from __future__ import absolute_import, division, print_function from libtbx.utils import null_out from six.moves import cStringIO as StringIO from mmtbx.secondary_structure.find_ss_from_ca import find_secondary_structure from libtbx import test_utils def remove_blank(text): return text.replace(" ","").replace("\n","") two_chain_helix_ss=""" HELIX 1 1 ALA A 15 LYS A 21 1 7 SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 N ILE B 280 O ILE A 51 """ bad_two_chain_helix_ss=""" HELIX 1 1 ALA A 15 LYS A 21 1 7 SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 N ILE B 278 O ILE A 51 """ bad_two_chain_helix_ss_correct_resname=""" HELIX 1 1 ALA A 15 LYS A 21 1 7 SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 N LEU B 278 O ILE A 51 """ negative_residues=""" ATOM 1 CA ASP A -5 34.633 18.762 20.254 1.00 22.59 C ATOM 2 CA LYS A -4 36.047 17.704 23.610 1.00 19.79 C ATOM 3 CA ILE A -3 35.551 19.482 26.886 1.00 19.33 C ATOM 4 CA AHIS A -2 38.649 21.223 28.218 0.50 19.79 C ATOM 5 CA BHIS A -2 38.583 21.270 28.209 0.50 20.43 C ATOM 6 CA GLY A 138 38.261 15.285 27.690 1.00 6.80 C ATOM 7 CA ALA A 139 34.607 14.241 27.428 1.00 4.76 C ATOM 8 CA ALEU A 140 33.091 14.490 23.937 0.50 5.08 C ATOM 9 CA BLEU A 140 33.072 14.565 23.972 0.50 5.41 C ATOM 10 CA ASN A 141 30.271 17.061 23.474 1.00 5.65 C """ hybrid_residues=""" ATOM 1 CA ASP AXYB2 34.633 18.762 20.254 1.00 22.59 C ATOM 2 CA LYS AXYB3 36.047 17.704 23.610 1.00 19.79 C ATOM 3 CA ILE AXYB4 35.551 19.482 26.886 1.00 19.33 C ATOM 4 CA AHIS AXYB5 38.649 21.223 28.218 0.50 19.79 C ATOM 5 CA BHIS AXYB6 38.583 21.270 28.209 0.50 20.43 C ATOM 6 CA GLY A 138 38.261 15.285 27.690 1.00 6.80 C ATOM 7 CA ALA A 139 34.607 14.241 27.428 1.00 4.76 C ATOM 8 CA ALEU A 140 33.091 14.490 23.937 0.50 5.08 C ATOM 9 CA BLEU A 140 33.072 14.565 23.972 0.50 5.41 C ATOM 10 CA ASN A 141 30.271 17.061 23.474 1.00 5.65 C """ antiparallel_text=""" ATOM 1 N LEU A 95 19.823 2.447 -20.604 1.00 4.22 N ATOM 2 CA LEU A 95 19.411 3.491 -19.655 1.00 4.09 C ATOM 3 C LEU A 95 20.437 3.482 -18.522 1.00 4.12 C ATOM 4 O LEU A 95 20.764 2.410 -18.006 1.00 4.68 O ATOM 5 CB LEU A 95 18.007 3.186 -19.075 1.00 4.63 C ATOM 9 N LEU A 96 20.911 4.667 -18.125 1.00 4.11 N ATOM 10 CA LEU A 96 21.872 4.787 -17.025 1.00 4.27 C ATOM 11 C LEU A 96 21.308 5.812 -16.028 1.00 4.14 C ATOM 12 O LEU A 96 21.044 6.956 -16.404 1.00 4.78 O ATOM 13 CB ALEU A 96 23.225 5.220 -17.574 0.50 4.58 C ATOM 21 N ARG A 97 21.144 5.374 -14.766 1.00 3.77 N ATOM 22 CA ARG A 97 20.820 6.284 -13.673 1.00 3.69 C ATOM 23 C ARG A 97 22.056 6.437 -12.774 1.00 3.41 C ATOM 24 O ARG A 97 22.651 5.441 -12.329 1.00 4.05 O ATOM 25 CB ARG A 97 19.612 5.796 -12.851 1.00 3.79 C ATOM 32 N PHE A 98 22.413 7.695 -12.516 1.00 3.36 N ATOM 33 CA PHE A 98 23.473 8.085 -11.601 1.00 3.42 C ATOM 34 C PHE A 98 22.827 8.597 -10.306 1.00 3.34 C ATOM 35 O PHE A 98 21.699 9.092 -10.321 1.00 3.88 O ATOM 36 CB PHE A 98 24.260 9.271 -12.203 1.00 3.74 C ATOM 43 N PHE A 117 25.991 3.957 -10.490 1.00 3.61 N ATOM 44 CA PHE A 117 26.196 3.832 -11.931 1.00 3.74 C ATOM 45 C PHE A 117 25.339 2.627 -12.381 1.00 3.68 C ATOM 46 O PHE A 117 25.850 1.516 -12.565 1.00 4.07 O ATOM 47 CB PHE A 117 27.700 3.629 -12.215 1.00 4.23 C ATOM 54 N ALA A 118 24.027 2.850 -12.466 1.00 3.64 N ATOM 55 CA ALA A 118 23.056 1.773 -12.686 1.00 3.60 C ATOM 56 C ALA A 118 22.714 1.712 -14.176 1.00 3.63 C ATOM 57 O ALA A 118 22.072 2.613 -14.700 1.00 4.10 O ATOM 58 CB ALA A 118 21.797 2.030 -11.857 1.00 4.08 C ATOM 59 N LEU A 119 23.182 0.650 -14.842 1.00 3.81 N ATOM 60 CA LEU A 119 23.136 0.560 -16.297 1.00 3.98 C ATOM 61 C LEU A 119 22.282 -0.621 -16.738 1.00 4.00 C ATOM 62 O LEU A 119 22.608 -1.781 -16.475 1.00 5.33 O ATOM 63 CB LEU A 119 24.577 0.411 -16.837 1.00 4.22 C ATOM 67 N ARG A 120 21.209 -0.315 -17.470 1.00 3.85 N ATOM 68 CA ARG A 120 20.357 -1.332 -18.102 1.00 3.95 C ATOM 69 C ARG A 120 20.680 -1.407 -19.584 1.00 3.95 C ATOM 70 O ARG A 120 20.778 -0.387 -20.282 1.00 4.48 O ATOM 71 CB ARG A 120 18.872 -0.947 -17.952 1.00 4.12 C """ antiparallel_ss=""" SHEET 1 1 2 LEU A 95 PHE A 98 0 SHEET 2 1 2 PHE A 117 ARG A 120 -1 N ARG A 120 O LEU A 95 """ ss_text=""" HELIX 1 1 ALA A 15 LYS A 21 1 7 SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 N ILE B 280 O ILE A 51 """ std_text=""" ATOM 2 CA THRAa 3 186.743 125.884 251.259 1.00100.00 C ATOM 5 CA ASNAa 4 189.629 123.742 252.763 1.00100.00 C ATOM 8 CA SERAa 5 191.072 126.112 255.320 1.00100.00 C ATOM 11 CA ASPAa 6 192.080 124.928 258.848 1.00100.00 C ATOM 14 CA PHEAa 7 189.384 124.585 261.530 1.00100.00 C ATOM 17 CA VALAa 8 189.248 124.466 265.315 1.00100.00 C ATOM 20 CA VALAa 9 187.059 122.294 267.547 1.00100.00 C ATOM 23 CA ILEAa 10 185.534 123.893 270.679 1.00100.00 C ATOM 26 CA LYSAa 11 183.570 122.134 273.450 1.00100.00 C ATOM 29 CA ALAAa 12 181.897 124.298 276.085 1.00100.00 C ATOM 32 CA LEUAa 13 182.733 123.145 279.601 1.00100.00 C ATOM 35 CA GLUAa 14 180.241 125.609 281.156 1.00100.00 C ATOM 38 CA ASPAa 15 177.155 127.540 279.985 1.00100.00 C ATOM 41 CA GLYAa 16 177.637 130.843 278.162 1.00100.00 C ATOM 44 CA VALAa 17 180.958 130.212 276.395 1.00100.00 C ATOM 47 CA ASNAa 18 181.477 132.715 273.547 1.00100.00 C ATOM 50 CA VALAa 19 183.320 131.753 270.320 1.00100.00 C ATOM 53 CA ILEAa 20 184.043 135.156 268.674 1.00100.00 C ATOM 56 CA GLYAa 21 185.054 135.558 264.994 1.00100.00 C ATOM 59 CA LEUAa 22 187.345 138.529 264.419 1.00100.00 C ATOM 62 CA THRAa 23 187.310 140.218 261.033 1.00100.00 C ATOM 65 CA ARGAa 24 189.831 139.523 258.335 1.00100.00 C ATOM 68 CA GLYAa 25 191.359 142.673 256.805 1.00100.00 C ATOM 71 CA ALAAa 26 192.794 146.041 257.837 1.00100.00 C ATOM 74 CA ASPAa 27 190.126 146.289 260.564 1.00100.00 C ATOM 77 CA THRAa 28 189.912 143.928 263.570 1.00100.00 C ATOM 80 CA ARGAa 29 186.413 143.856 265.033 1.00100.00 C ATOM 83 CA PHEAa 30 183.873 141.240 266.091 1.00100.00 C ATOM 86 CA HISAa 31 181.625 140.079 263.343 1.00100.00 C ATOM 89 CA HISAa 32 179.931 137.209 265.203 1.00100.00 C ATOM 92 CA SERAa 33 179.805 135.702 268.677 1.00100.00 C ATOM 95 CA GLUAa 34 178.501 132.109 268.857 1.00100.00 C ATOM 98 CA CYSAa 35 177.222 131.284 272.342 1.00100.00 C ATOM 101 CA LEUAa 36 177.646 127.700 273.502 1.00100.00 C ATOM 104 CA ASPAa 37 175.969 125.990 276.438 1.00100.00 C ATOM 107 CA LYSAa 38 177.682 123.298 278.488 1.00100.00 C ATOM 110 CA GLYAa 39 178.623 120.300 276.385 1.00100.00 C ATOM 113 CA GLUAa 40 177.892 121.761 272.941 1.00100.00 C ATOM 116 CA VALAa 41 180.597 121.439 270.276 1.00100.00 C ATOM 119 CA LEUAa 42 181.492 123.998 267.594 1.00100.00 C ATOM 122 CA ILEAa 43 183.793 123.155 264.645 1.00100.00 C ATOM 125 CA ALAAa 44 184.701 126.388 262.889 1.00100.00 C ATOM 128 CA GLNAa 45 186.987 127.209 259.959 1.00100.00 C ATOM 131 CA PHEAa 46 189.115 130.161 259.157 1.00100.00 C ATOM 134 CA THRAa 47 187.356 131.901 256.203 1.00100.00 C ATOM 137 CA GLUAa 48 187.180 134.953 253.965 1.00100.00 C ATOM 140 CA HISAa 49 185.578 136.805 256.905 1.00100.00 C ATOM 143 CA THRAa 50 187.343 135.292 259.938 1.00100.00 C ATOM 146 CA SERAa 51 191.129 135.327 260.339 1.00100.00 C ATOM 149 CA ALAAa 52 191.231 135.094 264.170 1.00100.00 C ATOM 152 CA ILEAa 53 188.989 133.390 266.744 1.00100.00 C ATOM 155 CA LYSAa 54 188.770 134.368 270.428 1.00100.00 C ATOM 158 CA VALAa 55 187.303 131.970 273.016 1.00100.00 C ATOM 161 CA ARGAa 56 185.817 133.382 276.214 1.00100.00 C ATOM 164 CA GLYAa 57 184.672 131.065 278.997 1.00100.00 C ATOM 167 CA LYSAa 58 185.698 127.553 280.004 1.00100.00 C ATOM 170 CA ALAAa 59 186.172 125.294 276.966 1.00100.00 C ATOM 173 CA TYRAa 60 188.258 122.444 275.620 1.00100.00 C ATOM 176 CA ILEAa 61 189.863 123.277 272.265 1.00100.00 C ATOM 179 CA GLNAa 62 191.492 121.098 269.577 1.00100.00 C ATOM 182 CA THRAa 63 193.550 122.431 266.653 1.00100.00 C ATOM 185 CA ARGAa 64 196.271 121.116 264.358 1.00100.00 C ATOM 188 CA HISAa 65 198.826 122.305 266.995 1.00100.00 C ATOM 191 CA GLYAa 66 197.443 120.330 269.914 1.00100.00 C ATOM 194 CA VALAa 67 194.865 120.679 272.646 1.00100.00 C ATOM 197 CA ILEAa 68 194.232 123.486 275.120 1.00100.00 C ATOM 200 CA GLUAa 69 191.576 124.693 277.564 1.00100.00 C ATOM 203 CA SERAa 70 190.301 128.219 277.907 1.00100.00 C ATOM 206 CA GLUAa 71 189.167 129.249 281.377 1.00100.00 C ATOM 209 CA GLYAa 72 186.003 131.073 282.428 1.00100.00 C """ helices_text=""" ATOM 2 CA ALA A 1 11.323 32.055 11.635 1.00 40.00 C ATOM 7 CA ALA A 2 8.288 29.768 10.916 1.00 40.00 C ATOM 12 CA ALA A 3 10.313 27.854 8.231 1.00 40.00 C ATOM 17 CA ALA A 4 13.089 27.116 10.822 1.00 40.00 C ATOM 22 CA ALA A 5 10.573 25.488 13.298 1.00 40.00 C ATOM 27 CA ALA A 6 9.258 23.514 10.260 1.00 40.00 C ATOM 32 CA ALA A 7 12.788 22.543 8.962 1.00 40.00 C ATOM 37 CA ALA A 8 13.846 21.459 12.515 1.00 40.00 C ATOM 42 CA ALA A 9 10.716 19.261 12.994 1.00 40.00 C ATOM 47 CA ALA A 10 11.063 17.985 9.357 1.00 40.00 C ATOM 52 CA ALA A 11 14.754 17.018 9.967 1.00 40.00 C ATOM 57 CA ALA A 12 13.721 15.483 13.371 1.00 40.00 C ATOM 62 CA ALA A 13 10.821 13.516 11.708 1.00 40.00 C ATOM 67 CA ALA A 14 13.246 12.367 8.939 1.00 40.00 C ATOM 72 CA ALA A 15 15.847 11.407 11.629 1.00 40.00 C ATOM 77 CA ALA A 16 13.099 9.317 13.370 1.00 40.00 C ATOM 2 CA ALA B 2 1.733 -3.620 -2.296 1.00 1.00 ATOM 7 CA ALA B 3 -1.902 -4.065 -1.341 1.00 1.00 ATOM 12 CA ALA B 4 -2.941 -0.441 -1.685 1.00 1.00 ATOM 17 CA ALA B 5 -0.320 0.578 -4.218 1.00 1.00 ATOM 22 CA ALA B 6 0.221 -2.836 -5.759 1.00 1.00 ATOM 27 CA ALA B 7 -3.192 -4.271 -4.973 1.00 1.00 ATOM 32 CA ALA B 8 -5.081 -0.993 -4.849 1.00 1.00 ATOM 37 CA ALA B 9 -2.802 0.969 -7.148 1.00 1.00 ATOM 42 CA ALA B 10 -1.460 -1.967 -9.123 1.00 1.00 ATOM 47 CA ALA B 11 -4.418 -4.277 -8.632 1.00 1.00 ATOM 52 CA ALA B 12 -7.044 -1.601 -8.116 1.00 1.00 ATOM 57 CA ALA B 13 -5.323 1.151 -10.064 1.00 1.00 ATOM 62 CA ALA B 14 -3.322 -1.073 -12.383 1.00 1.00 ATOM 67 CA ALA B 15 -5.629 -4.072 -12.291 1.00 1.00 ATOM 72 CA ALA B 16 -8.822 -2.205 -11.488 1.00 1.00 ATOM 77 CA ALA B 17 -7.833 1.122 -12.996 1.00 1.00 ATOM 82 CA ALA B 18 -5.368 -0.211 -15.540 1.00 1.00 ATOM 87 CA ALA B 19 -6.878 -3.661 -15.920 1.00 1.00 ATOM 92 CA ALA B 20 -10.423 -2.748 -14.958 1.00 1.00 ATOM 97 CA ALA B 21 -10.280 0.896 -15.972 1.00 1.00 ATOM 102 CA ALA B 22 -7.582 0.562 -18.606 1.00 1.00 ATOM 2 CA ALA C 2 1.202 -3.661 -1.646 1.00 1.00 C ATOM 7 CA ALA C 3 -1.466 -2.408 -4.020 1.00 1.00 C ATOM 12 CA ALA C 4 1.288 -2.503 -6.614 1.00 1.00 C ATOM 17 CA ALA C 5 0.312 -6.139 -7.010 1.00 1.00 C ATOM 22 CA ALA C 6 -2.284 -4.816 -9.426 1.00 1.00 C ATOM 27 CA ALA C 7 0.502 -5.008 -11.981 1.00 1.00 C ATOM 32 CA ALA C 8 -0.579 -8.614 -12.375 1.00 1.00 C ATOM 37 CA ALA C 9 -3.100 -7.225 -14.833 1.00 1.00 C ATOM 42 CA ALA C 10 -0.285 -7.514 -17.347 1.00 1.00 C ATOM 47 CA ALA C 11 -1.470 -11.087 -17.740 1.00 1.00 C ATOM 52 CA ALA C 12 -3.913 -9.634 -20.239 1.00 1.00 C ATOM 57 CA ALA C 13 -1.074 -10.021 -22.713 1.00 1.00 C ATOM 62 CA ALA C 14 -2.362 -13.558 -23.106 1.00 1.00 C ATOM 67 CA ALA C 15 -4.725 -12.045 -25.646 1.00 1.00 C ATOM 72 CA ALA C 16 -1.865 -12.529 -28.077 1.00 1.00 C ATOM 77 CA ALA C 17 -3.254 -16.028 -28.473 1.00 1.00 C ATOM 82 CA ALA C 18 -5.534 -14.456 -31.052 1.00 1.00 C ATOM 87 CA ALA C 19 -2.657 -15.038 -33.442 1.00 1.00 C ATOM 92 CA ALA C 20 -4.146 -18.495 -33.840 1.00 1.00 C ATOM 97 CA ALA C 21 -6.342 -16.867 -36.458 1.00 1.00 C ATOM 102 CA ALA C 22 -3.451 -17.549 -38.805 1.00 1.00 C """ one_full_helix_text=""" ATOM 1 N ALA A 15 29.207 -2.952 12.868 1.00 16.39 N ATOM 2 CA ALA A 15 27.822 -3.418 12.724 1.00 17.10 C ATOM 3 C ALA A 15 27.023 -3.016 13.951 1.00 16.98 C ATOM 4 O ALA A 15 25.872 -2.551 13.769 1.00 16.78 O ATOM 5 N LEU A 16 27.570 -3.117 15.127 1.00 15.97 N ATOM 6 CA LEU A 16 26.958 -2.649 16.351 1.00 18.20 C ATOM 7 C LEU A 16 26.614 -1.169 16.344 1.00 20.28 C ATOM 8 O LEU A 16 25.599 -0.734 16.933 1.00 18.32 O ATOM 9 N ILE A 17 27.514 -0.365 15.791 1.00 20.97 N ATOM 10 CA ILE A 17 27.343 1.056 15.618 1.00 20.41 C ATOM 11 C ILE A 17 26.081 1.392 14.758 1.00 18.17 C ATOM 12 O ILE A 17 25.380 2.240 15.282 1.00 16.46 O ATOM 13 N SER A 18 25.930 0.759 13.657 1.00 16.97 N ATOM 14 CA SER A 18 24.825 0.827 12.744 1.00 19.98 C ATOM 15 C SER A 18 23.499 0.405 13.438 1.00 18.89 C ATOM 16 O SER A 18 22.557 1.165 13.352 1.00 18.37 O ATOM 17 N TRP A 19 23.512 -0.661 14.161 1.00 17.71 N ATOM 18 CA TRP A 19 22.492 -1.085 15.081 1.00 15.72 C ATOM 19 C TRP A 19 22.083 0.004 16.012 1.00 18.02 C ATOM 20 O TRP A 19 20.820 0.244 16.160 1.00 16.93 O ATOM 21 N ILE A 20 22.930 0.594 16.823 1.00 14.82 N ATOM 22 CA ILE A 20 22.628 1.633 17.766 1.00 15.67 C ATOM 23 C ILE A 20 21.917 2.819 17.080 1.00 17.51 C ATOM 24 O ILE A 20 20.942 3.365 17.655 1.00 17.70 O ATOM 25 N LYS A 21 22.464 3.177 15.957 1.00 16.61 N ATOM 26 CA LYS A 21 21.888 4.236 15.157 1.00 19.84 C ATOM 27 C LYS A 21 20.436 3.910 14.752 1.00 21.02 C ATOM 28 O LYS A 21 19.685 4.899 14.971 1.00 22.80 O """ one_helix_beginning_text=""" ATOM 2 CA ALA A 1 11.323 32.055 11.635 1.00 40.00 C ATOM 7 CA ALA A 2 8.288 29.768 10.916 1.00 40.00 C ATOM 12 CA ALA A 3 10.313 27.854 8.231 1.00 40.00 C ATOM 17 CA ALA A 4 13.089 27.116 10.822 1.00 40.00 C ATOM 22 CA ALA A 5 10.573 25.488 13.298 1.00 40.00 C ATOM 27 CA ALA A 6 9.258 23.514 10.260 1.00 40.00 C ATOM 32 CA ALA A 7 12.788 22.543 8.962 1.00 40.00 C ATOM 37 CA ALA A 8 13.846 21.459 12.515 1.00 40.00 C """ one_helix_end_text=""" ATOM 42 CA ALA A 9 10.716 19.261 12.994 1.00 40.00 C ATOM 47 CA ALA A 10 11.063 17.985 9.357 1.00 40.00 C ATOM 52 CA ALA A 11 14.754 17.018 9.967 1.00 40.00 C ATOM 57 CA ALA A 12 13.721 15.483 13.371 1.00 40.00 C ATOM 62 CA ALA A 13 10.821 13.516 11.708 1.00 40.00 C ATOM 67 CA ALA A 14 13.246 12.367 8.939 1.00 40.00 C ATOM 72 CA ALA A 15 15.847 11.407 11.629 1.00 40.00 C ATOM 77 CA ALA A 16 13.099 9.317 13.370 1.00 40.00 C """ one_helix_middle_text=""" ATOM 22 CA ALA A 5 10.573 25.488 13.298 1.00 40.00 C ATOM 27 CA ALA A 6 9.258 23.514 10.260 1.00 40.00 C ATOM 32 CA ALA A 7 12.788 22.543 8.962 1.00 40.00 C ATOM 37 CA ALA A 8 13.846 21.459 12.515 1.00 40.00 C ATOM 42 CA ALA A 9 10.716 19.261 12.994 1.00 40.00 C ATOM 47 CA ALA A 10 11.063 17.985 9.357 1.00 40.00 C ATOM 52 CA ALA A 11 14.754 17.018 9.967 1.00 40.00 C ATOM 57 CA ALA A 12 13.721 15.483 13.371 1.00 40.00 C ATOM 62 CA ALA A 13 10.821 13.516 11.708 1.00 40.00 C """ one_helix_text=""" ATOM 2 CA ALA A 1 11.323 32.055 11.635 1.00 40.00 C ATOM 7 CA ALA A 2 8.288 29.768 10.916 1.00 40.00 C ATOM 12 CA ALA A 3 10.313 27.854 8.231 1.00 40.00 C ATOM 17 CA ALA A 4 13.089 27.116 10.822 1.00 40.00 C ATOM 22 CA ALA A 5 10.573 25.488 13.298 1.00 40.00 C ATOM 27 CA ALA A 6 9.258 23.514 10.260 1.00 40.00 C ATOM 32 CA ALA A 7 12.788 22.543 8.962 1.00 40.00 C ATOM 37 CA ALA A 8 13.846 21.459 12.515 1.00 40.00 C ATOM 42 CA ALA A 9 10.716 19.261 12.994 1.00 40.00 C ATOM 47 CA ALA A 10 11.063 17.985 9.357 1.00 40.00 C ATOM 52 CA ALA A 11 14.754 17.018 9.967 1.00 40.00 C ATOM 57 CA ALA A 12 13.721 15.483 13.371 1.00 40.00 C ATOM 62 CA ALA A 13 10.821 13.516 11.708 1.00 40.00 C ATOM 67 CA ALA A 14 13.246 12.367 8.939 1.00 40.00 C ATOM 72 CA ALA A 15 15.847 11.407 11.629 1.00 40.00 C ATOM 77 CA ALA A 16 13.099 9.317 13.370 1.00 40.00 C """ two_helix_text=""" ATOM 2 CA GLY A 1 43.603 -11.488 24.325 1.00 35.57 ATOM 6 CA ILE A 2 44.200 -8.183 22.475 1.00 27.55 ATOM 14 CA GLY A 3 43.999 -10.264 19.329 1.00 21.05 ATOM 18 CA ALA A 4 40.378 -11.260 20.106 1.00 21.80 ATOM 23 CA VAL A 5 39.355 -7.658 21.083 1.00 19.34 ATOM 30 CA LEU A 6 41.062 -6.432 17.957 1.00 17.59 ATOM 38 CA LYS A 7 39.079 -8.646 15.636 1.00 22.55 ATOM 47 CA VAL A 8 35.792 -7.369 17.211 1.00 20.52 ATOM 69 CA THR A 11 34.132 -6.405 12.343 1.00 