from __future__ import absolute_import, division, print_function import iotbx.pdb import time from cctbx import maptbx from libtbx.test_utils import approx_equal import mmtbx.masks pdb_str_1 = """ CRYST1 13.475 30.191 11.490 90.00 90.00 90.00 P 1 ATOM 1 N ALA E 1 6.622 27.477 5.274 1.00 50.00 N ATOM 2 CA ALA E 1 6.323 27.055 6.635 1.00 50.00 C ATOM 3 C ALA E 1 5.442 25.808 6.656 1.00 50.00 C ATOM 4 O ALA E 1 5.848 24.796 7.227 1.00 50.00 O ATOM 5 CB ALA E 1 5.675 28.191 7.414 1.00 50.00 C ATOM 6 N ALA E 2 4.256 25.870 6.012 1.00 50.00 N ATOM 7 CA ALA E 2 3.288 24.768 5.916 1.00 50.00 C ATOM 8 C ALA E 2 3.847 23.573 5.125 1.00 50.00 C ATOM 9 O ALA E 2 3.553 22.422 5.462 1.00 50.00 O ATOM 10 CB ALA E 2 2.000 25.267 5.276 1.00 50.00 C ATOM 11 N ALA E 3 4.664 23.856 4.084 1.00 50.00 N ATOM 12 CA ALA E 3 5.313 22.854 3.231 1.00 50.00 C ATOM 13 C ALA E 3 6.391 22.082 3.994 1.00 50.00 C ATOM 14 O ALA E 3 6.616 20.906 3.687 1.00 50.00 O ATOM 15 CB ALA E 3 5.915 23.517 2.000 1.00 50.00 C ATOM 16 N ALA E 4 7.063 22.744 4.976 1.00 50.00 N ATOM 17 CA ALA E 4 8.089 22.116 5.822 1.00 50.00 C ATOM 18 C ALA E 4 7.441 21.043 6.703 1.00 50.00 C ATOM 19 O ALA E 4 7.888 19.897 6.671 1.00 50.00 O ATOM 20 CB ALA E 4 8.785 23.160 6.683 1.00 50.00 C ATOM 21 N ALA E 5 6.338 21.398 7.423 1.00 50.00 N ATOM 22 CA ALA E 5 5.573 20.488 8.298 1.00 50.00 C ATOM 23 C ALA E 5 5.042 19.288 7.513 1.00 50.00 C ATOM 24 O ALA E 5 4.981 18.179 8.048 1.00 50.00 O ATOM 25 CB ALA E 5 4.433 21.233 8.975 1.00 50.00 C ATOM 26 N ALA E 6 4.715 19.518 6.221 1.00 50.00 N ATOM 27 CA ALA E 6 4.258 18.514 5.260 1.00 50.00 C ATOM 28 C ALA E 6 5.440 17.620 4.865 1.00 50.00 C ATOM 29 O ALA E 6 5.361 16.405 5.060 1.00 50.00 O ATOM 30 CB ALA E 6 3.664 19.193 4.032 1.00 50.00 C ATOM 31 N ALA E 7 6.556 18.234 4.374 1.00 50.00 N ATOM 32 CA ALA E 7 7.788 17.543 3.962 1.00 50.00 C ATOM 33 C ALA E 7 8.411 16.694 5.075 1.00 50.00 C ATOM 34 O ALA E 7 8.954 15.625 4.782 1.00 50.00 O ATOM 35 CB ALA E 7 8.806 18.540 3.433 1.00 50.00 C ATOM 36 N ALA E 8 8.327 17.168 6.343 1.00 50.00 N ATOM 37 CA ALA E 8 8.846 16.459 7.515 1.00 50.00 C ATOM 38 C ALA E 8 8.009 15.197 7.768 1.00 50.00 C ATOM 39 O ALA E 8 8.568 14.097 7.858 1.00 50.00 O ATOM 40 CB ALA E 8 8.833 17.368 8.742 1.00 50.00 C ATOM 41 N ALA E 9 6.664 15.357 7.803 1.00 50.00 N ATOM 42 CA ALA E 9 5.716 14.261 7.994 1.00 50.00 C ATOM 43 C ALA E 9 5.754 13.279 