from __future__ import absolute_import, division, print_function import iotbx.ncs import iotbx.ncs as ncs from iotbx import pdb pdb_str_1="""\ ATOM 1 N GLU A 3 189.385 151.249 151.584 1.00100.71 N ATOM 2 CA GLU A 3 190.604 152.017 151.807 1.00100.71 C ATOM 3 C GLU A 3 191.582 151.843 150.650 1.00100.71 C ATOM 4 O GLU A 3 191.527 150.846 149.929 1.00100.71 O ATOM 5 CB GLU A 3 191.266 151.602 153.123 1.00 81.32 C ATOM 6 N LYS A 4 192.471 152.820 150.489 1.00113.71 N ATOM 7 CA LYS A 4 193.464 152.823 149.414 1.00113.71 C ATOM 8 C LYS A 4 192.807 152.666 148.045 1.00113.71 C ATOM 9 O LYS A 4 191.719 153.194 147.810 1.00113.71 O ATOM 10 CB LYS A 4 194.500 151.716 149.633 1.00 74.77 C ATOM 11 N ARG A 5 193.479 151.939 147.155 1.00126.03 N ATOM 12 CA ARG A 5 192.989 151.690 145.800 1.00126.03 C ATOM 13 C ARG A 5 192.651 152.988 145.072 1.00126.03 C ATOM 14 O ARG A 5 191.677 153.056 144.321 1.00126.03 O ATOM 15 CB ARG A 5 191.763 150.772 145.832 1.00 91.24 C ATOM 16 N LEU A 6 193.465 154.014 145.302 1.00134.86 N ATOM 17 CA LEU A 6 193.232 155.328 144.718 1.00126.46 C ATOM 18 C LEU A 6 193.464 155.328 143.211 1.00118.31 C ATOM 19 O LEU A 6 194.543 154.966 142.738 1.00116.86 O ATOM 20 CB LEU A 6 194.129 156.372 145.384 1.00128.29 C ATOM 21 N SER A 7 192.446 155.734 142.460 1.00127.84 N ATOM 22 CA SER A 7 192.556 155.843 141.011 1.00123.16 C ATOM 23 C SER A 7 193.118 157.206 140.626 1.00118.42 C ATOM 24 O SER A 7 192.423 158.219 140.706 1.00104.49 O ATOM 25 CB SER A 7 191.195 155.625 140.347 1.00121.63 C ATOM 26 OG SER A 7 190.259 156.601 140.769 1.00106.82 O ATOM 27 N ALA A 8 194.380 157.227 140.210 1.00118.32 N ATOM 28 CA ALA A 8 195.053 158.483 139.901 1.00111.32 C ATOM 29 C ALA A 8 195.632 158.502 138.491 1.00106.60 C ATOM 30 O ALA A 8 195.140 159.230 137.629 1.00102.40 O ATOM 31 CB ALA A 8 196.149 158.752 140.922 1.00102.52 C ATOM 32 N LYS A 9 196.672 157.693 138.277 1.00107.25 N ATOM 33 CA LYS A 9 197.479 157.673 137.046 1.00101.87 C ATOM 34 C LYS A 9 197.684 159.066 136.442 1.00 99.64 C ATOM 35 O LYS A 9 197.682 159.240 135.222 1.00 96.65 O ATOM 36 CB LYS A 9 196.865 156.721 136.003 1.00116.20 C ATOM 37 CG LYS A 9 195.479 157.086 135.482 1.00116.20 C ATOM 38 CD LYS A 9 195.039 156.146 134.370 1.00116.20 C ATOM 39 CE LYS A 9 194.946 154.712 134.860 1.00116.20 C ATOM 40 NZ LYS A 9 194.513 153.782 133.781 1.00116.20 N ATOM 41 N LYS A 10 197.886 160.050 137.313 1.00105.36 N ATOM 42 CA LYS A 10 198.013 161.443 136.902 1.00 98.00 C ATOM 43 C LYS A 10 199.366 161.728 136.262 1.00100.41 C ATOM 44 O LYS A 10 200.353 