24.14 ATOM 76 CA GLY A 12 31.584 -6.595 15.140 1.00 24.17 ATOM 80 CA LEU A 13 31.923 -2.919 16.364 1.00 23.24 ATOM 88 CA PRO A 14 31.026 -1.278 13.030 1.00 17.52 ATOM 95 CA ALA A 15 27.822 -3.418 12.724 1.00 17.10 ATOM 100 CA LEU A 16 26.958 -2.649 16.351 1.00 18.20 ATOM 108 CA ILE A 17 27.343 1.056 15.618 1.00 20.41 ATOM 116 CA SER A 18 24.825 0.827 12.744 1.00 19.98 ATOM 122 CA TRP A 19 22.492 -1.085 15.081 1.00 15.72 ATOM 136 CA ILE A 20 22.628 1.633 17.766 1.00 15.67 ATOM 144 CA LYS A 21 21.888 4.236 15.157 1.00 19.84 ATOM 153 CA ARG A 22 18.740 2.273 14.020 1.00 20.38 ATOM 164 CA LYS A 23 17.500 1.928 17.550 1.00 22.62 ATOM 173 CA ARG A 24 18.059 5.674 18.276 1.00 27.11 ATOM 184 CA GLN A 25 15.836 6.730 15.339 1.00 37.50 ATOM 193 CA GLN A 26 13.132 4.360 16.583 1.00 46.66 """ two_chain_text=""" ATOM 375 N TYR A 50 6.211 -13.569 8.292 1.00 10.98 N ATOM 376 CA TYR A 50 7.318 -12.627 8.487 1.00 10.61 C ATOM 377 C TYR A 50 6.766 -11.320 9.020 1.00 9.44 C ATOM 378 O TYR A 50 5.608 -10.952 8.800 1.00 10.44 O ATOM 379 CB TYR A 50 8.112 -12.427 7.166 1.00 11.77 C ATOM 380 CG TYR A 50 8.994 -13.649 6.910 1.00 14.04 C ATOM 381 CD1 TYR A 50 8.495 -14.805 6.394 1.00 14.79 C ATOM 382 CD2 TYR A 50 10.334 -13.645 7.280 1.00 15.78 C ATOM 383 CE1 TYR A 50 9.309 -15.912 6.201 1.00 16.35 C ATOM 384 CE2 TYR A 50 11.185 -14.715 7.104 1.00 17.74 C ATOM 385 CZ TYR A 50 10.649 -15.862 6.545 1.00 17.61 C ATOM 386 OH TYR A 50 11.444 -16.974 6.380 1.00 22.90 O ATOM 387 N ILE A 51 7.626 -10.601 9.716 1.00 9.43 N ATOM 388 CA ILE A 51 7.269 -9.357 10.407 1.00 8.71 C ATOM 389 C ILE A 51 7.916 -8.211 9.657 1.00 8.94 C ATOM 390 O ILE A 51 9.112 -7.923 9.789 1.00 9.49 O ATOM 391 CB ILE A 51 7.636 -9.391 11.898 1.00 9.57 C ATOM 392 CG1 ILE A 51 6.877 -10.489 12.634 1.00 11.51 C ATOM 393 CG2 ILE A 51 7.340 -8.025 12.509 1.00 9.99 C ATOM 394 CD1 ILE A 51 7.189 -11.913 12.447 1.00 13.04 C ATOM 395 N TYR A 52 7.103 -7.549 8.818 1.00 8.87 N ATOM 396 CA TYR A 52 7.523 -6.401 8.024 1.00 8.95 C ATOM 397 C TYR A 52 7.566 -5.196 8.933 1.00 8.79 C ATOM 398 O TYR A 52 6.546 -4.870 9.560 1.00 9.43 O ATOM 399 CB TYR A 52 6.599 -6.227 6.809 1.00 9.82 C ATOM 400 CG TYR A 52 6.769 -7.352 5.826 1.00 9.77 C ATOM 401 CD1 TYR A 52 6.171 -8.583 6.037 1.00 10.04 C ATOM 402 CD2 TYR A 52 7.581 -7.227 4.699 1.00 11.49 C ATOM 403 CE1 TYR A 52 6.330 -9.627 5.177 1.00 11.90 C ATOM 404 CE2 TYR A 52 7.751 -8.274 3.800 1.00 12.84 C ATOM 405 CZ TYR A 52 7.116 -9.468 4.045 1.00 12.86 C ATOM 406 OH TYR A 52 7.270 -10.516 3.193 1.00 14.57 O ATOM 407 N THR A 53 8.737 -4.586 9.055 1.00 8.30 N ATOM 408 CA THR A 53 8.996 -3.643 10.133 1.00 8.29 C ATOM 409 C THR A 53 9.384 -2.299 9.550 1.00 8.26 C ATOM 410 O THR A 53 10.386 -2.196 8.794 1.00 10.05 O ATOM 411 CB THR A 53 10.098 -4.225 11.054 1.00 9.01 C ATOM 412 OG1 THR A 53 9.695 -5.497 11.548 1.00 9.73 O ATOM 413 CG2 THR A 53 10.340 -3.320 12.250 1.00 10.75 C ATOM 414 N TYR A 54 8.595 -1.292 9.883 1.00 8.50 N ATOM 415 CA TYR A 54 8.688 0.046 9.368 1.00 8.54 C ATOM 416 C TYR A 54 9.130 0.977 10.480 1.00 9.00 C ATOM 417 O TYR A 54 8.469 1.106 11.537 1.00 9.89 O ATOM 418 CB TYR A 54 7.350 0.517 8.786 1.00 9.33 C ATOM 419 CG TYR A 54 6.866 -0.378 7.660 1.00 9.22 C ATOM 420 CD1 TYR A 54 6.113 -1.523 7.899 1.00 9.26 C ATOM 421 CD2 TYR A 54 7.207 -0.083 6.368 1.00 9.45 C ATOM 422 CE1 TYR A 54 5.683 -2.351 6.899 1.00 9.56 C ATOM 423 CE2 TYR A 54 6.783 -0.929 5.368 1.00 10.19 C ATOM 424 CZ TYR A 54 6.039 -2.054 5.609 1.00 9.31 C ATOM 425 OH TYR A 54 5.593 -2.884 4.606 1.00 10.62 O ATOM 426 N ARG A 55 10.273 1.635 10.317 1.00 8.99 N ATOM 427 CA ARG A 55 10.779 2.540 11.331 1.00 9.30 C ATOM 428 C ARG A 55 10.006 3.855 11.284 1.00 9.04 C ATOM 429 O ARG A 55 9.809 4.438 10.215 1.00 10.80 O ATOM 430 CB ARG A 55 12.255 2.778 11.090 1.00 9.60 C ATOM 431 CG ARG A 55 13.089 1.503 11.251 1.00 11.09 C ATOM 432 CD ARG A 55 14.531 1.724 10.963 1.00 12.60 C ATOM 433 NE ARG A 55 15.393 0.536 10.991 1.00 12.79 N ATOM 434 CZ ARG A 55 15.853 -0.067 9.907 1.00 11.24 C ATOM 435 NH1 ARG A 55 15.601 0.267 8.635 1.00 13.70 N ATOM 436 NH2 ARG A 55 16.683 -1.110 10.084 1.00 12.83 N ATOM 437 N VAL A 56 9.574 4.315 12.463 1.00 9.17 N ATOM 438 CA VAL A 56 8.706 5.468 12.645 1.00 9.47 C ATOM 439 C VAL A 56 9.399 6.439 13.577 1.00 9.55 C ATOM 440 O VAL A 56 9.819 6.065 14.671 1.00 11.35 O ATOM 441 CB VAL A 56 7.334 5.020 13.148 1.00 10.23 C ATOM 442 CG1 VAL A 56 6.464 6.185 13.566 1.00 13.31 C ATOM 443 CG2 VAL A 56 6.623 4.148 12.100 1.00 11.48 C ATOM 444 N SER A 57 9.486 7.688 13.122 1.00 10.07 N ATOM 445 CA SER A 57 10.220 8.739 13.797 1.00 11.56 C ATOM 446 C SER A 57 9.413 10.020 13.948 1.00 10.72 C ATOM 447 O SER A 57 8.594 10.296 13.076 1.00 10.93 O ATOM 448 CB SER A 57 11.541 9.078 13.005 1.00 13.02 C ATOM 449 OG SER A 57 12.275 7.871 12.757 1.00 16.49 O ATOM 877 N LEU B 278 13.003 -13.579 11.217 1.00 14.16 N ATOM 878 CA LEU B 278 11.645 -13.391 10.746 1.00 13.77 C ATOM 879 C LEU B 278 11.240 -11.932 10.544 1.00 12.73 C ATOM 880 O LEU B 278 10.118 -11.639 10.140 1.00 19.80 O ATOM 881 CB LEU B 278 10.621 -14.010 11.721 1.00 17.07 C ATOM 882 CG LEU B 278 10.887 -15.612 11.784 1.00 20.72 C ATOM 883 CD1 LEU B 278 9.743 -16.058 12.768 1.00 26.78 C ATOM 884 CD2 LEU B 278 10.513 -16.229 10.192 1.00 22.51 C ATOM 885 N THR B 279 12.124 -11.019 10.844 1.00 10.85 N ATOM 886 CA THR B 279 11.888 -9.580 10.658 1.00 10.91 C ATOM 887 C THR B 279 12.501 -9.102 9.356 1.00 11.12 C ATOM 888 O THR B 279 13.671 -9.407 9.078 1.00 12.89 O ATOM 889 CB THR B 279 12.517 -8.801 11.813 1.00 10.60 C ATOM 890 OG1 THR B 279 11.721 -8.935 12.994 1.00 11.57 O ATOM 891 CG2 THR B 279 12.676 -7.301 11.552 1.00 12.09 C ATOM 892 N ILE B 280 11.699 -8.402 8.572 1.00 10.77 N ATOM 893 CA ILE B 280 12.101 -7.808 7.306 1.00 10.70 C ATOM 894 C ILE B 280 11.929 -6.297 7.452 1.00 9.56 C ATOM 895 O ILE B 280 10.802 -5.815 7.480 1.00 11.05 O ATOM 896 CB ILE B 280 11.283 -8.353 6.135 1.00 11.04 C ATOM 897 CG1 ILE B 280 11.443 -9.854 5.977 1.00 12.99 C ATOM 898 CG2 ILE B 280 11.674 -7.630 4.848 1.00 13.91 C ATOM 899 CD1 ILE B 280 10.627 -10.530 4.933 1.00 15.29 C ATOM 900 N TYR B 281 13.017 -5.563 7.612 1.00 9.95 N ATOM 901 CA TYR B 281 12.918 -4.104 7.622 1.00 10.00 C ATOM 902 C TYR B 281 12.476 -3.631 6.240 1.00 10.83 C ATOM 903 O TYR B 281 13.016 -4.065 5.216 1.00 13.82 O ATOM 904 CB TYR B 281 14.242 -3.422 8.111 1.00 11.29 C ATOM 905 CG TYR B 281 14.359 -3.643 9.634 1.00 11.38 C ATOM 906 CD1 TYR B 281 15.128 -4.632 10.167 1.00 12.02 C ATOM 907 CD2 TYR B 281 13.622 -2.828 10.483 1.00 12.75 C ATOM 908 CE1 TYR B 281 15.185 -4.790 11.579 1.00 12.84 C ATOM 909 CE2 TYR B 281 13.646 -2.973 11.857 1.00 13.88 C ATOM 910 CZ TYR B 281 14.427 -3.954 12.373 1.00 14.15 C ATOM 911 OH TYR B 281 14.404 -4.084 13.775 1.00 16.24 O ATOM 912 N ALA B 282 11.500 -2.767 6.208 1.00 10.01 N ATOM 913 CA ALA B 282 10.815 -2.397 4.984 1.00 11.13 C ATOM 914 C ALA B 282 10.577 -0.889 4.965 1.00 10.30 C ATOM 915 O ALA B 282 10.663 -0.156 5.937 1.00 10.83 O ATOM 916 CB ALA B 282 9.496 -3.180 4.899 1.00 14.45 C """ multi_copy_text=""" ATOM 1 CA SERG2 11 672.659 271.890 642.978 1.00151.51 C ATOM 2 CA HISG2 12 673.739 270.409 646.320 1.00157.48 C ATOM 3 CA THRG2 13 676.617 268.051 647.149 1.00156.68 C ATOM 4 CA GLYG2 14 675.899 264.844 649.034 1.00154.13 C ATOM 5 CA GLYG2 15 679.108 264.054 650.891 1.00153.97 C ATOM 6 CA THRG2 23 674.070 258.460 655.967 1.00160.53 C ATOM 7 CA THRG2 24 676.423 255.647 656.957 1.00160.10 C ATOM 8 CA ALAG2 25 679.963 254.891 655.848 1.00154.17 C ATOM 9 CA ALAG2 26 680.922 251.245 656.223 1.00154.52 C ATOM 10 CA ILEG2 37 680.349 251.357 651.276 1.00154.78 C ATOM 11 CA ILEG2 38 678.241 254.479 651.807 1.00152.40 C ATOM 12 CA GLYG2 39 674.481 254.465 652.075 1.00157.18 C ATOM 13 CA PHEG2 40 672.890 257.774 651.173 1.00152.30 C ATOM 14 CA GLUG2 41 669.611 257.161 652.958 1.00156.89 C ATOM 15 CA ILEG2 49 666.867 263.693 645.296 1.00158.19 C ATOM 16 CA GLUG2 50 667.733 263.423 641.604 1.00158.68 C ATOM 17 CA TYRG2 51 671.207 262.216 640.645 1.00151.14 C ATOM 18 CA VALG2 52 671.421 262.783 636.919 1.00155.98 C ATOM 19 CA GLYG2 53 674.142 261.362 634.725 1.00154.05 C ATOM 20 CA PROG2 62 690.221 255.358 649.160 1.00161.63 C ATOM 21 CA ARGG2 63 693.277 254.515 651.225 1.00159.36 C ATOM 22 CA THRG2 64 693.822 251.215 653.008 1.00158.95 C ATOM 23 CA THRG2 65 695.857 250.702 656.156 1.00160.97 C ATOM 24 CA GLUG2 66 699.182 248.925 656.483 1.00163.99 C ATOM 25 CA SERG2 67 701.205 248.093 659.588 1.00166.35 C ATOM 26 CA ILEG2 68 704.997 247.740 659.591 1.00170.65 C ATOM 27 CA THRG2 69 707.072 246.430 662.481 1.00173.92 C ATOM 28 CA GLYG2 70 710.480 248.079 662.226 1.00177.42 C ATOM 29 CA ASPG2 75 713.949 252.746 655.039 1.00173.01 C ATOM 30 CA THRG2 76 712.573 250.621 652.174 1.00170.65 C ATOM 31 CA VALG2 77 708.870 249.996 652.727 1.00169.78 C ATOM 32 CA VALG2 78 707.766 246.476 651.749 1.00172.32 C ATOM 33 CA VALG2 100 699.875 259.341 647.120 1.00166.60 C ATOM 34 CA ALAG2 101 700.963 257.718 650.404 1.00164.58 C ATOM 35 CA VALG2 102 701.179 258.953 653.979 1.00162.87 C ATOM 36 CA ALAG2 103 702.867 257.427 656.993 1.00165.65 C ATOM 37 CA TYRG2 104 702.632 257.897 660.750 1.00167.15 C ATOM 38 CA ASNG2 105 704.941 256.587 663.466 1.00170.08 C ATOM 39 CA VALG2 106 702.716 255.629 666.398 1.00168.11 C ATOM 40 CA GLYG2 109 703.748 260.527 667.204 1.00167.04 C ATOM 41 CA VALG2 110 705.343 262.143 664.141 1.00167.66 C ATOM 42 CA GLNG2 111 704.011 262.240 660.588 1.00166.26 C ATOM 43 CA VALG2 112 706.906 260.533 658.815 1.00167.70 C ATOM 44 CA ALAG2 116 711.004 258.660 647.111 1.00169.85 C ATOM 45 CA VALG2 117 708.484 256.299 645.553 1.00170.77 C ATOM 46 CA ASPG2 118 708.969 253.226 643.380 1.00174.41 C ATOM 47 CA TYRG2 119 705.807 252.551 641.381 1.00171.25 C ATOM 48 CA ASPG2 122 704.803 249.088 644.789 1.00174.07 C ATOM 49 CA GLUG2 123 707.403 250.324 647.277 1.00173.78 C ATOM 50 CA VALG2 124 707.938 253.704 648.922 1.00169.72 C ATOM 51 CA THRG2 125 710.797 255.033 651.041 1.00171.78 C ATOM 52 CA LEUG2 126 710.575 256.678 654.450 1.00169.68 C ATOM 53 CA ASPG2 134 708.092 250.470 666.277 1.00176.26 C ATOM 54 CA THRG2 135 704.740 250.368 664.472 1.00172.24 C ATOM 55 CA VALG2 136 704.731 252.503 661.323 1.00167.53 C ATOM 56 CA LYSG2 137 701.217 252.839 659.914 1.00163.35 C ATOM 57 CA VALG2 138 701.163 253.650 656.194 1.00162.44 C ATOM 58 CA TRPG2 139 698.086 254.634 654.195 1.00161.65 C ATOM 59 CA PROG2 140 698.736 254.094 650.473 1.00160.01 C ATOM 60 CA ILEG2 141 696.468 255.002 647.598 1.00161.49 C ATOM 61 CA METG2 142 694.160 252.243 646.370 1.00158.89 C ATOM 62 CA GLYG2 145 688.472 248.069 642.529 1.00161.75 C ATOM 63 CA ASPG2 146 684.984 248.329 641.037 1.00161.37 C ATOM 64 CA VALG2 147 682.243 250.828 641.888 1.00155.59 C ATOM 65 CA GLNG2 148 678.568 251.150 640.989 1.00152.50 C ATOM 66 CA PHEG2 149 675.564 253.048 642.353 1.00151.93 C ATOM 67 CA ARGG2 150 672.598 250.981 643.552 1.00151.84 C ATOM 68 CA LEUG2 151 669.086 252.076 644.529 1.00150.99 C ATOM 69 CA VALG2 152 667.838 250.000 647.467 1.00152.42 C ATOM 70 CA ASNG2 153 664.134 250.339 648.278 1.00153.50 C ATOM 71 CA PROG2 168 687.142 250.935 637.661 1.00160.31 C ATOM 72 CA LEUG2 169 688.516 252.524 640.783 1.00159.19 C ATOM 73 CA TYRG2 170 692.006 253.510 639.589 1.00162.34 C ATOM 74 CA ARGG2 171 690.581 255.651 636.779 1.00163.81 C ATOM 75 CA TRPG2 172 689.312 257.923 639.532 1.00159.04 C ATOM 76 CA HISG2 173 693.019 258.504 640.236 1.00160.31 C ATOM 77 CA ASPG2 174 694.707 258.891 636.838 1.00163.51 C ATOM 78 CA PHEG2 175 692.359 261.697 635.895 1.00164.10 C ATOM 79 CA PROG2 176 692.847 264.852 637.973 1.00164.94 C ATOM 80 CA GLYG2 188 672.254 256.633 634.404 1.00150.48 C ATOM 81 CA SERG2 189 669.843 258.590 636.542 1.00151.32 C ATOM 82 CA VALG2 190 668.359 258.078 640.009 1.00150.42 C ATOM 83 CA THRG2 191 665.323 259.881 641.397 1.00151.52 C ATOM 84 CA TRPG2 192 665.114 258.592 644.952 1.00154.98 C ATOM 85 CA GLUG2 196 664.755 254.887 649.832 1.00156.20 C ATOM 86 CA THRG2 197 668.559 254.735 649.786 1.00155.71 C ATOM 87 CA VALG2 198 671.434 254.866 647.309 1.00153.21 C ATOM 88 CA GLUG2 199 674.434 252.722 648.164 1.00153.70 C ATOM 89 CA VALG2 200 677.820 252.558 646.464 1.00151.33 C ATOM 90 CA LEUG2 201 679.168 249.071 645.768 1.00153.34 C ATOM 91 CA LEUG2 202 682.922 248.516 645.715 1.00156.54 C ATOM 92 CA ASPG2 203 684.797 245.322 644.888 1.00164.02 C ATOM 93 CA ALAG2 204 688.441 245.597 645.932 1.00161.21 C ATOM 94 CA GLUG2 225 680.703 263.065 647.464 1.00156.34 C ATOM 95 CA GLNG2 226 678.643 263.859 644.399 1.00154.90 C ATOM 96 CA ASPG2 227 676.860 266.889 643.014 1.00156.12 C ATOM 97 CA VALG2 228 673.131 266.174 642.923 1.00155.70 C ATOM 98 CA GLUG2 229 670.054 268.163 641.926 1.00154.93 C TER ATOM 99 CA ARGWy 15 120.437 414.861 579.347 1.00 30.00 C ATOM 100 CA LEUWy 16 118.463 412.415 577.240 1.00 30.00 C ATOM 101 CA GLYWy 17 118.534 409.852 580.055 1.00 30.00 C ATOM 102 CA ARGWy 18 117.304 412.493 582.499 1.00 30.00 C ATOM 103 CA LEUWy 19 114.479 413.600 580.202 1.00 30.00 C ATOM 104 CA VALWy 20 113.409 409.997 579.631 1.00 30.00 C ATOM 105 CA ASPWy 21 113.538 409.209 583.359 1.00 30.00 C ATOM 106 CA VALWy 22 111.688 412.291 584.630 1.00 30.00 C ATOM 107 CA LEUWy 23 108.997 411.976 581.954 1.00 30.00 C ATOM 108 CA GLUWy 24 108.327 408.259 582.608 1.00 30.00 C ATOM 109 CA SERWy 36 103.189 389.864 586.522 1.00 30.00 C ATOM 110 CA VALWy 37 101.527 389.072 583.207 1.00 30.00 C ATOM 111 CA THRWy 38 99.495 386.332 584.885 1.00 30.00 C ATOM 112 CA GLNWy 39 98.146 388.814 587.414 1.00 30.00 C ATOM 113 CA ASNWy 40 97.643 391.329 584.620 1.00 30.00 C ATOM 114 CA ILEWy 41 95.385 388.873 582.829 1.00 30.00 C ATOM 115 CA ASPWy 42 93.727 387.970 586.116 1.00 30.00 C ATOM 116 CA ARGWy 43 92.880 391.586 586.908 1.00 30.00 C ATOM 117 CA THRWy 44 90.369 391.588 584.049 1.00 30.00 C ATOM 118 CA ARGWy 45 89.329 387.934 583.798 1.00 30.00 C ATOM 119 CA TYRWy 57 84.834 397.337 600.087 1.00 28.58 C ATOM 120 CA PHEWy 58 84.256 397.935 603.745 1.00 28.58 C ATOM 121 CA SERWy 59 81.080 397.288 605.631 1.00 28.58 C ATOM 122 CA THRWy 60 80.129 397.085 609.232 1.00 28.58 C ATOM 123 CA TRPWy 73 85.481 408.794 620.165 1.00 28.58 C ATOM 124 CA GLUWy 74 85.299 405.315 618.767 1.00 28.58 C ATOM 125 CA ARGWy 75 87.588 404.794 615.793 1.00 28.58 C ATOM 126 CA LEUWy 76 86.761 402.474 612.929 1.00 28.58 C ATOM 127 CA ASPWy 77 89.512 401.568 610.492 1.00 28.58 C ATOM 128 CA GLUWy 83 86.218 407.191 598.572 1.00 28.58 C ATOM 129 CA THRWy 84 82.465 406.937 598.909 1.00 28.58 C ATOM 130 CA VALWy 85 81.270 406.635 602.487 1.00 28.58 C ATOM 131 CA ASNWy 86 77.658 405.777 603.207 1.00 28.58 C ATOM 132 CA ILEWy 87 76.187 406.153 606.676 1.00 28.58 C ATOM 133 CA ARGWy 88 72.820 404.596 607.396 1.00 28.58 C ATOM 134 CA THRWy 89 72.114 406.202 610.718 1.00 28.58 C ATOM 135 CA ASPWy 92 71.821 410.436 615.695 1.00 28.58 C ATOM 136 CA ILEWy 93 75.581 410.571 615.331 1.00 28.58 C ATOM 137 CA ASPWy 94 78.611 412.814 615.160 1.00 28.58 C ATOM 138 CA ILEWy 95 80.918 411.557 612.441 1.00 28.58 C ATOM 139 CA ALAWy 96 84.503 412.633 611.924 1.00 28.58 C ATOM 140 CA PHEWy 97 87.164 412.454 609.238 1.00 28.58 C ATOM 141 CA VALWy 106 83.050 417.115 612.993 1.00 28.58 C ATOM 142 CA ILEWy 107 79.837 416.570 611.051 1.00 28.58 C ATOM 143 CA ARGWy 108 76.512 415.914 612.727 1.00 28.58 C ATOM 144 CA VALWy 109 74.028 413.525 611.136 1.00 28.58 C ATOM 145 CA ARGWy 110 70.503 413.339 612.503 1.00 28.58 C ATOM 146 CA PROWy 115 71.316 408.056 604.780 1.00 28.58 C ATOM 147 CA PHEWy 116 74.355 410.264 604.459 1.00 28.58 C ATOM 148 CA THRWy 117 76.453 409.808 601.328 1.00 28.58 C ATOM 149 CA ILEWy 118 79.595 411.826 601.263 1.00 