6.822 1.00 50.00 C ATOM 44 O ALA E 9 5.654 12.075 7.051 1.00 50.00 O ATOM 45 CB ALA E 9 4.314 14.805 8.193 1.00 50.00 C ATOM 46 N ALA E 10 5.942 13.791 5.578 1.00 50.00 N ATOM 47 CA ALA E 10 6.063 12.985 4.357 1.00 50.00 C ATOM 48 C ALA E 10 7.322 12.116 4.421 1.00 50.00 C ATOM 49 O ALA E 10 7.235 10.910 4.169 1.00 50.00 O ATOM 50 CB ALA E 10 6.105 13.881 3.130 1.00 50.00 C ATOM 51 N ALA E 11 8.480 12.722 4.803 1.00 50.00 N ATOM 52 CA ALA E 11 9.754 12.018 4.967 1.00 50.00 C ATOM 53 C ALA E 11 9.631 10.976 6.089 1.00 50.00 C ATOM 54 O ALA E 11 10.074 9.837 5.908 1.00 50.00 O ATOM 55 CB ALA E 11 10.870 13.004 5.279 1.00 50.00 C ATOM 56 N ALA E 12 8.972 11.356 7.217 1.00 50.00 N ATOM 57 CA ALA E 12 8.721 10.483 8.371 1.00 50.00 C ATOM 58 C ALA E 12 7.851 9.277 7.972 1.00 50.00 C ATOM 59 O ALA E 12 8.201 8.140 8.310 1.00 50.00 O ATOM 60 CB ALA E 12 8.052 11.269 9.490 1.00 50.00 C ATOM 61 N ALA E 13 6.748 9.535 7.215 1.00 50.00 N ATOM 62 CA ALA E 13 5.821 8.516 6.708 1.00 50.00 C ATOM 63 C ALA E 13 6.530 7.563 5.752 1.00 50.00 C ATOM 64 O ALA E 13 6.266 6.360 5.793 1.00 50.00 O ATOM 65 CB ALA E 13 4.636 9.173 6.008 1.00 50.00 C ATOM 66 N ALA E 14 7.437 8.112 4.903 1.00 50.00 N ATOM 67 CA ALA E 14 8.246 7.367 3.939 1.00 50.00 C ATOM 68 C ALA E 14 9.277 6.511 4.676 1.00 50.00 C ATOM 69 O ALA E 14 9.512 5.363 4.286 1.00 50.00 O ATOM 70 CB ALA E 14 8.942 8.329 2.986 1.00 50.00 C ATOM 71 N ALA E 15 9.863 7.069 5.767 1.00 50.00 N ATOM 72 CA ALA E 15 10.847 6.407 6.629 1.00 50.00 C ATOM 73 C ALA E 15 10.213 5.257 7.427 1.00 50.00 C ATOM 74 O ALA E 15 10.922 4.322 7.816 1.00 50.00 O ATOM 75 CB ALA E 15 11.475 7.418 7.573 1.00 50.00 C ATOM 76 N ALA E 16 8.879 5.325 7.652 1.00 50.00 N ATOM 77 CA ALA E 16 8.099 4.317 8.370 1.00 50.00 C ATOM 78 C ALA E 16 7.822 3.106 7.488 1.00 50.00 C ATOM 79 O ALA E 16 7.658 2.000 7.999 1.00 50.00 O ATOM 80 CB ALA E 16 6.790 4.918 8.852 1.00 50.00 C TER END """ pdb_str_2 = """ CRYST1 13.475 30.191 11.490 90.00 90.00 90.00 P 1 ATOM 1 N ALA E 1 11.622 32.477 10.274 1.00 50.00 N ATOM 2 CA ALA E 1 11.323 32.055 11.635 1.00 50.00 C ATOM 3 C ALA E 1 10.442 30.808 11.656 1.00 50.00 C ATOM 4 O ALA E 1 10.848 29.796 12.227 1.00 50.00 O ATOM 5 CB ALA E 1 10.675 33.191 12.414 1.00 50.00 C ATOM 6 N ALA E 2 9.256 30.870 11.012 1.00 50.00 N ATOM 7 CA ALA E 2 8.288 29.768 10.916 1.00 50.00 C ATOM 8 C ALA E 2 8.847 28.573 10.125 1.00 