from __future__ import division from libtbx import easy_run from libtbx.test_utils import approx_equal pdb_str_1 = """ CRYST1 50.273 31.111 38.194 90.00 90.00 90.00 P 1 ATOM 1 N ALA A 1 45.103 22.406 32.854 1.00 1.00 ATOM 2 CA ALA A 1 44.740 21.164 32.193 1.00 1.00 ATOM 3 C ALA A 1 43.346 21.306 31.578 1.00 1.00 ATOM 4 O ALA A 1 43.133 20.945 30.422 1.00 1.00 ATOM 5 CB ALA A 1 44.821 20.010 33.194 1.00 1.00 ATOM 6 N ALA A 2 42.432 21.834 32.380 1.00 1.00 ATOM 7 CA ALA A 2 41.065 22.029 31.929 1.00 1.00 ATOM 8 C ALA A 2 41.064 22.917 30.683 1.00 1.00 ATOM 9 O ALA A 2 40.403 22.606 29.694 1.00 1.00 ATOM 10 CB ALA A 2 40.231 22.620 33.067 1.00 1.00 ATOM 11 N ALA A 3 41.815 24.006 30.772 1.00 1.00 ATOM 12 CA ALA A 3 41.909 24.941 29.664 1.00 1.00 ATOM 13 C ALA A 3 42.418 24.205 28.422 1.00 1.00 ATOM 14 O ALA A 3 41.862 24.354 27.336 1.00 1.00 ATOM 15 CB ALA A 3 42.812 26.111 30.059 1.00 1.00 ATOM 16 N ALA A 4 43.471 23.427 28.626 1.00 1.00 ATOM 17 CA ALA A 4 44.061 22.667 27.537 1.00 1.00 ATOM 18 C ALA A 4 42.999 21.751 26.925 1.00 1.00 ATOM 19 O ALA A 4 42.854 21.689 25.705 1.00 1.00 ATOM 20 CB ALA A 4 45.273 21.890 28.054 1.00 1.00 ATOM 21 N ALA A 5 42.282 21.062 27.802 1.00 1.00 ATOM 22 CA ALA A 5 41.237 20.153 27.363 1.00 1.00 ATOM 23 C ALA A 5 40.213 20.923 26.527 1.00 1.00 ATOM 24 O ALA A 5 39.820 20.475 25.451 1.00 1.00 ATOM 25 CB ALA A 5 40.605 19.475 28.580 1.00 1.00 ATOM 26 N ALA A 6 39.811 22.071 27.055 1.00 1.00 ATOM 27 CA ALA A 6 38.840 22.908 26.370 1.00 1.00 ATOM 28 C ALA A 6 39.374 23.272 24.983 1.00 1.00 ATOM 29 O ALA A 6 38.655 23.168 23.990 1.00 1.00 ATOM 30 CB ALA A 6 38.541 24.144 27.222 1.00 1.00 ATOM 31 N ALA A 7 40.631 23.689 24.959 1.00 1.00 ATOM 32 CA ALA A 7 41.270 24.068 23.710 1.00 1.00 ATOM 33 C ALA A 7 41.223 22.887 22.739 1.00 1.00 ATOM 34 O ALA A 7 40.866 23.049 21.573 1.00 1.00 ATOM 35 CB ALA A 7 42.699 24.537 23.988 1.00 1.00 ATOM 36 N ALA A 8 41.588 21.722 23.256 1.00 1.00 ATOM 37 CA ALA A 8 41.591 20.514 22.449 1.00 1.00 ATOM 38 C ALA A 8 40.189 20.278 21.885 1.00 1.00 ATOM 39 O ALA A 8 40.031 20.003 20.696 1.00 1.00 ATOM 40 CB ALA A 8 42.085 19.337 23.293 1.00 1.00 ATOM 41 N ALA A 9 39.204 20.394 22.765 1.00 1.00 ATOM 42 CA ALA A 9 37.820 20.198 22.369 1.00 1.00 ATOM 43 C ALA A 9 37.471 21.177 21.246 1.00 1.00 ATOM 44 O ALA A 9 36.882 20.789 20.239 1.00 1.00 ATOM 45 CB ALA A 9 36.912 20.361 23.589 1.00 1.00 ATOM 46 N ALA A 10 37.849 22.430 21.459 1.00 1.00 ATOM 47 CA ALA A 10 37.584 23.468 20.477 1.00 1.00 ATOM 48 C ALA A 10 38.222 23.078 19.143 1.00 1.00 ATOM 49 O ALA A 10 37.585 23.167 18.095 1.00 1.00 ATOM 50 CB ALA A 10 38.099 24.810 21.001 1.00 1.00 ATOM 51 N ALA A 11 39.475 22.654 19.225 1.00 1.00 ATOM 52 CA ALA A 11 40.208 22.250 18.037 1.00 1.00 ATOM 53 C ALA A 11 39.449 21.122 17.334 1.00 1.00 ATOM 54 O ALA A 11 39.260 21.158 16.119 1.00 1.00 ATOM 55 CB ALA A 11 41.629 21.842 18.427 1.00 1.00 ATOM 56 N ALA A 12 39.035 20.146 18.129 1.00 1.00 ATOM 57 CA ALA A 12 38.301 19.010 17.599 1.00 1.00 ATOM 58 C ALA A 12 37.041 19.508 16.888 1.00 1.00 ATOM 59 O ALA A 12 36.744 19.086 15.771 1.00 1.00 ATOM 60 CB ALA A 12 37.983 18.032 18.732 1.00 1.00 ATOM 61 N ALA A 13 36.333 20.401 