.00 10.00 N ATOM 12 N ALA A 2 29.223 13.907 2.474 1.00 0.00 N ATOM 13 CA ALA A 2 30.455 14.351 1.832 1.00 0.00 C ATOM 14 C ALA A 2 31.652 14.171 2.758 1.00 0.00 C ATOM 15 O ALA A 2 31.775 14.859 3.772 1.00 0.00 O ATOM 16 CB ALA A 2 30.331 15.807 1.408 1.00 0.00 C ATOM 17 N HIS A 3 32.534 13.242 2.403 1.00 0.00 N ATOM 18 CA HIS A 3 33.724 12.970 3.202 1.00 0.00 C ATOM 19 C HIS A 3 34.993 13.295 2.422 1.00 0.00 C ATOM 20 O HIS A 3 35.327 12.618 1.450 1.00 0.00 O ATOM 21 CB HIS A 3 33.744 11.503 3.640 1.00 0.00 C ATOM 22 CG HIS A 3 32.618 11.130 4.554 1.00 0.00 C ATOM 23 ND1 HIS A 3 32.586 11.494 5.882 1.00 0.00 N ATOM 24 CD2 HIS A 3 31.485 10.424 4.330 1.00 0.00 C ATOM 25 CE1 HIS A 3 31.481 11.029 6.437 1.00 0.00 C ATOM 26 NE2 HIS A 3 30.795 10.375 5.517 1.00 0.00 N ATOM 27 N ALA A 4 35.698 14.335 2.856 1.00 0.00 N ATOM 28 CA ALA A 4 36.932 14.752 2.201 1.00 0.00 C ATOM 29 C ALA A 4 38.127 14.604 3.136 1.00 0.00 C ATOM 30 O ALA A 4 38.248 15.329 4.124 1.00 0.00 O ATOM 31 CB ALA A 4 36.812 16.192 1.723 1.00 0.00 C ATOM 32 N ASP A 5 39.007 13.660 2.818 1.00 0.00 N ATOM 33 CA ASP A 5 40.194 13.415 3.630 1.00 0.00 C ATOM 34 C ASP A 5 41.467 13.708 2.841 1.00 0.00 C ATOM 35 O ASP A 5 41.801 12.995 1.896 1.00 0.00 O ATOM 36 CB ASP A 5 40.211 11.966 4.122 1.00 0.00 C ATOM 37 CG ASP A 5 41.346 11.691 5.089 1.00 0.00 C ATOM 38 OD1 ASP A 5 41.256 12.134 6.254 1.00 0.00 O ATOM 39 OD2 ASP A 5 42.327 11.032 4.685 1.00 0.00 O ATOM 40 N ALA A 6 42.172 14.763 3.238 1.00 0.00 N ATOM 41 CA ALA A 6 43.409 15.152 2.570 1.00 0.00 C ATOM 42 C ALA A 6 44.601 15.036 3.514 1.00 0.00 C ATOM 43 O ALA A 6 44.722 15.797 4.474 1.00 0.00 O ATOM 44 CB ALA A 6 43.294 16.573 2.039 1.00 0.00 C ATOM 45 N GLU A 7 45.480 14.079 3.234 1.00 0.00 N ATOM 46 CA GLU A 7 46.665 13.862 4.057 1.00 0.00 C ATOM 47 C GLU A 7 47.940 14.122 3.261 1.00 0.00 C ATOM 48 O GLU A 7 48.275 13.373 2.344 1.00 0.00 O ATOM 49 CB GLU A 7 46.677 12.432 4.604 1.00 0.00 C ATOM 50 CG GLU A 7 45.565 12.140 5.599 1.00 0.00 C ATOM 51 CD GLU A 7 45.595 10.711 6.103 1.00 0.00 C ATOM 52 OE1 GLU A 7 46.403 9.912 5.585 1.00 0.00 O ATOM 53 OE2 GLU A 7 44.809 10.384 7.019 1.00 0.00 O ATOM 54 N ALA A 8 48.647 15.189 3.620 1.00 0.00 N ATOM 55 