161.046 136.539 1.00103.97 O ATOM 45 CB LYS A 10 197.802 162.367 138.102 1.00106.11 C ATOM 46 CG LYS A 10 198.764 162.114 139.252 1.00113.17 C ATOM 47 CD LYS A 10 198.481 163.034 140.428 1.00110.08 C ATOM 48 CE LYS A 10 199.445 162.775 141.574 1.00119.94 C ATOM 49 NZ LYS A 10 199.358 161.373 142.069 1.00128.24 N TER ATOM 50 N GLU B 3 159.932 134.609 151.533 1.00114.47 N ATOM 51 CA GLU B 3 161.039 133.685 151.754 1.00114.47 C ATOM 52 C GLU B 3 161.174 132.703 150.594 1.00114.47 C ATOM 53 O GLU B 3 160.207 132.450 149.874 1.00114.47 O ATOM 54 CB GLU B 3 160.850 132.926 153.068 1.00 84.70 C ATOM 55 N LYS B 4 162.377 132.158 150.430 1.00120.40 N ATOM 56 CA LYS B 4 162.683 131.217 149.354 1.00120.40 C ATOM 57 C LYS B 4 162.331 131.796 147.986 1.00120.40 C ATOM 58 O LYS B 4 162.498 132.994 147.754 1.00120.40 O ATOM 59 CB LYS B 4 161.949 129.891 149.570 1.00 79.41 C ATOM 60 N ARG B 5 161.843 130.935 147.095 1.00131.79 N ATOM 61 CA ARG B 5 161.454 131.328 145.741 1.00131.79 C ATOM 62 C ARG B 5 162.586 132.049 145.013 1.00131.79 C ATOM 63 O ARG B 5 162.351 132.998 144.265 1.00131.79 O ATOM 64 CB ARG B 5 160.204 132.212 145.776 1.00 94.80 C ATOM 65 N LEU B 6 163.811 131.590 145.241 1.00136.38 N ATOM 66 CA LEU B 6 164.990 132.218 144.659 1.00127.98 C ATOM 67 C LEU B 6 165.062 131.999 143.151 1.00119.83 C ATOM 68 O LEU B 6 165.053 130.863 142.677 1.00118.38 O ATOM 69 CB LEU B 6 166.259 131.684 145.325 1.00129.41 C ATOM 70 N SER B 7 165.131 133.095 142.403 1.00127.99 N ATOM 71 CA SER B 7 165.270 133.027 140.954 1.00123.31 C ATOM 72 C SER B 7 166.741 132.912 140.572 1.00118.57 C ATOM 73 O SER B 7 167.493 133.882 140.667 1.00104.64 O ATOM 74 CB SER B 7 164.644 134.257 140.292 1.00117.80 C ATOM 75 OG SER B 7 165.285 135.447 140.717 1.00102.99 O ATOM 76 N ALA B 8 167.147 131.722 140.141 1.00124.82 N ATOM 77 CA ALA B 8 168.549 131.469 139.833 1.00117.82 C ATOM 78 C ALA B 8 168.746 130.925 138.421 1.00113.10 C ATOM 79 O ALA B 8 169.288 131.619 137.560 1.00108.90 O ATOM 80 CB ALA B 8 169.143 130.509 140.852 1.00108.04 C ATOM 81 N LYS B 9 168.295 129.687 138.206 1.00118.88 N ATOM 82 CA LYS B 9 168.523 128.914 136.975 1.00113.50 C ATOM 83 C LYS B 9 169.913 129.148 136.371 1.00111.27 C ATOM 84 O LYS B 9 170.076 129.209 135.151 1.00108.28 O ATOM 85 CB LYS B 9 167.429 129.207 135.932 1.00136.65 C ATOM 86 CG LYS B 9 167.347 130.639 135.415 1.00136.65 C ATOM 87 CD LYS B 9 166.317 130.771 134.304 1.00136.65 C ATOM 88 CE LYS B 9 164.925 130.416 134.796 1.00136.65 C ATOM 89 NZ LYS B 9 163.904 130.545 133.719 1.00136.65 N ATOM 