from __future__ import absolute_import, division, print_function from six.moves import cStringIO as StringIO from mmtbx.validation.chain_comparison import run def remove_blank(text): return text.replace(" ","").replace("\n","") model=""" CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4 ATOM 9 CA LYS 4 109.976 18.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP 5 109.182 21.755 43.110 1.00 47.90 P9 ATOM 25 CA VAL 6 110.823 23.654 40.250 1.00 46.89 P9 ATOM 32 CA MET 7 108.936 26.802 39.218 1.00 45.06 P9 ATOM 40 CA SER 8 105.419 28.211 39.036 1.00 41.81 P9 ATOM 46 CA THR 9 103.906 27.616 35.600 1.00 37.71 P9 ATOM 53 CA LYS 10 103.277 30.858 33.696 1.00 33.20 P9 ATOM 62 CA TYR 11 100.215 31.269 31.467 1.00 29.03 P9 ATOM 74 CA VAL 12 98.628 33.636 28.957 1.00 24.81 P9 ATOM 81 CA GLU 13 95.372 33.451 27.024 1.00 21.62 P9 ATOM 90 CA ALA 14 95.648 31.766 23.627 1.00 21.34 P9 ATOM 95 CA GLY 15 94.222 34.881 22.004 1.00 22.33 P9 ATOM 99 CA GLU 16 97.221 36.890 23.214 1.00 23.17 P9 ATOM 108 CA LEU 17 99.807 34.753 21.414 1.00 23.42 P9 ATOM 116 CA LYS 18 101.429 36.062 18.237 1.00 24.53 P9 ATOM 125 CA GLU 19 103.948 34.832 15.691 1.00 24.34 P9 ATOM 134 CA GLY 20 107.227 34.699 17.578 1.00 22.47 P9 ATOM 138 CA SER 21 105.632 33.977 20.956 1.00 20.20 P9 ATOM 144 CA TYR 22 106.668 30.890 22.912 1.00 19.09 P9 ATOM 156 CA VAL 23 104.283 28.225 24.176 1.00 18.63 P9 ATOM 163 CA VAL 24 104.403 24.711 25.602 1.00 16.73 P9 ATOM 170 CA ILE 25 102.485 22.073 23.645 1.00 16.21 P9 ATOM 178 CA ASP 26 102.424 18.531 25.042 1.00 17.02 P9 ATOM 186 CA GLY 27 105.535 19.131 27.135 1.00 19.18 P9 ATOM 190 CA GLU 28 107.647 20.739 24.398 1.00 18.42 P9 ATOM 200 CA PRO 29 108.490 24.457 24.454 1.00 17.13 P9 ATOM 206 CA CYS 30 107.738 25.793 20.958 1.00 18.27 P9 ATOM 212 CA ARG 31 108.013 29.010 18.950 1.00 18.81 P9 ATOM 223 CA VAL 32 104.720 30.074 17.348 1.00 18.68 P9 ATOM 230 CA VAL 33 104.990 30.324 13.554 1.00 21.62 P9 ATOM 237 CA GLU 34 101.337 30.903 12.676 1.00 22.97 P9 ATOM 246 CA ILE 35 97.990 31.567 14.325 1.00 23.13 P9 ATOM 254 CA GLU 36 94.516 31.390 12.807 1.00 22.64 P9 ATOM 263 CA LYS 37 91.314 32.656 14.422 1.00 21.25 P9 ATOM 272 CA SER 38 87.754 31.489 13.758 1.00 20.23 P9 ATOM 278 CA LYS 39 84.259 31.708 15.215 1.00 22.33 P9 ATOM 287 CA THR 40 81.571 29.194 14.236 1.00 25.52 P9 ATOM 294 CA GLY 41 79.184 29.756 17.114 0.93 29.60 P9 ATOM 298 CA LYS 42 76.787 32.652 16.597 0.89 32.20 P9 ATOM 307 CA HIS 43 77.170 33.509 20.288 1.00 31.87 P9 ATOM 317 CA GLY 44 80.141 31.264 20.999 0.65 28.63 P9 ATOM 321 CA SER 45 83.784 31.911 21.813 1.00 23.69 P9 ATOM 327 CA ALA 46 86.373 32.582 19.132 1.00 18.89 P9 ATOM 332 CA LYS 47 88.902 29.776 18.670 1.00 17.38 P9 ATOM 341 CA ALA 48 92.611 29.914 17.899 1.00 17.02 P9 ATOM 346 CA ARG 49 94.612 27.386 15.893 1.00 17.11 P9 ATOM 357 CA ILE 50 98.284 27.635 16.768 1.00 17.68 P9 ATOM 365 CA VAL 51 101.124 26.174 14.718 1.00 17.34 P9 ATOM 372 CA ALA 52 104.518 26.094 16.413 1.00 17.71 P9 ATOM 377 CA VAL 53 107.935 24.470 16.254 1.00 17.54 P9 ATOM 384 CA GLY 54 109.704 22.649 19.055 1.00 18.35 P9 ATOM 388 CA VAL 55 112.688 24.550 20.407 1.00 19.01 P9 ATOM 395 CA PHE 56 114.509 21.294 21.108 1.00 19.90 P9 ATOM 406 CA ASP 57 113.198 18.603 18.749 1.00 21.17 P9 ATOM 414 CA GLY 58 112.293 20.976 15.923 1.00 21.69 P9 ATOM 418 CA GLY 59 108.988 19.187 15.479 1.00 21.62 P9 ATOM 422 CA LYS 60 105.864 20.872 14.151 1.00 20.30 P9 ATOM 431 CA ARG 61 103.024 20.971 16.667 1.00 18.60 P9 ATOM 442 CA THR 62 99.517 22.398 16.607 1.00 17.44 P9 ATOM 449 CA LEU 63 96.998 23.440 19.242 1.00 16.19 P9 ATOM 457 CA SER 64 93.370 24.446 18.716 1.00 15.39 P9 ATOM 463 CA LEU 65 91.433 25.924 21.644 1.00 14.67 P9 ATOM 472 CA PRO 66 89.260 28.905 22.730 1.00 14.79 P9 ATOM 478 CA VAL 67 90.940 32.325 22.634 1.00 15.74 P9 ATOM 485 CA ASP 68 90.325 32.738 26.369 1.00 17.10 P9 ATOM 493 CA ALA 69 91.793 29.371 27.372 1.00 16.26 P9 ATOM 498 CA GLN 70 95.115 29.425 29.223 1.00 18.00 P9 ATOM 507 CA VAL 71 98.237 28.190 27.463 1.00 19.41 P9 ATOM 514 CA GLU 72 101.563 27.596 29.201 1.00 21.29 P9 ATOM 523 CA VAL 73 104.492 29.822 28.262 1.00 21.83 P9 ATOM 531 CA PRO 74 108.047 28.603 28.963 0.94 22.19 P9 ATOM 537 CA ILE 75 110.436 30.660 31.072 1.00 23.67 P9 ATOM 545 CA ILE 76 113.508 31.336 28.943 0.96 24.46 P9 ATOM 553 CA GLU 77 116.735 32.457 30.611 1.00 24.69 P9 ATOM 562 CA LYS 78 119.294 33.935 28.213 1.00 24.12 P9 ATOM 571 CA PHE 79 123.013 34.160 28.959 1.00 21.39 P9 ATOM 582 CA THR 80 126.479 34.196 27.404 1.00 19.30 P9 ATOM 589 CA ALA 81 128.958 31.320 27.436 1.00 17.03 P9 ATOM 594 CA GLN 82 132.421 30.668 25.993 1.00 15.83 P9 ATOM 603 CA ILE 83 133.128 27.536 23.964 1.00 14.35 P9 ATOM 611 CA LEU 84 135.770 25.349 25.639 1.00 14.01 P9 ATOM 619 CA SER 85 135.720 22.442 23.163 1.00 14.77 P9 ATOM 625 CA VAL 86 133.697 21.017 20.292 1.00 15.76 P9 ATOM 632 CA SER 87 133.246 17.344 19.410 1.00 15.97 P9 ATOM 638 