17.565 1.00 1.00 ATOM 62 CA ALA A 13 35.112 20.962 17.012 1.00 1.00 ATOM 63 C ALA A 13 35.424 21.632 15.672 1.00 1.00 ATOM 64 O ALA A 13 34.716 21.422 14.688 1.00 1.00 ATOM 65 CB ALA A 13 34.494 21.933 18.019 1.00 1.00 ATOM 66 N ALA A 14 36.486 22.426 15.677 1.00 1.00 ATOM 67 CA ALA A 14 36.900 23.127 14.474 1.00 1.00 ATOM 68 C ALA A 14 37.166 22.111 13.361 1.00 1.00 ATOM 69 O ALA A 14 36.709 22.286 12.233 1.00 1.00 ATOM 70 CB ALA A 14 38.126 23.989 14.783 1.00 1.00 ATOM 71 N ALA A 15 37.905 21.070 13.719 1.00 1.00 ATOM 72 CA ALA A 15 38.237 20.026 12.765 1.00 1.00 ATOM 73 C ALA A 15 36.947 19.426 12.202 1.00 1.00 ATOM 74 O ALA A 15 36.813 19.254 10.992 1.00 1.00 ATOM 75 CB ALA A 15 39.121 18.977 13.443 1.00 1.00 ATOM 76 N ALA A 16 36.028 19.124 13.109 1.00 1.00 ATOM 77 CA ALA A 16 34.753 18.547 12.718 1.00 1.00 ATOM 78 C ALA A 16 34.051 19.488 11.736 1.00 1.00 ATOM 79 O ALA A 16 33.555 19.052 10.699 1.00 1.00 ATOM 80 CB ALA A 16 33.912 18.273 13.966 1.00 1.00 ATOM 81 N ALA A 17 34.033 20.763 12.099 1.00 1.00 ATOM 82 CA ALA A 17 33.401 21.769 11.263 1.00 1.00 ATOM 83 C ALA A 17 34.050 21.757 9.878 1.00 1.00 ATOM 84 O ALA A 17 33.357 21.760 8.862 1.00 1.00 ATOM 85 CB ALA A 17 33.503 23.136 11.943 1.00 1.00 ATOM 86 N ALA A 18 35.376 21.744 9.881 1.00 1.00 ATOM 87 CA ALA A 18 36.127 21.731 8.637 1.00 1.00 ATOM 88 C ALA A 18 35.717 20.510 7.811 1.00 1.00 ATOM 89 O ALA A 18 35.455 20.624 6.615 1.00 1.00 ATOM 90 CB ALA A 18 37.625 21.751 8.945 1.00 1.00 ATOM 91 N ALA A 19 35.674 19.368 8.483 1.00 1.00 ATOM 92 CA ALA A 19 35.299 18.128 7.827 1.00 1.00 ATOM 93 C ALA A 19 33.908 18.281 7.209 1.00 1.00 ATOM 94 O ALA A 19 33.693 17.917 6.054 1.00 1.00 ATOM 95 CB ALA A 19 35.368 16.977 8.832 1.00 1.00 ATOM 96 N ALA A 20 32.998 18.820 8.008 1.00 1.00 ATOM 97 CA ALA A 20 31.633 19.027 7.555 1.00 1.00 ATOM 98 C ALA A 20 31.642 19.910 6.305 1.00 1.00 ATOM 99 O ALA A 20 30.979 19.602 5.317 1.00 1.00 ATOM 100 CB ALA A 20 30.804 19.630 8.690 1.00 1.00 TER ATOM 1 N ALA B 1 5.652 7.138 18.311 1.00 1.00 N ATOM 2 CA ALA B 1 6.710 6.420 17.620 1.00 1.00 C ATOM 3 C ALA B 1 7.114 7.197 16.366 1.00 1.00 C ATOM 4 O ALA B 1 8.300 7.396 16.108 1.00 1.00 O ATOM 5 CB ALA B 1 6.239 5.000 17.301 1.00 1.00 C ATOM 6 N ALA B 2 6.103 7.617 15.618 1.00 1.00 N ATOM 7 CA ALA B 2 6.338 8.368 14.397 1.00 1.00 C ATOM 8 C ALA B 2 7.143 9.628 14.724 1.00 1.00 C ATOM 9 O ALA B 2 8.122 9.938 14.047 1.00 1.00 O ATOM 10 CB ALA B 2 5.000 8.689 13.729 1.00 1.00 C ATOM 11 N ALA B 3 6.700 10.320 15.765 1.00 1.00 N ATOM 12 CA ALA B 3 7.367 11.539 16.190 1.00 1.00 C ATOM 13 C ALA B 3 8.832 11.229 16.510 1.00 1.00 C ATOM 14 O ALA B 3 9.731 11.947 16.077 1.00 1.00 O ATOM 15 CB ALA B 3 6.624 12.137 17.385 1.00 1.00 C ATOM 16 N ALA B 4 9.024 10.158 17.267 1.00 1.00 N ATOM 17 CA ALA B 4 10.363 9.744 17.649 1.00 1.00 C ATOM 18 C ALA B 4 11.197 9.499 16.390 1.00 1.00 C ATOM 19 O ALA B 4 12.332 9.963 16.290 1.00 1.00 O ATOM 20 CB ALA B 4 10.279 8.506 18.543 1.00 1.00 C ATOM 21 N ALA B 5 10.600 8.770 15.457 1.00 1.00 N ATOM 22 CA ALA B 5 11.273 8.458 14.208 1.00 1.00 C ATOM 23 C ALA B 5 11.667 9.759 13.506 1.00 1.00 C ATOM 24 O ALA B 5 12.799 9.904 13.047 1.00 1.00 O ATOM 25 CB ALA