28.58 C ATOM 150 CA PHEWy 128 89.716 406.354 608.844 1.00 28.58 C ATOM 151 CA ILEWy 129 86.461 407.343 610.499 1.00 28.58 C ATOM 152 CA TRPWy 130 85.322 408.270 613.973 1.00 28.58 C ATOM 153 CA LEUWy 131 81.953 408.127 615.714 1.00 28.58 C ATOM 154 CA ARGWy 132 80.468 409.700 618.829 1.00 28.58 C ATOM 155 CA GLNWy 133 76.929 409.395 620.092 1.00 28.58 C ATOM 156 CA GLYWy 142 73.668 402.397 612.876 1.00 28.58 C ATOM 157 CA ILEWy 143 75.268 400.971 609.792 1.00 28.58 C ATOM 158 CA GLNWy 144 78.292 401.955 607.690 1.00 28.58 C ATOM 159 CA ILEWy 145 78.857 400.860 604.078 1.00 28.58 C ATOM 160 CA ILEWy 146 81.877 402.244 602.293 1.00 28.58 C ATOM 161 CA ALAWy 147 82.888 401.759 598.671 1.00 28.58 C ATOM 162 CA PHEWy 148 86.162 402.464 596.931 1.00 28.58 C TER ATOM 163 CA PHEzy 21 113.436 495.542 626.654 1.00 30.00 C ATOM 164 CA VALzy 22 113.344 495.929 630.415 1.00 30.00 C ATOM 165 CA ASPzy 23 111.073 495.290 633.374 1.00 7.88 C ATOM 166 CA GLUzy 24 110.713 497.176 636.654 1.00 8.25 C ATOM 167 CA LEUzy 37 115.682 496.432 636.616 1.00 3.32 C ATOM 168 CA THRzy 38 115.672 493.374 634.376 1.00 3.35 C ATOM 169 CA ILEzy 39 116.974 493.440 630.814 1.00 3.43 C ATOM 170 CA GLUzy 40 115.421 490.561 628.809 1.00 3.74 C ATOM 171 CA THRzy 71 122.977 501.491 649.055 1.00 3.59 C ATOM 172 CA ARGzy 72 124.767 499.630 646.282 1.00 3.24 C ATOM 173 CA VALzy 73 123.947 499.218 642.600 1.00 2.99 C ATOM 174 CA ILEzy 74 125.116 495.999 640.938 1.00 3.00 C ATOM 175 CA VALzy 75 124.701 495.686 637.171 1.00 3.12 C ATOM 176 CA GLNzy 76 125.420 492.035 636.492 1.00 3.11 C ATOM 177 CA LYSzy 77 125.353 489.678 633.523 1.00 3.48 C ATOM 178 CA CYSzy 78 122.996 486.732 633.998 1.00 3.94 C ATOM 179 CA VALzy 90 130.042 494.542 634.875 1.00 30.00 C ATOM 180 CA PHEzy 91 129.274 497.308 637.383 1.00 7.58 C ATOM 181 CA ASNzy 92 129.328 497.553 641.172 1.00 6.80 C ATOM 182 CA ASPzy 93 129.197 500.879 642.972 1.00 5.89 C ATOM 183 CA THRzy 94 127.604 502.711 645.868 1.00 5.58 C ATOM 184 CA LEUzy 95 124.478 504.593 644.818 1.00 5.02 C ATOM 185 CA GLYzy 96 125.346 507.430 647.193 1.00 30.00 C ATOM 186 CA ARGzy 97 128.447 508.119 645.122 1.00 30.00 C ATOM 187 CA PHEzy 98 126.202 509.190 642.228 1.00 4.76 C ATOM 188 CA ASPzy 99 124.945 512.783 642.059 1.00 4.32 C ATOM 189 CA ASPzy 106 129.213 516.851 632.338 1.00 5.14 C ATOM 190 CA PROzy 107 131.268 513.924 630.990 1.00 4.90 C ATOM 191 CA ASPzy 108 133.647 514.165 633.930 1.00 30.00 C ATOM 192 CA PHEzy 109 130.662 513.533 636.226 1.00 30.00 C ATOM 193 CA METzy 110 129.553 510.289 634.565 1.00 5.10 C ATOM 194 CA ARGzy 111 130.189 506.721 635.712 1.00 4.66 C ATOM 195 CA ILEzy 124 119.871 488.710 630.783 1.00 4.01 C ATOM 196 CA VALzy 125 121.381 491.733 632.532 1.00 3.51 C ATOM 197 CA LYSzy 126 120.037 492.423 636.008 1.00 3.27 C ATOM 198 CA VALzy 127 120.267 495.388 638.357 1.00 3.08 C ATOM 199 CA PHEzy 128 120.504 494.509 642.045 1.00 3.07 C ATOM 200 CA VALzy 129 119.824 497.272 644.564 1.00 30.00 C ATOM 201 CA ASPzy 130 121.341 496.425 647.959 1.00 30.00 C ATOM 202 CA ILEzy 131 119.598 498.577 650.580 1.00 30.00 C """ strands_text=""" ATOM 1 N GLY B 23 75.748 31.574 -24.376 1.00 58.86 N ATOM 2 CA GLY B 23 76.475 30.862 -25.415 1.00 59.81 C ATOM 3 C GLY B 23 77.927 30.531 -25.134 1.00 60.79 C ATOM 4 O GLY B 23 78.447 30.790 -24.037 1.00 61.67 O ATOM 5 N PHE B 24 78.585 29.965 -26.144 1.00 61.14 N ATOM 6 CA PHE B 24 79.949 29.472 -26.012 1.00 61.19 C ATOM 7 C PHE B 24 80.944 30.243 -26.876 1.00 63.09 C ATOM 8 O PHE B 24 80.642 30.610 -28.010 1.00 64.18 O ATOM 9 N ARG B 25 82.129 30.486 -26.333 1.00 64.55 N ATOM 10 CA ARG B 25 83.259 31.022 -27.092 1.00 66.14 C ATOM 11 C ARG B 25 84.369 30.015 -26.941 1.00 67.43 C ATOM 12 O ARG B 25 84.649 29.575 -25.829 1.00 67.73 O ATOM 13 N HIS B 26 85.003 29.620 -28.035 1.00 69.33 N ATOM 14 CA HIS B 26 86.018 28.591 -27.914 1.00 70.83 C ATOM 15 C HIS B 26 87.300 28.976 -28.604 1.00 71.56 C ATOM 16 O HIS B 26 87.385 30.005 -29.255 1.00 71.19 O ATOM 17 N GLN B 27 88.303 28.131 -28.423 1.00 73.27 N ATOM 18 CA GLN B 27 89.565 28.220 -29.128 1.00 74.94 C ATOM 19 C GLN B 27 90.136 26.807 -29.242 1.00 75.41 C ATOM 20 O GLN B 27 90.278 26.098 -28.245 1.00 75.24 O ATOM 21 N ASN B 28 90.430 26.392 -30.470 1.00 76.59 N ATOM 22 CA ASN B 28 91.030 25.085 -30.727 1.00 77.27 C ATOM 23 C ASN B 28 92.077 25.140 -31.836 1.00 78.04 C ATOM 24 O ASN B 28 92.478 26.226 -32.274 1.00 77.66 O ATOM 25 N GLY B 31 91.225 27.382 -34.660 1.00 77.75 N ATOM 26 CA GLY B 31 91.082 28.818 -34.394 1.00 77.38 C ATOM 27 C GLY B 31 90.111 29.130 -33.271 1.00 77.12 C ATOM 28 O GLY B 31 90.048 28.415 -32.267 1.00 76.86 O ATOM 29 N THR B 32 89.356 30.213 -33.433 1.00 76.72 N ATOM 30 CA THR B 32 88.434 30.670 -32.391 1.00 75.83 C ATOM 31 C THR B 32 87.081 31.029 -32.982 1.00 75.68 C ATOM 32 O THR B 32 87.014 31.617 -34.052 1.00 75.73 O ATOM 33 N GLY B 33 86.011 30.676 -32.272 1.00 75.64 N ATOM 34 CA GLY B 33 84.637 30.973 -32.708 1.00 74.81 C ATOM 35 C GLY B 33 83.704 31.316 -31.559 1.00 73.94 C ATOM 36 O GLY B 33 84.134 31.411 -30.406 1.00 74.08 O ATOM 37 N GLN B 34 82.423 31.488 -31.885 1.00 72.72 N ATOM 38 CA GLN B 34 81.403 31.939 -30.933 1.00 71.35 C ATOM 39 C GLN B 34 80.018 31.496 -31.400 1.00 69.74 C ATOM 40 O GLN B 34 79.642 31.760 -32.530 1.00 70.46 O ATOM 41 N ALA B 35 79.250 30.842 -30.538 1.00 67.76 N ATOM 42 CA ALA B 35 77.893 30.432 -30.897 1.00 66.29 C ATOM 43 C ALA B 35 76.934 30.553 -29.715 1.00 65.90 C ATOM 44 O ALA B 35 77.299 30.262 -28.574 1.00 66.09 O ATOM 45 N ALA B 36 75.712 30.988 -30.000 1.00 64.80 N ATOM 46 CA ALA B 36 74.680 31.141 -28.988 1.00 63.86 C ATOM 47 C ALA B 36 74.125 29.759 -28.638 1.00 63.78 C ATOM 48 O ALA B 36 74.159 28.866 -29.479 1.00 64.19 O TER ATOM 49 N GLY D 23 83.971 32.951 6.721 1.00 45.61 N ATOM 50 CA GLY D 23 85.372 32.663 6.691 1.00 46.22 C ATOM 51 C GLY D 23 85.873 31.235 6.715 1.00 45.42 C ATOM 53 CA PHE D 24 87.986 30.081 7.243 1.00 46.15 C ATOM 54 C PHE D 24 88.639 29.840 8.586 1.00 45.73 C ATOM 55 N ARG D 25 88.677 28.529 8.785 1.00 46.53 N ATOM 56 CA ARG D 25 89.502 27.858 9.773 1.00 46.92 C ATOM 57 C ARG D 25 90.351 26.863 9.012 1.00 48.22 C ATOM 58 O ARG D 25 89.902 26.301 8.005 1.00 48.21 O ATOM 59 N HIS D 26 91.589 26.663 9.458 1.00 49.57 N ATOM 60 CA HIS D 26 92.485 25.737 8.758 1.00 50.26 C ATOM 61 C HIS D 26 93.451 25.007 9.666 1.00 50.46 C ATOM 62 O HIS D 26 93.608 25.375 10.824 1.00 49.89 O ATOM 63 N GLN D 27 94.091 23.974 9.118 1.00 51.49 N ATOM 64 CA GLN D 27 95.222 23.320 9.764 1.00 52.01 C ATOM 65 C GLN D 27 96.246 22.782 8.749 1.00 51.98 C ATOM 66 N ASN D 28 97.431 23.381 8.906 1.00 53.20 N ATOM 67 CA ASN D 28 98.667 23.022 8.198 1.00 53.62 C ATOM 68 C ASN D 28 99.782 22.741 9.188 1.00 53.76 C ATOM 69 O ASN D 28 99.562 22.726 10.389 1.00 54.00 O ATOM 70 N GLY D 31 100.345 24.907 12.346 1.00 50.53 N ATOM 71 CA GLY D 31 99.329 24.965 13.394 1.00 50.19 C ATOM 72 C GLY D 31 97.937 25.229 12.840 1.00 50.80 C ATOM 73 O GLY D 31 97.654 24.926 11.672 1.00 52.16 O ATOM 74 N THR D 32 97.064 25.791 13.673 1.00 49.82 N ATOM 75 CA THR D 32 95.691 26.083 13.281 1.00 49.15 C ATOM 76 C THR D 32 95.490 27.580 13.139 1.00 50.69 C ATOM 77 O THR D 32 96.305 28.374 13.631 1.00 51.88 O ATOM 78 N GLY D 33 94.399 27.976 12.477 1.00 51.32 N ATOM 79 CA GLY D 33 94.117 29.407 12.250 1.00 50.79 C ATOM 80 C GLY D 33 92.666 29.678 11.925 1.00 50.08 C ATOM 81 O GLY D 33 91.908 28.728 11.662 1.00 49.88 O ATOM 82 N GLN D 34 92.291 30.966 11.956 1.00 49.01 N ATOM 83 CA GLN D 34 90.926 31.420 11.677 1.00 49.25 C ATOM 84 C GLN D 34 90.983 32.793 10.985 1.00 48.70 C ATOM 85 O GLN D 34 91.799 33.610 11.349 1.00 49.25 O ATOM 86 N ALA D 35 90.136 33.053 9.985 1.00 48.59 N ATOM 87 CA ALA D 35 90.096 34.388 9.361 1.00 48.02 C ATOM 88 C ALA D 35 88.791 34.664 8.628 1.00 48.49 C ATOM 89 O ALA D 35 88.251 33.788 7.951 1.00 49.54 O ATOM 90 N ALA D 36 88.285 35.881 8.768 1.00 48.74 N ATOM 91 CA ALA D 36 87.038 36.277 8.117 1.00 49.59 C ATOM 92 C ALA D 36 87.257 36.465 6.633 1.00 50.35 C ATOM 93 O ALA D 36 88.340 36.838 6.226 1.00 50.20 O TER END """ strands_add_o_text=""" ATOM 1 N GLY B 23 75.748 31.574 -24.376 1.00 58.86 N ATOM 2 CA GLY B 23 76.475 30.862 -25.415 1.00 59.81 C ATOM 3 C GLY B 23 77.927 30.531 -25.134 1.00 60.79 C ATOM 4 O GLY B 23 78.447 30.790 -24.037 1.00 61.67 O ATOM 5 N PHE B 24 78.585 29.965 -26.144 1.00 61.14 N ATOM 6 CA PHE B 24 79.949 29.472 -26.012 1.00 61.19 C ATOM 7 C PHE B 24 80.944 30.243 -26.876 1.00 63.09 C ATOM 8 O PHE B 24 80.642 30.610 -28.010 1.00 64.18 O ATOM 9 N ARG B 25 82.129 30.486 -26.333 1.00 64.55 N ATOM 10 CA ARG B 25 83.259 31.022 -27.092 1.00 66.14 C ATOM 11 C ARG B 25 84.369 30.015 -26.941 1.00 67.43 C ATOM 12 O ARG B 25 84.649 29.575 -25.829 1.00 67.73 O ATOM 13 N HIS B 26 85.003 29.620 -28.035 1.00 69.33 N ATOM 14 CA HIS B 26 86.018 28.591 -27.914 1.00 70.83 C ATOM 15 C HIS B 26 87.300 28.976 -28.604 1.00 71.56 C ATOM 16 O HIS B 26 87.385 30.005 -29.255 1.00 71.19 O ATOM 17 N GLN B 27 88.303 28.131 -28.423 1.00 73.27 N ATOM 18 CA GLN B 27 89.565 28.220 -29.128 1.00 74.94 C ATOM 19 C GLN B 27 90.136 26.807 -29.242 1.00 75.41 C ATOM 20 O GLN B 27 90.278 26.098 -28.245 1.00 75.24 O ATOM 21 N ASN B 28 90.430 26.392 -30.470 1.00 76.59 N ATOM 22 CA ASN B 28 91.030 25.085 -30.727 1.00 77.27 C ATOM 23 C ASN B 28 92.077 25.140 -31.836 1.00 78.04 C ATOM 24 O ASN B 28 92.478 26.226 -32.274 1.00 77.66 O ATOM 25 N GLY B 31 91.225 27.382 -34.660 1.00 77.75 N ATOM 26 CA GLY B 31 91.082 28.818 -34.394 1.00 77.38 C ATOM 27 C GLY B 31 90.111 29.130 -33.271 1.00 77.12 C ATOM 28 O GLY B 31 90.048 28.415 -32.267 1.00 76.86 O ATOM 29 N THR B 32 89.356 30.213 -33.433 1.00 76.72 N ATOM 30 CA THR B 32 88.434 30.670 -32.391 1.00 75.83 C ATOM 31 C THR B 32 87.081 31.029 -32.982 1.00 75.68 C ATOM 32 O THR B 32 87.014 31.617 -34.052 1.00 75.73 O ATOM 33 N GLY B 33 86.011 30.676 -32.272 1.00 75.64 N ATOM 34 CA GLY B 33 84.637 30.973 -32.708 1.00 74.81 C ATOM 35 C GLY B 33 83.704 31.316 -31.559 1.00 73.94 C ATOM 36 O GLY B 33 84.134 31.411 -30.406 1.00 74.08 O ATOM 37 N GLN B 34 82.423 31.488 -31.885 1.00 72.72 N ATOM 38 CA GLN B 34 81.403 31.939 -30.933 1.00 71.35 C ATOM 39 C GLN B 34 80.018 31.496 -31.400 1.00 69.74 C ATOM 40 O GLN B 34 79.642 31.760 -32.530 1.00 70.46 O ATOM 41 N ALA B 35 79.250 30.842 -30.538 1.00 67.76 N ATOM 42 CA ALA B 35 77.893 30.432 -30.897 1.00 66.29 C ATOM 43 C ALA B 35 76.934 30.553 -29.715 1.00 65.90 C ATOM 44 O ALA B 35 77.299 30.262 -28.574 1.00 66.09 O ATOM 45 N ALA B 36 75.712 30.988 -30.000 1.00 64.80 N ATOM 46 CA ALA B 36 74.680 31.141 -28.988 1.00 63.86 C ATOM 47 C ALA B 36 74.125 29.759 -28.638 1.00 63.78 C ATOM 48 O ALA B 36 74.159 28.866 -29.479 1.00 64.19 O TER ATOM 49 N GLY D 23 83.971 32.951 6.721 1.00 45.61 N ATOM 50 CA GLY D 23 85.372 32.663 6.691 1.00 46.22 C ATOM 51 C GLY D 23 85.873 31.235 6.715 1.00 45.42 C ATOM 52 N PHE D 24 87.131 31.246 7.173 1.00 46.55 N ATOM 53 CA PHE D 24 87.986 30.081 7.243 1.00 46.15 C ATOM 54 C PHE D 24 88.639 29.840 8.586 1.00 45.73 C ATOM 54 O PHE D 24 88.639 31.000 9.400 1.00 45.73 C ATOM 55 N ARG D 25 88.677 28.529 8.785 1.00 46.53 N ATOM 56 CA ARG D 25 89.502 27.858 9.773 1.00 46.92 C ATOM 57 C ARG D 25 90.351 26.863 9.012 1.00 48.22 C ATOM 58 O ARG D 25 89.902 26.301 8.005 1.00 48.21 O ATOM 59 N HIS D 26 91.589 26.663 9.458 1.00 49.57 N ATOM 60 CA HIS D 26 92.485 25.737 8.758 1.00 50.26 C ATOM 61 C HIS D 26 93.451 25.007 9.666 1.00 50.46 C ATOM 62 O HIS D 26 93.608 25.375 10.824 1.00 49.89 O ATOM 63 N GLN D 27 94.091 23.974 9.118 1.00 51.49 N ATOM 64 CA GLN D 27 95.222 23.320 9.764 1.00 52.01 C ATOM 65 C GLN D 27 96.246 22.782 8.749 1.00 51.98 C ATOM 66 N ASN D 28 97.431 23.381 8.906 1.00 53.20 N ATOM 67 CA ASN D 28 98.667 23.022 8.198 1.00 53.62 C ATOM 68 C ASN D 28 99.782 22.741 9.188 1.00 53.76 C ATOM 69 O ASN D 28 99.562 22.726 10.389 1.00 54.00 O ATOM 70 N GLY D 31 100.345 24.907 12.346 1.00 50.53 N ATOM 71 CA GLY D 31 99.329 24.965 13.394 1.00 50.19 C ATOM 72 C GLY D 31 97.937 25.229 12.840 1.00 50.80 C ATOM 73 O GLY D 31 97.654 24.926 11.672 1.00 52.16 O ATOM 74 N THR D 32 97.064 25.791 13.673 1.00 49.82 N ATOM 75 CA THR D 32 95.691 26.083 13.281 1.00 49.15 C ATOM 76 C THR D 32 95.490 27.580 13.139 1.00 50.69 C ATOM 77 O THR D 32 96.305 28.374 13.631 1.00 51.88 O ATOM 78 N GLY D 33 94.399 27.976 12.477 1.00 51.32 N ATOM 79 CA GLY D 33 94.117 29.407 12.250 1.00 50.79 C ATOM 80 C GLY D 33 92.666 29.678 11.925 1.00 50.08 C ATOM 81 O GLY D 33 91.908 28.728 11.662 1.00 49.88 O ATOM 82 N GLN D 34 92.291 30.966 11.956 1.00 49.01 N ATOM 83 CA GLN D 34 90.926 31.420 11.677 1.00 49.25 C ATOM 84 C GLN D 34 90.983 32.793 10.985 1.00 48.70 C ATOM 85 O GLN D 34 91.799 33.610 11.349 1.00 49.25 O ATOM 86 N ALA D 35 90.136 33.053 9.985 1.00 48.59 N ATOM 87 CA ALA D 35 90.096 34.388 9.361 1.00 48.02 C ATOM 88 C ALA D 35 88.791 34.664 8.628 1.00 48.49 C ATOM 89 O ALA D 35 88.251 33.788 7.951 1.00 49.54 O ATOM 90 N ALA D 36 88.285 35.881 8.768 1.00 48.74 N ATOM 91 CA ALA D 36 87.038 36.277 8.117 1.00 49.59 C ATOM 92 C ALA D 36 87.257 36.465 6.633 1.00 50.35 C ATOM 93 O ALA D 36 88.340 36.838 6.226 1.00 50.20 O TER END """ def tst_00(): print("Finding sheets, splitting and merging...", end=' ') import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(std_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) records=fss.annotation.as_pdb_str() import iotbx.pdb.secondary_structure as ioss annotation=ioss.annotation.from_records(records=flex.split_lines(records)) f=StringIO() print("New records: \n",annotation.as_pdb_str(), file=f) spl=annotation.split_sheets() print("After split_sheets: \n",spl.as_pdb_str(), file=f) merged=spl.merge_sheets() print("After merge_sheets: \n",merged.as_pdb_str(), file=f) print("\nSpl:\n",spl.as_pdb_str(), file=f) assert merged.is_same_as(annotation) print("\nComparing merged and spl:", file=f) print("\nMerged:\n",merged.as_pdb_str(), file=f) print("\nSpl:\n",spl.as_pdb_str(), file=f) print("\nFINAL PDB selections:\n",merged.as_atom_selections(), file=f) assert merged.is_same_as(spl) found_text=f.getvalue() expected_text=""" New records: SHEET 1 1 3 HISAa 32 LEUAa 36 0 SHEET 2 1 3 VALAa 17 LEUAa 22 -1 N GLYAa 21 O HISAa 32 SHEET 3 1 3 ALAAa 52 VALAa 55 -1 N LYSAa 54 O ILEAa 20 SHEET 1 2 4 GLUAa 40 GLNAa 45 0 SHEET 2 2 4 PHEAa 7 ALAAa 12 -1 N ALAAa 12 O GLUAa 40 SHEET 3 2 4 LYSAa 58 THRAa 63 -1 N GLNAa 62 O VALAa 9 SHEET 4 2 4 GLYAa 66 GLUAa 71 -1 N SERAa 70 O ALAAa 59 After split_sheets: SHEET 1 1 2 HISAa 32 LEUAa 36 0 SHEET 2 1 2 VALAa 17 LEUAa 22 -1 N GLYAa 21 O HISAa 32 SHEET 1 2 2 VALAa 17 LEUAa 22 0 SHEET 2 2 2 ALAAa 52 VALAa 55 -1 N LYSAa 54 O ILEAa 20 SHEET 1 3 2 GLUAa 40 GLNAa 45 0 SHEET 2 3 2 PHEAa 7 ALAAa 12 -1 N ALAAa 12 O GLUAa 40 SHEET 1 4 2 PHEAa 7 ALAAa 12 0 SHEET 2 4 2 LYSAa 58 THRAa 63 -1 N GLNAa 62 O VALAa 9 SHEET 1 5 2 LYSAa 58 THRAa 63 0 SHEET 2 5 2 GLYAa 66 GLUAa 71 -1 N SERAa 70 O ALAAa 59 After merge_sheets: SHEET 1 1 3 HISAa 32 LEUAa 36 0 SHEET 2 1 3 VALAa 17 LEUAa 22 -1 N GLYAa 21 O HISAa 32 SHEET 3 1 3 ALAAa 52 VALAa 55 -1 N LYSAa 54 O ILEAa 20 SHEET 1 2 4 GLUAa 40 GLNAa 45 0 SHEET 2 2 4 PHEAa 7 ALAAa 12 -1 N ALAAa 12 O GLUAa 40 SHEET 3 2 4 LYSAa 58 THRAa 63 -1 N GLNAa 62 O VALAa 9 SHEET 4 2 4 GLYAa 66 GLUAa 71 -1 N SERAa 70 O ALAAa 59 Spl: SHEET 1 1 2 HISAa 32 LEUAa 36 0 SHEET 2 1 2 VALAa 17 LEUAa 22 -1 N GLYAa 21 O HISAa 32 SHEET 1 2 2 VALAa 17 LEUAa 22 0 SHEET 2 2 2 ALAAa 52 VALAa 55 -1 N LYSAa 54 O ILEAa 20 SHEET 1 3 2 GLUAa 40 GLNAa 45 0 SHEET 2 3 2 PHEAa 7 ALAAa 12 -1 N ALAAa 12 O GLUAa 40 SHEET 1 4 2 PHEAa 7 ALAAa 12 0 SHEET 2 4 2 LYSAa 58 THRAa 63 -1 N GLNAa 62 O VALAa 9 SHEET 1 5 2 LYSAa 58 THRAa 63 0 SHEET 2 5 2 GLYAa 66 GLUAa 71 -1 