CA GLY 88 130.905 15.871 16.836 1.00 16.65 P9 ATOM 642 CA ASP 89 128.352 15.243 19.587 1.00 17.36 P9 ATOM 650 CA VAL 90 128.894 17.746 22.389 1.00 16.73 P9 ATOM 657 CA ILE 91 129.780 21.401 22.870 1.00 16.05 P9 ATOM 665 CA GLN 92 131.584 22.059 26.178 1.00 16.32 P9 ATOM 674 CA LEU 93 130.870 25.590 27.465 1.00 15.69 P9 ATOM 682 CA MET 94 131.982 27.904 30.270 1.00 17.32 P9 ATOM 690 CA ASP 95 129.006 29.830 31.697 1.00 19.94 P9 ATOM 698 CA MET 96 130.333 33.412 31.817 1.00 22.68 P9 ATOM 706 CA ARG 97 128.065 34.204 34.767 1.00 24.59 P9 ATOM 717 CA ASP 98 129.544 31.755 37.283 0.96 24.84 P9 ATOM 725 CA TYR 99 132.285 30.135 35.175 0.99 24.06 P9 ATOM 737 CA LYS 100 130.841 26.625 35.550 1.00 22.14 P9 ATOM 746 CA THR 101 131.149 24.064 32.761 1.00 20.84 P9 ATOM 753 CA ILE 102 127.988 23.035 30.916 1.00 19.78 P9 ATOM 761 CA GLU 103 127.678 20.418 28.177 1.00 19.97 P9 ATOM 770 CA VAL 104 125.251 20.963 25.299 1.00 18.00 P9 ATOM 778 CA PRO 105 124.362 18.242 22.754 1.00 18.24 P9 ATOM 784 CA MET 106 125.166 19.138 19.128 1.00 18.91 P9 ATOM 792 CA LYS 107 121.491 18.558 18.303 1.00 19.94 P9 ATOM 801 CA TYR 108 120.616 21.558 20.496 1.00 20.72 P9 ATOM 813 CA VAL 109 122.621 24.018 18.411 1.00 23.20 P9 ATOM 820 CA GLU 110 120.751 26.260 15.961 1.00 28.03 P9 ATOM 829 CA GLU 111 121.704 25.099 12.460 0.74 31.85 P9 ATOM 838 CA GLU 112 122.954 28.554 11.512 1.00 33.44 P9 ATOM 847 CA ALA 113 125.368 28.615 14.458 1.00 31.90 P9 ATOM 852 CA LYS 114 126.911 25.180 13.906 0.92 31.27 P9 ATOM 861 CA GLY 115 129.136 26.579 11.174 1.00 30.17 P9 ATOM 865 CA ARG 116 130.956 29.004 13.463 1.00 27.89 P9 ATOM 876 CA LEU 117 131.365 26.777 16.514 1.00 25.28 P9 ATOM 884 CA ALA 118 134.998 27.063 17.578 1.00 23.01 P9 ATOM 890 CA PRO 119 136.912 26.997 20.869 1.00 21.21 P9 ATOM 896 CA GLY 120 137.158 30.500 22.308 1.00 21.69 P9 ATOM 900 CA ALA 121 134.046 31.875 20.620 1.00 21.58 P9 ATOM 905 CA GLU 122 131.240 33.298 22.745 1.00 22.41 P9 ATOM 914 CA VAL 123 127.678 32.132 22.205 1.00 20.97 P9 ATOM 921 CA GLU 124 124.171 33.150 23.219 1.00 20.32 P9 ATOM 930 CA VAL 125 122.627 30.323 25.229 1.00 19.82 P9 ATOM 937 CA TRP 126 119.012 29.745 26.239 1.00 21.08 P9 ATOM 951 CA GLN 127 118.027 27.643 29.216 1.00 22.22 P9 ATOM 960 CA ILE 128 114.538 26.200 29.585 1.00 22.80 P9 ATOM 968 CA LEU 129 114.153 24.029 32.671 1.00 24.59 P9 ATOM 976 CA ASP 130 117.058 21.551 32.616 0.99 24.90 P9 ATOM 984 CA ARG 131 117.952 21.918 28.938 1.00 22.57 P9 ATOM 995 CA TYR 132 120.128 24.357 27.016 1.00 21.18 P9 ATOM 1007 CA LYS 133 120.153 25.537 23.432 1.00 21.22 P9 ATOM 1016 CA ILE 134 122.957 27.373 21.662 1.00 20.82 P9 ATOM 1024 CA ILE 135 121.298 30.133 19.637 1.00 24.27 P9 ATOM 1032 CA ARG 136 124.175 31.872 17.866 1.00 28.80 P9 ATOM 1043 CA VAL 137 127.877 32.680 17.955 1.00 32.92 P9 ATOM 1050 CA LYS 138 128.895 35.931 19.718 1.00 36.89 P9 ATOM 1059 CA GLY 139 126.242 36.878 22.264 0.67 38.21 P9 """ query=""" ATOM 2 CA HIS A 7 47.968 37.350 1.343 1.00 30.00 C ATOM 12 CA ILE A 8 46.579 37.684 4.402 1.00 30.00 C ATOM 20 CA LYS A 9 47.784 38.702 7.227 1.00 30.00 C ATOM 29 CA LEU A 10 45.288 36.534 8.774 1.00 30.00 C ATOM 37 CA MET A 11 43.852 36.569 12.293 1.00 30.00 C ATOM 45 CA ASN A 12 42.415 33.671 14.884 1.00 30.00 C ATOM 53 CA ALA U 31 39.285 33.668 16.254 1.00 30.00 UNK C ATOM 58 CA CYS U 32 40.481 30.632 18.193 1.00 30.00 UNK C ATOM 64 CA LYS U 33 38.694 27.705 19.208 1.00 30.00 UNK C ATOM 73 CA GLY U 34 41.530 25.709 20.615 1.00 30.00 UNK C ATOM 77 CA LEU U 35 42.598 23.279 18.933 1.00 30.00 UNK C ATOM 85 CA GLY U 36 45.899 23.083 17.741 1.00 30.00 UNK C ATOM 89 CA HIS U 37 47.964 25.323 17.214 1.00 30.00 UNK C ATOM 99 CA TRP U 41 49.522 32.736 0.687 1.00 30.00 UNK C ATOM 113 CA PRO U 42 46.846 33.404 2.158 1.00 30.00 UNK C ATOM 120 CA GLY U 43 49.716 33.742 4.809 1.00 30.00 UNK C ATOM 124 CA MET U 44 50.275 36.496 3.408 1.00 30.00 UNK C ATOM 132 CA ARG U 51 66.471 31.618 0.165 1.00 30.00 UNK C ATOM 143 CA THR U 52 62.673 32.286 0.000 1.00 30.00 UNK C ATOM 150 CA TRP U 53 60.396 33.791 2.514 1.00 30.00 UNK C ATOM 164 CA PRO U 54 56.975 33.518 4.059 1.00 30.00 UNK C ATOM 171 CA GLY U 55 56.742 37.050 3.683 1.00 30.00 UNK C ATOM 175 CA HIS U 56 58.241 37.385 0.677 1.00 30.00 UNK C ATOM 185 CA GLY U 57 60.259 36.521 -2.061 1.00 30.00 UNK C ATOM 189 CA TRP U 58 63.306 36.585 -0.658 1.00 30.00 UNK C ATOM 203 CA HIS U 59 66.371 36.917 -1.353 1.00 30.00 UNK C ATOM 213 CA ARG U 71 33.885 27.955 5.046 1.00 30.00 UNK C ATOM 224 CA PRO U 72 34.112 31.066 3.070 1.00 30.00 UNK C ATOM 231 CA GLY U 73 37.023 30.068 0.698 1.00 30.00 UNK C ATOM 235 CA ASN U 74 40.330 31.142 0.443 1.00 30.00 UNK C ATOM 243 CA GLY U 75 39.883 28.291 -1.998 1.00 30.00 UNK C ATOM 247 CA ALA U 76 40.699 29.754 -4.736 1.00 30.00 UNK C ATOM 252 CA TYR U 77 42.908 31.262 -3.328 1.00 30.00 UNK C ATOM 264 CA GLY U 78 44.842 29.020 -1.084 1.00 30.00 UNK C ATOM 268 CA ALA U 79 46.698 