B 5 10.365 7.581 13.343 1.00 1.00 C ATOM 26 N ALA B 6 10.710 10.674 13.446 1.00 1.00 N ATOM 27 CA ALA B 6 10.944 11.959 12.808 1.00 1.00 C ATOM 28 C ALA B 6 12.121 12.657 13.492 1.00 1.00 C ATOM 29 O ALA B 6 13.019 13.166 12.823 1.00 1.00 O ATOM 30 CB ALA B 6 9.662 12.794 12.858 1.00 1.00 C ATOM 31 N ALA B 7 12.079 12.657 14.816 1.00 1.00 N ATOM 32 CA ALA B 7 13.131 13.284 15.598 1.00 1.00 C ATOM 33 C ALA B 7 14.475 12.646 15.241 1.00 1.00 C ATOM 34 O ALA B 7 15.458 13.347 15.005 1.00 1.00 O ATOM 35 CB ALA B 7 12.805 13.160 17.087 1.00 1.00 C ATOM 36 N ALA B 8 14.475 11.320 15.211 1.00 1.00 N ATOM 37 CA ALA B 8 15.682 10.580 14.886 1.00 1.00 C ATOM 38 C ALA B 8 16.184 11.010 13.507 1.00 1.00 C ATOM 39 O ALA B 8 17.372 11.280 13.329 1.00 1.00 O ATOM 40 CB ALA B 8 15.396 9.079 14.960 1.00 1.00 C ATOM 41 N ALA B 9 15.254 11.061 12.563 1.00 1.00 N ATOM 42 CA ALA B 9 15.588 11.455 11.205 1.00 1.00 C ATOM 43 C ALA B 9 16.218 12.850 11.222 1.00 1.00 C ATOM 44 O ALA B 9 17.248 13.078 10.591 1.00 1.00 O ATOM 45 CB ALA B 9 14.333 11.392 10.332 1.00 1.00 C ATOM 46 N ALA B 10 15.569 13.747 11.951 1.00 1.00 N ATOM 47 CA ALA B 10 16.053 15.113 12.060 1.00 1.00 C ATOM 48 C ALA B 10 17.479 15.103 12.612 1.00 1.00 C ATOM 49 O ALA B 10 18.360 15.777 12.082 1.00 1.00 O ATOM 50 CB ALA B 10 15.095 15.927 12.932 1.00 1.00 C ATOM 51 N ALA B 11 17.663 14.329 13.672 1.00 1.00 N ATOM 52 CA ALA B 11 18.968 14.221 14.304 1.00 1.00 C ATOM 53 C ALA B 11 19.990 13.737 13.273 1.00 1.00 C ATOM 54 O ALA B 11 21.079 14.297 13.161 1.00 1.00 O ATOM 55 CB ALA B 11 18.875 13.292 15.514 1.00 1.00 C ATOM 56 N ALA B 12 19.602 12.699 12.545 1.00 1.00 N ATOM 57 CA ALA B 12 20.470 12.133 11.527 1.00 1.00 C ATOM 58 C ALA B 12 20.836 13.218 10.513 1.00 1.00 C ATOM 59 O ALA B 12 22.003 13.372 10.155 1.00 1.00 O ATOM 60 CB ALA B 12 19.779 10.933 10.875 1.00 1.00 C ATOM 61 N ALA B 13 19.815 13.943 10.077 1.00 1.00 N ATOM 62 CA ALA B 13 20.014 15.010 9.111 1.00 1.00 C ATOM 63 C ALA B 13 21.014 16.023 9.674 1.00 1.00 C ATOM 64 O ALA B 13 21.945 16.433 8.983 1.00 1.00 O ATOM 65 CB ALA B 13 18.667 15.648 8.770 1.00 1.00 C ATOM 66 N ALA B 14 20.785 16.398 10.926 1.00 1.00 N ATOM 67 CA ALA B 14 21.654 17.355 11.589 1.00 1.00 C ATOM 68 C ALA B 14 23.089 16.823 11.587 1.00 1.00 C ATOM 69 O ALA B 14 24.025 17.550 11.258 1.00 1.00 O ATOM 70 CB ALA B 14 21.133 17.622 13.002 1.00 1.00 C ATOM 71 N ALA B 15 23.217 15.556 11.958 1.00 1.00 N ATOM 72 CA ALA B 15 24.521 14.919 12.002 1.00 1.00 C ATOM 73 C ALA B 15 25.171 14.997 10.619 1.00 1.00 C ATOM 74 O ALA B 15 26.340 15.358 10.497 1.00 1.00 O ATOM 75 CB ALA B 15 24.369 13.478 12.494 1.00 1.00 C ATOM 76 N ALA B 16 24.382 14.654 9.610 1.00 1.00 N ATOM 77 CA ALA B 16 24.866 14.682 8.240 1.00 1.00 C ATOM 78 C ALA B 16 25.353 16.093 7.904 1.00 1.00 C ATOM 79 O ALA B 16 26.437 16.263 7.348 1.00 1.00 O ATOM 80 CB ALA B 16 23.758 14.207 7.298 1.00 1.00 C ATOM 81 N ALA B 17 24.528 17.069 8.256 1.00 1.00 N ATOM 82 CA ALA B 17 24.862 18.459 7.998 1.00 1.00 C ATOM 83 C ALA B 17 26.190 18.795 8.678 1.00 1.00 C ATOM 84 O ALA B 17 27.071 19.398 8.067 1.00 1.00 O ATOM 85 CB ALA B 17 23.719 19.356 8.478 1.00 1.00 C ATOM 86 N ALA B 18 26.294 18.388 