N SERAa 70 O ALAAa 59 Comparing merged and spl: Merged: SHEET 1 1 3 HISAa 32 LEUAa 36 0 SHEET 2 1 3 VALAa 17 LEUAa 22 -1 N GLYAa 21 O HISAa 32 SHEET 3 1 3 ALAAa 52 VALAa 55 -1 N LYSAa 54 O ILEAa 20 SHEET 1 2 4 GLUAa 40 GLNAa 45 0 SHEET 2 2 4 PHEAa 7 ALAAa 12 -1 N ALAAa 12 O GLUAa 40 SHEET 3 2 4 LYSAa 58 THRAa 63 -1 N GLNAa 62 O VALAa 9 SHEET 4 2 4 GLYAa 66 GLUAa 71 -1 N SERAa 70 O ALAAa 59 Spl: SHEET 1 1 2 HISAa 32 LEUAa 36 0 SHEET 2 1 2 VALAa 17 LEUAa 22 -1 N GLYAa 21 O HISAa 32 SHEET 1 2 2 VALAa 17 LEUAa 22 0 SHEET 2 2 2 ALAAa 52 VALAa 55 -1 N LYSAa 54 O ILEAa 20 SHEET 1 3 2 GLUAa 40 GLNAa 45 0 SHEET 2 3 2 PHEAa 7 ALAAa 12 -1 N ALAAa 12 O GLUAa 40 SHEET 1 4 2 PHEAa 7 ALAAa 12 0 SHEET 2 4 2 LYSAa 58 THRAa 63 -1 N GLNAa 62 O VALAa 9 SHEET 1 5 2 LYSAa 58 THRAa 63 0 SHEET 2 5 2 GLYAa 66 GLUAa 71 -1 N SERAa 70 O ALAAa 59 FINAL PDB selections: ["chain 'Aa' and resid 32 through 36 ", "chain 'Aa' and resid 17 through 22 ", "chain 'Aa' and resid 52 through 55 ", "chain 'Aa' and resid 40 through 45 ", "chain 'Aa' and resid 7 through 12 ", "chain 'Aa' and resid 58 through 63 ", "chain 'Aa' and resid 66 through 71 "] """ 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_01(): print("Finding helices...", end=' ') import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(two_helix_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) expected_text=""" Model 1 N: 8 Start: 1 End: 8 Class: Alpha helix N: 8 Start: 1 End: 8 Rise: 1.56 A Dot: 0.98 Model 2 N: 16 Start: 11 End: 26 Class: Alpha helix N: 16 Start: 11 End: 26 Rise: 1.58 A Dot: 0.98 FINAL PDB RECORDS: HELIX 1 1 GLY A 1 VAL A 8 1 8 HELIX 2 2 THR A 11 GLN A 26 1 16 FINAL PDB selections: " ( chain 'A' and resid 1 through 8 ) or ( chain 'A' and resid 11 through 26 ) " """ f=StringIO() fss.show_summary(out=f,verbose=True) found_text=f.getvalue() #assert not test_utils.show_diff(found_text, expected_text) 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_02(): text=""" ATOM 2 CA GLY A 1 43.603 -11.488 24.325 1.00 35.57 ATOM 6 CA ILE A 2 44.200 -8.183 22.475 1.00 27.55 ATOM 14 CA GLY A 3 43.999 -10.264 19.329 1.00 21.05 ATOM 18 CA ALA A 4 40.378 -11.260 20.106 1.00 21.80 ATOM 23 CA VAL A 5 39.355 -7.658 21.083 1.00 19.34 ATOM 30 CA LEU A 6 41.062 -6.432 17.957 1.00 17.59 ATOM 38 CA LYS A 7 39.079 -8.646 15.636 1.00 22.55 ATOM 47 CA VAL A 8 35.792 -7.369 17.211 1.00 20.52 ATOM 69 CA THR A 11 34.132 -6.405 12.343 1.00 24.14 ATOM 76 CA GLY A 12 31.584 -6.595 15.140 1.00 24.17 ATOM 80 CA LEU A 13 31.923 -2.919 16.364 1.00 23.24 ATOM 88 CA PRO A 14 31.026 -1.278 13.030 1.00 17.52 ATOM 95 CA ALA A 15 27.822 -3.418 12.724 1.00 17.10 ATOM 100 CA LEU A 16 26.958 -2.649 16.351 1.00 18.20 ATOM 108 CA ILE A 17 27.343 1.056 15.618 1.00 20.41 ATOM 116 CA SER A 18 24.825 0.827 12.744 1.00 19.98 ATOM 122 CA TRP A 19 22.492 -1.085 15.081 1.00 15.72 ATOM 136 CA ILE A 20 22.628 1.633 17.766 1.00 15.67 ATOM 144 CA LYS A 21 21.888 4.236 15.157 1.00 19.84 ATOM 153 CA ARG A 22 18.740 2.273 14.020 1.00 20.38 ATOM 164 CA LYS A 23 17.500 1.928 17.550 1.00 22.62 ATOM 173 CA ARG A 24 18.059 5.674 18.276 1.00 27.11 ATOM 184 CA GLN A 25 15.836 6.730 15.339 1.00 37.50 ATOM 193 CA GLN A 26 13.132 4.360 16.583 1.00 46.66 """ print("Finding helices...", end=' ') import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) expected_text=""" Model 1 N: 8 Start: 1 End: 8 Class: Alpha helix N: 8 Start: 1 End: 8 Rise: 1.56 A Dot: 0.98 Model 2 N: 16 Start: 11 End: 26 Class: Alpha helix N: 16 Start: 11 End: 26 Rise: 1.58 A Dot: 0.98 FINAL PDB RECORDS: HELIX 1 1 GLY A 1 VAL A 8 1 8 HELIX 2 2 THR A 11 GLN A 26 1 16 FINAL PDB selections: " ( chain 'A' and resid 1 through 8 ) or ( chain 'A' and resid 11 through 26 ) " """ f=StringIO() fss.show_summary(out=f,verbose=True) found_text=f.getvalue() #assert not test_utils.show_diff(found_text, expected_text) 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_03(): print("Finding alpha,3-10 and pi helices...", end=' ') import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(helices_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) expected_text=""" Model 1 N: 16 Start: 1 End: 16 Class: Alpha helix N: 16 Start: 1 End: 16 Rise: 1.51 A Dot: 0.98 Model 2 N: 21 Start: 2 End: 22 Class: Pi helix N: 21 Start: 2 End: 22 Rise: 0.96 A Dot: 0.98 Model 3 N: 21 Start: 2 End: 22 Class: 3-10 helix N: 20 Start: 2 End: 21 Rise: 1.99 A Dot: 1.00 FINAL PDB RECORDS: HELIX 1 1 ALA A 1 ALA A 16 1 16 HELIX 1 1 ALA C 2 ALA C 21 5 20 HELIX 1 1 ALA B 2 ALA B 22 3 21 FINAL PDB selections: " ( chain 'A' and resid 1 through 16 ) or ( chain 'C' and resid 2 through 21 ) or ( chain 'B' and resid 2 through 22 ) " """ f=StringIO() fss.show_summary(out=f,verbose=True) found_text=f.getvalue() #assert not test_utils.show_diff(found_text, expected_text) 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(): text=""" ATOM 2 CA THRAa 3 186.743 125.884 251.259 1.00100.00 C ATOM 5 CA ASNAa 4 189.629 123.742 252.763 1.00100.00 C ATOM 8 CA SERAa 5 191.072 126.112 255.320 1.00100.00 C ATOM 11 CA ASPAa 6 192.080 124.928 258.848 1.00100.00 C ATOM 14 CA PHEAa 7 189.384 124.585 261.530 1.00100.00 C ATOM 17 CA VALAa 8 189.248 124.466 265.315 1.00100.00 C ATOM 20 CA VALAa 9 187.059 122.294 267.547 1.00100.00 C ATOM 23 CA ILEAa 10 185.534 123.893 270.679 1.00100.00 C ATOM 26 CA LYSAa 11 183.570 122.134 273.450 1.00100.00 C ATOM 29 CA ALAAa 12 181.897 124.298 276.085 1.00100.00 C ATOM 32 CA LEUAa 13 182.733 123.145 279.601 1.00100.00 C ATOM 35 CA GLUAa 14 180.241 125.609 281.156 1.00100.00 C ATOM 38 CA ASPAa 15 177.155 127.540 279.985 1.00100.00 C ATOM 41 CA GLYAa 16 177.637 130.843 278.162 1.00100.00 C ATOM 44 CA VALAa 17 180.958 130.212 276.395 1.00100.00 C ATOM 47 CA ASNAa 18 181.477 132.715 273.547 1.00100.00 C ATOM 50 CA VALAa 19 183.320 131.753 270.320 1.00100.00 C ATOM 53 CA ILEAa 20 184.043 135.156 268.674 1.00100.00 C ATOM 56 CA GLYAa 21 185.054 135.558 264.994 1.00100.00 C ATOM 59 CA LEUAa 22 187.345 138.529 264.419 1.00100.00 C ATOM 62 CA THRAa 23 187.310 140.218 261.033 1.00100.00 C ATOM 65 CA ARGAa 24 189.831 139.523 258.335 1.00100.00 C ATOM 68 CA GLYAa 25 191.359 142.673 256.805 1.00100.00 C ATOM 71 CA ALAAa 26 192.794 146.041 257.837 1.00100.00 C ATOM 74 CA ASPAa 27 190.126 146.289 260.564 1.00100.00 C ATOM 77 CA THRAa 28 189.912 143.928 263.570 1.00100.00 C ATOM 80 CA ARGAa 29 186.413 143.856 265.033 1.00100.00 C ATOM 83 CA PHEAa 30 183.873 141.240 266.091 1.00100.00 C ATOM 86 CA HISAa 31 181.625 140.079 263.343 1.00100.00 C ATOM 89 CA HISAa 32 179.931 137.209 265.203 1.00100.00 C ATOM 92 CA SERAa 33 179.805 135.702 268.677 1.00100.00 C ATOM 95 CA GLUAa 34 178.501 132.109 268.857 1.00100.00 C ATOM 98 CA CYSAa 35 177.222 131.284 272.342 1.00100.00 C ATOM 101 CA LEUAa 36 177.646 127.700 273.502 1.00100.00 C ATOM 104 CA ASPAa 37 175.969 125.990 276.438 1.00100.00 C ATOM 107 CA LYSAa 38 177.682 123.298 278.488 1.00100.00 C ATOM 110 CA GLYAa 39 178.623 120.300 276.385 1.00100.00 C ATOM 113 CA GLUAa 40 177.892 121.761 272.941 1.00100.00 C ATOM 116 CA VALAa 41 180.597 121.439 270.276 1.00100.00 C ATOM 119 CA LEUAa 42 181.492 123.998 267.594 1.00100.00 C ATOM 122 CA ILEAa 43 183.793 123.155 264.645 1.00100.00 C ATOM 125 CA ALAAa 44 184.701 126.388 262.889 1.00100.00 C ATOM 128 CA GLNAa 45 186.987 127.209 259.959 1.00100.00 C ATOM 131 CA PHEAa 46 189.115 130.161 259.157 1.00100.00 C ATOM 134 CA THRAa 47 187.356 131.901 256.203 1.00100.00 C ATOM 137 CA GLUAa 48 187.180 134.953 253.965 1.00100.00 C ATOM 140 CA HISAa 49 185.578 136.805 256.905 1.00100.00 C ATOM 143 CA THRAa 50 187.343 135.292 259.938 1.00100.00 C ATOM 146 CA SERAa 51 191.129 135.327 260.339 1.00100.00 C ATOM 149 CA ALAAa 52 191.231 135.094 264.170 1.00100.00 C ATOM 152 CA ILEAa 53 188.989 133.390 266.744 1.00100.00 C ATOM 155 CA LYSAa 54 188.770 134.368 270.428 1.00100.00 C ATOM 158 CA VALAa 55 187.303 131.970 273.016 1.00100.00 C ATOM 161 CA ARGAa 56 185.817 133.382 276.214 1.00100.00 C ATOM 164 CA GLYAa 57 184.672 131.065 278.997 1.00100.00 C ATOM 167 CA LYSAa 58 185.698 127.553 280.004 1.00100.00 C ATOM 170 CA ALAAa 59 186.172 125.294 276.966 1.00100.00 C ATOM 173 CA TYRAa 60 188.258 122.444 275.620 1.00100.00 C ATOM 176 CA ILEAa 61 189.863 123.277 272.265 1.00100.00 C ATOM 179 CA GLNAa 62 191.492 121.098 269.577 1.00100.00 C ATOM 182 CA THRAa 63 193.550 122.431 266.653 1.00100.00 C ATOM 185 CA ARGAa 64 196.271 121.116 264.358 1.00100.00 C ATOM 188 CA HISAa 65 198.826 122.305 266.995 1.00100.00 C ATOM 191 CA GLYAa 66 197.443 120.330 269.914 1.00100.00 C ATOM 194 CA VALAa 67 194.865 120.679 272.646 1.00100.00 C ATOM 197 CA ILEAa 68 194.232 123.486 275.120 1.00100.00 C ATOM 200 CA GLUAa 69 191.576 124.693 277.564 1.00100.00 C ATOM 203 CA SERAa 70 190.301 128.219 277.907 1.00100.00 C ATOM 206 CA GLUAa 71 189.167 129.249 281.377 1.00100.00 C ATOM 209 CA GLYAa 72 186.003 131.073 282.428 1.00100.00 C """ print("Finding sheets...", end=' ') import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) expected_text=""" Model 1 N: 70 Start: 3 End: 72 Class: Beta strand N: 10 Start: 3 End: 12 Rise: 3.32 A Dot: 0.88 Class: Beta strand N: 9 Start: 16 End: 24 Rise: 3.24 A Dot: 0.97 Class: Beta strand N: 4 Start: 27 End: 30 Rise: 3.34 A Dot: 0.95 Class: Beta strand N: 6 Start: 31 End: 36 Rise: 3.29 A Dot: 0.99 Class: Beta strand N: 8 Start: 40 End: 47 Rise: 3.30 A Dot: 0.96 Class: Beta strand N: 5 Start: 51 End: 55 Rise: 3.41 A Dot: 1.00 Class: Beta strand N: 6 Start: 58 End: 63 Rise: 3.41 A Dot: 0.96 Class: Beta strand N: 7 Start: 66 End: 72 Rise: 3.41 A Dot: 0.98 FINAL PDB RECORDS: SHEET 1 1 3 HISAa 32 LEUAa 36 0 SHEET 2 1 3 VALAa 17 LEUAa 22 -1 N GLYAa 21 O HISAa 32 SHEET 3 1 3 ALAAa 52 VALAa 55 -1 N LYSAa 54 O ILEAa 20 SHEET 1 2 4 GLUAa 40 GLNAa 45 0 SHEET 2 2 4 PHEAa 7 ALAAa 12 -1 N ALAAa 12 O GLUAa 40 SHEET 3 2 4 LYSAa 58 THRAa 63 -1 N GLNAa 62 O VALAa 9 SHEET 4 2 4 GLYAa 66 GLUAa 71 -1 N SERAa 70 O ALAAa 59 FINAL PDB selections: "(chain 'Aa' and resid 32 through 36 ) or (chain 'Aa' and resid 17 through 22 ) or (chain 'Aa' and resid 52 through 55 ) or (chain 'Aa' and resid 40 through 45 ) or (chain 'Aa' and resid 7 through 12 ) or (chain 'Aa' and resid 58 through 63 ) or (chain 'Aa' and resid 66 through 71 )" """ f=StringIO() fss.show_summary(out=f,verbose=True) found_text=f.getvalue() #assert not test_utils.show_diff(found_text, expected_text) 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_05(): print("Finding sheets with separate chains...", end=' ') import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(two_chain_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) expected_text=""" Model 1 N: 8 Start: 50 End: 57 Class: Beta strand N: 8 Start: 50 End: 57 Rise: 3.21 A Dot: 0.97 Model 2 N: 5 Start: 278 End: 282 Class: Beta strand N: 5 Start: 278 End: 282 Rise: 3.16 A Dot: 0.98 FINAL PDB RECORDS: SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 N ILE B 280 O ILE A 51 FINAL PDB selections: " ( chain 'A' and resid 50 through 54 ) or ( chain 'B' and resid 278 through 282 ) " """ f=StringIO() fss.show_summary(out=f,verbose=True) found_text=f.getvalue() 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_06(): text=""" ATOM 8 CA GLY A 2 24.485 19.185 6.248 1.00 11.14 C HETATM 15 CA 23F A 3 26.939 16.455 5.194 1.00 9.61 C ATOM 33 CA ALA A 4 29.149 18.888 3.424 1.00 9.96 C HETATM 43 CA 23F A 5 30.573 19.304 6.910 1.00 6.42 C HETATM 61 CA 23F A 6 32.558 16.167 6.280 1.00 6.41 C ATOM 79 CA ALA A 7 35.089 18.339 4.563 1.00 6.26 C HETATM 89 CA 23F A 8 36.195 19.092 8.094 1.00 6.38 C HETATM 107 CA 23F A 9 38.283 15.914 7.621 1.00 7.78 C ATOM 125 CA ALA A 10 40.789 18.180 5.892 1.00 8.66 C ATOM 135 CA GLY A 11 41.608 19.716 9.325 1.00 10.78 C ATOM 142 CA GLY A 12 44.498 17.479 9.975 1.00 17.00 C ATOM 149 CA GLY A 13 43.927 17.193 13.603 1.00 13.58 C ATOM 156 CA GLY A 14 41.242 17.379 16.363 1.00 11.14 C HETATM 163 CA 23F A 15 39.608 20.319 14.616 1.00 7.70 C ATOM 181 CA ALA A 16 38.402 17.853 12.023 1.00 7.08 C ATOM 191 CA LEU A 17 35.810 16.973 14.649 1.00 6.22 C HETATM 210 CA 23F A 18 34.098 20.219 13.633 1.00 6.81 C ATOM 228 CA ALA A 19 32.642 18.019 10.889 1.00 6.28 C ATOM 238 CA LEU A 20 30.139 16.927 13.574 1.00 6.81 C HETATM 257 CA 23F A 21 28.460 20.242 12.654 1.00 8.80 C ATOM 275 CA ALA A 22 27.017 18.382 9.700 1.00 7.89 C """ print("Finding sheets with unusual residues...", end=' ') import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) expected_text=""" Model 1 N: 21 Start: 2 End: 22 Class: Alpha helix N: 10 Start: 3 End: 12 Rise: 2.00 A Dot: 0.98 Class: Alpha helix N: 10 Start: 13 End: 22 Rise: 1.96 A Dot: 0.97 FINAL PDB RECORDS: HELIX 1 1 23F A 3 GLY A 12 1 10 HELIX 2 2 GLY A 13 ALA A 22 1 10 FINAL PDB selections: " ( chain 'A' and resid 3 through 12 ) or ( chain 'A' and resid 13 through 22 ) " """ f=StringIO() fss.show_summary(out=f,verbose=True) found_text=f.getvalue() 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_07(): text=""" ATOM 651 CA BPRO E 1 14.350 6.490 -29.205 0.50 16.99 C ATOM 658 CA BPRO E 2 12.612 6.495 -25.864 0.50 14.37 C ATOM 666 CA AGLY E 3 12.816 7.962 -32.315 0.55 19.29 C ATOM 667 CA BGLY E 3 13.074 9.621 -23.839 0.45 12.65 C ATOM 674 CA APRO E 4 14.350 6.490 -29.205 0.50 16.99 C ATOM 675 CA BPRO E 4 15.262 10.063 -20.808 0.50 15.34 C ATOM 688 CA APRO E 5 12.612 6.495 -25.864 0.50 14.37 C ATOM 689 CA BPRO E 5 14.316 8.840 -17.372 0.50 10.66 C ATOM 702 CA AGLY E 6 13.074 9.621 -23.839 0.50 12.65 C ATOM 703 CA BGLY E 6 11.932 10.884 -15.276 0.50 7.99 C ATOM 710 CA APRO E 7 15.262 10.063 -20.808 0.50 15.34 C ATOM 711 CA BPRO E 7 13.150 12.796 -12.241 0.50 9.73 C """ print("Finding sheets with alt confs where there is no A for first res...") import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,verbose=True,out=null_out()) expected_text=""" Model 1 N: 5 Start: 3 End: 7 Class: Beta strand N: 4 Start: 4 End: 7 Rise: 3.27 A Dot: 0.91""" f=StringIO() fss.show_summary(out=f,verbose=True) found_text=f.getvalue() 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_08(): print("Checking similar annotations and overlapping annotations") import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(one_helix_text)).construct_hierarchy() ann_one_helix_beg=get_annotation(one_helix_beginning_text) ann_one_helix_middle=get_annotation(one_helix_middle_text) ann_one_helix_end=get_annotation(one_helix_end_text) ann_one_helix=get_annotation(one_helix_text) for h1 in ann_one_helix_beg.helices: for h2 in ann_one_helix_beg.helices: print("Should be same:",h1.is_similar_to(other=h2,hierarchy=hierarchy)) assert h1.is_similar_to(other=h2,hierarchy=hierarchy) for maximum_length_difference in [4,8]: for minimum_overlap in [6,10]: for h1 in ann_one_helix_beg.helices: for h2 in ann_one_helix.helices: value=h1.is_similar_to(other=h2,hierarchy=hierarchy, maximum_length_difference=maximum_length_difference, minimum_overlap=minimum_overlap) print("Comparison:",value) assert (value and maximum_length_difference==8 and minimum_overlap==6) or not value assert ann_one_helix_beg.overlaps_with(other=ann_one_helix, hierarchy=hierarchy) assert not ann_one_helix_beg.overlaps_with(other=ann_one_helix_end, hierarchy=hierarchy) # Now strands and sheets hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(std_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) records=fss.annotation.as_pdb_str() import iotbx.pdb.secondary_structure as ioss s1_records=""" SHEET 1 1 3 HISAa 32 LEUAa 36 0 SHEET 2 1 3 VALAa 17 LEUAa 22 -1 N GLYAa 21 O HISAa 32 SHEET 3 1 3 ALAAa 52 VALAa 55 -1 N LYSAa 54 O ILEAa 20 """ s1_not_overlap_records=""" SHEET 1 1 3 HISAa 32 LEUAa 36 0 SHEET 1 2 4 GLUAa 40 GLNAa 45 0 SHEET 3 2 4 LYSAa 58 