27.855 -3.383 1.00 30.00 UNK C ATOM 273 CA VAL U 91 51.081 32.321 8.150 1.00 30.00 UNK C ATOM 280 CA ARG U 92 51.757 33.221 11.457 1.00 30.00 UNK C ATOM 291 CA TYR U 93 53.177 35.451 14.207 1.00 30.00 UNK C ATOM 303 CA GLY U 94 55.930 33.240 16.341 1.00 30.00 UNK C ATOM 307 CA LYS U 95 56.538 31.836 13.500 1.00 30.00 UNK C ATOM 316 CA GLU U 96 53.605 29.086 13.128 1.00 30.00 UNK C ATOM 325 CA TRP U 97 52.331 28.161 9.983 1.00 30.00 UNK C ATOM 339 CA ASP U 98 49.378 26.104 9.729 1.00 30.00 UNK C ATOM 347 CA GLU U 99 47.812 25.689 7.165 1.00 30.00 UNK C ATOM 356 CA GLY U 111 34.962 41.965 -2.040 1.00 30.00 UNK C ATOM 360 CA GLY U 112 34.552 41.382 1.896 1.00 30.00 UNK C ATOM 364 CA PHE U 113 32.652 38.617 2.536 1.00 30.00 UNK C ATOM 375 CA GLY U 114 33.035 35.430 1.690 1.00 30.00 UNK C ATOM 379 CA LEU U 115 31.413 34.883 5.090 1.00 30.00 UNK C ATOM 387 CA SER U 116 29.190 32.919 6.131 1.00 30.00 UNK C ATOM 393 CA LEU U 117 25.231 33.701 6.955 1.00 30.00 UNK C ATOM 401 CA PRO U 118 24.358 32.286 10.112 1.00 30.00 UNK C ATOM 408 CA TYR U 119 26.935 34.425 10.677 1.00 30.00 UNK C ATOM 420 CA GLY U 131 38.770 41.005 4.746 1.00 30.00 UNK C ATOM 424 CA GLN U 132 39.116 39.652 2.001 1.00 30.00 UNK C ATOM 433 CA TRP U 133 36.781 37.434 3.332 1.00 30.00 UNK C ATOM 447 CA TYR U 134 37.051 34.918 6.022 1.00 30.00 UNK C ATOM 459 CA ALA U 135 34.718 33.052 8.152 1.00 30.00 UNK C ATOM 464 CA CYS U 136 35.953 32.045 10.889 1.00 30.00 UNK C ATOM 470 CA GLY U 137 37.106 29.541 8.056 1.00 30.00 UNK C ATOM 474 CA TYR U 138 39.250 29.269 5.412 1.00 30.00 UNK C """ model1=""" CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4 ATOM 1 CA LYS A 4 109.976 18.221 44.266 1.00 48.61 P9 ATOM 2 CA TRP A 5 109.182 21.755 43.110 1.00 47.90 P9 ATOM 3 CA VAL A 6 110.823 23.654 40.250 1.00 46.89 P9 ATOM 4 CA MET A 7 108.936 26.802 39.218 1.00 45.06 P9 ATOM 5 CA SER A 8 105.419 28.211 39.036 1.00 41.81 P9 ATOM 6 CA THR A 9 103.906 27.616 35.600 1.00 37.71 P9 ATOM 7 CA LYS A 10 103.277 30.858 33.696 1.00 33.20 P9 ATOM 8 CA TYR A 11 100.215 31.269 31.467 1.00 29.03 P9 ATOM 9 CA VAL A 12 98.628 33.636 28.957 1.00 24.81 P9 ATOM 10 CA GLU A 13 95.372 33.451 27.024 1.00 21.62 P9 ATOM 11 CA ALA A 14 95.648 31.766 23.627 1.00 21.34 P9 ATOM 12 CA GLY A 15 94.222 34.881 22.004 1.00 22.33 P9 ATOM 13 CA GLU A 16 97.221 36.890 23.214 1.00 23.17 P9 ATOM 14 CA LEU A 17 99.807 34.753 21.414 1.00 23.42 P9 ATOM 15 CA LYS A 18 101.429 36.062 18.237 1.00 24.53 P9 ATOM 16 CA GLU A 19 103.948 34.832 15.691 1.00 24.34 P9 ATOM 17 CA GLY A 20 107.227 34.699 17.578 1.00 22.47 P9 ATOM 18 CA SER A 21 105.632 33.977 20.956 1.00 20.20 P9 ATOM 19 CA TYR A 22 106.668 30.890 22.912 1.00 19.09 P9 ATOM 20 CA VAL A 23 104.283 28.225 24.176 1.00 18.63 P9 ATOM 21 CA VAL A 24 104.403 24.711 25.602 1.00 16.73 P9 ATOM 22 CA ILE A 25 102.485 22.073 23.645 1.00 16.21 P9 ATOM 23 CA ASP A 26 102.424 18.531 25.042 1.00 17.02 P9 ATOM 24 CA GLY A 27 105.535 19.131 27.135 1.00 19.18 P9 ATOM 25 CA GLU A 28 107.647 20.739 24.398 1.00 18.42 P9 ATOM 26 CA PRO A 29 108.490 24.457 24.454 1.00 17.13 P9 ATOM 27 CA CYS A 30 107.738 25.793 20.958 1.00 18.27 P9 ATOM 28 CA ARG A 31 108.013 29.010 18.950 1.00 18.81 P9 ATOM 29 CA VAL A 32 104.720 30.074 17.348 1.00 18.68 P9 ATOM 30 CA VAL A 33 104.990 30.324 13.554 1.00 21.62 P9 ATOM 31 CA GLU A 34 101.337 30.903 12.676 1.00 22.97 P9 ATOM 32 CA ILE A 35 97.990 31.567 14.325 1.00 23.13 P9 ATOM 33 CA GLU A 36 94.516 31.390 12.807 1.00 22.64 P9 ATOM 34 CA LYS A 37 91.314 32.656 14.422 1.00 21.25 P9 ATOM 35 CA SER A 38 87.754 31.489 13.758 1.00 20.23 P9 ATOM 36 CA LYS A 39 84.259 31.708 15.215 1.00 22.33 P9 ATOM 37 CA THR A 40 81.571 29.194 14.236 1.00 25.52 P9 ATOM 38 CA GLY A 41 79.184 29.756 17.114 0.93 29.60 P9 ATOM 39 CA LYS A 42 76.787 32.652 16.597 0.89 32.20 P9 ATOM 40 CA HIS A 43 77.170 33.509 20.288 1.00 31.87 P9 ATOM 41 CA GLY A 44 80.141 31.264 20.999 0.65 28.63 P9 ATOM 42 CA SER A 45 83.784 31.911 21.813 1.00 23.69 P9 ATOM 43 CA ALA A 46 86.373 32.582 19.132 1.00 18.89 P9 ATOM 44 CA LYS A 47 88.902 29.776 18.670 1.00 17.38 P9 ATOM 45 CA ALA A 48 92.611 29.914 17.899 1.00 17.02 P9 ATOM 46 CA ARG A 49 94.612 27.386 15.893 1.00 17.11 P9 ATOM 47 CA ILE A 50 98.284 27.635 16.768 1.00 17.68 P9 ATOM 48 CA VAL A 51 101.124 26.174 14.718 1.00 17.34 P9 ATOM 49 CA ALA A 52 104.518 26.094 16.413 1.00 17.71 P9 ATOM 50 CA VAL A 53 107.935 24.470 16.254 1.00 17.54 P9 ATOM 51 CA GLY A 54 109.704 22.649 19.055 1.00 18.35 P9 ATOM 52 CA VAL A 55 112.688 24.550 20.407 1.00 19.01 P9 ATOM 53 CA PHE A 56 114.509 21.294 21.108 1.00 19.90 P9 ATOM 54 CA ASP A 57 113.198 18.603 18.749 1.00 21.17 P9 ATOM 55 CA GLY A 58 112.293 20.976 15.923 1.00 21.69 P9 ATOM 56 CA GLY A 59 108.988 19.187 15.479 1.00 21.62 P9 ATOM 57 CA LYS A 60 105.864 20.872 14.151 1.00 20.30 P9 ATOM 58 CA ARG A 61 103.024 20.971 16.667 1.00 18.60 P9 ATOM 59 CA THR A 62 99.517 22.398 