9.936 1.00 1.00 N ATOM 87 CA ALA B 18 27.502 18.638 10.705 1.00 1.00 C ATOM 88 C ALA B 18 28.699 18.017 9.984 1.00 1.00 C ATOM 89 O ALA B 18 29.736 18.659 9.826 1.00 1.00 O ATOM 90 CB ALA B 18 27.326 18.091 12.123 1.00 1.00 C ATOM 91 N ALA B 19 28.517 16.772 9.566 1.00 1.00 N ATOM 92 CA ALA B 19 29.568 16.057 8.864 1.00 1.00 C ATOM 93 C ALA B 19 29.971 16.844 7.615 1.00 1.00 C ATOM 94 O ALA B 19 31.157 17.040 7.355 1.00 1.00 O ATOM 95 CB ALA B 19 29.091 14.642 8.533 1.00 1.00 C ATOM 96 N ALA B 20 28.959 17.273 6.875 1.00 1.00 N ATOM 97 CA ALA B 20 29.191 18.036 5.660 1.00 1.00 C ATOM 98 C ALA B 20 30.003 19.289 5.995 1.00 1.00 C ATOM 99 O ALA B 20 30.979 19.602 5.317 1.00 1.00 O ATOM 100 CB ALA B 20 27.852 18.366 5.000 1.00 1.00 C TER END """ pdb_str_2 = """ CRYST1 20.469 15.134 33.877 90.00 90.00 90.00 P 1 ATOM 1 N ALA A 1 17.299 8.429 30.537 1.00 1.00 ATOM 2 CA ALA A 1 16.936 7.187 29.876 1.00 1.00 ATOM 3 C ALA A 1 15.542 7.329 29.261 1.00 1.00 ATOM 4 O ALA A 1 15.329 6.968 28.105 1.00 1.00 ATOM 5 CB ALA A 1 17.017 6.033 30.877 1.00 1.00 ATOM 6 N ALA A 2 14.628 7.857 30.063 1.00 1.00 ATOM 7 CA ALA A 2 13.261 8.052 29.612 1.00 1.00 ATOM 8 C ALA A 2 13.260 8.940 28.366 1.00 1.00 ATOM 9 O ALA A 2 12.599 8.629 27.377 1.00 1.00 ATOM 10 CB ALA A 2 12.427 8.643 30.750 1.00 1.00 ATOM 11 N ALA A 3 14.011 10.029 28.455 1.00 1.00 ATOM 12 CA ALA A 3 14.105 10.964 27.347 1.00 1.00 ATOM 13 C ALA A 3 14.614 10.228 26.105 1.00 1.00 ATOM 14 O ALA A 3 14.058 10.377 25.019 1.00 1.00 ATOM 15 CB ALA A 3 15.008 12.134 27.742 1.00 1.00 ATOM 16 N ALA A 4 15.667 9.450 26.309 1.00 1.00 ATOM 17 CA ALA A 4 16.257 8.690 25.220 1.00 1.00 ATOM 18 C ALA A 4 15.195 7.774 24.608 1.00 1.00 ATOM 19 O ALA A 4 15.050 7.712 23.388 1.00 1.00 ATOM 20 CB ALA A 4 17.469 7.913 25.737 1.00 1.00 ATOM 21 N ALA A 5 14.478 7.085 25.485 1.00 1.00 ATOM 22 CA ALA A 5 13.433 6.176 25.046 1.00 1.00 ATOM 23 C ALA A 5 12.409 6.946 24.210 1.00 1.00 ATOM 24 O ALA A 5 12.016 6.498 23.134 1.00 1.00 ATOM 25 CB ALA A 5 12.801 5.498 26.263 1.00 1.00 ATOM 26 N ALA A 6 12.007 8.094 24.738 1.00 1.00 ATOM 27 CA ALA A 6 11.036 8.931 24.053 1.00 1.00 ATOM 28 C ALA A 6 11.570 9.295 22.666 1.00 1.00 ATOM 29 O ALA A 6 10.851 9.191 21.673 1.00 1.00 ATOM 30 CB ALA A 6 10.737 10.167 24.905 1.00 1.00 ATOM 31 N ALA A 7 12.827 9.712 22.642 1.00 1.00 ATOM 32 CA ALA A 7 13.466 10.091 21.393 1.00 1.00 ATOM 33 C ALA A 7 13.419 8.910 20.422 1.00 1.00 ATOM 34 O ALA A 7 13.062 9.072 19.256 1.00 1.00 ATOM 35 CB ALA A 7 14.895 10.560 21.671 1.00 1.00 ATOM 36 N ALA A 8 13.784 7.745 20.939 1.00 1.00 ATOM 37 CA ALA A 8 13.787 6.537 20.132 1.00 1.00 ATOM 38 C ALA A 8 12.385 6.301 19.568 1.00 1.00 ATOM 39 O ALA A 8 12.227 6.026 18.379 1.00 1.00 ATOM 40 CB ALA A 8 14.281 5.360 20.976 1.00 1.00 ATOM 41 N ALA A 9 11.400 6.417 20.448 1.00 1.00 ATOM 42 CA ALA A 9 10.016 6.221 20.052 1.00 1.00 ATOM 43 C ALA A 9 9.667 7.200 18.929 1.00 1.00 ATOM 44 O ALA A 9 9.078 6.812 17.922 1.00 1.00 ATOM 45 CB ALA A 9 9.108 6.384 21.272 1.00 1.00 ATOM 46 N ALA A 10 10.045 8.453 19.142 1.00 1.00 ATOM 47 CA ALA A 10 9.780 9.491 18.160 1.00 1.00 ATOM 48 C ALA A 10 10.418 9.101 16.826 1.00 1.00 ATOM 49 O ALA A 10 9.781 9.190 