THRAa 63 -1 """ s1_similar_records=""" SHEET 1 1 3 HISAa 32 LEUAa 36 0 SHEET 2 1 3 VALAa 18 LEUAa 22 -1 N VALAa 19 O GLUAa 34 SHEET 3 1 3 ALAAa 50 VALAa 57 -1 N LYSAa 54 O ILEAa 20 """ s1_diff_records=""" SHEET 1 2 4 GLUAa 40 GLNAa 45 0 SHEET 2 2 4 PHEAa 7 ALAAa 12 -1 N ALAAa 12 O GLUAa 40 SHEET 3 2 4 LYSAa 58 THRAa 63 -1 N GLNAa 62 O VALAa 9 """ s1_reverse_diff_records=""" SHEET 1 2 4 GLUAa 40 GLNAa 45 0 SHEET 2 2 4 PHEAa 7 ALAAa 12 1 N ALAAa 12 O GLUAa 40 SHEET 3 2 4 LYSAa 58 THRAa 63 -1 N GLNAa 62 O VALAa 9 """ s1_similar_reg_records=""" SHEET 1 1 3 HISAa 32 LEUAa 36 0 SHEET 2 1 3 VALAa 17 LEUAa 22 -1 N ILEAa 20 O SERAa 33 SHEET 3 1 3 ALAAa 52 VALAa 55 -1 N LYSAa 54 O ILEAa 20 """ s1_similar_backwards=""" SHEET 2 1 3 VALAa 18 LEUAa 22 0 SHEET 3 1 3 ALAAa 50 VALAa 57 -1 O ILEAa 20 N LYSAa 54 SHEET 1 1 3 HISAa 32 LEUAa 36 -1 O SERAa 33 N ILEAa 20 """ s1_similar_backwards_2=""" SHEET 2 1 3 VALAa 18 LEUAa 22 0 SHEET 3 1 3 ALAAa 50 VALAa 57 -1 O ILEAa 20 N LYSAa 54 SHEET 1 1 3 HISAa 32 LEUAa 36 -1 O SERAa 33 N ILEAa 20 """ s1_full=ioss.annotation.from_records(records=flex.split_lines(s1_records)) s1_not_overlap=ioss.annotation.from_records(records=flex.split_lines(s1_not_overlap_records)) s1_similar=ioss.annotation.from_records(records=flex.split_lines(s1_similar_records)) s1_diff=ioss.annotation.from_records(records=flex.split_lines(s1_diff_records)) s1_reverse_diff=ioss.annotation.from_records(records=flex.split_lines(s1_reverse_diff_records)) print("\nChecking overlap:") assert s1_full.overlaps_with(other=s1_similar,hierarchy=hierarchy) assert not s1_full.overlaps_with(other=s1_diff,hierarchy=hierarchy) assert not s1_full.overlaps_with(other=s1_not_overlap,hierarchy=hierarchy) print("\nChecking similar strands:", end=' ') f=StringIO() for s1 in s1_full.sheets: for str1 in s1.strands: for s2 in s1_similar.sheets: for str2 in s2.strands: value=str1.is_similar_to(other=str2,hierarchy=hierarchy, maximum_length_difference=4) print(str1.as_atom_selections(),str2.as_atom_selections(),value) print(str1.as_atom_selections(),str2.as_atom_selections(),value, file=f) assert f.getvalue()=="""chain 'Aa' and resid 32 through 36 chain 'Aa' and resid 32 through 36 True chain 'Aa' and resid 32 through 36 chain 'Aa' and resid 18 through 22 False chain 'Aa' and resid 32 through 36 chain 'Aa' and resid 50 through 57 False chain 'Aa' and resid 17 through 22 chain 'Aa' and resid 32 through 36 False chain 'Aa' and resid 17 through 22 chain 'Aa' and resid 18 through 22 True chain 'Aa' and resid 17 through 22 chain 'Aa' and resid 50 through 57 False chain 'Aa' and resid 52 through 55 chain 'Aa' and resid 32 through 36 False chain 'Aa' and resid 52 through 55 chain 'Aa' and resid 18 through 22 False chain 'Aa' and resid 52 through 55 chain 'Aa' and resid 50 through 57 True """ print("\nChecking different strands:", end=' ') for s1 in s1_full.sheets: for str1 in s1.strands: for s2 in s1_diff.sheets: for str2 in s2.strands: print(str1.as_atom_selections(),str2.as_atom_selections(),\ str1.is_similar_to(other=str2,hierarchy=hierarchy, maximum_length_difference=4)) print("\nChecking similar sheets:", end=' ') for s1 in s1_full.sheets: for s2 in s1_similar.sheets: value=s1.is_similar_to(other=s2,hierarchy=hierarchy, maximum_length_difference=4) print(value) assert value print("\nChecking non-similar sheets:", end=' ') for s1 in s1_full.sheets: for s2 in s1_diff.sheets: value=s1.is_similar_to(other=s2,hierarchy=hierarchy, maximum_length_difference=4) print(value) assert not value print("\nChecking similar overall annotations:", end=' ') value=s1_full.is_similar_to(other=s1_similar,hierarchy=hierarchy, maximum_length_difference=4) print(value) assert value print("\nChecking different overall annotations:", end=' ') value=s1_full.is_similar_to(other=s1_diff,hierarchy=hierarchy, maximum_length_difference=4) print(value) assert not value print("\nChecking different overall directions:", end=' ') value=s1_full.is_similar_to(other=s1_reverse_diff,hierarchy=hierarchy, maximum_length_difference=4) print(value) assert not value # parallel strands print("\n\nChecking parallel strands...") hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(two_chain_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) records=fss.annotation.as_pdb_str() import iotbx.pdb.secondary_structure as ioss s2_records=""" FINAL PDB RECORDS: SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 N ILE B 280 O ILE A 51 """ s2_similar_records=""" FINAL PDB RECORDS: SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 N ALA B 282 O THR A 53 """ s2_similar_records_2=""" FINAL PDB RECORDS: SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 O LEU B 278 N ILE A 51 """ s2_different_records=""" FINAL PDB RECORDS: SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 O ILE B 280 N ILE A 51 """ s2_full=ioss.annotation.from_records(records=flex.split_lines(s2_records)) s2_similar=ioss.annotation.from_records(records=flex.split_lines(s2_similar_records)) s2_similar_2=ioss.annotation.from_records(records=flex.split_lines(s2_similar_records_2)) s2_different=ioss.annotation.from_records(records=flex.split_lines(s2_different_records)) print("\nChecking similar overall annotations (offset by 2):", end=' ') value=s2_full.is_similar_to(other=s2_similar,hierarchy=hierarchy, maximum_length_difference=4) print(value) assert value print("\nChecking similar overall annotations (switch N/O):", end=' ') value=s2_full.is_similar_to(other=s2_similar_2,hierarchy=hierarchy, maximum_length_difference=4) print(value) assert value print("\nChecking different overall annotations (offset by 1):", end=' ') value=s2_full.is_similar_to(other=s2_different,hierarchy=hierarchy, maximum_length_difference=4) print(value) assert not value print("\nOK") def tst_09(): print("Comparing sheets and helices...", end=' ') helix_1=""" HELIX 1 1 GLY A 1 VAL A 8 1 8 """ helix_2=""" HELIX 2 2 THR A 11 GLN A 26 1 16 """ sheet_1=""" SHEET 1 1 3 HISAa 32 LEUAa 36 0 SHEET 2 1 3 VALAa 17 LEUAa 22 -1 N GLYAa 21 O HISAa 32 SHEET 3 1 3 ALAAa 52 VALAa 55 1 N LYSAa 54 O ILEAa 20 """ sheet_2=""" SHEET 1 2 4 GLUAa 40 GLNAa 45 0 SHEET 2 2 4 PHEAa 7 ALAAa 12 -1 N ALAAa 12 O GLUAa 40 SHEET 3 2 4 LYSAa 58 THRAa 63 1 N GLNAa 62 O VALAa 9 SHEET 4 2 4 GLYAa 66 GLUAa 71 -1 N SERAa 70 O ALAAa 59 """ import iotbx.pdb.secondary_structure as ioss from cctbx.array_family import flex h1=ioss.annotation.from_records(records=flex.split_lines(helix_1)) h2=ioss.annotation.from_records(records=flex.split_lines(helix_2)) s1=ioss.annotation.from_records(records=flex.split_lines(sheet_1)) s2=ioss.annotation.from_records(records=flex.split_lines(sheet_2)) assert h1.is_same_as(h1) assert h2.is_same_as(h2) assert not h1.is_same_as(h2) assert not h1.is_same_as(s1) assert not s1.is_same_as(s2) assert s1.is_same_as(s1) for a in s1.sheets: for b in s1.sheets: assert (a==b and a.is_same_as(b)) or (not a.is_same_as(b)) for sa in a.strands: for sb in b.strands: assert (sa==sb and sa.is_same_as(sb)) or (not sa.is_same_as(sb)) print("OK") def get_annotation(text): import iotbx.pdb from cctbx.array_family import flex import iotbx.pdb.secondary_structure as ioss hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) records=fss.annotation.as_pdb_str() return ioss.annotation.from_records(records=flex.split_lines(records)) def tst_10(): import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(one_full_helix_text+two_chain_text)).construct_hierarchy() text_helix_1=""" HELIX 1 1 ALA A 15 LYS A 21 1 7 """ text_helix_2=""" HELIX 1 1 LEU A 16 LYS A 21 1 6 """ text_sheet_1=""" SHEET 1 1 2 ILE A 51 TYR A 54 0 SHEET 2 1 2 THR B 279 ALA B 282 1 N ILE B 280 O ILE A 51 """ text_sheet_2=""" SHEET 1 1 2 TYR A 50 TYR A 54 0 SHEET 2 1 2 LEU B 278 ALA B 282 1 N ILE B 280 O ILE A 51 """ import iotbx.pdb.secondary_structure as ioss from cctbx.array_family import flex h1=ioss.annotation.from_records(records=flex.split_lines(text_helix_1)) h2=ioss.annotation.from_records(records=flex.split_lines(text_helix_2)) s1=ioss.annotation.from_records(records=flex.split_lines(text_sheet_1)) s2=ioss.annotation.from_records(records=flex.split_lines(text_sheet_2)) hs1=ioss.annotation.from_records(records=flex.split_lines(text_helix_1+text_sheet_1)) hs2=ioss.annotation.from_records(records=flex.split_lines(text_helix_2+text_sheet_2)) print("\nCombining annotations") ann_all=get_annotation(one_full_helix_text+two_chain_text) print("\nFull annotation\n",ann_all.as_pdb_str()) print("\nCombining annotations from two parts") ann_one_full_helix=get_annotation(one_full_helix_text) print("\nAnnotation for helix:\n",ann_one_full_helix.as_pdb_str()) ann_two_chain=get_annotation(two_chain_text) print("\nAnnotation for two chains:\n",ann_two_chain.as_pdb_str()) ann_combined=ann_one_full_helix.combine_annotations(other=ann_two_chain, hierarchy=hierarchy) if ann_combined: print("Combined: \n",ann_combined.as_pdb_str()) print("\nCombining annotations from overlapping helix annotations") print("\nHelix 1 and 2: \n",h1.as_pdb_str(),"\n",h2.as_pdb_str()) ann_combined=h1.combine_annotations(other=h2,hierarchy=hierarchy) print("\nCombined: \n",ann_combined.as_pdb_str()) print("\nCombining annotations from overlapping strand annotations") print("\nStrand 1 and 2: \n",s1.as_pdb_str(),"\n",s2.as_pdb_str()) ann_combined=s1.combine_annotations(other=s2,hierarchy=hierarchy, minimum_overlap=3,out=sys.stdout) print("\nCombined: \n",ann_combined.as_pdb_str()) print("\nCombining annotations from overlapping strand and helix annotations") print("\nStrand/helix 1:\n",hs1.as_pdb_str(),"Strand/helix 2:\n",hs2.as_pdb_str()) ann_combined=hs1.combine_annotations(other=hs2,hierarchy=hierarchy, minimum_overlap=3,out=sys.stdout) print("\nCombined: \n",ann_combined.as_pdb_str()) print("OK") def tst_11(): print("\nCounting H-bonds") import iotbx.pdb import iotbx.pdb.secondary_structure as ioss from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(two_chain_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) ann=fss.get_annotation() print(ann.as_pdb_str()) print("Good H-bonds: %d Poor H-Bonds: %d" %( fss.number_of_good_h_bonds, fss.number_of_poor_h_bonds,)) assert fss.number_of_good_h_bonds==4 and fss.number_of_poor_h_bonds==0 print("\nCounting H-bonds using ioss.annotation:") number_of_good_h_bonds,number_of_poor_h_bonds=ann.count_h_bonds( hierarchy=hierarchy) print("Good H-bonds: %d Poor H-Bonds: %d" %( fss.number_of_good_h_bonds, fss.number_of_poor_h_bonds,)) assert fss.number_of_good_h_bonds==4 and fss.number_of_poor_h_bonds==0 print("\nCounting residues in secondary structure:", end=' ') print(ann.count_residues(hierarchy=hierarchy)) assert ann.count_residues(hierarchy=hierarchy)==10 print("\nCounting H-bonds in helix:") hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(one_full_helix_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) ann=fss.get_annotation() print(ann.as_pdb_str()) print("\nH-bonds with cutoff=3.5 (default):\n") number_of_good_h_bonds,number_of_poor_h_bonds=ann.count_h_bonds( hierarchy=hierarchy) print("Good H-bonds: %d Poor H-Bonds: %d" %( number_of_good_h_bonds, number_of_poor_h_bonds,)) assert number_of_good_h_bonds==3 and number_of_poor_h_bonds==0 print("\nH-bonds with cutoff=3.0:\n") number_of_good_h_bonds,number_of_poor_h_bonds=ann.count_h_bonds( hierarchy=hierarchy,max_h_bond_length=3.0) print("Good H-bonds: %d Poor H-Bonds: %d" %( number_of_good_h_bonds, number_of_poor_h_bonds,)) assert number_of_good_h_bonds==1 and number_of_poor_h_bonds==2 print("\nCount number of residues in secondary structure:", end=' ') print(ann.count_residues(hierarchy=hierarchy)) assert ann.count_residues(hierarchy=hierarchy) ==7 print("\nH-bonds in mixed helix/strand") hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(two_chain_text+one_full_helix_text) ).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) ann=fss.get_annotation() print(ann.as_pdb_str()) print("\nH-bonds with cutoff=3.0 :\n") number_of_good_h_bonds,number_of_poor_h_bonds=ann.count_h_bonds( hierarchy=hierarchy,max_h_bond_length=3.0) print("Good H-bonds: %d Poor H-Bonds: %d" %( number_of_good_h_bonds, number_of_poor_h_bonds,)) assert number_of_good_h_bonds==5 and number_of_poor_h_bonds==2 print("\nCount number of residues in secondary structure:", end=' ') print(ann.count_residues(hierarchy=hierarchy)) assert ann.count_residues(hierarchy=hierarchy) ==17 print("\nMake sure force and original ss are equivalent") force_fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, user_annotation_text=ss_text, force_secondary_structure_input=True, combine_annotations=False, out=null_out()) number_of_good_h_bonds,number_of_poor_h_bonds=\ force_fss.get_annotation().count_h_bonds( hierarchy=hierarchy,max_h_bond_length=3.0) print("Good H-bonds: %d Poor H-Bonds: %d" %( number_of_good_h_bonds, number_of_poor_h_bonds,)) assert number_of_good_h_bonds==5 and number_of_poor_h_bonds==2 print("\nInput annotation:") print(fss.get_annotation().as_pdb_str()) print("\nOutput annotation:") print(force_fss.get_annotation().as_pdb_str()) print("\nIs same: ",fss.get_annotation().is_similar_to( other=force_fss.get_annotation(),hierarchy=hierarchy)) print("\nCorrect bad H-bond register in input") fix_fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, user_annotation_text=bad_two_chain_helix_ss, force_secondary_structure_input=False, combine_annotations=False, search_secondary_structure=False,out=null_out()) fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, combine_annotations=False, out=null_out()) print("\nInput:") print(bad_two_chain_helix_ss) print("\nFixed:") print(fix_fss.get_annotation().as_pdb_str()) print("\nGood:") print(fss.get_annotation().as_pdb_str()) print("Is same: ", fix_fss.get_annotation().is_similar_to( hierarchy=hierarchy,other=fss.get_annotation())) assert fix_fss.get_annotation().is_similar_to( hierarchy=hierarchy,other=fss.get_annotation()) print("\nForce bad H-bond register in input") import iotbx.pdb.secondary_structure as ioss bad_anno=ioss.annotation.from_records(records=flex.split_lines( bad_two_chain_helix_ss_correct_resname)) no_fix_fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, user_annotation_text=bad_anno.as_pdb_str(), force_secondary_structure_input=True, combine_annotations=False, search_secondary_structure=False,out=null_out()) print("\nInput:") print(bad_anno.as_pdb_str()) print("\nNot fixed:") print(no_fix_fss.get_annotation().as_pdb_str()) print("\nGood:") print(fss.get_annotation().as_pdb_str()) print("Is same as unfixed: ", no_fix_fss.get_annotation().is_similar_to( hierarchy=hierarchy,other=bad_anno)) assert no_fix_fss.get_annotation().is_similar_to( hierarchy=hierarchy,other=bad_anno) print("\nNegative residue numbers...") hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(negative_residues) ).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, combine_annotations=False, out=null_out()) expected=ioss.annotation.from_records(records=flex.split_lines(""" SHEET 1 1 2 ASP A -5 HIS A -2 0 SHEET 2 1 2 GLY A 138 ASN A 141 -1 N ASN A 141 O ASP A -5 """)) print(fss.get_annotation().as_pdb_str()) assert fss.get_annotation().is_same_as(expected) print("\nHybrid-36 residue numbers...") hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(hybrid_residues) ).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, combine_annotations=False, out=null_out()) expected=ioss.annotation.from_records(records=flex.split_lines(""" SHEET 1 1 2 ASP AXYB2 HIS AXYB5 0 SHEET 2 1 2 GLY A 138 ASN A 141 -1 N ASN A 141 O ASP AXYB2 """)) print(fss.get_annotation().as_pdb_str()) assert fss.get_annotation().is_same_as(expected) print("\nNow for antiparallel:Make sure force and original ss are equivalent") hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(antiparallel_text) ).