CA ALA A 8 49.886 15.550 2.941 1.00 0.00 C ATOM 56 C ALA A 8 51.076 15.468 3.892 1.00 0.00 C ATOM 57 O ALA A 8 51.196 16.264 4.823 1.00 0.00 O ATOM 58 CB ALA A 8 49.776 16.951 2.356 1.00 0.00 C ATOM 59 N ALA A 10 55.122 15.615 4.002 1.00 0.00 N ATOM 60 CA ALA A 10 56.363 15.948 3.313 1.00 0.00 C ATOM 61 C ALA A 10 57.551 15.898 4.269 1.00 0.00 C ATOM 62 O ALA A 10 57.671 16.728 5.170 1.00 0.00 O ATOM 63 CB ALA A 10 56.258 17.326 2.676 1.00 0.00 C ATOM 64 N ASN A 11 58.427 14.919 4.065 1.00 0.00 N ATOM 65 CA ASN A 11 59.606 14.759 4.908 1.00 0.00 C ATOM 66 C ASN A 11 60.886 14.953 4.102 1.00 0.00 C ATOM 67 O ASN A 11 61.222 14.136 3.244 1.00 0.00 O ATOM 68 CB ASN A 11 59.609 13.379 5.562 1.00 0.00 C ATOM 69 CG ASN A 11 58.532 13.236 6.620 1.00 0.00 C ATOM 70 OD1 ASN A 11 58.296 14.149 7.410 1.00 0.00 O ATOM 71 ND2 ASN A 11 57.872 12.083 6.640 1.00 0.00 N ATOM 72 N ALA A 12 61.597 16.041 4.383 1.00 0.00 N ATOM 73 CA ALA A 12 62.841 16.345 3.686 1.00 0.00 C ATOM 74 C ALA A 12 64.025 16.328 4.646 1.00 0.00 C ATOM 75 O ALA A 12 64.145 17.191 5.515 1.00 0.00 O ATOM 76 CB ALA A 12 62.740 17.698 2.997 1.00 0.00 C ATOM 77 N GLN A 13 64.899 15.340 4.481 1.00 0.00 N ATOM 78 CA GLN A 13 66.076 15.209 5.332 1.00 0.00 C ATOM 79 C GLN A 13 67.359 15.370 4.522 1.00 0.00 C ATOM 80 O GLN A 13 67.695 14.521 3.697 1.00 0.00 O ATOM 81 CB GLN A 13 66.071 13.849 6.037 1.00 0.00 C ATOM 82 CG GLN A 13 67.212 13.651 7.023 1.00 0.00 C ATOM 83 CD GLN A 13 67.140 12.317 7.739 1.00 0.00 C ATOM 84 OE1 GLN A 13 66.251 11.506 7.477 1.00 0.00 O ATOM 85 NE2 GLN A 13 68.078 12.082 8.650 1.00 0.00 N ATOM 86 N ALA A 14 68.071 16.466 4.765 1.00 0.00 N ATOM 87 CA ALA A 14 69.318 16.740 4.059 1.00 0.00 C ATOM 88 C ALA A 14 70.500 16.757 5.022 1.00 0.00 C ATOM 89 O ALA A 14 70.620 17.652 5.859 1.00 0.00 O ATOM 90 CB ALA A 14 69.222 18.067 3.320 1.00 0.00 C ATOM 91 N LEU A 15 71.372 15.761 4.897 1.00 0.00 N ATOM 92 CA LEU A 15 72.547 15.660 5.755 1.00 0.00 C ATOM 93 C LEU A 15 73.832 15.788 4.943 1.00 0.00 C ATOM 94 O LEU A 15 74.168 14.907 4.151 1.00 0.00 O ATOM 95 CB LEU A 15 72.541 14.325 6.508 1.00 0.00 C ATOM 96 CG LEU A 15 71.415 14.114 7.526 1.00 0.00 C ATOM 97 CD1 LEU A 15 71.462 12.699 8.081 