15.778 1.00 1.00 ATOM 50 CB ALA A 10 10.295 10.833 18.684 1.00 1.00 ATOM 51 N ALA A 11 11.671 8.677 16.908 1.00 1.00 ATOM 52 CA ALA A 11 12.404 8.273 15.720 1.00 1.00 ATOM 53 C ALA A 11 11.645 7.145 15.017 1.00 1.00 ATOM 54 O ALA A 11 11.456 7.181 13.802 1.00 1.00 ATOM 55 CB ALA A 11 13.825 7.865 16.110 1.00 1.00 ATOM 56 N ALA A 12 11.231 6.169 15.812 1.00 1.00 ATOM 57 CA ALA A 12 10.497 5.033 15.282 1.00 1.00 ATOM 58 C ALA A 12 9.237 5.531 14.571 1.00 1.00 ATOM 59 O ALA A 12 8.940 5.109 13.454 1.00 1.00 ATOM 60 CB ALA A 12 10.179 4.055 16.415 1.00 1.00 ATOM 61 N ALA A 13 8.529 6.424 15.248 1.00 1.00 ATOM 62 CA ALA A 13 7.308 6.985 14.695 1.00 1.00 ATOM 63 C ALA A 13 7.620 7.655 13.355 1.00 1.00 ATOM 64 O ALA A 13 6.912 7.445 12.371 1.00 1.00 ATOM 65 CB ALA A 13 6.690 7.956 15.702 1.00 1.00 ATOM 66 N ALA A 14 8.682 8.449 13.360 1.00 1.00 ATOM 67 CA ALA A 14 9.096 9.150 12.157 1.00 1.00 ATOM 68 C ALA A 14 9.362 8.134 11.044 1.00 1.00 ATOM 69 O ALA A 14 8.905 8.309 9.916 1.00 1.00 ATOM 70 CB ALA A 14 10.322 10.012 12.466 1.00 1.00 ATOM 71 N ALA A 15 10.101 7.093 11.402 1.00 1.00 ATOM 72 CA ALA A 15 10.433 6.049 10.448 1.00 1.00 ATOM 73 C ALA A 15 9.143 5.449 9.885 1.00 1.00 ATOM 74 O ALA A 15 9.009 5.277 8.675 1.00 1.00 ATOM 75 CB ALA A 15 11.317 5.000 11.126 1.00 1.00 ATOM 76 N ALA A 16 8.224 5.147 10.792 1.00 1.00 ATOM 77 CA ALA A 16 6.949 4.570 10.401 1.00 1.00 ATOM 78 C ALA A 16 6.247 5.511 9.419 1.00 1.00 ATOM 79 O ALA A 16 5.751 5.075 8.382 1.00 1.00 ATOM 80 CB ALA A 16 6.108 4.296 11.649 1.00 1.00 ATOM 81 N ALA A 17 6.229 6.786 9.782 1.00 1.00 ATOM 82 CA ALA A 17 5.597 7.792 8.946 1.00 1.00 ATOM 83 C ALA A 17 6.246 7.780 7.561 1.00 1.00 ATOM 84 O ALA A 17 5.553 7.783 6.545 1.00 1.00 ATOM 85 CB ALA A 17 5.699 9.159 9.626 1.00 1.00 ATOM 86 N ALA A 18 7.572 7.767 7.564 1.00 1.00 ATOM 87 CA ALA A 18 8.323 7.754 6.320 1.00 1.00 ATOM 88 C ALA A 18 7.913 6.533 5.494 1.00 1.00 ATOM 89 O ALA A 18 7.651 6.647 4.298 1.00 1.00 ATOM 90 CB ALA A 18 9.821 7.774 6.628 1.00 1.00 ATOM 91 N ALA A 19 7.870 5.391 6.166 1.00 1.00 ATOM 92 CA ALA A 19 7.495 4.151 5.510 1.00 1.00 ATOM 93 C ALA A 19 6.104 4.304 4.892 1.00 1.00 ATOM 94 O ALA A 19 5.889 3.940 3.737 1.00 1.00 ATOM 95 CB ALA A 19 7.564 3.000 6.515 1.00 1.00 ATOM 96 N ALA A 20 5.194 4.843 5.691 1.00 1.00 ATOM 97 CA ALA A 20 3.829 5.050 5.238 1.00 1.00 ATOM 98 C ALA A 20 3.838 5.933 3.988 1.00 1.00 ATOM 99 O ALA A 20 3.175 5.625 3.000 1.00 1.00 ATOM 100 CB ALA A 20 3.000 5.653 6.373 1.00 1.00 TER ATOM 1 N ALA B 1 -22.152 -6.839 15.994 1.00 1.00 N ATOM 2 CA ALA B 1 -21.094 -7.557 15.303 1.00 1.00 C ATOM 3 C ALA B 1 -20.690 -6.780 14.049 1.00 1.00 C ATOM 4 O ALA B 1 -19.504 -6.581 13.791 1.00 1.00 O ATOM 5 CB ALA B 1 -21.565 -8.977 14.984 1.00 1.00 C ATOM 6 N ALA B 2 -21.701 -6.360 13.301 1.00 1.00 N ATOM 7 CA ALA B 2 -21.466 -5.609 12.080 1.00 1.00 C ATOM 8 C ALA B 2 -20.661 -4.349 12.407 1.00 1.00 C ATOM 9 O ALA B 2 -19.682 -4.039 11.730 1.00 1.00 O ATOM 10 CB ALA B 2 -22.804 -5.288 11.412 1.00 1.00 C ATOM 11 N ALA B 3 -21.104 -3.657 13.448 1.00 1.00 N ATOM 12 CA ALA B 3 -20.437 -2.438 13.873 1.00 1.00 C ATOM 13 C ALA B 3 -18.972 -2.748 14.193 1.00 1.00 C ATOM 14 O ALA B 3 -18.073 -2.030 13.760 1.00 1.00 O ATOM 15 CB ALA B 3 -21.180 -1.840 15.068 1.00 1.00 C ATOM 16 N ALA B 4 -18.780 -3.819 14.950 1.00 1.00 N ATOM 17 CA ALA B 4 -17.441 -4.233 15.332 1.00 1.00 C ATOM 18 C ALA B 4 -16.607 -4.478 14.073 1.00 1.00 C ATOM 19 O ALA B 4 -15.472 -4.014 13.973 1.00 1.00 O ATOM 20 CB ALA B 4 -17.525 -5.471 16.226 1.00 1.00 C ATOM 21 N ALA B 5 -17.204 -5.207 13.140 1.00 1.00 N ATOM 22 CA ALA B 5 -16.531 -5.519 11.891 1.00 1.00 C ATOM 23 C ALA B 5 -16.137 -4.218 11.189 1.00 1.00 C ATOM 24 O ALA B 5 -15.005 -4.073 10.730 1.00 1.00 O ATOM 25 CB ALA B 5 -17.439 -6.396 11.026 1.00 1.00 C ATOM 26 N ALA B 6 -17.094 -3.303 11.129 1.00 1.00 N ATOM 27 CA ALA B 6 -16.860 -2.018 10.491 1.00 1.00 C ATOM 28 C ALA B 6 -15.683 -1.320 11.175 1.00 1.00 C ATOM 29 O ALA B 6 -14.785 -0.811 10.506 1.00 1.00 O ATOM 30 CB ALA B 6 -18.142 -1.183 10.541 1.00 1.00 C ATOM 31 N ALA B 7 -15.725 -1.320 12.499 1.00 1.00 N ATOM 32 CA ALA B 7 -14.673 -0.693 13.281 1.00 1.00 C ATOM 33 C ALA B 7 -13.329 -1.331 12.924 1.00 1.00 C ATOM 34 O ALA B 7 -12.346 -0.630 12.688 1.00 1.00 O ATOM 35 CB ALA B 7 -14.999 -0.817 14.770 1.00 1.00 C ATOM 36 N ALA B 8 -13.329 -2.657 12.894 1.00 1.00 N ATOM 37 CA ALA B 8 -12.122 -3.397 12.569 1.00 1.00 C ATOM 38 C ALA B 8 -11.620 -2.967 11.190 1.00 1.00 C ATOM 39 O ALA B 8 -10.432 -2.697 11.012 1.00 1.00 O ATOM 40 CB ALA B 8 -12.408 -4.898 12.643 1.00 1.00 C ATOM 41 N ALA B 9 -12.550 -2.916 10.246 1.00 1.00 N ATOM 42 CA ALA B 9 -12.216 -2.522 8.888 1.00 1.00 C ATOM 43 C ALA B 9 -11.586 -1.127 8.905 1.00 1.00 C ATOM 44 O ALA B 9 -10.556 -0.899 8.274 1.00 1.00 O ATOM 45 CB ALA B 9 -13.471 -2.585 8.015 1.00 1.00 C ATOM 46 N ALA B 10 -12.235 -0.230 9.634 1.00 1.00 N ATOM 47 CA ALA B 10 -11.751 1.136 9.743 1.00 1.00 C ATOM 48 C ALA B 10 -10.325 1.126 10.295 1.00 1.00 C ATOM 49 O ALA B 10 -9.444 1.800 9.765 1.00 1.00 O ATOM 50 CB ALA B 10 -12.709 1.950 10.615 1.00 1.00 C ATOM 51 N ALA B 11 -10.141 0.352 11.355 1.00 1.00 N ATOM 52 CA ALA B 11 -8.836 0.244 11.987 1.00 1.00 C ATOM 53 C ALA B 11 -7.814 -0.240 10.956 1.00 1.00 C ATOM 54 O ALA B 11 -6.725 0.320 10.844 1.00 1.00 O ATOM 55 CB ALA B 11 -8.929 -0.685 13.197 1.00 1.00 C ATOM 56 N ALA B 12 -8.202 -1.278 10.228 1.00 1.00 N ATOM 57 CA ALA B 12 -7.334 -1.844 9.210 1.00 1.00 C ATOM 58 C ALA B 12 -6.968 -0.759 8.196 1.00 1.00 C ATOM 59 O ALA B 12 -5.801 -0.605 7.838 1.00 1.00 O ATOM 60 CB ALA B 12 -8.025 -3.044 8.558 1.00 1.00 C ATOM 61 N ALA B 13 -7.989 -0.034 7.760 1.00 1.00 N ATOM 62 CA ALA B 13 -7.790 1.033 6.794 1.00 1.00 C ATOM 63 C ALA B 13 -6.790 2.046 7.357 1.00 1.00 C ATOM 64 O ALA B 13 -5.859 2.456 6.666 1.00 1.00 O ATOM 65 CB ALA B 13 -9.137 1.671 6.453 1.00 1.00 C ATOM 66 N ALA B 14 -7.019 2.421 8.609 1.00 1.00 N ATOM 67 CA ALA B 14 -6.150 3.378 9.272 1.00 1.00 C ATOM 68 C ALA B 14 -4.715 2.846 9.270 1.00 1.00 C ATOM 69 O ALA B 14 -3.779 3.573 8.941 1.00 1.00 O ATOM 70 CB ALA B 14 -6.671 3.645 10.685 1.00 1.00 C ATOM 71 N ALA B 15 -4.587 1.579 9.641 1.00 1.00 N ATOM 72 CA ALA B 15 -3.283 0.942 9.685 1.00 1.00 C ATOM 73 C ALA B 15 -2.633 1.020 8.302 1.00 1.00 C ATOM 74 O ALA B 15 -1.464 1.381 8.180 1.00 1.00 O ATOM 75 CB ALA B 15 -3.435 -0.499 10.177 