16.607 1.00 17.44 P9 ATOM 60 CA LEU A 63 96.998 23.440 19.242 1.00 16.19 P9 ATOM 61 CA SER A 64 93.370 24.446 18.716 1.00 15.39 P9 ATOM 62 CA LEU A 65 91.433 25.924 21.644 1.00 14.67 P9 ATOM 63 CA PRO A 66 89.260 28.905 22.730 1.00 14.79 P9 ATOM 64 CA VAL A 67 90.940 32.325 22.634 1.00 15.74 P9 ATOM 65 CA ASP A 68 90.325 32.738 26.369 1.00 17.10 P9 ATOM 66 CA ALA A 69 91.793 29.371 27.372 1.00 16.26 P9 ATOM 67 CA GLN A 70 95.115 29.425 29.223 1.00 18.00 P9 ATOM 68 CA VAL A 71 98.237 28.190 27.463 1.00 19.41 P9 ATOM 69 CA GLU A 72 101.563 27.596 29.201 1.00 21.29 P9 ATOM 70 CA VAL A 73 104.492 29.822 28.262 1.00 21.83 P9 ATOM 71 CA PRO A 74 108.047 28.603 28.963 0.94 22.19 P9 ATOM 72 CA ILE A 75 110.436 30.660 31.072 1.00 23.67 P9 ATOM 73 CA ILE A 76 113.508 31.336 28.943 0.96 24.46 P9 ATOM 74 CA GLU A 77 116.735 32.457 30.611 1.00 24.69 P9 ATOM 75 CA LYS A 78 119.294 33.935 28.213 1.00 24.12 P9 ATOM 76 CA PHE A 79 123.013 34.160 28.959 1.00 21.39 P9 ATOM 77 CA THR A 80 126.479 34.196 27.404 1.00 19.30 P9 ATOM 78 CA ALA A 81 128.958 31.320 27.436 1.00 17.03 P9 ATOM 79 CA GLN A 82 132.421 30.668 25.993 1.00 15.83 P9 ATOM 80 CA ILE A 83 133.128 27.536 23.964 1.00 14.35 P9 ATOM 81 CA LEU A 84 135.770 25.349 25.639 1.00 14.01 P9 ATOM 82 CA SER A 85 135.720 22.442 23.163 1.00 14.77 P9 ATOM 83 CA VAL A 86 133.697 21.017 20.292 1.00 15.76 P9 ATOM 84 CA SER A 87 133.246 17.344 19.410 1.00 15.97 P9 ATOM 85 CA GLY A 88 130.905 15.871 16.836 1.00 16.65 P9 ATOM 86 CA ASP A 89 128.352 15.243 19.587 1.00 17.36 P9 ATOM 87 CA VAL A 90 128.894 17.746 22.389 1.00 16.73 P9 ATOM 88 CA ILE A 91 129.780 21.401 22.870 1.00 16.05 P9 ATOM 89 CA GLN A 92 131.584 22.059 26.178 1.00 16.32 P9 ATOM 90 CA LEU A 93 130.870 25.590 27.465 1.00 15.69 P9 ATOM 91 CA MET A 94 131.982 27.904 30.270 1.00 17.32 P9 ATOM 92 CA ASP A 95 129.006 29.830 31.697 1.00 19.94 P9 ATOM 93 CA MET A 96 130.333 33.412 31.817 1.00 22.68 P9 ATOM 94 CA ARG A 97 128.065 34.204 34.767 1.00 24.59 P9 ATOM 95 CA ASP A 98 129.544 31.755 37.283 0.96 24.84 P9 ATOM 96 CA TYR A 99 132.285 30.135 35.175 0.99 24.06 P9 ATOM 97 CA LYS A 100 130.841 26.625 35.550 1.00 22.14 P9 ATOM 98 CA THR A 101 131.149 24.064 32.761 1.00 20.84 P9 ATOM 99 CA ILE A 102 127.988 23.035 30.916 1.00 19.78 P9 ATOM 100 CA GLU A 103 127.678 20.418 28.177 1.00 19.97 P9 ATOM 101 CA VAL A 104 125.251 20.963 25.299 1.00 18.00 P9 ATOM 102 CA PRO A 105 124.362 18.242 22.754 1.00 18.24 P9 ATOM 103 CA MET A 106 125.166 19.138 19.128 1.00 18.91 P9 ATOM 104 CA LYS A 107 121.491 18.558 18.303 1.00 19.94 P9 ATOM 105 CA TYR A 108 120.616 21.558 20.496 1.00 20.72 P9 ATOM 106 CA VAL A 109 122.621 24.018 18.411 1.00 23.20 P9 ATOM 107 CA GLU A 110 120.751 26.260 15.961 1.00 28.03 P9 ATOM 108 CA GLU A 111 121.704 25.099 12.460 0.74 31.85 P9 ATOM 109 CA GLU A 112 122.954 28.554 11.512 1.00 33.44 P9 ATOM 110 CA ALA A 113 125.368 28.615 14.458 1.00 31.90 P9 ATOM 111 CA LYS A 114 126.911 25.180 13.906 0.92 31.27 P9 ATOM 112 CA GLY A 115 129.136 26.579 11.174 1.00 30.17 P9 ATOM 113 CA ARG A 116 130.956 29.004 13.463 1.00 27.89 P9 ATOM 114 CA LEU A 117 131.365 26.777 16.514 1.00 25.28 P9 ATOM 115 CA ALA A 118 134.998 27.063 17.578 1.00 23.01 P9 ATOM 116 CA PRO A 119 136.912 26.997 20.869 1.00 21.21 P9 ATOM 117 CA GLY A 120 137.158 30.500 22.308 1.00 21.69 P9 ATOM 118 CA ALA A 121 134.046 31.875 20.620 1.00 21.58 P9 ATOM 119 CA GLU A 122 131.240 33.298 22.745 1.00 22.41 P9 ATOM 120 CA VAL A 123 127.678 32.132 22.205 1.00 20.97 P9 ATOM 121 CA GLU A 124 124.171 33.150 23.219 1.00 20.32 P9 ATOM 122 CA VAL A 125 122.627 30.323 25.229 1.00 19.82 P9 ATOM 123 CA TRP A 126 119.012 29.745 26.239 1.00 21.08 P9 ATOM 124 CA GLN A 127 118.027 27.643 29.216 1.00 22.22 P9 ATOM 125 CA ILE A 128 114.538 26.200 29.585 1.00 22.80 P9 ATOM 126 CA LEU A 129 114.153 24.029 32.671 1.00 24.59 P9 ATOM 127 CA ASP A 130 117.058 21.551 32.616 0.99 24.90 P9 ATOM 128 CA ARG A 131 117.952 21.918 28.938 1.00 22.57 P9 ATOM 129 CA TYR A 132 120.128 24.357 27.016 1.00 21.18 P9 ATOM 130 CA LYS A 133 120.153 25.537 23.432 1.00 21.22 P9 ATOM 131 CA ILE A 134 122.957 27.373 21.662 1.00 20.82 P9 ATOM 132 CA ILE A 135 121.298 30.133 19.637 1.00 24.27 P9 ATOM 133 CA ARG A 136 124.175 31.872 17.866 1.00 28.80 P9 ATOM 134 CA VAL A 137 127.877 32.680 17.955 1.00 32.92 P9 ATOM 135 CA LYS A 138 128.895 35.931 19.718 1.00 36.89 P9 ATOM 136 CA GLY A 139 126.242 36.878 22.264 0.67 38.21 P9 ATOM 1 CA LYS B 4 514.976 423.221 449.266 1.00 48.61 P9 ATOM 2 CA TRP B 5 514.182 426.755 448.110 1.00 47.90 P9 ATOM 3 CA VAL B 6 515.823 428.654 445.250 1.00 46.89 P9 ATOM 4 CA MET B 7 513.936 431.802 444.218 1.00 45.06 P9 ATOM 5 CA SER B 8 510.419 433.211 444.036 1.00 41.81 P9 ATOM 6 CA THR B 9 508.906 432.616 440.600 1.00 37.71 P9 ATOM 7 CA LYS B 10 508.277 435.858 438.696 1.00 33.20 P9 ATOM 8 CA TYR B 11 505.215 436.269 436.467 1.00 29.03 P9 ATOM 9 CA VAL B 12 503.628 438.636 