1.00 0.00 C ATOM 98 CD2 LEU A 15 71.487 15.136 8.654 1.00 0.00 C ATOM 99 N ALA A 16 74.546 16.890 5.146 1.00 0.00 N ATOM 100 CA ALA A 16 75.795 17.135 4.434 1.00 0.00 C ATOM 101 C ALA A 16 76.975 17.185 5.399 1.00 0.00 C ATOM 102 O ALA A 16 77.095 18.110 6.202 1.00 0.00 O ATOM 103 CB ALA A 16 75.704 18.434 3.646 1.00 0.00 C ATOM 104 N PHE A 17 77.845 16.184 5.313 1.00 0.00 N ATOM 105 CA PHE A 17 79.018 16.111 6.177 1.00 0.00 C ATOM 106 C PHE A 17 80.304 16.206 5.364 1.00 0.00 C ATOM 107 O PHE A 17 80.640 15.296 4.606 1.00 0.00 O ATOM 108 CB PHE A 17 79.005 14.807 6.980 1.00 0.00 C ATOM 109 CG PHE A 17 77.889 14.721 7.981 1.00 0.00 C ATOM 110 CD1 PHE A 17 77.992 15.351 9.210 1.00 0.00 C ATOM 111 CD2 PHE A 17 76.735 14.009 7.693 1.00 0.00 C ATOM 112 CE1 PHE A 17 76.966 15.272 10.133 1.00 0.00 C ATOM 113 CE2 PHE A 17 75.706 13.927 8.612 1.00 0.00 C ATOM 114 CZ PHE A 17 75.822 14.560 9.833 1.00 0.00 C ATOM 115 N ALA A 18 81.021 17.314 5.528 1.00 0.00 N ATOM 116 CA ALA A 18 82.272 17.529 4.810 1.00 0.00 C ATOM 117 C ALA A 18 83.450 17.613 5.775 1.00 0.00 C ATOM 118 O ALA A 18 83.570 18.567 6.543 1.00 0.00 O ATOM 119 CB ALA A 18 82.186 18.797 3.973 1.00 0.00 C ATOM 120 N TYR A 19 84.318 16.606 5.729 1.00 0.00 N ATOM 121 CA TYR A 19 85.488 16.564 6.598 1.00 0.00 C ATOM 122 C TYR A 19 86.777 16.625 5.785 1.00 0.00 C ATOM 123 O TYR A 19 87.113 15.687 5.063 1.00 0.00 O ATOM 124 CB TYR A 19 85.471 15.292 7.450 1.00 0.00 C ATOM 125 CG TYR A 19 84.363 15.258 8.479 1.00 0.00 C ATOM 126 CD1 TYR A 19 83.662 16.411 8.812 1.00 0.00 C ATOM 127 CD2 TYR A 19 84.016 14.074 9.116 1.00 0.00 C ATOM 128 CE1 TYR A 19 82.648 16.386 9.751 1.00 0.00 C ATOM 129 CE2 TYR A 19 83.002 14.039 10.057 1.00 0.00 C ATOM 130 CZ TYR A 19 82.323 15.197 10.369 1.00 0.00 C ATOM 131 OH TYR A 19 81.313 15.166 11.305 1.00 0.00 O ATOM 132 N ALA A 20 87.496 17.737 5.909 1.00 0.00 N ATOM 133 CA ALA A 20 88.749 17.922 5.187 1.00 0.00 C ATOM 134 C ALA A 20 89.925 18.039 6.151 1.00 0.00 C ATOM 135 O ALA A 20 90.046 19.021 6.883 1.00 0.00 O ATOM 136 CB ALA A 20 88.668 19.159 4.303 1.00 0.00 C ATOM 137 N VAL A 21 90.791 17.030 6.145 1.00 0.00 N ATOM 138 CA VAL A 21 91.959 17.017 7.018 1.00 0.00 C ATOM 139 C VAL A 21 