1.00 1.00 C ATOM 76 N ALA B 16 -3.422 0.677 7.293 1.00 1.00 N ATOM 77 CA ALA B 16 -2.938 0.705 5.923 1.00 1.00 C ATOM 78 C ALA B 16 -2.451 2.116 5.587 1.00 1.00 C ATOM 79 O ALA B 16 -1.367 2.286 5.031 1.00 1.00 O ATOM 80 CB ALA B 16 -4.046 0.230 4.981 1.00 1.00 C ATOM 81 N ALA B 17 -3.276 3.092 5.939 1.00 1.00 N ATOM 82 CA ALA B 17 -2.942 4.482 5.681 1.00 1.00 C ATOM 83 C ALA B 17 -1.614 4.818 6.361 1.00 1.00 C ATOM 84 O ALA B 17 -0.733 5.421 5.750 1.00 1.00 O ATOM 85 CB ALA B 17 -4.085 5.379 6.161 1.00 1.00 C ATOM 86 N ALA B 18 -1.510 4.411 7.619 1.00 1.00 N ATOM 87 CA ALA B 18 -0.302 4.661 8.388 1.00 1.00 C ATOM 88 C ALA B 18 0.895 4.040 7.667 1.00 1.00 C ATOM 89 O ALA B 18 1.932 4.682 7.509 1.00 1.00 O ATOM 90 CB ALA B 18 -0.478 4.114 9.806 1.00 1.00 C ATOM 91 N ALA B 19 0.713 2.795 7.249 1.00 1.00 N ATOM 92 CA ALA B 19 1.764 2.080 6.547 1.00 1.00 C ATOM 93 C ALA B 19 2.167 2.867 5.298 1.00 1.00 C ATOM 94 O ALA B 19 3.353 3.063 5.038 1.00 1.00 O ATOM 95 CB ALA B 19 1.287 0.665 6.216 1.00 1.00 C ATOM 96 N ALA B 20 1.155 3.296 4.558 1.00 1.00 N ATOM 97 CA ALA B 20 1.387 4.059 3.343 1.00 1.00 C ATOM 98 C ALA B 20 2.199 5.312 3.678 1.00 1.00 C ATOM 99 O ALA B 20 3.175 5.625 3.000 1.00 1.00 O ATOM 100 CB ALA B 20 0.048 4.389 2.683 1.00 1.00 C END """ pdb_str_3 = """ CRYST1 50.273 31.111 38.194 90.00 90.00 90.00 P 1 ATOM 1 N ALA A 1 45.103 22.406 32.854 1.00 1.00 ATOM 2 CA ALA A 1 44.740 21.164 32.193 1.00 1.00 ATOM 3 C ALA A 1 43.346 21.306 31.578 1.00 1.00 ATOM 4 O ALA A 1 43.133 20.945 30.422 1.00 1.00 ATOM 5 CB ALA A 1 44.821 20.010 33.194 1.00 1.00 ATOM 6 N ALA A 2 42.432 21.834 32.380 1.00 1.00 ATOM 7 CA ALA A 2 41.065 22.029 31.929 1.00 1.00 ATOM 8 C ALA A 2 41.064 22.917 30.683 1.00 1.00 ATOM 9 O ALA A 2 40.403 22.606 29.694 1.00 1.00 ATOM 10 CB ALA A 2 40.231 22.620 33.067 1.00 1.00 ATOM 11 N ALA A 3 41.815 24.006 30.772 1.00 1.00 ATOM 12 CA ALA A 3 41.909 24.941 29.664 1.00 1.00 ATOM 13 C ALA A 3 42.418 24.205 28.422 1.00 1.00 ATOM 14 O ALA A 3 41.862 24.354 27.336 1.00 1.00 ATOM 15 CB ALA A 3 42.812 26.111 30.059 1.00 1.00 ATOM 16 N ALA A 4 43.471 23.427 28.626 1.00 1.00 ATOM 17 CA ALA A 4 44.061 22.667 27.537 1.00 1.00 ATOM 18 C ALA A 4 42.999 21.751 26.925 1.00 1.00 ATOM 19 O ALA A 4 42.854 21.689 25.705 1.00 1.00 ATOM 20 CB ALA A 4 45.273 21.890 28.054 1.00 1.00 ATOM 21 N ALA A 5 42.282 21.062 27.802 1.00 1.00 ATOM 22 CA ALA A 5 41.237 20.153 27.363 1.00 1.00 ATOM 23 C ALA A 5 40.213 20.923 26.527 1.00 1.00 ATOM 24 O ALA A 5 39.820 20.475 25.451 1.00 1.00 ATOM 25 CB ALA A 5 40.605 19.475 28.580 1.00 1.00 ATOM 26 N ALA A 6 39.811 22.071 27.055 1.00 1.00 ATOM 27 CA ALA A 6 38.840 22.908 26.370 1.00 1.00 ATOM 28 C ALA A 6 39.374 23.272 24.983 1.00 1.00 ATOM 29 O ALA A 6 38.655 23.168 23.990 1.00 1.00 ATOM 30 CB ALA A 6 38.541 24.144 27.222 1.00 1.00 TER ATOM 1 N ALA B 1 5.652 7.138 18.311 1.00 1.00 N ATOM 2 CA ALA B 1 6.710 6.420 17.620 1.00 1.00 C ATOM 3 C ALA B 1 7.114 7.197 16.366 1.00 1.00 C ATOM 4 O ALA B 1 8.300 7.396 16.108 1.00 1.00 O ATOM 5 CB ALA B 1 6.239 5.000 17.301 1.00 1.00 C ATOM 6 N ALA B 2 6.103 7.617 15.618 1.00 1.00 N ATOM 7 CA ALA B 2 6.338 8.368 14.397 1.00 1.00 C ATOM 8 C ALA B 2 