433.957 1.00 24.81 P9 ATOM 10 CA GLU B 13 500.372 438.451 432.024 1.00 21.62 P9 ATOM 11 CA ALA B 14 500.648 436.766 428.627 1.00 21.34 P9 ATOM 12 CA GLY B 15 499.222 439.881 427.004 1.00 22.33 P9 ATOM 13 CA GLU B 16 502.221 441.890 428.214 1.00 23.17 P9 ATOM 14 CA LEU B 17 504.807 439.753 426.414 1.00 23.42 P9 ATOM 15 CA LYS B 18 506.429 441.062 423.237 1.00 24.53 P9 ATOM 16 CA GLU B 19 508.948 439.832 420.691 1.00 24.34 P9 ATOM 17 CA GLY B 20 512.227 439.699 422.578 1.00 22.47 P9 ATOM 18 CA SER B 21 510.632 438.977 425.956 1.00 20.20 P9 ATOM 19 CA TYR B 22 511.668 435.890 427.912 1.00 19.09 P9 ATOM 20 CA VAL B 23 509.283 433.225 429.176 1.00 18.63 P9 ATOM 21 CA VAL B 24 509.403 429.711 430.602 1.00 16.73 P9 ATOM 22 CA ILE B 25 507.485 427.073 428.645 1.00 16.21 P9 ATOM 23 CA ASP B 26 507.424 423.531 430.042 1.00 17.02 P9 ATOM 24 CA GLY B 27 510.535 424.131 432.135 1.00 19.18 P9 ATOM 25 CA GLU B 28 512.647 425.739 429.398 1.00 18.42 P9 ATOM 26 CA PRO B 29 513.490 429.457 429.454 1.00 17.13 P9 ATOM 27 CA CYS B 30 512.738 430.793 425.958 1.00 18.27 P9 ATOM 28 CA ARG B 31 513.013 434.010 423.950 1.00 18.81 P9 ATOM 29 CA VAL B 32 509.720 435.074 422.348 1.00 18.68 P9 ATOM 30 CA VAL B 33 509.990 435.324 418.554 1.00 21.62 P9 ATOM 31 CA GLU B 34 506.337 435.903 417.676 1.00 22.97 P9 ATOM 32 CA ILE B 35 502.990 436.567 419.325 1.00 23.13 P9 ATOM 33 CA GLU B 36 499.516 436.390 417.807 1.00 22.64 P9 ATOM 34 CA LYS B 37 496.314 437.656 419.422 1.00 21.25 P9 ATOM 35 CA SER B 38 492.754 436.489 418.758 1.00 20.23 P9 ATOM 36 CA LYS B 39 489.259 436.708 420.215 1.00 22.33 P9 ATOM 37 CA THR B 40 486.571 434.194 419.236 1.00 25.52 P9 ATOM 38 CA GLY B 41 484.184 434.756 422.114 0.93 29.60 P9 ATOM 39 CA LYS B 42 481.787 437.652 421.597 0.89 32.20 P9 ATOM 40 CA HIS B 43 482.170 438.509 425.288 1.00 31.87 P9 ATOM 41 CA GLY B 44 485.141 436.264 425.999 0.65 28.63 P9 ATOM 42 CA SER B 45 488.784 436.911 426.813 1.00 23.69 P9 ATOM 43 CA ALA B 46 491.373 437.582 424.132 1.00 18.89 P9 ATOM 44 CA LYS B 47 493.902 434.776 423.670 1.00 17.38 P9 ATOM 45 CA ALA B 48 497.611 434.914 422.899 1.00 17.02 P9 ATOM 46 CA ARG B 49 499.612 432.386 420.893 1.00 17.11 P9 ATOM 47 CA ILE B 50 503.284 432.635 421.768 1.00 17.68 P9 ATOM 48 CA VAL B 51 506.124 431.174 419.718 1.00 17.34 P9 ATOM 49 CA ALA B 52 509.518 431.094 421.413 1.00 17.71 P9 ATOM 50 CA VAL B 53 512.935 429.470 421.254 1.00 17.54 P9 ATOM 51 CA GLY B 54 514.704 427.649 424.055 1.00 18.35 P9 ATOM 52 CA VAL B 55 517.688 429.550 425.407 1.00 19.01 P9 ATOM 53 CA PHE B 56 519.509 426.294 426.108 1.00 19.90 P9 ATOM 54 CA ASP B 57 518.198 423.603 423.749 1.00 21.17 P9 ATOM 55 CA GLY B 58 517.293 425.976 420.923 1.00 21.69 P9 ATOM 56 CA GLY B 59 513.988 424.187 420.479 1.00 21.62 P9 ATOM 57 CA LYS B 60 510.864 425.872 419.151 1.00 20.30 P9 ATOM 58 CA ARG B 61 508.024 425.971 421.667 1.00 18.60 P9 ATOM 59 CA THR B 62 504.517 427.398 421.607 1.00 17.44 P9 ATOM 60 CA LEU B 63 501.998 428.440 424.242 1.00 16.19 P9 ATOM 61 CA SER B 64 498.370 429.446 423.716 1.00 15.39 P9 ATOM 62 CA LEU B 65 496.433 430.924 426.644 1.00 14.67 P9 ATOM 63 CA PRO B 66 494.260 433.905 427.730 1.00 14.79 P9 ATOM 64 CA VAL B 67 495.940 437.325 427.634 1.00 15.74 P9 ATOM 65 CA ASP B 68 495.325 437.738 431.369 1.00 17.10 P9 ATOM 66 CA ALA B 69 496.793 434.371 432.372 1.00 16.26 P9 ATOM 67 CA GLN B 70 500.115 434.425 434.223 1.00 18.00 P9 ATOM 68 CA VAL B 71 503.237 433.190 432.463 1.00 19.41 P9 ATOM 69 CA GLU B 72 506.563 432.596 434.201 1.00 21.29 P9 ATOM 70 CA VAL B 73 509.492 434.822 433.262 1.00 21.83 P9 ATOM 71 CA PRO B 74 513.047 433.603 433.963 0.94 22.19 P9 ATOM 72 CA ILE B 75 515.436 435.660 436.072 1.00 23.67 P9 ATOM 73 CA ILE B 76 518.508 436.336 433.943 0.96 24.46 P9 ATOM 74 CA GLU B 77 521.735 437.457 435.611 1.00 24.69 P9 ATOM 75 CA LYS B 78 524.294 438.935 433.213 1.00 24.12 P9 ATOM 76 CA PHE B 79 528.013 439.160 433.959 1.00 21.39 P9 ATOM 77 CA THR B 80 531.479 439.196 432.404 1.00 19.30 P9 ATOM 78 CA ALA B 81 533.958 436.320 432.436 1.00 17.03 P9 ATOM 79 CA GLN B 82 537.421 435.668 430.993 1.00 15.83 P9 ATOM 80 CA ILE B 83 538.128 432.536 428.964 1.00 14.35 P9 ATOM 81 CA LEU B 84 540.770 430.349 430.639 1.00 14.01 P9 ATOM 82 CA SER B 85 540.720 427.442 428.163 1.00 14.77 P9 ATOM 83 CA VAL B 86 538.697 426.017 425.292 1.00 15.76 P9 ATOM 84 CA SER B 87 538.246 422.344 424.410 1.00 15.97 P9 ATOM 85 CA GLY B 88 535.905 420.871 421.836 1.00 16.65 P9 ATOM 86 CA ASP B 89 533.352 420.243 424.587 1.00 17.36 P9 ATOM 87 CA VAL B 90 533.894 422.746 427.389 1.00 16.73 P9 ATOM 88 CA ILE B 91 534.780 426.401 427.870 1.00 16.05 P9 ATOM 89 CA GLN B 92 536.584 427.059 431.178 1.00 16.32 P9 ATOM 90 CA LEU B 93 535.870 430.590 432.465 1.00 15.69 P9 ATOM 91 CA MET B 94 536.982 432.904 435.270 1.00 17.32 P9 ATOM 92 CA ASP B 95 534.006 434.830 436.697 1.00 19.94 P9 ATOM 93 CA MET B 96 535.333 438.412 436.817 1.00 