50.00 C ATOM 9 O ALA E 2 8.553 27.422 10.462 1.00 50.00 O ATOM 10 CB ALA E 2 7.000 30.267 10.276 1.00 50.00 C ATOM 11 N ALA E 3 9.664 28.856 9.084 1.00 50.00 N ATOM 12 CA ALA E 3 10.313 27.854 8.231 1.00 50.00 C ATOM 13 C ALA E 3 11.391 27.082 8.994 1.00 50.00 C ATOM 14 O ALA E 3 11.616 25.906 8.687 1.00 50.00 O ATOM 15 CB ALA E 3 10.915 28.517 7.000 1.00 50.00 C ATOM 16 N ALA E 4 12.063 27.744 9.976 1.00 50.00 N ATOM 17 CA ALA E 4 13.089 27.116 10.822 1.00 50.00 C ATOM 18 C ALA E 4 12.441 26.043 11.703 1.00 50.00 C ATOM 19 O ALA E 4 12.888 24.897 11.671 1.00 50.00 O ATOM 20 CB ALA E 4 13.785 28.160 11.683 1.00 50.00 C ATOM 21 N ALA E 5 11.338 26.398 12.423 1.00 50.00 N ATOM 22 CA ALA E 5 10.573 25.488 13.298 1.00 50.00 C ATOM 23 C ALA E 5 10.042 24.288 12.513 1.00 50.00 C ATOM 24 O ALA E 5 9.981 23.179 13.048 1.00 50.00 O ATOM 25 CB ALA E 5 9.433 26.233 13.975 1.00 50.00 C ATOM 26 N ALA E 6 9.715 24.518 11.221 1.00 50.00 N ATOM 27 CA ALA E 6 9.258 23.514 10.260 1.00 50.00 C ATOM 28 C ALA E 6 10.440 22.620 9.865 1.00 50.00 C ATOM 29 O ALA E 6 10.361 21.405 10.060 1.00 50.00 O ATOM 30 CB ALA E 6 8.664 24.193 9.032 1.00 50.00 C ATOM 31 N ALA E 7 11.556 23.234 9.374 1.00 50.00 N ATOM 32 CA ALA E 7 12.788 22.543 8.962 1.00 50.00 C ATOM 33 C ALA E 7 13.411 21.694 10.075 1.00 50.00 C ATOM 34 O ALA E 7 13.954 20.625 9.782 1.00 50.00 O ATOM 35 CB ALA E 7 13.806 23.540 8.433 1.00 50.00 C ATOM 36 N ALA E 8 13.327 22.168 11.343 1.00 50.00 N ATOM 37 CA ALA E 8 13.846 21.459 12.515 1.00 50.00 C ATOM 38 C ALA E 8 13.009 20.197 12.768 1.00 50.00 C ATOM 39 O ALA E 8 13.568 19.097 12.858 1.00 50.00 O ATOM 40 CB ALA E 8 13.833 22.368 13.742 1.00 50.00 C ATOM 41 N ALA E 9 11.664 20.357 12.803 1.00 50.00 N ATOM 42 CA ALA E 9 10.716 19.261 12.994 1.00 50.00 C ATOM 43 C ALA E 9 10.754 18.279 11.822 1.00 50.00 C ATOM 44 O ALA E 9 10.654 17.075 12.051 1.00 50.00 O ATOM 45 CB ALA E 9 9.314 19.805 13.193 1.00 50.00 C ATOM 46 N ALA E 10 10.942 18.791 10.578 1.00 50.00 N ATOM 47 CA ALA E 10 11.063 17.985 9.357 1.00 50.00 C ATOM 48 C ALA E 10 12.322 17.116 9.421 1.00 50.00 C ATOM 49 O ALA E 10 12.235 15.910 9.169 1.00 50.00 O ATOM 50 CB ALA E 10 11.105 18.881 8.130 1.00 50.00 C ATOM 51 N ALA E 11 13.480 17.722 9.803 1.00 50.00 N ATOM 52 CA ALA E 11 14.754 17.018 9.967 1.00 50.00 C ATOM 53 C ALA E 11 14.631 15.976 11.089 1.00 50.00 C ATOM 54 O ALA E 11 15.074 14.837 10.908 