7.143 9.628 14.724 1.00 1.00 C ATOM 9 O ALA B 2 8.122 9.938 14.047 1.00 1.00 O ATOM 10 CB ALA B 2 5.000 8.689 13.729 1.00 1.00 C ATOM 11 N ALA B 3 6.700 10.320 15.765 1.00 1.00 N ATOM 12 CA ALA B 3 7.367 11.539 16.190 1.00 1.00 C ATOM 13 C ALA B 3 8.832 11.229 16.510 1.00 1.00 C ATOM 14 O ALA B 3 9.731 11.947 16.077 1.00 1.00 O ATOM 15 CB ALA B 3 6.624 12.137 17.385 1.00 1.00 C ATOM 16 N ALA B 4 9.024 10.158 17.267 1.00 1.00 N ATOM 17 CA ALA B 4 10.363 9.744 17.649 1.00 1.00 C ATOM 18 C ALA B 4 11.197 9.499 16.390 1.00 1.00 C ATOM 19 O ALA B 4 12.332 9.963 16.290 1.00 1.00 O ATOM 20 CB ALA B 4 10.279 8.506 18.543 1.00 1.00 C ATOM 21 N ALA B 5 10.600 8.770 15.457 1.00 1.00 N ATOM 22 CA ALA B 5 11.273 8.458 14.208 1.00 1.00 C ATOM 23 C ALA B 5 11.667 9.759 13.506 1.00 1.00 C ATOM 24 O ALA B 5 12.799 9.904 13.047 1.00 1.00 O ATOM 25 CB ALA B 5 10.365 7.581 13.343 1.00 1.00 C ATOM 26 N ALA B 6 10.710 10.674 13.446 1.00 1.00 N ATOM 27 CA ALA B 6 10.944 11.959 12.808 1.00 1.00 C ATOM 28 C ALA B 6 12.121 12.657 13.492 1.00 1.00 C ATOM 29 O ALA B 6 13.019 13.166 12.823 1.00 1.00 O ATOM 30 CB ALA B 6 9.662 12.794 12.858 1.00 1.00 C TER END """ pdb_str_4 = """ CRYST1 18.000 18.000 18.000 90.00 90.00 90.00 P 1 ATOM 0 O HOH A 0 5.000 5.000 5.000 1.00 40.00 O ATOM 2 O HOH A 2 5.000 7.000 7.000 1.00 40.00 O ATOM 4 O HOH A 4 5.000 9.000 9.000 1.00 40.00 O ATOM 6 O HOH A 6 5.000 11.000 11.000 1.00 40.00 O ATOM 8 O HOH A 8 5.000 13.000 13.000 1.00 40.00 O TER ATOM 0 O HOH B 0 5.000 5.000 5.000 1.00 40.00 O ATOM 2 O HOH B 2 7.000 5.000 7.000 1.00 40.00 O ATOM 4 O HOH B 4 9.000 5.000 9.000 1.00 40.00 O ATOM 6 O HOH B 6 11.000 5.000 11.000 1.00 40.00 O ATOM 8 O HOH B 8 13.000 5.000 13.000 1.00 40.00 O TER ATOM 0 O HOH C 0 5.000 5.000 5.000 1.00 40.00 O ATOM 2 O HOH C 2 7.000 7.000 5.000 1.00 40.00 O ATOM 4 O HOH C 4 9.000 9.000 5.000 1.00 40.00 O ATOM 6 O HOH C 6 11.000 11.000 5.000 1.00 40.00 O ATOM 8 O HOH C 8 13.000 13.000 5.000 1.00 40.00 O TER END """ def run_cmd(fn, log, s1, s2): cmd = " ".join([ "phenix.angle", "%s"%fn, "'%s'"%s1, "'%s'"%s2, ">%s"%log]) easy_run.call(cmd) return float(easy_run.go( command="grep 'Angle :' "+log).stdout_lines[0].split()[2]) def exercise_00(prefix="tst_phenix_angle_cmd_00"): for i, pdb_str in enumerate([pdb_str_1, pdb_str_2, pdb_str_3, pdb_str_4]): prefix_i = prefix + str(i) fn = prefix_i + ".pdb" log = "%s.log"%prefix_i of = open(fn, "w") print >> of, pdb_str of.close() r = run_cmd(fn=fn, log=log, s1="chain A", s2="chain B") if (i==0 or i==1): assert approx_equal(r, 87, 1) elif(i==2): assert approx_equal(r, 90, 1) elif(i==3): assert approx_equal(r, 60, 0.001) else: assert 0 if(i==3): r = run_cmd(fn=fn, log=log, s1="chain A", s2="chain C") assert approx_equal(r, 60, 0.001) r = run_cmd(fn=fn, log=log, s1="chain B", s2="chain C") assert approx_equal(r, 60, 0.001) def exercise_01(prefix="tst_phenix_angle_cmd_01"): fn = prefix + ".pdb" log = "%s.log"%prefix of = open(fn, "w") print >> of, pdb_str_4 of.close() r = run_cmd(fn=fn, log=log, s1="chain A and (resseq 0 or resseq 8)", s2="chain B and (resseq 0 or resseq 8)") assert approx_equal(r, 60, 0.001) if (__name__ == "__main__"): exercise_00() exercise_01()