22.68 P9 ATOM 94 CA ARG B 97 533.065 439.204 439.767 1.00 24.59 P9 ATOM 95 CA ASP B 98 534.544 436.755 442.283 0.96 24.84 P9 ATOM 96 CA TYR B 99 537.285 435.135 440.175 0.99 24.06 P9 ATOM 97 CA LYS B 100 535.841 431.625 440.550 1.00 22.14 P9 ATOM 98 CA THR B 101 536.149 429.064 437.761 1.00 20.84 P9 ATOM 99 CA ILE B 102 532.988 428.035 435.916 1.00 19.78 P9 ATOM 100 CA GLU B 103 532.678 425.418 433.177 1.00 19.97 P9 ATOM 101 CA VAL B 104 530.251 425.963 430.299 1.00 18.00 P9 ATOM 102 CA PRO B 105 529.362 423.242 427.754 1.00 18.24 P9 ATOM 103 CA MET B 106 530.166 424.138 424.128 1.00 18.91 P9 ATOM 104 CA LYS B 107 526.491 423.558 423.303 1.00 19.94 P9 ATOM 105 CA TYR B 108 525.616 426.558 425.496 1.00 20.72 P9 ATOM 106 CA VAL B 109 527.621 429.018 423.411 1.00 23.20 P9 ATOM 107 CA GLU B 110 525.751 431.260 420.961 1.00 28.03 P9 ATOM 108 CA GLU B 111 526.704 430.099 417.460 0.74 31.85 P9 ATOM 109 CA GLU B 112 527.954 433.554 416.512 1.00 33.44 P9 ATOM 110 CA ALA B 113 530.368 433.615 419.458 1.00 31.90 P9 ATOM 111 CA LYS B 114 531.911 430.180 418.906 0.92 31.27 P9 ATOM 112 CA GLY B 115 534.136 431.579 416.174 1.00 30.17 P9 ATOM 113 CA ARG B 116 535.956 434.004 418.463 1.00 27.89 P9 ATOM 114 CA LEU B 117 536.365 431.777 421.514 1.00 25.28 P9 ATOM 115 CA ALA B 118 539.998 432.063 422.578 1.00 23.01 P9 ATOM 116 CA PRO B 119 541.912 431.997 425.869 1.00 21.21 P9 ATOM 117 CA GLY B 120 542.158 435.500 427.308 1.00 21.69 P9 ATOM 118 CA ALA B 121 539.046 436.875 425.620 1.00 21.58 P9 ATOM 119 CA GLU B 122 536.240 438.298 427.745 1.00 22.41 P9 ATOM 120 CA VAL B 123 532.678 437.132 427.205 1.00 20.97 P9 ATOM 121 CA GLU B 124 529.171 438.150 428.219 1.00 20.32 P9 ATOM 122 CA VAL B 125 527.627 435.323 430.229 1.00 19.82 P9 ATOM 123 CA TRP B 126 524.012 434.745 431.239 1.00 21.08 P9 ATOM 124 CA GLN B 127 523.027 432.643 434.216 1.00 22.22 P9 ATOM 125 CA ILE B 128 519.538 431.200 434.585 1.00 22.80 P9 ATOM 126 CA LEU B 129 519.153 429.029 437.671 1.00 24.59 P9 ATOM 127 CA ASP B 130 522.058 426.551 437.616 0.99 24.90 P9 ATOM 128 CA ARG B 131 522.952 426.918 433.938 1.00 22.57 P9 ATOM 129 CA TYR B 132 525.128 429.357 432.016 1.00 21.18 P9 ATOM 130 CA LYS B 133 525.153 430.537 428.432 1.00 21.22 P9 ATOM 131 CA ILE B 134 527.957 432.373 426.662 1.00 20.82 P9 ATOM 132 CA ILE B 135 526.298 435.133 424.637 1.00 24.27 P9 ATOM 133 CA ARG B 136 529.175 436.872 422.866 1.00 28.80 P9 ATOM 134 CA VAL B 137 532.877 437.680 422.955 1.00 32.92 P9 ATOM 135 CA LYS B 138 533.895 440.931 424.718 1.00 36.89 P9 ATOM 136 CA GLY B 139 531.242 441.878 427.264 0.67 38.21 P9 """ def tst_01(): print("Comparing mixed model with target...") import iotbx.pdb from cctbx.array_family import flex model_pdb_inp=iotbx.pdb.input(source_info='model', lines=flex.split_lines(model)) crystal_symmetry=model_pdb_inp.crystal_symmetry() model_hierarchy=model_pdb_inp.construct_hierarchy() query_hierarchy=iotbx.pdb.input(source_info='query', lines=flex.split_lines(query)).construct_hierarchy() f=StringIO() r=run(crystal_symmetry=crystal_symmetry, chain_hierarchy=query_hierarchy,target_hierarchy=model_hierarchy,out=f) expected_text=\ """SEQ SCORE is fraction (close and matching target sequence). MEAN LENGTH is the mean length of contiguous segments in the match with target sequence. (Each gap/reverse of direction starts new segment). ----ALL RESIDUES--- CLOSE RESIDUES ONLY % MODEL --CLOSE- --FAR-- FORWARD REVERSE MIXED FOUND CA SEQ RMSD N N N N N SCORE SEQ MATCH(%) SCORE MEAN LENGTH FRAGMENTS BAD CONNECTIONS Unique_target 1.55 54 7 14 29 11 39.7 0.26 9.3 0.04 6.0 7 6""" found_text="\n".join(f.getvalue().splitlines()[-10:]) if remove_blank(found_text)!=remove_blank(expected_text): print("Expected: \n%s \nFound: \n%s" %(expected_text,found_text)) raise AssertionError("FAILED") from libtbx.test_utils import approx_equal print(r.get_values("forward")) assert approx_equal(r.get_values("forward"),(1.6751069901864204, 14)) print(r.get_values("reverse")) assert approx_equal(r.get_values("reverse"),(1.388466550576198, 29)) print(r.get_values("close")) assert approx_equal(r.get_values("close"),(1.545835235099158, 54)) print(r.get_values("all_far")) assert approx_equal(r.get_values("all_far"),(0,0)) print("OK") def tst_02(): print("Comparing mixed model with target with 2 chains...") import iotbx.pdb from cctbx.array_family import flex model_pdb_inp=iotbx.pdb.input(source_info='model', lines=flex.split_lines(model1)) crystal_symmetry=model_pdb_inp.crystal_symmetry() model_hierarchy=model_pdb_inp.construct_hierarchy() query_hierarchy=iotbx.pdb.input(source_info='query', lines=flex.split_lines(query)).construct_hierarchy() f=StringIO() r=run(crystal_symmetry=crystal_symmetry, chain_hierarchy=query_hierarchy,target_hierarchy=model_hierarchy,out=f) expected_text=""" SEQ SCORE is fraction (close and matching target sequence). MEAN LENGTH is the mean length of contiguous segments in the match with target sequence. (Each gap/reverse of direction starts new segment). ----ALL RESIDUES--- CLOSE RESIDUES ONLY % MODEL --CLOSE- --FAR-- FORWARD REVERSE MIXED FOUND CA SEQ RMSD N N N N N SCORE SEQ MATCH(%) SCORE MEAN LENGTH FRAGMENTS BAD CONNECTIONS Unique_target 1.55 54 7 14 29 11 39.7 0.26 9.3 0.04 6.0 7 6""" found_text="\n".join(f.getvalue().splitlines()[-10:]) if remove_blank(found_text)!