93.250 17.045 6.207 1.00 0.00 C ATOM 140 O VAL A 21 93.585 16.079 5.521 1.00 0.00 O ATOM 141 CB VAL A 21 91.967 15.769 7.925 1.00 0.00 C ATOM 142 CG1 VAL A 21 93.241 15.722 8.760 1.00 0.00 C ATOM 143 CG2 VAL A 21 90.735 15.749 8.820 1.00 0.00 C ATOM 144 N ALA A 22 93.971 18.159 6.291 1.00 0.00 N ATOM 145 CA ALA A 22 95.226 18.315 5.565 1.00 0.00 C ATOM 146 C ALA A 22 96.400 18.465 6.527 1.00 0.00 C ATOM 147 O ALA A 22 96.521 19.473 7.222 1.00 0.00 O ATOM 148 CB ALA A 22 95.150 19.517 4.636 1.00 0.00 C TER ATOM 149 N ARG B 1 27.961 0.504 1.988 1.00 0.00 N ATOM 150 CA ARG B 1 29.153 0.205 2.773 1.00 0.00 C ATOM 151 C ARG B 1 30.420 0.562 2.003 1.00 0.00 C ATOM 152 O ARG B 1 30.753 -0.077 1.005 1.00 0.00 O ATOM 153 CB ARG B 1 29.180 -1.279 3.156 1.00 10.00 C ATOM 154 CG ARG B 1 28.007 -1.729 4.022 1.00 10.00 C ATOM 155 CD ARG B 1 28.018 -1.090 5.409 1.00 10.00 C ATOM 156 NE ARG B 1 29.183 -1.492 6.201 1.00 10.00 N ATOM 157 CZ ARG B 1 29.635 -0.879 7.298 1.00 10.00 C ATOM 158 NH1 ARG B 1 30.708 -1.364 7.908 1.00 10.00 N ATOM 159 NH2 ARG B 1 29.046 0.205 7.803 1.00 10.00 N ATOM 160 N ALA B 2 31.123 1.587 2.474 1.00 0.00 N ATOM 161 CA ALA B 2 32.355 2.031 1.832 1.00 0.00 C ATOM 162 C ALA B 2 33.552 1.851 2.758 1.00 0.00 C ATOM 163 O ALA B 2 33.675 2.539 3.772 1.00 0.00 O ATOM 164 CB ALA B 2 32.231 3.487 1.408 1.00 0.00 C ATOM 165 N HIS B 3 34.434 0.922 2.403 1.00 0.00 N ATOM 166 CA HIS B 3 35.624 0.650 3.202 1.00 0.00 C ATOM 167 C HIS B 3 36.893 0.975 2.422 1.00 0.00 C ATOM 168 O HIS B 3 37.227 0.298 1.450 1.00 0.00 O ATOM 169 CB HIS B 3 35.644 -0.817 3.640 1.00 0.00 C ATOM 170 CG HIS B 3 34.518 -1.190 4.554 1.00 0.00 C ATOM 171 ND1 HIS B 3 34.311 -0.928 5.866 1.00 0.00 C ATOM 172 CD2 HIS B 3 33.431 -1.925 4.134 1.00 0.00 N ATOM 173 CE1 HIS B 3 33.113 -1.504 6.211 1.00 0.00 N ATOM 174 NE2 HIS B 3 32.603 -2.100 5.148 1.00 0.00 C ATOM 175 N ALA B 4 37.598 2.015 2.856 1.00 0.00 N ATOM 176 CA ALA B 4 38.832 2.432 2.201 1.00 0.00 C ATOM 177 C ALA B 4 40.027 2.284 3.136 1.00 0.00 C ATOM 178 O ALA B 4 40.148 3.009 4.124 1.00 0.00 O ATOM 179 CB ALA B 4 38.712 3.872 1.723 1.00 0.00 C ATOM 180 N ASP B 5 40.907 1.340 2.818 1.00 0.00 N ATOM 181 CA ASP B 5 42.094 1.095 3.630 1.00 