90 N LYS B 10 170.911 129.255 137.242 1.00117.26 N ATOM 91 CA LYS B 10 172.276 129.563 136.831 1.00109.90 C ATOM 92 C LYS B 10 172.964 128.366 136.185 1.00112.31 C ATOM 93 O LYS B 10 172.620 127.216 136.458 1.00115.87 O ATOM 94 CB LYS B 10 173.091 130.044 138.033 1.00114.70 C ATOM 95 CG LYS B 10 173.145 129.047 139.180 1.00121.76 C ATOM 96 CD LYS B 10 173.936 129.596 140.357 1.00118.67 C ATOM 97 CE LYS B 10 173.984 128.597 141.501 1.00128.53 C ATOM 98 NZ LYS B 10 172.623 128.251 141.996 1.00136.83 N TER ATOM 99 N GLU C 3 135.020 157.489 151.546 1.00 97.12 N ATOM 100 CA GLU C 3 134.486 156.151 151.769 1.00 97.12 C ATOM 101 C GLU C 3 133.592 155.717 150.612 1.00 97.12 C ATOM 102 O GLU C 3 133.050 156.556 149.891 1.00 97.12 O ATOM 103 CB GLU C 3 133.707 156.096 153.084 1.00 78.85 C ATOM 104 N LYS C 4 133.446 154.403 150.449 1.00109.02 N ATOM 105 CA LYS C 4 132.646 153.820 149.375 1.00109.02 C ATOM 106 C LYS C 4 133.085 154.333 148.006 1.00109.02 C ATOM 107 O LYS C 4 134.276 154.544 147.772 1.00109.02 O ATOM 108 CB LYS C 4 131.157 154.106 149.593 1.00 74.21 C ATOM 109 N ARG C 5 132.114 154.528 147.117 1.00123.74 N ATOM 110 CA ARG C 5 132.365 155.018 145.760 1.00123.74 C ATOM 111 C ARG C 5 133.399 154.165 145.034 1.00123.74 C ATOM 112 O ARG C 5 134.229 154.680 144.283 1.00123.74 O ATOM 113 CB ARG C 5 132.819 156.480 145.794 1.00 88.74 C ATOM 114 N LEU C 6 133.343 152.857 145.263 1.00134.34 N ATOM 115 CA LEU C 6 134.303 151.929 144.680 1.00125.94 C ATOM 116 C LEU C 6 134.118 151.794 143.172 1.00117.79 C ATOM 117 O LEU C 6 133.035 151.448 142.699 1.00116.34 O ATOM 118 CB LEU C 6 134.187 150.557 145.347 1.00128.27 C ATOM 119 N SER C 7 135.180 152.070 142.425 1.00122.42 N ATOM 120 CA SER C 7 135.159 151.916 140.975 1.00117.74 C ATOM 121 C SER C 7 135.505 150.483 140.593 1.00113.00 C ATOM 122 O SER C 7 136.662 150.071 140.680 1.00 99.07 O ATOM 123 CB SER C 7 136.133 152.893 140.314 1.00118.03 C ATOM 124 OG SER C 7 137.463 152.652 140.736 1.00103.22 O ATOM 125 N ALA C 8 134.499 149.725 140.169 1.00116.62 N ATOM 126 CA ALA C 8 134.694 148.314 139.861 1.00109.62 C ATOM 127 C ALA C 8 134.235 147.958 138.451 1.00104.90 C ATOM 128 O ALA C 8 135.061 147.658 137.588 1.00100.70 O ATOM 129 CB ALA C 8 133.968 147.451 140.881 1.00105.20 C ATOM 130 N LYS C 9 132.918 148.001 138.237 1.00110.41 N ATOM 131 CA LYS C 9 132.253 147.544 137.008 1.00105.03 C ATOM 132 C LYS C 9 132.904 146.294 136.405 1.00102.80 C ATOM 133 O LYS C 9 133.005 146.153 135.186 1.00 99.81 O ATOM 134 CB LYS C 9 132.189 148.673 135.963 1.00112.95 C ATOM 