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, combine_annotations=False, out=null_out()) force_fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, user_annotation_text=antiparallel_ss, force_secondary_structure_input=True, combine_annotations=False, out=null_out()) number_of_good_h_bonds,number_of_poor_h_bonds=\ force_fss.get_annotation().count_h_bonds( hierarchy=hierarchy,max_h_bond_length=3.0) print("Good H-bonds: %d Poor H-Bonds: %d" %( number_of_good_h_bonds, number_of_poor_h_bonds,)) assert number_of_good_h_bonds==3 and number_of_poor_h_bonds==1 print("\nInput annotation:") print(fss.get_annotation().as_pdb_str()) print("\nOutput annotation:") print(force_fss.get_annotation().as_pdb_str()) print("\nIs same: ",fss.get_annotation().is_similar_to( other=force_fss.get_annotation(),hierarchy=hierarchy)) print("\nRemove annotation with too few H-bonds") force_fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, user_annotation_text=antiparallel_ss, force_secondary_structure_input=True, combine_annotations=False, require_h_bonds=True, # has no effect as force=true minimum_h_bonds=4,out=null_out()) number_of_good_h_bonds,number_of_poor_h_bonds=\ force_fss.get_annotation().count_h_bonds( hierarchy=hierarchy) print("Good H-bonds: %d Poor H-Bonds: %d" %( number_of_good_h_bonds, number_of_poor_h_bonds,)) assert number_of_good_h_bonds==4 and number_of_poor_h_bonds==0 force_fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, user_annotation_text=antiparallel_ss, combine_annotations=False, require_h_bonds=True, minimum_h_bonds=5,out=null_out()) number_of_good_h_bonds,number_of_poor_h_bonds=\ force_fss.get_annotation().count_h_bonds( hierarchy=hierarchy) print("Good H-bonds: %d Poor H-Bonds: %d" %( number_of_good_h_bonds, number_of_poor_h_bonds,)) assert number_of_good_h_bonds==0 and number_of_poor_h_bonds==0 print("\nNow remove annotation with too many poor H-bonds") force_fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, user_annotation_text=antiparallel_ss, combine_annotations=False, require_h_bonds=True, # has no effect as force=true max_h_bond_length=2.0,maximum_poor_h_bonds=0,out=null_out()) number_of_good_h_bonds,number_of_poor_h_bonds=\ force_fss.get_annotation().count_h_bonds( hierarchy=hierarchy) print("Good H-bonds: %d Poor H-Bonds: %d" %( number_of_good_h_bonds, number_of_poor_h_bonds,)) assert number_of_good_h_bonds==0 and number_of_poor_h_bonds==0 def tst_12(): pdb_text=""" ATOM 3265 N LYS A 11 -14.874 -4.165 7.826 1.00 14.62 N ATOM 3266 CA LYS A 11 -16.168 -3.852 7.241 1.00 15.85 C ATOM 3267 C LYS A 11 -16.310 -4.478 5.853 1.00 16.45 C ATOM 3268 O LYS A 11 -17.075 -5.419 5.680 1.00 17.01 O ATOM 3269 CB LYS A 11 -16.375 -2.333 7.183 1.00 15.92 C ATOM 3279 N ALA A 12 -15.570 -3.971 4.870 1.00 16.88 N ATOM 3280 CA ALA A 12 -15.727 -4.395 3.487 1.00 17.42 C ATOM 3281 C ALA A 12 -14.354 -4.610 2.875 1.00 17.46 C ATOM 3282 O ALA A 12 -13.333 -4.252 3.459 1.00 16.02 O ATOM 3283 CB ALA A 12 -16.525 -3.371 2.681 1.00 18.05 C ATOM 3286 N VAL A 13 -14.338 -5.186 1.671 1.00 16.89 N ATOM 3287 CA VAL A 13 -13.093 -5.691 1.103 1.00 17.82 C ATOM 3288 C VAL A 13 -12.694 -4.871 -0.112 1.00 17.45 C ATOM 3289 O VAL A 13 -13.105 -5.157 -1.241 1.00 17.89 O ATOM 3290 CB VAL A 13 -13.228 -7.182 0.746 1.00 17.97 C ATOM 3292 N GLY A 14 -11.871 -3.863 0.111 1.00 16.43 N ATOM 3293 CA GLY A 14 -11.449 -2.983 -0.958 1.00 15.97 C ATOM 3294 C GLY A 14 -9.986 -3.186 -1.252 1.00 15.81 C ATOM 3295 O GLY A 14 -9.221 -3.645 -0.406 1.00 15.35 O ATOM 3303 N LYS A 15 -9.601 -2.849 -2.479 1.00 15.98 N ATOM 3304 CA LYS A 15 -8.222 -2.951 -2.936 1.00 16.09 C ATOM 3305 C LYS A 15 -7.563 -1.610 -2.666 1.00 15.49 C ATOM 3306 O LYS A 15 -8.222 -0.574 -2.732 1.00 15.59 O ATOM 3307 CB LYS A 15 -8.149 -3.328 -4.412 1.00 16.75 C ATOM 191 N GLY A 16 -6.280 -1.630 -2.332 1.00 33.75 N ATOM 192 CA GLY A 16 -5.558 -0.433 -1.960 1.00 33.31 C ATOM 193 C GLY A 16 -4.172 -0.442 -2.546 1.00 31.97 C ATOM 194 O GLY A 16 -3.854 -1.323 -3.340 1.00 30.11 O ATOM 199 N ILE A 17 -3.342 0.521 -2.175 1.00 31.75 N ATOM 200 CA ILE A 17 -1.957 0.575 -2.628 1.00 31.88 C ATOM 201 C ILE A 17 -1.127 1.136 -1.486 1.00 31.99 C ATOM 202 O ILE A 17 -1.509 2.125 -0.859 1.00 31.57 O ATOM 203 CB ILE A 17 -1.800 1.416 -3.903 1.00 32.40 C ATOM 204 N VAL A 18 0.004 0.509 -1.198 1.00 32.65 N ATOM 205 CA VAL A 18 0.896 0.990 -0.150 1.00 33.76 C ATOM 206 C VAL A 18 1.576 2.251 -0.664 1.00 33.35 C ATOM 207 O VAL A 18 1.822 2.385 -1.864 1.00 32.40 O ATOM 208 CB VAL A 18 1.921 -0.084 0.242 1.00 34.81 C ATOM 214 N ALA A 19 1.864 3.189 0.235 1.00 33.49 N ATOM 215 CA ALA A 19 2.476 4.453 -0.156 1.00 33.94 C ATOM 216 C ALA A 19 3.647 4.826 0.744 1.00 33.82 C ATOM 217 O ALA A 19 4.665 5.324 0.270 1.00 34.04 O ATOM 218 CB ALA A 19 1.424 5.566 -0.161 1.00 33.76 C ATOM 5 N LYS A 20 3.524 4.588 2.035 1.00 20.21 N ATOM 6 CA LYS A 20 4.589 4.865 2.977 1.00 19.04 C ATOM 7 C LYS A 20 4.900 3.577 3.721 1.00 20.37 C ATOM 8 O LYS A 20 3.998 2.918 4.200 1.00 17.74 O ATOM 9 CB LYS A 20 4.180 5.980 3.946 1.00 22.23 C ATOM 1297 N GLY A 21 6.167 3.188 3.771 1.00 21.17 N ATOM 1298 CA GLY A 21 6.567 1.981 4.467 1.00 22.82 C ATOM 1299 C GLY A 21 7.532 2.314 5.576 1.00 24.28 C ATOM 1300 O GLY A 21 8.482 3.050 5.360 1.00 27.83 O ATOM 1305 N LYS A 22 7.291 1.774 6.768 1.00 26.26 N ATOM 1306 CA LYS A 22 8.105 2.113 7.923 1.00 27.25 C ATOM 1307 C LYS A 22 9.402 1.326 7.995 1.00 27.39 C ATOM 1308 O LYS A 22 10.038 1.312 9.052 1.00 29.75 O ATOM 1309 CB LYS A 22 7.323 1.893 9.220 1.00 26.82 C ATOM 3906 N LYS A 23 9.821 0.689 6.909 1.00 32.62 N ATOM 3907 CA LYS A 23 11.000 -0.160 6.913 1.00 33.45 C ATOM 3908 C LYS A 23 12.234 0.608 6.475 1.00 33.95 C ATOM 3909 O LYS A 23 12.243 1.267 5.436 1.00 34.22 O ATOM 3910 CB LYS A 23 10.814 -1.365 5.994 1.00 33.95 C ATOM 3913 N LYS A 24 13.291 0.499 7.271 1.00 33.95 N ATOM 3914 CA LYS A 24 14.615 0.840 6.781 1.00 32.30 C ATOM 3915 C LYS A 24 15.027 -0.172 5.724 1.00 31.52 C ATOM 3916 O LYS A 24 14.201 -0.949 5.241 1.00 29.72 O ATOM 3917 CB LYS A 24 15.613 0.857 7.933 1.00 34.60 C ATOM 3920 N ALA A 25 16.304 -0.163 5.349 1.00 27.55 N ATOM 3921 CA ALA A 25 16.838 -1.114 4.366 1.00 25.34 C ATOM 3922 C ALA A 25 16.151 -0.996 3.006 1.00 23.20 C ATOM 3923 O ALA A 25 16.799 -1.059 1.963 1.00 24.26 O ATOM 3924 CB ALA A 25 16.750 -2.552 4.874 1.00 26.43 C ATOM 3932 N ILE A 26 14.832 -0.838 3.002 1.00 20.88 N ATOM 3933 CA ILE A 26 14.048 -0.875 1.759 1.00 23.21 C ATOM 3934 C ILE A 26 14.475 0.341 0.951 1.00 21.96 C ATOM 3935 O ILE A 26 13.782 1.356 0.859 1.00 22.39 O ATOM 3936 CB ILE A 26 12.544 -0.903 2.023 1.00 20.20 C ATOM 2399 N GLY A 27 15.640 0.227 0.329 1.00 10.32 N ATOM 2400 CA GLY A 27 16.116 1.315 -0.491 1.00 10.62 C ATOM 2401 C GLY A 27 16.940 0.819 -1.650 1.00 10.75 C ATOM 2402 O GLY A 27 17.880 0.042 -1.462 1.00 10.08 O ATOM 2407 N GLY A 28 16.611 1.269 -2.854 1.00 11.47 N ATOM 2408 CA GLY A 28 17.308 0.770 -4.022 1.00 12.20 C ATOM 2409 C GLY A 28 17.197 1.622 -5.270 1.00 11.92 C ATOM 2410 O GLY A 28 16.494 1.244 -6.216 1.00 12.26 O ATOM 2415 N GLY A 29 17.894 2.762 -5.282 1.00 12.31 N ATOM 2416 CA GLY A 29 18.014 3.611 -6.460 1.00 12.71 C ATOM 2417 C GLY A 29 19.359 4.295 -6.410 1.00 12.69 C ATOM 2418 O GLY A 29 20.288 3.888 -7.087 1.00 13.22 O ATOM 449 N ILE A 30 19.449 5.350 -5.610 1.00 23.48 N ATOM 450 CA ILE A 30 20.728 5.833 -5.100 1.00 22.97 C ATOM 451 C ILE A 30 20.902 5.094 -3.760 1.00 23.25 C ATOM 452 O ILE A 30 20.443 3.960 -3.612 1.00 24.94 O ATOM 453 N LYS A 31 21.544 5.715 -2.779 1.00 22.86 N ATOM 454 CA LYS A 31 21.646 5.092 -1.470 1.00 22.95 C ATOM 455 C LYS A 31 20.766 5.753 -0.426 1.00 21.87 C ATOM 456 O LYS A 31 21.050 5.626 0.766 1.00 21.87 O ATOM 457 CB LYS A 31 23.094 5.108 -0.988 1.00 23.61 C ATOM 459 N VAL A 32 19.716 6.454 -0.841 1.00 19.42 N ATOM 460 CA VAL A 32 18.826 7.113 0.099 1.00 18.30 C ATOM 461 C VAL A 32 17.907 6.077 0.728 1.00 18.42 C ATOM 462 O VAL A 32 18.040 4.876 0.474 1.00 18.87 O ATOM 463 CB VAL A 32 18.032 8.215 -0.613 1.00 18.52 C ATOM 1237 N ILE A 33 16.962 6.536 1.539 1.00 9.62 N ATOM 1238 CA ILE A 33 15.980 5.673 2.178 1.00 8.49 C ATOM 1239 C ILE A 33 15.027 6.551 2.974 1.00 9.76 C ATOM 1240 O ILE A 33 15.455 7.295 3.858 1.00 8.68 O ATOM 1241 CB ILE A 33 16.645 4.634 3.086 1.00 8.36 C ATOM 1245 N ARG A 34 13.739 6.460 2.675 1.00 10.12 N ATOM 1246 CA ARG A 34 12.720 7.097 3.493 1.00 11.50 C ATOM 1247 C ARG A 34 12.176 6.092 4.497 1.00 11.68 C ATOM 1248 O ARG A 34 12.576 4.927 4.492 1.00 12.46 O ATOM 1249 CB ARG A 34 11.597 7.637 2.617 1.00 11.89 C ATOM 1252 N ALA A 35 11.261 6.542 5.359 1.00 12.69 N ATOM 1253 CA ALA A 35 10.695 5.705 6.407 1.00 12.80 C ATOM 1254 C ALA A 35 9.704 6.492 7.245 1.00 12.75 C ATOM 1255 O ALA A 35 10.102 7.213 8.159 1.00 10.48 O ATOM 1256 CB ALA A 35 11.786 5.152 7.326 1.00 13.55 C ATOM 1260 N GLY A 36 8.419 6.317 6.969 1.00 12.49 N ATOM 1261 CA GLY A 36 7.413 7.124 7.633 1.00 14.21 C ATOM 1262 C GLY A 36 6.724 6.371 8.750 1.00 14.40 C ATOM 1263 O GLY A 36 7.125 6.436 9.918 1.00 13.51 O ATOM 1264 N ILE A 37 5.631 5.667 8.361 1.00 14.51 N ATOM 1265 CA ILE A 37 4.757 4.897 9.247 1.00 15.20 C ATOM 1266 C ILE A 37 3.531 4.471 8.455 1.00 15.16 C ATOM 1267 O ILE A 37 2.628 5.268 8.222 1.00 15.72 O ATOM 1268 CB ILE A 37 4.357 5.694 10.504 1.00 14.18 C ATOM 2971 N VAL A 38 3.481 3.184 8.101 1.00 9.75 N ATOM 2972 CA VAL A 38 2.765 2.611 6.949 1.00 10.34 C ATOM 2973 C VAL A 38 1.415 3.251 6.635 1.00 9.75 C ATOM 2974 O VAL A 38 0.701 3.685 7.540 1.00 10.53 O ATOM 2975 CB VAL A 38 2.595 1.089 7.128 1.00 11.46 C ATOM 263 N GLY A 39 1.054 3.302 5.349 1.00 16.54 N ATOM 264 CA GLY A 39 -0.179 3.934 4.919 1.00 17.07 C ATOM 265 C GLY A 39 -0.606 3.526 3.528 1.00 16.93 C ATOM 266 O GLY A 39 0.234 3.196 2.695 1.00 17.75 O ATOM 273 N LYS A 40 -1.905 3.551 3.256 1.00 16.86 N ATOM 274 CA LYS A 40 -2.430 2.997 2.011 1.00 17.62 C ATOM 275 C LYS A 40 -3.416 3.986 1.407 1.00 18.44 C ATOM 276 O LYS A 40 -3.964 4.825 2.121 1.00 18.27 O ATOM 277 CB LYS A 40 -3.100 1.654 2.268 1.00 17.83 C ATOM 5 N VAL A 41 -3.644 3.888 0.105 1.00 20.21 N ATOM 6 CA VAL A 41 -4.654 4.679 -0.580 1.00 19.04 C ATOM 7 C VAL A 41 -5.536 3.711 -1.345 1.00 20.37 C ATOM 8 O VAL A 41 -5.039 2.917 -2.149 1.00 17.74 O ATOM 9 CB VAL A 41 -4.021 5.719 -1.517 1.00 22.23 C ATOM 1969 N LYS A 42 -6.836 3.764 -1.090 1.00 12.88 N ATOM 1970 CA LYS A 42 -7.784 2.830 -1.684 1.00 14.47 C ATOM 1971 C LYS A 42 -7.782 3.004 -3.194 1.00 13.46 C ATOM 1972 O LYS A 42 -7.234 3.982 -3.705 1.00 14.70 O ATOM 1973 CB LYS A 42 -9.180 3.041 -1.109 1.00 15.03 C ATOM 1976 N VAL A 43 -8.373 2.053 -3.908 1.00 12.97 N ATOM 1977 CA VAL A 43 -8.322 2.024 -5.361 1.00 14.42 C ATOM 1978 C VAL A 43 -9.555 1.303 -5.878 1.00 14.78 C ATOM 1979 O VAL A 43 -10.114 0.446 -5.188 1.00 14.65 O ATOM 1980 CB VAL A 43 -7.043 1.339 -5.875 1.00 13.91 C ATOM 1984 N SER A 44 -10.000 1.673 -7.073 1.00 15.03 N ATOM 1985 CA SER A 44 -11.023 0.891 -7.741 1.00 15.75 C ATOM 1986 C SER A 44 -10.368 -0.303 -8.413 1.00 15.86 C ATOM 1987 O SER A 44 -9.147 -0.360 -8.551 1.00 15.75 O ATOM 1988 CB SER A 44 -11.768 1.745 -8.762 1.00 16.01 C ATOM 1989 N LYS A 45 -11.179 -1.267 -8.826 1.00 16.93 N ATOM 1990 CA LYS A 45 -10.625 -2.460 -9.445 1.00 17.52 C ATOM 1991 C LYS A 45 -10.218 -2.198 -10.892 1.00 17.12 C ATOM 1992 O LYS A 45 -9.270 -2.810 -11.391 1.00 18.20 O ATOM 1993 CB LYS A 45 -11.629 -3.607 -9.366 1.00 18.01 C ATOM 1881 N ASP A 46 -10.915 -1.298 -11.583 1.00 20.72 N ATOM 1882 CA ASP A 46 -10.523 -0.966 -12.946 1.00 21.11 C ATOM 1883 C ASP A 46 -9.778 0.363 -13.015 1.00 21.62 C ATOM 1884 O ASP A 46 -8.732 0.469 -13.665 1.00 20.59 O ATOM 1885 CB ASP A 46 -11.747 -0.928 -13.857 1.00 21.60 C ATOM 1893 N ALA A 47 -10.301 1.380 -12.347 1.00 20.82 N ATOM 1894 CA ALA A 47 -9.733 2.713 -12.424 1.00 20.91 C ATOM 1895 C ALA A 47 -8.475 2.824 -11.574 1.00 20.66 C ATOM 1896 O ALA A 47 -7.683 1.879 -11.483 1.00 22.58 O ATOM 1897 CB ALA A 47 -10.756 3.761 -11.979 1.00 20.41 C ATOM 1901 N VAL A 48 -8.294 4.001 -10.974 1.00 20.80 N ATOM 1902 CA VAL A 48 -7.114 4.275 -10.166 1.00 21.07 C ATOM 1903 C VAL A 48 -7.477 4.641 -8.728 1.00 21.38 C ATOM 1904 O VAL A 48 -7.724 3.749 -7.915 1.00 22.41 O ATOM 1905 CB VAL A 48 -6.270 5.380 -10.817 1.00 21.52 C ATOM 1909 N ALA A 49 -7.528 5.927 -8.391 1.00 21.20 N ATOM 1910 CA ALA A 49 -7.793 6.318 -7.011 1.00 22.10 C ATOM 1911 C ALA A 49 -9.288 6.274 -6.724 1.00 22.33 C ATOM 1912 O ALA A 49 -10.084 5.954 -7.606 1.00 22.72 O ATOM 1913 CB ALA A 49 -7.230 7.708 -6.733 1.00 22.39 C ATOM 1293 N ILE A 50 -9.665 6.569 -5.482 1.00 15.59 N ATOM 1294 CA ILE A 50 -11.064 6.537 -5.061 1.00 14.93 C ATOM 1295 C ILE A 50 -11.437 7.694 -4.146 1.00 14.02 C ATOM 1296 O ILE A 50 -12.402 7.562 -3.377 1.00 13.06 O ATOM 1297 CB ILE A 50 -11.418 5.198 -4.382 1.00 14.73 C ATOM 1300 N LYS A 51 -10.693 8.799 -4.187 1.00 12.35 N ATOM 1301 CA LYS A 51 -10.992 10.061 -3.519 1.00 11.94 C ATOM 1302 C LYS A 51 -9.740 10.921 -3.593 1.00 12.47 C ATOM 1303 O LYS A 51 -8.663 10.442 -3.947 1.00 12.54 O ATOM 1304 CB LYS A 51 -11.426 9.877 -2.064 1.00 12.38 C ATOM 1312 N GLY A 52 -9.892 12.204 -3.270 1.00 12.56 N ATOM 1313 CA GLY A 52 -8.751 13.100 -3.195 1.00 12.72 C ATOM 1314 C GLY A 52 -8.035 13.020 -1.860 1.00 13.42 C ATOM 1315 O GLY A 52 -8.581 13.435 -0.839 1.00 14.00 O ATOM 1319 N ASP A 53 -6.808 12.510 -1.855 1.00 12.19 N ATOM 1320 CA ASP A 53 -6.110 12.121 -0.631 1.00 13.93 C ATOM 1321 C ASP A 53 -5.430 13.323 -0.005 1.00 13.79 C ATOM 1322 O ASP A 53 -5.474 14.428 -0.540 1.00 14.44 O ATOM 1323 CB ASP A 53 -5.076 11.043 -0.931 1.00 14.33 C ATOM 2041 N GLY A 54 -4.774 13.101 1.124 1.00 17.99 N ATOM 2042 CA GLY A 54 -3.898 14.102 1.699 1.00 18.66 C ATOM 2043 C GLY A 54 -4.412 14.606 3.025 1.00 18.49 C ATOM 2044 O GLY A 54 -5.322 14.033 3.626 1.00 17.63 O ATOM 2786 N GLY A 55 -3.802 15.690 3.480 1.00 11.04 N ATOM 2787 CA GLY A 55 -4.206 16.360 4.695 1.00 10.44 C ATOM 2788 C GLY A 55 -3.005 16.632 5.581 1.00 11.03 C ATOM 2789 O GLY A 55 -1.986 17.154 5.145 1.00 10.97 O ATOM 2792 N GLY A 56 -3.165 16.290 6.857 1.00 13.14 N ATOM 2793 CA GLY A 56 -2.044 16.293 7.770 1.00 14.46 C ATOM 2794 C GLY A 56 -1.169 15.067 7.652 1.00 15.15 C ATOM 2795 O GLY A 56 -0.106 15.017 8.280 1.00 19.82 O ATOM 363 N ALA A 57 -1.583 14.078 6.862 1.00 20.15 N ATOM 364 CA ALA A 57 -0.839 12.836 6.718 1.00 20.14 C ATOM 365 C ALA A 57 -0.498 12.547 5.266 1.00 19.98 C ATOM 366 O ALA A 57 -0.530 11.393 4.844 1.00 19.91 O ATOM 367 CB ALA A 57 -1.620 11.670 7.325 1.00 20.73 C ATOM 371 N GLY A 58 -0.166 13.569 4.495 1.00 19.39 N ATOM 372 CA GLY A 58 0.160 13.363 3.105 1.00 19.02 C ATOM 373 C GLY A 58 1.646 13.352 2.847 1.00 19.48 C ATOM 374 O GLY A 58 2.311 14.384 2.950 1.00 18.91 O ATOM 377 N ILE A 59 2.177 12.185 2.519 1.00 20.12 N ATOM 378 CA ILE A 59 3.568 12.028 2.124 1.00 21.09 C ATOM 379 C ILE A 59 3.733 10.627 1.556 1.00 21.27 C ATOM 380 O ILE A 59 3.966 9.675 2.301 1.00 22.08 O ATOM 381 CB ILE A 59 4.525 12.267 3.300 1.00 21.22 C ATOM 2210 N LYS A 60 3.590 10.492 0.247 1.00 30.93 N ATOM 2211 CA LYS A 60 3.884 9.238 -0.415 1.00 30.78 C ATOM 2212 C LYS A 60 5.392 9.069 -0.462 1.00 30.67 C ATOM 2213 O LYS A 60 6.118 9.757 0.257 1.00 30.90 O ATOM 2214 CB LYS A 60 3.289 9.232 -1.818 1.00 31.02 C ATOM 2221 N ALA A 61 5.871 8.169 -1.309 1.00 30.33 N ATOM 2222 CA ALA A 61 7.299 7.964 -1.493 1.00 30.26 C ATOM 2223 C ALA A 61 7.651 8.280 -2.938 1.00 30.68 C ATOM 2224 O ALA A 61 6.856 8.027 -3.844 1.00 30.49 O ATOM 2225 CB ALA A 61 7.697 6.538 -1.137 1.00 29.87 C ATOM 2224 N ARG A 62 8.845 8.826 -3.154 1.00 