1.00 50.00 O ATOM 55 CB ALA E 11 15.870 18.004 10.279 1.00 50.00 C ATOM 56 N ALA E 12 13.972 16.356 12.217 1.00 50.00 N ATOM 57 CA ALA E 12 13.721 15.483 13.371 1.00 50.00 C ATOM 58 C ALA E 12 12.851 14.277 12.972 1.00 50.00 C ATOM 59 O ALA E 12 13.201 13.140 13.310 1.00 50.00 O ATOM 60 CB ALA E 12 13.052 16.269 14.490 1.00 50.00 C ATOM 61 N ALA E 13 11.748 14.535 12.215 1.00 50.00 N ATOM 62 CA ALA E 13 10.821 13.516 11.708 1.00 50.00 C ATOM 63 C ALA E 13 11.530 12.563 10.752 1.00 50.00 C ATOM 64 O ALA E 13 11.266 11.360 10.793 1.00 50.00 O ATOM 65 CB ALA E 13 9.636 14.173 11.008 1.00 50.00 C ATOM 66 N ALA E 14 12.437 13.112 9.903 1.00 50.00 N ATOM 67 CA ALA E 14 13.246 12.367 8.939 1.00 50.00 C ATOM 68 C ALA E 14 14.277 11.511 9.676 1.00 50.00 C ATOM 69 O ALA E 14 14.512 10.363 9.286 1.00 50.00 O ATOM 70 CB ALA E 14 13.942 13.329 7.986 1.00 50.00 C ATOM 71 N ALA E 15 14.863 12.069 10.767 1.00 50.00 N ATOM 72 CA ALA E 15 15.847 11.407 11.629 1.00 50.00 C ATOM 73 C ALA E 15 15.213 10.257 12.427 1.00 50.00 C ATOM 74 O ALA E 15 15.922 9.322 12.816 1.00 50.00 O ATOM 75 CB ALA E 15 16.475 12.418 12.573 1.00 50.00 C ATOM 76 N ALA E 16 13.879 10.325 12.652 1.00 50.00 N ATOM 77 CA ALA E 16 13.099 9.317 13.370 1.00 50.00 C ATOM 78 C ALA E 16 12.822 8.106 12.488 1.00 50.00 C ATOM 79 O ALA E 16 12.658 7.000 12.999 1.00 50.00 O ATOM 80 CB ALA E 16 11.790 9.918 13.852 1.00 50.00 C TER END """ pdb_str_3 = """ CRYST1 23.475 30.191 21.490 90.00 90.00 90.00 P 21 21 21 ATOM 1 N ALA E 1 11.658 32.727 10.658 1.00 50.00 N ATOM 2 CA ALA E 1 11.151 32.395 11.984 1.00 50.00 C ATOM 3 C ALA E 1 10.253 31.164 11.939 1.00 50.00 C ATOM 4 O ALA E 1 10.424 30.229 12.721 1.00 50.00 O ATOM 5 CB ALA E 1 10.402 33.579 12.578 1.00 50.00 C ATOM 6 N ALA E 2 9.294 31.170 11.018 1.00 50.00 N ATOM 7 CA ALA E 2 8.368 30.054 10.869 1.00 50.00 C ATOM 8 C ALA E 2 8.951 28.970 9.969 1.00 50.00 C ATOM 9 O ALA E 2 8.528 27.815 10.019 1.00 50.00 O ATOM 10 CB ALA E 2 7.035 30.542 10.321 1.00 50.00 C ATOM 11 N ALA E 3 9.923 29.350 9.147 1.00 50.00 N ATOM 12 CA ALA E 3 10.566 28.411 8.235 1.00 50.00 C ATOM 13 C ALA E 3 11.651 27.608 8.944 1.00 50.00 C ATOM 14 O ALA E 3 11.988 26.499 8.529 1.00 50.00 O ATOM 15 CB ALA E 3 11.145 29.148 7.037 1.00 50.00 C ATOM 16 N ALA E 4 12.196 28.176 10.015 1.00 50.00 N ATOM 17 CA ALA E 4 13.244 27.515 10.783 1.00 50.00 C ATOM 18 C ALA E 4 12.660 26.464 11.721 