0.00 C ATOM 182 C ASP B 5 43.367 1.388 2.841 1.00 0.00 C ATOM 183 O ASP B 5 43.701 0.675 1.896 1.00 0.00 O ATOM 184 CB ASP B 5 42.111 -0.354 4.122 1.00 0.00 C ATOM 185 CG ASP B 5 43.246 -0.629 5.089 1.00 0.00 C ATOM 186 OD1 ASP B 5 43.158 -0.186 6.253 1.00 0.00 O ATOM 187 OD2 ASP B 5 44.227 -1.288 4.683 1.00 0.00 O ATOM 188 N ALA B 6 44.072 2.443 3.238 1.00 0.00 N ATOM 189 CA ALA B 6 45.309 2.832 2.570 1.00 0.00 C ATOM 190 C ALA B 6 46.501 2.716 3.514 1.00 0.00 C ATOM 191 O ALA B 6 46.622 3.477 4.474 1.00 0.00 O ATOM 192 CB ALA B 6 45.194 4.253 2.039 1.00 0.00 C ATOM 193 N GLU B 7 47.380 1.759 3.234 1.00 0.00 N ATOM 194 CA GLU B 7 48.565 1.542 4.057 1.00 0.00 C ATOM 195 C GLU B 7 49.840 1.802 3.261 1.00 0.00 C ATOM 196 O GLU B 7 50.175 1.053 2.344 1.00 0.00 O ATOM 197 CB GLU B 7 48.577 0.112 4.604 1.00 0.00 C ATOM 198 CG GLU B 7 47.465 -0.180 5.599 1.00 0.00 C ATOM 199 CD GLU B 7 47.495 -1.609 6.103 1.00 0.00 C ATOM 200 OE1 GLU B 7 48.305 -2.409 5.584 1.00 0.00 O ATOM 201 OE2 GLU B 7 46.711 -1.936 7.018 1.00 0.00 O ATOM 202 N ALA B 8 50.547 2.869 3.620 1.00 0.00 N ATOM 203 CA ALA B 8 51.786 3.230 2.941 1.00 0.00 C ATOM 204 C ALA B 8 52.976 3.148 3.892 1.00 0.00 C ATOM 205 O ALA B 8 53.096 3.944 4.823 1.00 0.00 O ATOM 206 CB ALA B 8 51.676 4.631 2.356 1.00 0.00 C ATOM 207 N ALA B 10 57.022 3.295 4.002 1.00 0.00 N ATOM 208 CA ALA B 10 58.263 3.628 3.313 1.00 0.00 C ATOM 209 C ALA B 10 59.451 3.578 4.269 1.00 0.00 C ATOM 210 O ALA B 10 59.571 4.408 5.170 1.00 0.00 O ATOM 211 CB ALA B 10 58.158 5.006 2.676 1.00 0.00 C ATOM 212 N ASN B 11 60.327 2.599 4.065 1.00 0.00 N ATOM 213 CA ASN B 11 61.506 2.439 4.908 1.00 0.00 C ATOM 214 C ASN B 11 62.786 2.633 4.102 1.00 0.00 C ATOM 215 O ASN B 11 63.122 1.816 3.244 1.00 0.00 O ATOM 216 CB ASN B 11 61.509 1.059 5.562 1.00 0.00 C ATOM 217 CG ASN B 11 60.432 0.916 6.620 1.00 0.00 C ATOM 218 OD1 ASN B 11 60.252 1.957 7.425 1.00 0.00 N ATOM 219 ND2 ASN B 11 59.769 -0.116 6.713 1.00 0.00 O ATOM 220 N ALA B 12 63.497 3.721 4.383 1.00 0.00 N ATOM 221 CA ALA B 12 64.741 4.025 3.686 1.00 0.00 C ATOM 222 C ALA B 12 65.925 4.008 4.646 1.00 0.00 C ATOM 223 O ALA B 12 66.045 4.871 5.515 1.00 0.00 O ATOM 224 CB ALA B 12 64.640 5.378 2.997 