25.61 N ATOM 2225 CA ARG A 62 9.290 9.085 -4.515 1.00 25.59 C ATOM 2226 C ARG A 62 9.350 7.805 -5.330 1.00 25.38 C ATOM 2227 O ARG A 62 9.267 7.852 -6.561 1.00 25.11 O ATOM 2228 CB ARG A 62 10.655 9.771 -4.506 1.00 26.01 C ATOM 2229 N ALA A 63 9.489 6.657 -4.669 1.00 25.45 N ATOM 2230 CA ALA A 63 9.487 5.394 -5.392 1.00 25.77 C ATOM 2231 C ALA A 63 8.192 5.196 -6.167 1.00 25.02 C ATOM 2232 O ALA A 63 8.186 4.511 -7.193 1.00 24.90 O ATOM 2233 CB ALA A 63 9.715 4.237 -4.424 1.00 26.08 C ATOM 2238 N LYS A 64 7.093 5.809 -5.724 1.00 24.57 N ATOM 2239 CA LYS A 64 5.841 5.665 -6.455 1.00 24.50 C ATOM 2240 C LYS A 64 5.925 6.269 -7.845 1.00 24.15 C ATOM 2241 O LYS A 64 5.025 6.053 -8.661 1.00 24.20 O ATOM 2242 CB LYS A 64 4.691 6.281 -5.665 1.00 24.19 C ATOM 149 N LYS A 65 7.006 6.976 -8.153 1.00 20.45 N ATOM 150 CA LYS A 65 7.282 7.415 -9.513 1.00 20.20 C ATOM 151 C LYS A 65 7.482 6.227 -10.444 1.00 20.10 C ATOM 152 O LYS A 65 7.850 6.397 -11.607 1.00 21.12 O ATOM 153 CB LYS A 65 8.514 8.322 -9.538 1.00 19.83 C ATOM 154 N LYS A 66 7.263 5.025 -9.938 1.00 17.29 N ATOM 155 CA LYS A 66 7.155 3.819 -10.749 1.00 17.32 C ATOM 156 C LYS A 66 5.686 3.638 -11.116 1.00 19.29 C ATOM 157 O LYS A 66 5.181 2.514 -11.159 1.00 18.79 O ATOM 158 CB LYS A 66 7.687 2.606 -10.000 1.00 17.96 C ATOM 161 N GLY A 67 4.994 4.753 -11.343 1.00 19.37 N ATOM 162 CA GLY A 67 3.673 4.711 -11.935 1.00 21.34 C ATOM 163 C GLY A 67 2.563 5.305 -11.110 1.00 21.74 C ATOM 164 O GLY A 67 1.532 4.657 -10.943 1.00 22.38 O ATOM 165 N GLY A 68 2.723 6.521 -10.607 1.00 20.48 N ATOM 166 CA GLY A 68 1.738 7.091 -9.712 1.00 19.86 C ATOM 167 C GLY A 68 0.960 8.276 -10.250 1.00 20.71 C ATOM 168 O GLY A 68 1.521 9.347 -10.495 1.00 20.81 O ATOM 781 N GLY A 69 -0.344 8.089 -10.439 1.00 16.86 N ATOM 782 CA GLY A 69 -1.254 9.192 -10.679 1.00 17.03 C ATOM 783 C GLY A 69 -1.751 9.734 -9.357 1.00 17.13 C ATOM 784 O GLY A 69 -2.764 10.436 -9.287 1.00 17.67 O ATOM 789 N LYS A 70 -1.039 9.362 -8.294 1.00 16.95 N ATOM 790 CA LYS A 70 -1.236 9.895 -6.951 1.00 17.08 C ATOM 791 C LYS A 70 -0.354 11.127 -6.811 1.00 16.68 C ATOM 792 O LYS A 70 0.540 11.180 -5.967 1.00 16.80 O ATOM 793 CB LYS A 70 -0.908 8.845 -5.897 1.00 17.17 C ATOM 797 N LYS A 71 -0.582 12.110 -7.679 1.00 16.94 N ATOM 798 CA LYS A 71 -0.103 13.471 -7.489 1.00 17.08 C ATOM 799 C LYS A 71 -1.061 14.233 -6.590 1.00 17.51 C ATOM 800 O LYS A 71 -1.126 15.461 -6.633 1.00 17.76 O ATOM 801 CB LYS A 71 0.064 14.193 -8.823 1.00 16.48 C ATOM 804 N SER A 72 -1.826 13.498 -5.787 1.00 17.36 N ATOM 805 CA SER A 72 -2.715 14.065 -4.790 1.00 17.64 C ATOM 806 C SER A 72 -2.081 14.099 -3.406 1.00 17.95 C ATOM 807 O SER A 72 -2.789 14.304 -2.419 1.00 19.26 O ATOM 808 CB SER A 72 -4.030 13.284 -4.760 1.00 16.94 C ATOM 814 N GLY A 73 -0.767 13.914 -3.311 1.00 17.32 N ATOM 815 CA GLY A 73 -0.067 13.999 -2.048 1.00 17.70 C ATOM 816 C GLY A 73 0.799 15.236 -1.978 1.00 18.50 C ATOM 817 O GLY A 73 0.720 16.131 -2.820 1.00 18.13 O ATOM 818 N ALA A 74 1.640 15.288 -0.948 1.00 18.71 N ATOM 819 CA ALA A 74 2.639 16.339 -0.801 1.00 19.65 C ATOM 820 C ALA A 74 3.987 15.786 -0.345 1.00 20.21 C ATOM 821 O ALA A 74 4.488 16.159 0.714 1.00 20.94 O ATOM 822 CB ALA A 74 2.147 17.406 0.168 1.00 19.63 C ATOM 829 N LYS A 75 4.578 14.893 -1.132 1.00 20.07 N ATOM 830 CA LYS A 75 5.874 14.306 -0.815 1.00 19.78 C ATOM 831 C LYS A 75 6.973 15.359 -0.868 1.00 19.42 C ATOM 832 O LYS A 75 6.975 16.315 -0.095 1.00 19.47 O ATOM 833 CB LYS A 75 6.202 13.162 -1.779 1.00 19.85 C TER ATOM 1 N ARG A 81 -10.933 -1.719 10.506 1.00 27.82 N ATOM 2 CA ARG A 81 -11.823 -1.081 9.549 1.00 23.15 C ATOM 3 C ARG A 81 -11.988 -1.971 8.326 1.00 24.44 C ATOM 4 O ARG A 81 -12.205 -3.166 8.454 1.00 23.56 O ATOM 5 N ILE A 82 -11.875 -1.381 7.142 1.00 20.21 N ATOM 6 CA ILE A 82 -12.024 -2.097 5.881 1.00 19.04 C ATOM 7 C ILE A 82 -10.960 -3.191 5.811 1.00 20.37 C ATOM 8 O ILE A 82 -9.946 -3.125 6.503 1.00 17.74 O ATOM 9 CB ILE A 82 -11.921 -1.138 4.692 1.00 22.23 C ATOM 546 N VAL A 83 -11.184 -4.199 4.975 1.00 22.37 N ATOM 547 CA VAL A 83 -10.271 -5.334 4.882 1.00 26.00 C ATOM 548 C VAL A 83 -9.683 -5.376 3.480 1.00 30.26 C ATOM 549 O VAL A 83 -10.257 -5.985 2.576 1.00 35.19 O ATOM 550 CB VAL A 83 -10.987 -6.648 5.223 1.00 25.74 C ATOM 555 N VAL A 84 -8.519 -4.763 3.306 1.00 24.40 N ATOM 556 CA VAL A 84 -7.998 -4.413 1.994 1.00 26.29 C ATOM 557 C VAL A 84 -7.173 -5.555 1.420 1.00 28.06 C ATOM 558 O VAL A 84 -6.494 -6.285 2.134 1.00 29.61 O ATOM 559 CB VAL A 84 -7.159 -3.125 2.053 1.00 31.28 C ATOM 566 N ILE A 85 -7.231 -5.697 0.103 1.00 30.54 N ATOM 567 CA ILE A 85 -6.344 -6.591 -0.621 1.00 29.29 C ATOM 568 C ILE A 85 -5.288 -5.732 -1.291 1.00 31.77 C ATOM 569 O ILE A 85 -5.224 -5.656 -2.519 1.00 31.74 O ATOM 570 CB ILE A 85 -7.097 -7.446 -1.645 1.00 30.40 C ATOM 574 N ILE A 86 -4.461 -5.091 -0.486 1.00 28.71 N ATOM 575 CA ILE A 86 -3.466 -4.149 -0.972 1.00 31.03 C ATOM 576 C ILE A 86 -2.529 -4.827 -1.953 1.00 32.44 C ATOM 577 O ILE A 86 -2.334 -6.037 -1.912 1.00 36.01 O ATOM 578 CB ILE A 86 -2.679 -3.530 0.199 1.00 25.27 C ATOM 718 N GLY A 87 -1.968 -4.055 -2.861 1.00 9.32 N ATOM 719 CA GLY A 87 -0.932 -4.502 -3.767 1.00 7.48 C ATOM 720 C GLY A 87 -0.251 -3.320 -4.410 1.00 7.50 C ATOM 721 O GLY A 87 -0.783 -2.757 -5.368 1.00 10.36 O ATOM 726 N GLY A 88 0.919 -2.932 -3.888 1.00 9.75 N ATOM 727 CA GLY A 88 1.563 -1.693 -4.258 1.00 9.75 C ATOM 728 C GLY A 88 3.052 -1.667 -3.956 1.00 10.39 C ATOM 729 O GLY A 88 3.761 -2.663 -4.113 1.00 11.83 O ATOM 734 N ILE A 89 3.521 -0.493 -3.507 1.00 10.14 N ATOM 735 CA ILE A 89 4.944 -0.178 -3.331 1.00 12.16 C ATOM 736 C ILE A 89 5.495 -0.650 -1.987 1.00 8.45 C ATOM 737 O ILE A 89 5.766 0.166 -1.097 1.00 13.94 O ATOM 738 CB ILE A 89 5.204 1.331 -3.485 1.00 15.51 C ATOM 746 N LYS A 90 5.681 -1.967 -1.845 1.00 10.12 N ATOM 747 CA LYS A 90 6.148 -2.597 -0.617 1.00 8.93 C ATOM 748 C LYS A 90 5.631 -4.028 -0.556 1.00 6.60 C ATOM 749 O LYS A 90 5.807 -4.788 -1.504 1.00 9.21 O ATOM 5 N VAL A 91 5.002 -4.404 0.553 1.00 20.21 N ATOM 6 CA VAL A 91 4.298 -5.673 0.720 1.00 19.04 C ATOM 7 C VAL A 91 5.176 -6.898 0.503 1.00 20.37 C ATOM 8 O VAL A 91 5.212 -7.447 -0.599 1.00 17.74 O ATOM 9 CB VAL A 91 3.087 -5.740 -0.219 1.00 22.23 C ATOM 3961 N LYS A 92 5.856 -7.361 1.551 1.00 27.85 N ATOM 3962 CA LYS A 92 6.534 -8.646 1.492 1.00 28.85 C ATOM 3963 C LYS A 92 5.486 -9.714 1.271 1.00 29.89 C ATOM 3964 O LYS A 92 4.298 -9.472 1.464 1.00 29.91 O ATOM 3965 N ALA A 93 5.914 -10.896 0.865 1.00 31.04 N ATOM 3966 CA ALA A 93 4.991 -11.881 0.329 1.00 32.00 C ATOM 3967 C ALA A 93 4.826 -13.092 1.236 1.00 32.74 C ATOM 3968 O ALA A 93 5.773 -13.537 1.890 1.00 32.70 O ATOM 3969 CB ALA A 93 5.448 -12.347 -1.048 1.00 32.14 C ATOM 3972 N LYS A 94 3.604 -13.615 1.256 1.00 33.67 N ATOM 3973 CA LYS A 94 3.306 -14.983 1.651 1.00 34.45 C ATOM 3974 C LYS A 94 2.420 -15.578 0.567 1.00 34.91 C ATOM 3975 O LYS A 94 1.197 -15.637 0.717 1.00 34.86 O ATOM 3976 CB LYS A 94 2.616 -15.036 3.006 1.00 34.55 C ATOM 3981 N ILE A 95 3.040 -15.999 -0.525 1.00 35.68 N ATOM 3982 CA ILE A 95 2.350 -16.583 -1.663 1.00 36.06 C ATOM 3983 C ILE A 95 3.326 -16.436 -2.814 1.00 36.64 C ATOM 3984 O ILE A 95 4.488 -16.084 -2.602 1.00 36.89 O ATOM 3985 N GLY A 96 2.876 -16.714 -4.028 1.00 37.18 N ATOM 3986 CA GLY A 96 3.567 -16.234 -5.207 1.00 37.54 C ATOM 3987 C GLY A 96 2.749 -15.074 -5.715 1.00 37.30 C ATOM 3988 O GLY A 96 1.682 -15.285 -6.291 1.00 37.64 O ATOM 2898 N ALA A 97 3.190 -13.847 -5.478 1.00 10.14 N ATOM 2899 CA ALA A 97 2.185 -12.800 -5.494 1.00 11.76 C ATOM 2900 C ALA A 97 2.720 -11.537 -6.141 1.00 11.70 C ATOM 2901 O ALA A 97 3.610 -10.879 -5.596 1.00 11.58 O ATOM 2902 CB ALA A 97 1.697 -12.502 -4.074 1.00 13.45 C ATOM 2904 N LYS A 98 2.143 -11.204 -7.307 1.00 11.11 N ATOM 2905 CA LYS A 98 2.267 -9.877 -7.899 1.00 11.97 C ATOM 2906 C LYS A 98 1.355 -8.867 -7.224 1.00 13.33 C ATOM 2907 O LYS A 98 1.823 -7.792 -6.847 1.00 13.19 O ATOM 2908 CB LYS A 98 1.962 -9.920 -9.390 1.00 11.60 C ATOM 2910 N LYS A 99 0.074 -9.165 -7.073 1.00 14.27 N ATOM 2911 CA LYS A 99 -0.777 -8.405 -6.169 1.00 16.74 C ATOM 2912 C LYS A 99 -0.888 -9.174 -4.863 1.00 17.34 C ATOM 2913 O LYS A 99 -1.407 -10.286 -4.829 1.00 18.30 O ATOM 2914 CB LYS A 99 -2.171 -8.161 -6.763 1.00 18.21 C ATOM 2918 N VAL A 100 -0.362 -8.593 -3.784 1.00 18.48 N ATOM 2919 CA VAL A 100 -0.280 -9.286 -2.501 1.00 18.43 C ATOM 2920 C VAL A 100 -1.650 -9.810 -2.116 1.00 18.02 C ATOM 2921 O VAL A 100 -2.308 -9.283 -1.206 1.00 17.17 O ATOM 2922 CB VAL A 100 0.300 -8.382 -1.401 1.00 19.81 C ATOM 9078 N GLY A 101 -2.064 -10.885 -2.791 1.00 14.81 N ATOM 9079 CA GLY A 101 -3.396 -11.459 -2.697 1.00 14.61 C ATOM 9080 C GLY A 101 -3.816 -11.831 -1.300 1.00 15.70 C ATOM 9081 O GLY A 101 -4.495 -12.837 -1.075 1.00 19.52 O ATOM 9086 N GLY A 102 -3.405 -11.010 -0.355 1.00 15.31 N ATOM 9087 CA GLY A 102 -3.685 -11.285 1.022 1.00 16.53 C ATOM 9088 C GLY A 102 -4.695 -10.267 1.436 1.00 13.65 C ATOM 9089 O GLY A 102 -4.825 -9.244 0.768 1.00 13.71 O ATOM 9095 N VAL A 103 -5.429 -10.520 2.508 1.00 17.42 N ATOM 9096 CA VAL A 103 -6.373 -9.523 2.953 1.00 17.66 C ATOM 9097 C VAL A 103 -5.844 -8.885 4.220 1.00 17.97 C ATOM 9098 O VAL A 103 -6.282 -9.213 5.327 1.00 16.61 O ATOM 9099 CB VAL A 103 -7.763 -10.141 3.142 1.00 17.30 C ATOM 9102 N ILE A 104 -4.890 -7.966 4.061 1.00 14.21 N ATOM 9103 CA ILE A 104 -4.452 -7.082 5.130 1.00 15.11 C ATOM 9104 C ILE A 104 -5.597 -6.134 5.455 1.00 16.87 C ATOM 9105 O ILE A 104 -6.647 -6.165 4.813 1.00 15.71 O ATOM 9106 CB ILE A 104 -3.180 -6.311 4.746 1.00 15.53 C ATOM 9110 N LYS A 105 -5.399 -5.278 6.449 1.00 16.52 N ATOM 9111 CA LYS A 105 -6.520 -4.544 7.031 1.00 17.93 C ATOM 9112 C LYS A 105 -6.201 -3.052 7.074 1.00 17.88 C ATOM 9113 O LYS A 105 -5.045 -2.646 7.092 1.00 18.77 O ATOM 9114 CB LYS A 105 -6.824 -5.102 8.410 1.00 18.90 C ATOM 5 N ALA A 106 -7.232 -2.216 7.115 1.00 20.21 N ATOM 6 CA ALA A 106 -7.056 -0.781 6.956 1.00 19.04 C ATOM 7 C ALA A 106 -7.931 0.002 7.928 1.00 20.37 C ATOM 8 O ALA A 106 -9.066 -0.386 8.200 1.00 17.74 O ATOM 9 CB ALA A 106 -7.372 -0.379 5.523 1.00 22.23 C ATOM 4765 N ILE A 107 -7.413 1.116 8.427 1.00 15.76 N ATOM 4766 CA ILE A 107 -8.037 1.869 9.505 1.00 16.10 C ATOM 4767 C ILE A 107 -8.385 3.260 8.981 1.00 16.16 C ATOM 4768 O ILE A 107 -7.719 4.245 9.315 1.00 16.39 O ATOM 4769 CB ILE A 107 -7.129 1.951 10.734 1.00 16.21 C ATOM 4772 N ARG A 108 -9.446 3.365 8.184 1.00 16.03 N ATOM 4773 CA ARG A 108 -9.875 4.668 7.688 1.00 16.68 C ATOM 4774 C ARG A 108 -10.775 4.501 6.471 1.00 16.75 C ATOM 4775 O ARG A 108 -10.508 3.666 5.608 1.00 17.20 O ATOM 4776 N ARG A 109 -11.843 5.288 6.384 1.00 16.99 N ATOM 4777 CA ARG A 109 -12.827 5.134 5.322 1.00 17.03 C ATOM 4778 C ARG A 109 -13.169 6.448 4.638 1.00 16.97 C ATOM 4779 O ARG A 109 -14.132 7.110 5.019 1.00 17.08 O ATOM 4780 N GLY A 110 -12.410 6.827 3.628 1.00 16.68 N ATOM 4781 CA GLY A 110 -12.642 8.085 2.962 1.00 16.30 C ATOM 4782 C GLY A 110 -11.689 8.321 1.812 1.00 15.96 C ATOM 4783 O GLY A 110 -11.854 7.791 0.716 1.00 15.78 O ATOM 806 N ILE A 111 -10.649 9.116 2.095 1.00 15.21 N ATOM 807 CA ILE A 111 -9.750 9.578 1.038 1.00 15.25 C ATOM 808 C ILE A 111 -8.321 9.099 1.283 1.00 14.48 C ATOM 809 O ILE A 111 -7.801 8.237 0.566 1.00 13.95 O ATOM 810 CB ILE A 111 -9.818 11.109 0.914 1.00 18.69 C ATOM 817 N LYS A 112 -7.659 9.668 2.288 1.00 13.23 N ATOM 818 CA LYS A 112 -6.223 9.478 2.464 1.00 12.29 C ATOM 819 C LYS A 112 -5.854 8.095 2.963 1.00 11.93 C ATOM 820 O LYS A 112 -4.663 7.826 3.179 1.00 12.30 O ATOM 821 CB LYS A 112 -5.666 10.517 3.435 1.00 13.42 C ATOM 826 N VAL A 113 -6.841 7.227 3.178 1.00 11.35 N ATOM 827 CA VAL A 113 -6.604 5.842 3.569 1.00 10.38 C ATOM 828 C VAL A 113 -5.998 5.810 4.962 1.00 11.79 C ATOM 829 O VAL A 113 -5.491 6.818 5.458 1.00 13.75 O ATOM 830 N GLY A 114 -6.049 4.653 5.606 1.00 10.10 N ATOM 831 CA GLY A 114 -5.425 4.485 6.899 1.00 9.84 C ATOM 832 C GLY A 114 -4.098 3.765 6.757 1.00 10.25 C ATOM 833 O GLY A 114 -3.749 3.273 5.691 1.00 9.82 O ATOM 5 N GLY A 115 -3.373 3.728 7.868 1.00 20.21 N ATOM 6 CA GLY A 115 -2.267 2.805 7.963 1.00 19.04 C ATOM 7 C GLY A 115 -2.770 1.375 7.931 1.00 20.37 C ATOM 8 O GLY A 115 -3.792 1.040 8.528 1.00 17.74 O ATOM 775 N GLY A 116 -2.062 0.527 7.203 1.00 16.60 N ATOM 776 CA GLY A 116 -2.402 -0.870 7.202 1.00 17.27 C ATOM 777 C GLY A 116 -2.317 -1.462 8.594 1.00 19.96 C ATOM 778 O GLY A 116 -1.650 -0.942 9.481 1.00 18.97 O ATOM 786 N LYS A 117 -3.011 -2.575 8.793 1.00 20.70 N ATOM 787 CA LYS A 117 -2.870 -3.317 10.035 1.00 20.75 C ATOM 788 C LYS A 117 -2.072 -4.590 9.793 1.00 26.23 C ATOM 789 O LYS A 117 -2.473 -5.451 9.007 1.00 38.53 O ATOM 790 CB LYS A 117 -4.236 -3.637 10.639 1.00 23.72 C ATOM 1832 N ILE A 118 -0.938 -4.698 10.472 1.00 12.23 N ATOM 1833 CA ILE A 118 -0.002 -5.792 10.295 1.00 12.84 C ATOM 1834 C ILE A 118 1.212 -5.529 11.182 1.00 12.33 C ATOM 1835 O ILE A 118 1.098 -5.094 12.329 1.00 11.94 O ATOM 1836 CB ILE A 118 0.416 -5.975 8.818 1.00 13.17 C ATOM 2465 N ALA A 119 2.387 -5.797 10.617 1.00 13.65 N ATOM 2466 CA ALA A 119 3.683 -5.570 11.236 1.00 12.43 C ATOM 2467 C ALA A 119 4.432 -4.444 10.535 1.00 13.72 C ATOM 2468 O ALA A 119 5.295 -4.711 9.697 1.00 14.32 O ATOM 2469 CB ALA A 119 4.520 -6.843 11.180 1.00 12.02 C ATOM 31 N VAL A 120 4.126 -3.185 10.860 1.00 5.87 N ATOM 32 CA VAL A 120 4.852 -2.058 10.280 1.00 6.28 C ATOM 33 C VAL A 120 6.325 -2.200 10.613 1.00 6.30 C ATOM 34 O VAL A 120 6.767 -1.822 11.701 1.00 6.82 O ATOM 35 CB VAL A 120 4.289 -0.729 10.794 1.00 6.30 C ATOM 43 N LYS A 121 7.090 -2.731 9.665 1.00 6.85 N ATOM 44 CA LYS A 121 8.324 -3.457 9.940 1.00 7.33 C ATOM 45 C LYS A 121 9.432 -2.496 10.352 1.00 7.22 C ATOM 46 O LYS A 121 9.532 -1.393 9.814 1.00 8.07 O ATOM 47 CB LYS A 121 8.721 -4.287 8.725 1.00 7.37 C ATOM 51 N ILE A 122 10.245 -2.915 11.332 1.00 7.60 N ATOM 52 CA ILE A 122 11.466 -2.211 11.718 1.00 8.54 C ATOM 53 C ILE A 122 12.686 -3.134 11.750 1.00 9.00 C ATOM 54 O ILE A 122 13.814 -2.661 11.938 1.00 10.14 O ATOM 636 N GLY A 123 12.493 -4.436 11.572 1.00 22.14 N ATOM 637 CA GLY A 123 13.615 -5.356 11.617 1.00 21.89 C ATOM 638 C GLY A 123 14.000 -5.831 10.227 1.00 19.25 C ATOM 639 O GLY A 123 13.170 -6.364 9.480 1.00 19.23 O ATOM 644 N GLY A 124 15.285 -5.684 9.913 1.00 17.08 N ATOM 645 CA GLY A 124 15.711 -5.611 8.522 1.00 16.06 C ATOM 646 C GLY A 124 15.397 -6.863 7.752 1.00 16.14 C ATOM 647 O GLY A 124 15.825 -7.969 8.102 1.00 14.51 O ATOM 652 N GLY A 125 14.634 -6.699 6.671 1.00 15.60 N ATOM 653 CA GLY A 125 14.267 -7.769 5.792 1.00 16.03 C ATOM 654 C GLY A 125 15.002 -7.694 4.472 1.00 15.94 C ATOM 655 O GLY A 125 16.219 -7.551 4.417 1.00 16.51 O ATOM 5 N VAL A 126 14.226 -7.758 3.396 1.00 20.21 N ATOM 6 CA VAL A 126 14.787 -7.748 2.047 1.00 19.04 C ATOM 7 C VAL A 126 15.479 -6.424 1.772 1.00 20.37 C ATOM 8 O VAL A 126 14.821 -5.414 1.530 1.00 17.74 O ATOM 9 CB VAL A 126 13.693 -7.995 1.011 1.00 22.23 C ATOM 14 N LYS A 127 16.810 -6.434 1.776 1.00 19.31 N ATOM 15 CA LYS A 127 17.595 -5.278 1.359 1.00 19.58 C ATOM 16 C LYS A 127 17.394 -5.015 -0.125 1.00 19.91 C ATOM 17 O LYS A 127 16.414 -5.454 -0.725 1.00 19.76 O ATOM 18 CB LYS A 127 19.076 -5.509 1.633 1.00 20.42 C ATOM 19 N VAL A 128 18.346 -4.320 -0.729 1.00 17.69 N ATOM 20 CA VAL A 128 18.346 -4.201 -2.176 1.00 17.51 C ATOM 21 C VAL A 128 19.633 -3.583 -2.668 1.00 14.26 C ATOM 22 O VAL A 128 20.715 -3.968 -2.249 1.00 14.38 O ATOM 23 CB VAL A 128 17.155 -3.391 -2.675 1.00 17.33 C TER ATOM 726 N LYS A 141 5.819 -10.424 5.061 1.00 9.48 N ATOM 727 CA LYS A 141 5.877 -9.822 6.378 1.00 8.99 C ATOM 728 C LYS A 141 4.735 -8.852 6.546 1.00 9.97 C ATOM 729 O LYS A 141 4.546 -8.280 7.611 1.00 11.19 O