1.00 50.00 C ATOM 19 O ALA E 4 13.315 25.472 12.042 1.00 50.00 O ATOM 20 CB ALA E 4 14.053 28.538 11.566 1.00 50.00 C ATOM 21 N ALA E 5 11.425 26.688 12.157 1.00 50.00 N ATOM 22 CA ALA E 5 10.751 25.761 13.059 1.00 50.00 C ATOM 23 C ALA E 5 10.177 24.570 12.298 1.00 50.00 C ATOM 24 O ALA E 5 10.033 23.480 12.851 1.00 50.00 O ATOM 25 CB ALA E 5 9.654 26.477 13.833 1.00 50.00 C ATOM 26 N ALA E 6 9.852 24.787 11.028 1.00 50.00 N ATOM 27 CA ALA E 6 9.294 23.733 10.189 1.00 50.00 C ATOM 28 C ALA E 6 10.390 22.825 9.643 1.00 50.00 C ATOM 29 O ALA E 6 10.148 21.657 9.338 1.00 50.00 O ATOM 30 CB ALA E 6 8.484 24.334 9.051 1.00 50.00 C ATOM 31 N ALA E 7 11.597 23.369 9.521 1.00 50.00 N ATOM 32 CA ALA E 7 12.732 22.609 9.011 1.00 50.00 C ATOM 33 C ALA E 7 13.347 21.738 10.101 1.00 50.00 C ATOM 34 O ALA E 7 13.954 20.706 9.815 1.00 50.00 O ATOM 35 CB ALA E 7 13.777 23.547 8.425 1.00 50.00 C ATOM 36 N ALA E 8 13.185 22.160 11.351 1.00 50.00 N ATOM 37 CA ALA E 8 13.723 21.420 12.485 1.00 50.00 C ATOM 38 C ALA E 8 12.833 20.234 12.842 1.00 50.00 C ATOM 39 O ALA E 8 13.307 19.225 13.364 1.00 50.00 O ATOM 40 CB ALA E 8 13.894 22.339 13.685 1.00 50.00 C ATOM 41 N ALA E 9 11.542 20.363 12.558 1.00 50.00 N ATOM 42 CA ALA E 9 10.583 19.304 12.849 1.00 50.00 C ATOM 43 C ALA E 9 10.585 18.243 11.753 1.00 50.00 C ATOM 44 O ALA E 9 10.271 17.079 12.001 1.00 50.00 O ATOM 45 CB ALA E 9 9.189 19.884 13.027 1.00 50.00 C ATOM 46 N ALA E 10 10.940 18.654 10.540 1.00 50.00 N ATOM 47 CA ALA E 10 10.983 17.741 9.404 1.00 50.00 C ATOM 48 C ALA E 10 12.259 16.906 9.416 1.00 50.00 C ATOM 49 O ALA E 10 12.282 15.782 8.914 1.00 50.00 O ATOM 50 CB ALA E 10 10.864 18.512 8.099 1.00 50.00 C ATOM 51 N ALA E 11 13.320 17.463 9.992 1.00 50.00 N ATOM 52 CA ALA E 11 14.601 16.771 10.070 1.00 50.00 C ATOM 53 C ALA E 11 14.610 15.753 11.206 1.00 50.00 C ATOM 54 O ALA E 11 15.320 14.750 11.147 1.00 50.00 O ATOM 55 CB ALA E 11 15.734 17.771 10.241 1.00 50.00 C ATOM 56 N ALA E 12 13.817 16.020 12.238 1.00 50.00 N ATOM 57 CA ALA E 12 13.732 15.128 13.389 1.00 50.00 C ATOM 58 C ALA E 12 12.813 13.945 13.104 1.00 50.00 C ATOM 59 O ALA E 12 12.964 12.874 13.690 1.00 50.00 O ATOM 60 CB ALA E 12 13.254 15.890 14.615 1.00 50.00 C ATOM 61 N ALA E 13 11.860 14.147 12.200 1.00 50.00 N ATOM 62 CA ALA E 13 10.915 13.099 11.835 1.00 50.00 C ATOM 63 C ALA E 13 11.506 12.164 10.785 1.00 50.00 C ATOM 64 