1.00 0.00 C ATOM 225 N GLN B 13 66.799 3.020 4.481 1.00 0.00 N ATOM 226 CA GLN B 13 67.976 2.889 5.332 1.00 0.00 C ATOM 227 C GLN B 13 69.259 3.050 4.522 1.00 0.00 C ATOM 228 O GLN B 13 69.595 2.201 3.697 1.00 0.00 O ATOM 229 CB GLN B 13 67.971 1.529 6.037 1.00 0.00 C ATOM 230 CG GLN B 13 69.112 1.331 7.023 1.00 0.00 C ATOM 231 CD GLN B 13 69.040 -0.003 7.739 1.00 0.00 C ATOM 232 OE1 GLN B 13 68.046 -0.811 7.388 1.00 0.00 N ATOM 233 NE2 GLN B 13 69.869 -0.305 8.598 1.00 0.00 O ATOM 234 N ALA B 14 69.971 4.146 4.765 1.00 0.00 N ATOM 235 CA ALA B 14 71.218 4.420 4.059 1.00 0.00 C ATOM 236 C ALA B 14 72.400 4.437 5.022 1.00 0.00 C ATOM 237 O ALA B 14 72.520 5.332 5.859 1.00 0.00 O ATOM 238 CB ALA B 14 71.122 5.747 3.320 1.00 0.00 C ATOM 239 N LEU B 15 73.272 3.441 4.897 1.00 0.00 N ATOM 240 CA LEU B 15 74.447 3.340 5.755 1.00 0.00 C ATOM 241 C LEU B 15 75.732 3.468 4.943 1.00 0.00 C ATOM 242 O LEU B 15 76.068 2.587 4.151 1.00 0.00 O ATOM 243 CB LEU B 15 74.441 2.005 6.508 1.00 0.00 C ATOM 244 CG LEU B 15 73.315 1.794 7.526 1.00 0.00 C ATOM 245 CD1 LEU B 15 72.426 0.619 7.136 1.00 0.00 C ATOM 246 CD2 LEU B 15 72.491 3.063 7.674 1.00 0.00 C ATOM 247 N ALA B 16 76.446 4.570 5.146 1.00 0.00 N ATOM 248 CA ALA B 16 77.695 4.815 4.434 1.00 0.00 C ATOM 249 C ALA B 16 78.875 4.865 5.399 1.00 0.00 C ATOM 250 O ALA B 16 78.995 5.790 6.202 1.00 0.00 O ATOM 251 CB ALA B 16 77.604 6.114 3.646 1.00 0.00 C ATOM 252 N PHE B 17 79.745 3.864 5.313 1.00 0.00 N ATOM 253 CA PHE B 17 80.918 3.791 6.177 1.00 0.00 C ATOM 254 C PHE B 17 82.204 3.886 5.364 1.00 0.00 C ATOM 255 O PHE B 17 82.540 2.976 4.606 1.00 0.00 O ATOM 256 CB PHE B 17 80.905 2.487 6.980 1.00 0.00 C ATOM 257 CG PHE B 17 79.789 2.401 7.981 1.00 0.00 C ATOM 258 CD1 PHE B 17 79.893 3.032 9.211 1.00 0.00 C ATOM 259 CD2 PHE B 17 78.636 1.690 7.694 1.00 0.00 C ATOM 260 CE1 PHE B 17 78.868 2.956 10.134 1.00 0.00 C ATOM 261 CE2 PHE B 17 77.607 1.611 8.614 1.00 0.00 C ATOM 262 CZ PHE B 17 77.724 2.244 9.835 1.00 0.00 C ATOM 263 N ALA B 18 82.921 4.994 5.528 1.00 0.00 N ATOM 264 CA ALA B 18 84.172 5.209 4.810 1.00 0.00 C ATOM 265 C ALA B 18 85.350 5.293 5.775 1.00 0.00 C ATOM 266 O ALA B 18 85.470 6.247 6.543 1.00 0.00 O ATOM 267 