135 CG LYS C 9 133.525 149.191 135.441 1.00112.95 C ATOM 136 CD LYS C 9 133.328 150.209 134.328 1.00112.95 C ATOM 137 CE LYS C 9 132.560 151.424 134.819 1.00112.95 C ATOM 138 NZ LYS C 9 132.363 152.431 133.739 1.00112.95 N ATOM 139 N LYS C 10 133.322 145.383 137.277 1.00110.13 N ATOM 140 CA LYS C 10 134.037 144.180 136.866 1.00102.77 C ATOM 141 C LYS C 10 133.111 143.155 136.226 1.00105.18 C ATOM 142 O LYS C 10 131.911 143.125 136.504 1.00108.74 O ATOM 143 CB LYS C 10 134.751 143.556 138.067 1.00111.37 C ATOM 144 CG LYS C 10 133.823 143.193 139.216 1.00118.43 C ATOM 145 CD LYS C 10 134.592 142.612 140.391 1.00115.34 C ATOM 146 CE LYS C 10 133.659 142.253 141.535 1.00125.20 C ATOM 147 NZ LYS C 10 132.907 143.438 142.032 1.00133.50 N TER ATOM 148 N GLU D 3 149.071 188.264 151.543 1.00111.15 N ATOM 149 CA GLU D 3 147.633 188.359 151.765 1.00111.15 C ATOM 150 C GLU D 3 146.945 189.074 150.607 1.00111.15 C ATOM 151 O GLU D 3 147.575 189.848 149.885 1.00111.15 O ATOM 152 CB GLU D 3 147.340 189.084 153.079 1.00 85.33 C ATOM 153 N LYS D 4 145.651 188.806 150.445 1.00121.08 N ATOM 154 CA LYS D 4 144.847 189.386 149.369 1.00121.08 C ATOM 155 C LYS D 4 145.471 189.125 148.001 1.00121.08 C ATOM 156 O LYS D 4 146.041 188.058 147.767 1.00121.08 O ATOM 157 CB LYS D 4 144.659 190.890 149.587 1.00 80.08 C ATOM 158 N ARG D 5 145.357 190.109 147.110 1.00127.58 N ATOM 159 CA ARG D 5 145.900 190.021 145.755 1.00127.58 C ATOM 160 C ARG D 5 145.409 188.771 145.027 1.00127.58 C ATOM 161 O ARG D 5 146.157 188.143 144.278 1.00127.58 O ATOM 162 CB ARG D 5 147.431 190.042 145.788 1.00 92.50 C ATOM 163 N LEU D 6 144.148 188.421 145.256 1.00133.20 N ATOM 164 CA LEU D 6 143.564 187.219 144.673 1.00124.80 C ATOM 165 C LEU D 6 143.376 187.355 143.166 1.00116.65 C ATOM 166 O LEU D 6 142.718 188.282 142.693 1.00115.20 O ATOM 167 CB LEU D 6 142.224 186.904 145.341 1.00123.11 C ATOM 168 N SER D 7 143.963 186.427 142.417 1.00122.44 N ATOM 169 CA SER D 7 143.809 186.402 140.968 1.00117.76 C ATOM 170 C SER D 7 142.553 185.629 140.584 1.00113.02 C ATOM 171 O SER D 7 142.520 184.401 140.668 1.00 99.09 O ATOM 172 CB SER D 7 145.040 185.778 140.305 1.00114.82 C ATOM 173 OG SER D 7 145.223 184.439 140.728 1.00100.01 O ATOM 174 N ALA D 8 141.521 186.352 140.164 1.00110.90 N ATOM 175 CA ALA D 8 140.239 185.731 139.856 1.00103.90 C ATOM 176 C ALA D 8 139.759 186.055 138.445 1.00 99.18 C ATOM 177 O ALA D 8 139.729 185.175 137.584 1.00 94.98 O ATOM 178 CB ALA D 8 139.193 186.157 140.876 1.00100.30 C ATOM 179 N LYS D 9 139.393 187.321 138.229 1.00101.28 