=remove_blank(expected_text): print("\n\nExpected: \n%s \n\nFound: \n%s" %(expected_text,found_text)) raise AssertionError("FAILED") from libtbx.test_utils import approx_equal print(r.get_values("forward")) assert approx_equal(r.get_values("forward"),(1.6751069901864204, 14)) print(r.get_values("reverse")) assert approx_equal(r.get_values("reverse"),(1.388466550576198, 29)) print(r.get_values("close")) assert approx_equal(r.get_values("close"),(1.545835235099158, 54)) print(r.get_values("all_far")) assert approx_equal(r.get_values("all_far"),(0,0)) print("OK") def tst_03(): print("Comparing mixed model with target with 2 chains...as group") import iotbx.pdb from cctbx.array_family import flex model_pdb_inp=iotbx.pdb.input(source_info='model', lines=flex.split_lines(model1)) crystal_symmetry=model_pdb_inp.crystal_symmetry() model_hierarchy=model_pdb_inp.construct_hierarchy() query_hierarchy=iotbx.pdb.input(source_info='query', lines=flex.split_lines(query)).construct_hierarchy() import os if not os.path.isdir("files"): os.mkdir("files") ff=open(os.path.join("files","query.pdb"),'w') print("CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4", file=ff) print(query_hierarchy.as_pdb_string(), file=ff) ff.close() ff=open("model.pdb",'w') print(model_hierarchy.as_pdb_string(), file=ff) ff.close() f=StringIO() args=["query_dir=files","model.pdb"] r=run(args,out=f) expected_text=""" SEQ SCORE is fraction (close and matching target sequence). MEAN LENGTH is the mean length of contiguous segments in the match with target sequence. (Each gap/reverse of direction starts new segment). ----ALL RESIDUES--- CLOSE RESIDUES ONLY % MODEL --CLOSE- --FAR-- FORWARD REVERSE MIXED FOUND CA SEQ RMSD N N N N N SCORE SEQ MATCH(%) SCORE MEAN LENGTH FRAGMENTS BAD CONNECTIONS query.pdb 1.55 54 7 14 29 11 39.7 0.26 9.3 0.04 6.0 7 6""" found_text="\n".join(f.getvalue().splitlines()[-10:]) if remove_blank(found_text)!=remove_blank(expected_text): print("Expected: \n%s \nFound: \n%s" %(expected_text,found_text)) raise AssertionError("FAILED") print("OK") def tst_04(): print("Testing choosing unique sequences") from mmtbx.validation.chain_comparison import \ extract_unique_part_of_sequences as eups seqs=[ "abcdefgh","klafmalsd"] print() print(seqs) copies_in_unique,base_copies,unique_sequence_dict=eups(seqs) for seq in copies_in_unique.keys(): print(copies_in_unique[seq],base_copies,seq) seqs=[ "abcdefgh", "klafmalsd", "klafmalsd"] print() print(seqs) copies_in_unique,base_copies,unique_sequence_dict=eups(seqs) for seq in copies_in_unique.keys(): print(copies_in_unique[seq],base_copies,seq) seqs=[ "abcdefgh", "klafmalsd", ] print() print(seqs) copies_in_unique,base_copies,unique_sequence_dict=eups(seqs) for seq in copies_in_unique.keys(): print(copies_in_unique[seq],base_copies,seq) seqs=[ "abcdefgh", "klafmalsd", "abcdefgh", "klafmalsd", ] print() print(seqs) copies_in_unique,base_copies,unique_sequence_dict=eups(seqs) for seq in copies_in_unique.keys(): print(copies_in_unique[seq],base_copies,seq) seqs=[ "abcdefgh", "klafmalsd", "klafmalsd", "abcdefgh", "klafmalsd", "klafmalsd", ] print() print(seqs) copies_in_unique,base_copies,unique_sequence_dict=eups(seqs) for seq in copies_in_unique.keys(): print(copies_in_unique[seq],base_copies,seq) print("OK") target=""" CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4 ATOM 9 CA LYS U 4 109.976 18.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP U 5 109.182 21.755 43.110 1.00 47.90 P9 ATOM 25 CA VAL U 6 110.823 23.654 40.250 1.00 46.89 P9 ATOM 32 CA MET U 7 108.936 26.802 39.218 1.00 45.06 P9 """ modela=""" CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4 ATOM 9 CA LYS A 4 109.976 18.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP A 5 109.182 21.755 43.110 1.00 47.90 P9 ATOM 25 CA VAL A 6 110.823 23.654 40.250 1.00 46.89 P9 ATOM 32 CA MET A 7 108.936 26.802 39.218 1.00 45.06 P9 """ modelb=""" ATOM 40 CA SER B 8 205.419 28.211 39.036 1.00 41.81 P9 ATOM 46 CA THR B 9 203.906 27.616 35.600 1.00 37.71 P9 ATOM 53 CA LYS B 10 203.277 30.858 33.696 1.00 33.20 P9 ATOM 62 CA TYR B 11 200.215 31.269 31.467 1.00 29.03 P9 """ modelaa=""" ATOM 9 CA LYS A 4 109.976 18.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP A 5 109.182 21.755 43.110 1.00 47.90 P9 ATOM 25 CA VAL A 6 110.823 23.654 40.250 1.00 46.89 P9 ATOM 32 CA MET A 7 108.936 26.802 39.218 1.00 45.06 P9 ATOM 9 CA LYS C 14 209.976 18.