CB ALA B 18 84.086 6.477 3.973 1.00 0.00 C ATOM 268 N TYR B 19 86.218 4.286 5.729 1.00 0.00 N ATOM 269 CA TYR B 19 87.388 4.244 6.598 1.00 0.00 C ATOM 270 C TYR B 19 88.677 4.305 5.785 1.00 0.00 C ATOM 271 O TYR B 19 89.013 3.367 5.063 1.00 0.00 O ATOM 272 CB TYR B 19 87.371 2.972 7.450 1.00 0.00 C ATOM 273 CG TYR B 19 86.263 2.938 8.479 1.00 0.00 C ATOM 274 CD1 TYR B 19 85.564 4.090 8.814 1.00 0.00 C ATOM 275 CD2 TYR B 19 85.918 1.753 9.118 1.00 0.00 C ATOM 276 CE1 TYR B 19 84.550 4.063 9.756 1.00 0.00 C ATOM 277 CE2 TYR B 19 84.907 1.716 10.059 1.00 0.00 C ATOM 278 CZ TYR B 19 84.228 2.874 10.374 1.00 0.00 C ATOM 279 OH TYR B 19 83.220 2.843 11.312 1.00 0.00 O ATOM 280 N ALA B 20 89.396 5.417 5.909 1.00 0.00 N ATOM 281 CA ALA B 20 90.649 5.602 5.187 1.00 0.00 C ATOM 282 C ALA B 20 91.825 5.719 6.151 1.00 0.00 C ATOM 283 O ALA B 20 91.946 6.701 6.883 1.00 0.00 O ATOM 284 CB ALA B 20 90.568 6.839 4.303 1.00 0.00 C ATOM 285 N VAL B 21 92.691 4.710 6.145 1.00 0.00 N ATOM 286 CA VAL B 21 93.859 4.697 7.018 1.00 0.00 C ATOM 287 C VAL B 21 95.150 4.725 6.207 1.00 0.00 C ATOM 288 O VAL B 21 95.485 3.759 5.521 1.00 0.00 O ATOM 289 CB VAL B 21 93.867 3.449 7.925 1.00 0.00 C ATOM 290 CG1 VAL B 21 95.105 2.602 7.660 1.00 0.00 C ATOM 291 CG2 VAL B 21 92.599 2.630 7.720 1.00 0.00 C ATOM 292 N ALA B 22 95.871 5.839 6.291 1.00 0.00 N ATOM 293 CA ALA B 22 97.126 5.995 5.565 1.00 0.00 C ATOM 294 C ALA B 22 98.300 6.145 6.527 1.00 0.00 C ATOM 295 O ALA B 22 98.421 7.153 7.222 1.00 0.00 O ATOM 296 CB ALA B 22 97.050 7.197 4.636 1.00 0.00 C TER """ h = iotbx.pdb.input(source_info=None, lines=test_pdb_5).construct_hierarchy() anwer_h = iotbx.pdb.input(source_info=None, lines=answer_pdb_str).construct_hierarchy() h.write_pdb_file("test_8_before.pdb") ncs_inp = iotbx.ncs.input( hierarchy=h, params=ncs_pars.ncs_search) ncs_groups = ncs_inp.get_ncs_restraints_group_list() nu.flip_atoms_in_ncs_groups(h, ncs_groups) h.write_pdb_file("test_8_result.pdb") rmsd_smart = calculate_rmsd_smart(anwer_h, h) print(rmsd_smart) assert rmsd_smart < 0.01 if __name__=='__main__': test_1() test_2() # test_3() intentional, see docstring in the test. test_4() test_5() test_6() test_7() test_8() print("OK")