N ATOM 180 CA LYS D 9 138.753 187.810 136.999 1.00 95.90 C ATOM 181 C LYS D 9 137.768 186.804 136.395 1.00 93.67 C ATOM 182 O LYS D 9 137.670 186.658 135.176 1.00 90.68 O ATOM 183 CB LYS D 9 139.808 188.219 135.955 1.00108.30 C ATOM 184 CG LYS D 9 140.718 187.109 135.437 1.00108.30 C ATOM 185 CD LYS D 9 141.626 187.610 134.325 1.00108.30 C ATOM 186 CE LYS D 9 142.544 188.716 134.815 1.00108.30 C ATOM 187 NZ LYS D 9 143.443 189.213 133.736 1.00108.30 N ATOM 188 N LYS D 10 137.023 186.128 137.267 1.00 96.18 N ATOM 189 CA LYS D 10 136.102 185.076 136.857 1.00 88.82 C ATOM 190 C LYS D 10 134.841 185.639 136.213 1.00 91.23 C ATOM 191 O LYS D 10 134.442 186.771 136.486 1.00 94.79 O ATOM 192 CB LYS D 10 135.729 184.206 138.058 1.00 88.01 C ATOM 193 CG LYS D 10 135.099 184.979 139.206 1.00 95.07 C ATOM 194 CD LYS D 10 134.786 184.070 140.383 1.00 91.98 C ATOM 195 CE LYS D 10 134.160 184.848 141.529 1.00101.84 C ATOM 196 NZ LYS D 10 135.058 185.930 142.023 1.00110.14 N TER ATOM 197 N GLU E 3 182.665 184.397 151.568 1.00101.17 N ATOM 198 CA GLU E 3 182.312 185.794 151.790 1.00101.17 C ATOM 199 C GLU E 3 182.779 186.669 150.633 1.00101.17 C ATOM 200 O GLU E 3 183.711 186.309 149.911 1.00101.17 O ATOM 201 CB GLU E 3 182.910 186.296 153.105 1.00 79.37 C ATOM 202 N LYS E 4 182.124 187.817 150.471 1.00110.10 N ATOM 203 CA LYS E 4 182.429 188.761 149.395 1.00110.10 C ATOM 204 C LYS E 4 182.375 188.087 148.027 1.00110.10 C ATOM 205 O LYS E 4 181.536 187.216 147.793 1.00110.10 O ATOM 206 CB LYS E 4 183.802 189.404 149.613 1.00 77.29 C ATOM 207 N ARG E 5 183.275 188.499 147.136 1.00120.36 N ATOM 208 CA ARG E 5 183.360 187.955 145.781 1.00120.36 C ATOM 209 C ARG E 5 182.020 188.037 145.053 1.00120.36 C ATOM 210 O ARG E 5 181.654 187.131 144.304 1.00120.36 O ATOM 211 CB ARG E 5 183.852 186.505 145.814 1.00 88.94 C ATOM 212 N LEU E 6 181.298 189.128 145.281 1.00129.21 N ATOM 213 CA LEU E 6 179.976 189.314 144.698 1.00120.81 C ATOM 214 C LEU E 6 180.049 189.534 143.190 1.00112.66 C ATOM 215 O LEU E 6 180.727 190.446 142.718 1.00111.21 O ATOM 216 CB LEU E 6 179.263 190.492 145.364 1.00125.07 C ATOM 217 N SER E 7 179.346 188.691 142.442 1.00122.90 N ATOM 218 CA SER E 7 179.276 188.827 140.992 1.00118.22 C ATOM 219 C SER E 7 178.153 189.782 140.606 1.00113.48 C ATOM 220 O SER E 7 176.975 189.433 140.684 1.00 99.55 O ATOM 221 CB SER E 7 179.064 187.463 140.330 1.00118.74 C ATOM 222 OG SER E 7 177.846 186.876 140.753 1.00103.93 O ATOM 223 N ALA E 8 178.522 190.989 140.191 1.00119.02 N ATOM 224 CA ALA E 8 177.536 192.016 139.881 