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP C 15 209.182 21.755 43.110 1.00 47.90 P9 ATOM 15 CA VAL C 16 210.823 23.654 40.250 1.00 46.89 P9 ATOM 32 CA MET C 17 208.936 26.802 39.218 1.00 45.06 P9 """ modelaab=""" ATOM 9 CA LYS A 4 109.976 18.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP A 5 109.182 21.755 43.110 1.00 47.90 P9 ATOM 25 CA VAL A 6 110.823 23.654 40.250 1.00 46.89 P9 ATOM 32 CA MET A 7 108.936 26.802 39.218 1.00 45.06 P9 ATOM 9 CA LYS C 14 209.976 18.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP C 15 209.182 21.755 43.110 1.00 47.90 P9 ATOM 15 CA VAL C 16 210.823 23.654 40.250 1.00 46.89 P9 ATOM 32 CA MET C 17 208.936 26.802 39.218 1.00 45.06 P9 ATOM 40 CA SER B 8 205.419 28.211 39.036 1.00 41.81 P9 ATOM 46 CA THR B 9 203.906 27.616 35.600 1.00 37.71 P9 ATOM 53 CA LYS B 10 203.277 30.858 33.696 1.00 33.20 P9 ATOM 62 CA TYR B 11 200.215 31.269 31.467 1.00 29.03 P9 """ modelaabaab=""" ATOM 9 CA LYS A 4 109.976 18.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP A 5 109.182 21.755 43.110 1.00 47.90 P9 ATOM 25 CA VAL A 6 110.823 23.654 40.250 1.00 46.89 P9 ATOM 32 CA MET A 7 108.936 26.802 39.218 1.00 45.06 P9 ATOM 9 CA LYS C 14 209.976 18.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP C 15 209.182 21.755 43.110 1.00 47.90 P9 ATOM 15 CA VAL C 16 210.823 23.654 40.250 1.00 46.89 P9 ATOM 32 CA MET C 17 208.936 26.802 39.218 1.00 45.06 P9 ATOM 40 CA SER B 8 205.419 28.211 39.036 1.00 41.81 P9 ATOM 46 CA THR B 9 203.906 27.616 35.600 1.00 37.71 P9 ATOM 53 CA LYS B 10 203.277 30.858 33.696 1.00 33.20 P9 ATOM 62 CA TYR B 11 200.215 31.269 31.467 1.00 29.03 P9 ATOM 9 CA LYS F 4 109.976 118.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP F 5 109.182 121.755 43.110 1.00 47.90 P9 ATOM 25 CA VAL F 6 110.823 123.654 40.250 1.00 46.89 P9 ATOM 32 CA MET F 7 108.936 126.802 39.218 1.00 45.06 P9 ATOM 9 CA LYS H 14 209.976 118.221 44.266 1.00 48.61 P9 ATOM 11 CA TRP H 15 209.182 121.755 43.110 1.00 47.90 P9 ATOM 15 CA VAL H 16 210.823 123.654 40.250 1.00 46.89 P9 ATOM 32 CA MET H 17 208.936 126.802 39.218 1.00 45.06 P9 ATOM 40 CA SER G 8 205.419 128.211 39.036 1.00 41.81 P9 ATOM 46 CA THR G 9 203.906 127.616 35.600 1.00 37.71 P9 ATOM 53 CA LYS G 10 203.277 130.858 33.696 1.00 33.20 P9 ATOM 62 CA TYR G 11 200.215 131.269 31.467 1.00 29.03 P9 """ ncs_spec=""" Summary of NCS information Fri Jan 12 11:58:49 2018 /net/anaconda/raid1/terwill/misc/junk new_ncs_group new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 112.2897 27.5224 23.1305 CHAIN A RMSD 0 MATCHING 136 RESSEQ 4:139 new_operator rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth -405.0000 -405.0000 -405.0000 center_orth 517.2897 432.5224 428.1305 CHAIN B RMSD 4.32467304409e-13 MATCHING 136 RESSEQ 4:139 """ def tst_05(): from mmtbx.validation.chain_comparison import \ extract_unique_part_of_hierarchy as euph print("Testing extraction of unique part and unique matching") for m in [modela,modelb,modelaa,modelaab,modelaabaab]: import iotbx.pdb from cctbx.array_family import flex model_pdb_inp=iotbx.pdb.input(source_info='model', lines=flex.split_lines(m)) crystal_symmetry=model_pdb_inp.crystal_symmetry() model_hierarchy=model_pdb_inp.construct_hierarchy() print("\nExtraction of unique MODEL with %s residues" %( model_hierarchy.overall_counts().n_residues)) query_hierarchy=iotbx.pdb.input(source_info='query', lines=flex.split_lines(target)).construct_hierarchy() unique_hierarchy=euph(model_hierarchy,target_ph=query_hierarchy) print("FINAL chain ids: %s \n" %(" ".join(unique_hierarchy.chain_ids()))) print("OK") def tst_06(): print("Comparing mixed model with target with 2 chains...using ncs") import iotbx.pdb from cctbx.array_family import flex model_pdb_inp=iotbx.pdb.input(source_info='model', lines=flex.split_lines(model1)) crystal_symmetry=model_pdb_inp.crystal_symmetry() f=open('ncs.ncs_spec','w') print(ncs_spec, file=f) f.close() f=open('model.pdb','w') print(model1, file=f) #model_hierarchy.as_pdb_string() f.close() f=open('query.pdb','w') print(query, file=f) #query_hierarchy.as_pdb_string() f.close() f=StringIO() args=['model.pdb','query.pdb','ncs_file=ncs.ncs_spec'] r=run(args,out=f) expected_text=""" SEQ SCORE is fraction (close and matching target sequence). MEAN LENGTH is the mean length of contiguous segments in the match with target sequence. (Each gap/reverse of direction starts new segment). ----ALL RESIDUES--- CLOSE RESIDUES ONLY % MODEL --CLOSE- --FAR-- FORWARD REVERSE MIXED FOUND CA SEQ RMSD N N N N N SCORE SEQ MATCH(%) SCORE MEAN LENGTH FRAGMENTS BAD CONNECTIONS Unique_target 1.67 58 64 15 29 14 42.6 0.25 8.6 0.04 4.5 16 8""" found_text="\n".join(f.getvalue().splitlines()[-10:]) if remove_blank(found_text)!=remove_blank(expected_text): print("\n\nExpected: \n%s \n\nFound: \n%s" %(expected_text,found_text)) raise AssertionError("FAILED") print("OK") if __name__=="__main__": tst_01() tst_02() tst_03() tst_04() tst_05() tst_06()