O ALA E 13 11.087 11.013 10.658 1.00 50.00 O ATOM 65 CB ALA E 13 9.614 13.708 11.334 1.00 50.00 C ATOM 66 N ALA E 14 12.482 12.666 10.036 1.00 50.00 N ATOM 67 CA ALA E 14 13.132 11.877 8.996 1.00 50.00 C ATOM 68 C ALA E 14 14.227 10.991 9.580 1.00 50.00 C ATOM 69 O ALA E 14 14.585 9.966 9.000 1.00 50.00 O ATOM 70 CB ALA E 14 13.702 12.787 7.919 1.00 50.00 C ATOM 71 N ALA E 15 14.755 11.392 10.732 1.00 50.00 N ATOM 72 CA ALA E 15 15.809 10.636 11.397 1.00 50.00 C ATOM 73 C ALA E 15 15.227 9.611 12.365 1.00 50.00 C ATOM 74 O ALA E 15 15.925 8.704 12.818 1.00 50.00 O ATOM 75 CB ALA E 15 16.759 11.576 12.124 1.00 50.00 C ATOM 76 N ALA E 16 13.944 9.762 12.677 1.00 50.00 N ATOM 77 CA ALA E 16 13.265 8.851 13.591 1.00 50.00 C ATOM 78 C ALA E 16 12.707 7.641 12.849 1.00 50.00 C ATOM 79 O ALA E 16 12.597 6.552 13.413 1.00 50.00 O ATOM 80 CB ALA E 16 12.157 9.577 14.337 1.00 50.00 C TER """ def exercise(): """ Compare simple mask (maptbx/mask.h) with classic mask. Does not account for site multiplicity due to symmetry. Also, this is an alternative exercise for asu mask. """ for i_pdb, pdb_str in enumerate([pdb_str_1, pdb_str_2, pdb_str_3]): for solvent_radius in [0, 1.0]: print("file %d solvent_raius: %3.1f"%(i_pdb, solvent_radius)) xrs = iotbx.pdb.input(source_info = None, lines = pdb_str).xray_structure_simple() mp = mmtbx.masks.mask_master_params.extract() mp.solvent_radius=solvent_radius mp.shrink_truncation_radius=0.0 mp.grid_step_factor=4 mmtbx_masks_asu_mask_obj = mmtbx.masks.asu_mask( xray_structure = xrs.expand_to_p1(sites_mod_positive=True), # Must be P1 d_min = 1, mask_params = mp) mask_data = mmtbx_masks_asu_mask_obj.mask_data_whole_uc() c1o,c0o,s,csf = mask_data.count(1), mask_data.count(0), mask_data.size(),\ mmtbx_masks_asu_mask_obj.asu_mask.contact_surface_fraction assert c1o+c0o==s f1o, f0o = c1o*100./s, c0o*100./s print(" old", f1o, f0o, csf) mask_data = maptbx.mask( xray_structure = xrs, # Expanded to P1 internally n_real = mask_data.focus(), solvent_radius = solvent_radius) c1n, c0n, s = mask_data.count(1), mask_data.count(0), mask_data.size() assert c1n+c0n==s f1n, f0n = c1n*100./s, c0n*100./s print(" new:", f1n, f0n) assert approx_equal(f1o, f1n, 1) assert approx_equal(f0o, f0n, 1) assert approx_equal(f1o, csf*100, 1) if (__name__ == "__main__"): t0 = time.time() exercise() print("Total time: %-8.4f"%(time.time()-t0)) print("OK")