1.00112.02 C ATOM 225 C ALA E 8 177.696 192.572 138.470 1.00107.30 C ATOM 226 O ALA E 8 176.851 192.329 137.609 1.00103.10 O ATOM 227 CB ALA E 8 177.617 193.143 140.901 1.00107.03 C ATOM 228 N LYS E 9 178.787 193.311 138.255 1.00112.72 N ATOM 229 CA LYS E 9 179.055 194.071 137.025 1.00107.34 C ATOM 230 C LYS E 9 177.794 194.698 136.420 1.00105.11 C ATOM 231 O LYS E 9 177.627 194.746 135.201 1.00102.12 O ATOM 232 CB LYS E 9 179.771 193.193 135.981 1.00119.28 C ATOM 233 CG LYS E 9 178.996 191.986 135.462 1.00119.28 C ATOM 234 CD LYS E 9 179.753 191.277 134.350 1.00119.28 C ATOM 235 CE LYS E 9 181.089 190.746 134.841 1.00119.28 C ATOM 236 NZ LYS E 9 181.840 190.046 133.762 1.00119.28 N ATOM 237 N LYS E 10 176.921 195.194 137.291 1.00111.63 N ATOM 238 CA LYS E 10 175.636 195.745 136.880 1.00104.27 C ATOM 239 C LYS E 10 175.782 197.120 136.237 1.00106.68 C ATOM 240 O LYS E 10 176.736 197.848 136.513 1.00110.24 O ATOM 241 CB LYS E 10 174.691 195.831 138.080 1.00108.19 C ATOM 242 CG LYS E 10 175.230 196.669 139.229 1.00115.25 C ATOM 243 CD LYS E 10 174.268 196.685 140.406 1.00112.16 C ATOM 244 CE LYS E 10 174.812 197.522 141.551 1.00122.02 C ATOM 245 NZ LYS E 10 176.119 197.005 142.046 1.00130.32 N TER HETATM 246 MG MG A 401 195.263 159.228 130.323 1.00 89.18 MG HETATM 247 MG MG A 402 190.491 155.655 128.902 1.00 58.96 MG TER HETATM 248 MG MG B 401 169.312 131.516 130.255 1.00 89.18 MG HETATM 249 MG MG B 402 164.437 134.951 128.844 1.00 58.96 MG TER HETATM 250 MG MG C 401 134.961 147.586 130.281 1.00 89.18 MG HETATM 251 MG MG C 402 136.700 153.281 128.869 1.00 58.96 MG TER HETATM 252 MG MG E 402 178.823 186.803 128.888 1.00 58.96 MG TER HETATM 253 MG MG D 401 139.639 185.244 130.278 1.00 89.18 MG TER HETATM 254 MG MG E 501 163.180 163.256 210.123 1.00 53.90 MG TER HETATM 255 MG MG D 402 145.597 185.342 128.864 1.00 58.96 MG TER HETATM 256 MG MG E 502 163.175 163.242 206.503 1.00 53.90 MG HETATM 257 MG MG E 401 176.892 192.439 130.302 1.00 89.18 MG HETATM 258 MG MG E 503 163.118 163.159 156.463 1.00 53.90 MG TER """ def exercise_00(): """ Verify that strangely broken chain does not lead to crash """ pdb_inp = iotbx.pdb.input(lines=pdb_str_1,source_info=None) hierarchy = pdb_inp.construct_hierarchy() ncs_inp = iotbx.ncs.input(hierarchy = hierarchy) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 3, len(ncs_groups[0].copies) assert ncs_groups[0].master_iselection.size() == 51 # all chain assert ncs_groups[0].copies[0].iselection.size() == 51 # all chain print("OK") if(__name__=='__main__'): exercise_00()