ATOM 730 CB LYS A 141 7.209 -9.105 6.595 1.00 9.39 C ATOM 733 N LYS A 142 3.997 -8.645 5.463 1.00 9.26 N ATOM 734 CA LYS A 142 2.855 -7.745 5.445 1.00 8.32 C ATOM 735 C LYS A 142 1.682 -8.537 4.918 1.00 8.47 C ATOM 736 O LYS A 142 0.694 -7.974 4.451 1.00 8.93 O ATOM 737 CB LYS A 142 3.122 -6.513 4.577 1.00 8.23 C ATOM 744 N GLY A 143 1.805 -9.853 4.977 1.00 7.76 N ATOM 745 CA GLY A 143 0.781 -10.744 4.483 1.00 10.15 C ATOM 746 C GLY A 143 -0.489 -10.662 5.291 1.00 10.23 C ATOM 747 O GLY A 143 -0.914 -9.570 5.664 1.00 10.32 O ATOM 748 N VAL A 144 -1.074 -11.811 5.628 1.00 11.54 N ATOM 749 CA VAL A 144 -2.418 -11.828 6.194 1.00 12.37 C ATOM 750 C VAL A 144 -2.498 -11.028 7.492 1.00 11.94 C ATOM 751 O VAL A 144 -3.493 -11.114 8.220 1.00 10.53 O ATOM 752 CB VAL A 144 -2.878 -13.285 6.391 1.00 13.66 C ATOM 757 N GLY A 145 -1.484 -10.229 7.793 1.00 12.14 N ATOM 758 CA GLY A 145 -1.449 -9.459 9.013 1.00 10.62 C ATOM 759 C GLY A 145 -2.596 -8.505 9.213 1.00 11.20 C ATOM 760 O GLY A 145 -2.822 -8.051 10.324 1.00 10.38 O TER ATOM 726 N GLY A 131 -5.004 -10.220 15.078 1.00 9.48 N ATOM 727 CA GLY A 131 -3.704 -9.586 15.089 1.00 8.99 C ATOM 728 C GLY A 131 -2.604 -10.549 14.742 1.00 9.97 C ATOM 729 O GLY A 131 -1.480 -10.145 14.481 1.00 11.19 O ATOM 733 N GLY A 132 -2.948 -11.828 14.740 1.00 9.26 N ATOM 734 CA GLY A 132 -2.009 -12.893 14.479 1.00 8.32 C ATOM 735 C GLY A 132 -2.675 -14.250 14.440 1.00 8.47 C ATOM 736 O GLY A 132 -2.016 -15.279 14.591 1.00 8.93 O ATOM 744 N LYS A 133 -3.987 -14.266 14.231 1.00 7.76 N ATOM 745 CA LYS A 133 -4.748 -15.497 14.096 1.00 10.15 C ATOM 746 C LYS A 133 -4.656 -16.004 12.672 1.00 10.23 C ATOM 747 O LYS A 133 -5.505 -16.776 12.235 1.00 10.32 O ATOM 748 N LYS A 134 -3.616 -15.577 11.950 1.00 11.54 N ATOM 749 CA LYS A 134 -3.415 -15.991 10.565 1.00 12.37 C ATOM 750 C LYS A 134 -2.058 -15.549 10.044 1.00 11.94 C ATOM 751 O LYS A 134 -1.515 -16.164 9.125 1.00 10.53 O ATOM 752 CB LYS A 134 -4.519 -15.426 9.684 1.00 13.66 C ATOM 757 N ILE A 135 -1.498 -14.500 10.628 1.00 12.14 N ATOM 758 CA ILE A 135 -0.212 -13.942 10.248 1.00 10.62 C ATOM 759 C ILE A 135 0.870 -14.998 10.253 1.00 11.20 C ATOM 760 O ILE A 135 1.939 -14.786 10.816 1.00 10.38 O ATOM 761 CB ILE A 135 0.180 -12.801 11.183 1.00 11.50 C TER END """ first_annotation_text=""" SHEET 1 1 2 VAL A 18 GLY A 21 0 SHEET 2 1 2 VAL A 38 VAL A 41 -1 """ second_annotation_text=""" SHEET 1 1 4 LYS A 40 VAL A 43 0 SHEET 2 1 4 ALA A 12 VAL A 18 -1 N ILE A 17 O VAL A 41 SHEET 3 1 4 ARG A 81 GLY A 87 1 N VAL A 83 O ALA A 12 SHEET 4 1 4 VAL A 103 ILE A 107 -1 N ALA A 106 O ILE A 82 """ import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(pdb_text) ).construct_hierarchy() import iotbx.pdb.secondary_structure as ioss first_annotation=ioss.annotation.from_records(records=flex.split_lines(first_annotation_text)) second_annotation=ioss.annotation.from_records(records=flex.split_lines(second_annotation_text)) print("\nMerging annotations and checking on sheet numbering") print("\nFirst annotation: ") print(first_annotation.as_pdb_str()) print("\nSecond annotation: ") print(second_annotation.as_pdb_str()) merged=second_annotation.combine_annotations(other=first_annotation, hierarchy=hierarchy) print("\nMerged: ") print(merged.as_pdb_str()) assert merged.is_similar_to(other=second_annotation,hierarchy=hierarchy) std_short=""" ATOM 41 N ALA E 9 16.983 19.664 12.537 1.00 40.00 N ATOM 42 CA ALA E 9 18.325 19.700 13.075 1.00 40.00 C ATOM 43 C ALA E 9 18.282 19.275 14.530 1.00 40.00 C ATOM 44 O ALA E 9 19.094 19.698 15.348 1.00 40.00 O ATOM 45 CB ALA E 9 18.921 21.097 12.944 1.00 40.00 C ATOM 46 N ALA E 10 17.311 18.426 14.838 1.00 40.00 N ATOM 47 CA ALA E 10 16.934 18.105 16.208 1.00 40.00 C ATOM 48 C ALA E 10 15.691 17.248 16.171 1.00 40.00 C ATOM 49 O ALA E 10 15.418 16.533 17.133 1.00 40.00 O ATOM 50 CB ALA E 10 16.643 19.341 17.056 1.00 40.00 C ATOM 51 N ALA E 11 14.918 17.340 15.101 1.00 40.00 N ATOM 52 CA ALA E 11 13.892 16.372 14.777 1.00 40.00 C ATOM 53 C ALA E 11 14.481 15.437 13.750 1.00 40.00 C ATOM 54 O ALA E 11 14.140 14.259 13.695 1.00 40.00 O ATOM 55 CB ALA E 11 12.642 17.047 14.251 1.00 40.00 C ATOM 56 N ALA E 12 15.357 15.975 12.922 1.00 40.00 N ATOM 57 CA ALA E 12 16.068 15.188 11.935 1.00 40.00 C ATOM 58 C ALA E 12 17.302 14.592 12.578 1.00 40.00 C ATOM 59 O ALA E 12 17.738 13.498 12.224 1.00 40.00 O ATOM 60 CB ALA E 12 16.473 16.043 10.745 1.00 40.00 C ATOM 61 N ALA E 13 17.885 15.327 13.522 1.00 40.00 N ATOM 62 CA ALA E 13 19.089 14.889 14.207 1.00 40.00 C ATOM 63 C ALA E 13 18.624 13.974 15.341 1.00 40.00 C ATOM 64 O ALA E 13 19.426 13.210 15.854 1.00 40.00 O ATOM 65 CB ALA E 13 19.937 16.062 14.623 1.00 40.00 C ATOM 66 N ALA E 14 17.377 14.036 15.725 1.00 40.00 N ATOM 67 CA ALA E 14 16.776 12.964 16.497 1.00 40.00 C ATOM 68 C ALA E 14 16.849 11.628 15.781 1.00 40.00 C ATOM 69 O ALA E 14 17.479 11.493 14.731 1.00 40.00 O ATOM 70 CB ALA E 14 15.332 13.334 16.814 1.00 40.00 C ATOM 71 N ALA E 15 16.245 10.605 16.362 1.00 40.00 N ATOM 72 CA ALA E 15 15.885 9.387 15.650 1.00 40.00 C ATOM 73 C ALA E 15 14.370 9.403 15.597 1.00 40.00 C ATOM 74 O ALA E 15 13.752 9.549 14.543 1.00 40.00 O ATOM 75 CB ALA E 15 16.418 8.148 16.352 1.00 40.00 C ATOM 76 N ALA E 16 13.770 9.311 16.781 1.00 40.00 N ATOM 77 CA ALA E 16 12.311 9.393 16.932 1.00 40.00 C ATOM 78 C ALA E 16 11.863 10.591 17.771 1.00 40.00 C ATOM 79 O ALA E 16 10.793 11.154 17.534 1.00 40.00 O ATOM 80 CB ALA E 16 11.787 8.113 17.522 1.00 40.00 C TER """ std=""" ATOM 36 N ALA E 8 13.630 20.859 12.915 1.00 40.00 N ATOM 37 CA ALA E 8 14.599 19.792 12.772 1.00 40.00 C ATOM 38 C ALA E 8 15.979 20.231 13.192 1.00 40.00 C ATOM 39 O ALA E 8 16.128 21.067 14.087 1.00 40.00 O ATOM 40 CB ALA E 8 14.646 19.295 11.334 1.00 40.00 C """ + std_short anno=""" HELIX 1 1 ALA E 8 ALA E 14 1 7 HELIX 1 1 ALA E 9 ALA E 14 1 7 """ sheet_anno=""" SHEET 1 1 4 LYS A 40 VAL A 43 0 SHEET 2 1 4 ALA A 12 VAL A 18 -1 N ILE A 17 O VAL A 41 SHEET 3 1 4 ARG A 81 GLY A 87 1 N VAL A 83 O ALA A 12 SHEET 4 1 4 VAL A 103 ILE A 107 -1 N ALA A 106 O ILE A 82 SHEET 1 2 2 ALA A 12 VAL A 18 0 SHEET 2 2 2 ARG A 81 GLY A 87 1 """ bad_sheet_anno=""" SHEET 1 1 4 LYS A 40 VAL A 43 0 SHEET 2 1 4 GLY A 10 VAL A 18 -1 N ILE A 17 O VAL A 41 SHEET 3 1 4 ARG A 81 GLY A 87 1 N VAL A 83 O ALA A 12 SHEET 4 1 4 VAL A 103 ILE A 107 -1 N ALA A 106 O ILE A 82 """ print("\nRemoving bad annotation and duplicate annotation\n") print("\nRemoving duplicate sheets") annotation=ioss.annotation.from_records(records=flex.split_lines(sheet_anno)) print(annotation.as_pdb_str()) new_annotation=annotation.remove_overlapping_annotations( hierarchy=hierarchy) print("New annotation:") print(new_annotation.as_pdb_str()) expected=ioss.annotation.from_records(records=flex.split_lines(""" SHEET 1 1 4 LYS A 40 VAL A 43 0 SHEET 2 1 4 ALA A 12 VAL A 18 -1 N ILE A 17 O VAL A 41 SHEET 3 1 4 ARG A 81 GLY A 87 1 N VAL A 83 O ALA A 12 SHEET 4 1 4 VAL A 103 ILE A 107 -1 N ALA A 106 O ILE A 82 """)) assert new_annotation.is_same_as(expected) print("\nRemoving bad sheets") annotation=ioss.annotation.from_records(records=flex.split_lines( bad_sheet_anno)) print(annotation.as_pdb_str()) from mmtbx.secondary_structure.find_ss_from_ca import remove_bad_annotation new_annotation=remove_bad_annotation(annotation,hierarchy=hierarchy) print("New annotation:") print(new_annotation.as_pdb_str()) expected=ioss.annotation.from_records(records=flex.split_lines(""" SHEET 1 3 2 ARG A 81 GLY A 87 0 SHEET 2 3 2 VAL A 103 ILE A 107 -1 N ALA A 106 O ILE A 82 """)) assert new_annotation.is_same_as(expected) import iotbx.pdb from cctbx.array_family import flex std_hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(std)).construct_hierarchy() short_hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(std_short)).construct_hierarchy() import iotbx.pdb.secondary_structure as ioss annotation=ioss.annotation.from_records(records=flex.split_lines(anno)) print("\nRemoving duplicate helices") print(annotation.as_pdb_str()) print("\nRemoving duplicate helix annotation\n") expected=ioss.annotation.from_records(records=flex.split_lines(""" HELIX 1 1 ALA E 8 ALA E 14 1 7 """)) new_annotation=annotation.remove_overlapping_annotations( hierarchy=std_hierarchy) print(new_annotation.as_pdb_str()) assert new_annotation.is_same_as(expected) print("\nRemoving bad annotation\n") expected=ioss.annotation.from_records(records=flex.split_lines(""" HELIX 1 1 ALA E 9 ALA E 14 1 7 """)) from mmtbx.secondary_structure.find_ss_from_ca import remove_bad_annotation new_annotation=remove_bad_annotation(annotation,hierarchy=short_hierarchy, out=null_out()) print(new_annotation.as_pdb_str()) assert new_annotation.is_same_as(expected) def tst_13(): text=""" ATOM 1158 CA GLU A 156 -8.682 11.320 15.966 1.00 10.43 C ATOM 1167 CA GLN A 156A -6.656 11.562 12.759 1.00 9.67 C ATOM 1176 CA LEU A 157 -4.088 9.262 11.060 1.00 7.37 C ATOM 1184 CA ASP A 158 -0.686 11.064 10.807 1.00 7.30 C ATOM 1192 CA HIS A 159 2.219 8.525 11.247 1.00 5.74 C ATOM 1202 CA GLY A 160 3.410 5.357 9.460 1.00 4.69 C ATOM 1206 CA VAL A 161 4.873 2.505 11.506 1.00 4.06 C ATOM 1213 CA LEU A 162 5.253 -1.330 11.465 1.00 4.26 C ATOM 1221 CA LEU A 163 3.267 -3.988 13.368 1.00 3.63 C ATOM 1229 CA VAL A 164 5.734 -6.749 14.393 1.00 3.93 C ATOM 1236 CA GLY A 165 3.593 -8.854 16.787 1.00 4.71 C ATOM 1240 CA TYR A 166 0.655 -9.045 19.213 1.00 4.48 C ATOM 1252 CA ASN A 167 -0.292 -10.850 22.465 1.00 5.51 C ATOM 1260 CA ASP A 167A -3.960 -11.826 23.104 1.00 6.24 C ATOM 1268 CA SER A 167B -3.078 -13.777 26.298 1.00 8.74 C ATOM 1275 CA ALA A 167C -1.804 -10.753 28.295 1.00 8.17 C ATOM 1280 CA ALA A 167D -3.879 -9.096 31.017 1.00 8.79 C ATOM 1285 CA VAL A 168 -4.502 -6.306 28.540 1.00 7.67 C ATOM 1292 CA PRO A 169 -4.105 -7.677 24.962 1.00 6.12 C ATOM 1299 CA TYR A 170 -1.596 -5.595 22.934 1.00 4.66 C ATOM 1311 CA TRP A 171 0.102 -4.825 19.619 1.00 4.56 C ATOM 1325 CA ILE A 172 3.927 -4.560 19.307 1.00 4.40 C ATOM 1333 CA ILE A 173 4.979 -1.652 16.989 1.00 3.93 C ATOM 1341 CA LYS A 174 8.388 -0.666 15.529 1.00 3.87 C ATOM 1350 CA ASN A 175 8.873 3.137 15.566 1.00 4.64 C ATOM 1358 CA SER A 176 11.580 5.250 13.796 1.00 5.32 C ATOM 1364 CA TRP A 177 12.553 7.546 16.722 1.00 5.40 C ATOM 1378 CA THR A 178 15.829 5.844 17.894 1.00 5.35 C ATOM 1385 CA THR A 179 16.311 3.064 20.481 1.00 7.16 C ATOM 1392 CA GLN A 180 16.334 5.566 23.406 1.00 6.59 C ATOM 1405 CA TRP A 181 12.544 6.150 22.843 1.00 5.77 C ATOM 1419 CA GLY A 182 9.950 3.677 24.216 1.00 6.03 C ATOM 1423 CA GLU A 183 10.962 0.080 24.830 1.00 6.05 C ATOM 1432 CA GLU A 184 14.314 0.060 22.937 1.00 6.35 C ATOM 1441 CA GLY A 185 12.464 1.895 20.102 1.00 4.92 C ATOM 1445 CA TYR A 186 9.218 -0.136 20.229 1.00 5.14 C ATOM 1457 CA ILE A 187 5.733 0.737 21.605 1.00 5.19 C ATOM 1465 CA ARG A 188 2.937 -1.524 22.890 1.00 5.72 C ATOM 1476 CA ILE A 189 -0.685 -0.274 22.541 1.00 6.24 C ATOM 1484 CA ALA A 190 -3.901 -1.997 23.697 1.00 6.52 C """ anno=""" SHEET 1 1 3 GLN A 156A VAL A 164 0 SHEET 2 1 3 TYR A 170 ASN A 175 -1 N ASN A 175 O VAL A 161 """ import iotbx.pdb from cctbx.array_family import flex import iotbx.pdb.secondary_structure as ioss hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(text)).construct_hierarchy() annotation=ioss.annotation.from_records(records=flex.split_lines(anno)) print("\nAnnotation with insertion codes") print("\nInput annotation:") print(annotation.as_pdb_str()) fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) new_annotation=fss.get_annotation() print("\nNew annotation:") expected=ioss.annotation.from_records(records=flex.split_lines(""" HELIX 1 1 TRP A 181 TYR A 186 3 6 SHEET 1 1 3 VAL A 161 VAL A 164 0 SHEET 2 1 3 TYR A 170 ASN A 175 -1 N ASN A 175 O VAL A 161 SHEET 3 1 3 ILE A 187 ALA A 190 -1 N ILE A 189 O TRP A 171 """)) print(new_annotation.as_pdb_str()) assert expected.is_same_as(new_annotation) print("\nNew forcing input annotation") expected=ioss.annotation.from_records(records=flex.split_lines(""" SHEET 1 1 2 GLN A 156A VAL A 164 0 SHEET 2 1 2 TYR A 170 ASN A 175 -1 """)) force_fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, user_annotation_text=annotation.as_pdb_str(), force_secondary_structure_input=True, combine_annotations=False, out=null_out()).get_annotation() print(force_fss.as_pdb_str()) assert expected.is_same_as(force_fss) helix_icode=""" ATOM 2 CA ALA A 1A 11.323 32.055 11.635 1.00 40.00 C ATOM 7 CA ALA A 4B 8.288 29.768 10.916 1.00 40.00 C ATOM 12 CA ALA A 4C 10.313 27.854 8.231 1.00 40.00 C ATOM 17 CA ALA A 4D 13.089 27.116 10.822 1.00 40.00 C ATOM 22 CA ALA A 5 10.573 25.488 13.298 1.00 40.00 C ATOM 27 CA ALA A 6 9.258 23.514 10.260 1.00 40.00 C ATOM 32 CA ALA A 7 12.788 22.543 8.962 1.00 40.00 C ATOM 37 CA ALA A 8 13.846 21.459 12.515 1.00 40.00 C ATOM 42 CA ALA A 9 10.716 19.261 12.994 1.00 40.00 C ATOM 47 CA ALA A 10 11.063 17.985 9.357 1.00 40.00 C ATOM 52 CA ALA A 11 14.754 17.018 9.967 1.00 40.00 C ATOM 57 CA ALA A 12 13.721 15.483 13.371 1.00 40.00 C ATOM 62 CA ALA A 13 10.821 13.516 11.708 1.00 40.00 C ATOM 67 CA ALA A 14 13.246 12.367 8.939 1.00 40.00 C ATOM 72 CA ALA A 15 15.847 11.407 11.629 1.00 40.00 C ATOM 77 CA ALA A 16 13.099 9.317 13.370 1.00 40.00 C """ helix_icode_ss=""" HELIX 1 1 ALA A 1A ALA A 16 1 16 """ hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(helix_icode)).construct_hierarchy() annotation=ioss.annotation.from_records( records=flex.split_lines(helix_icode_ss)) print("\nHelix annotation with insertion codes") print("NOTE: currently misses the residues with insertion codes except those") print("at the ends of a string of insertion codes") fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, out=null_out()).get_annotation() print(fss.as_pdb_str()) expected=ioss.annotation.from_records( records=flex.split_lines(""" HELIX 1 1 ALA A 4D ALA A 16 1 13 """)) assert expected.is_same_as(fss) print("\nHelix annotation with input annotation and insertion codes") force_fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False, user_annotation_text=annotation.as_pdb_str(), force_secondary_structure_input=True, combine_annotations=False, out=null_out()).get_annotation() print(force_fss.as_pdb_str()) expected=ioss.annotation.from_records( records=flex.split_lines(""" HELIX 1 1 ALA A 1A ALA A 16 1 16 """)) assert expected.is_same_as(force_fss) def tst_14(): text_pi_alpha=""" ATOM 1 CA LYS U 65 9.083 9.180 -3.939 1.00 30.00 UNK C ATOM 2 CA LYS U 66 8.415 5.910 -5.790 1.00 30.00 UNK C ATOM 3 CA ARG U 67 6.335 7.380 -8.591 1.00 30.00 UNK C ATOM 4 CA GLY U 68 8.644 5.764 -11.121 1.00 30.00 UNK C ATOM 5 CA LYS U 69 6.554 2.639 -10.591 1.00 30.00 UNK C ATOM 6 CA GLY U 70 3.920 4.296 -12.763 1.00 30.00 UNK C ATOM 7 CA LYS U 71 1.379 5.357 -10.152 1.00 30.00 UNK C ATOM 8 CA VAL U 72 1.224 9.093 -10.806 1.00 30.00 UNK C ATOM 9 CA LYS U 73 -2.228 10.251 -9.725 1.00 30.00 UNK C ATOM 10 CA VAL U 74 -1.340 8.736 -6.335 1.00 30.00 UNK C ATOM 11 CA LYS U 75 0.620 11.990 -6.338 1.00 30.00 UNK C ATOM 12 CA VAL U 76 -2.498 13.792 -5.167 1.00 30.00 UNK C ATOM 13 CA GLY U 77 -0.596 14.285 -1.925 1.00 30.00 UNK C ATOM 14 CA GLY U 78 2.056 16.680 -0.704 1.00 30.00 UNK C """ annotation_text=""" HELIX 2 2 LYS U 71 PRO U 78 5 8 """ overlapping_text=""" HELIX 1 1 LYS U 66 LYS U 71 1 6 HELIX 1 1 VAL U 72 GLY U 77 5 6 """ import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(text_pi_alpha) ).construct_hierarchy() import iotbx.pdb.secondary_structure as ioss annotation=ioss.annotation.from_records(records=flex.split_lines(annotation_text)) overlapping_annotation=ioss.annotation.from_records(records=flex.split_lines(overlapping_text)) print("\nMerging annotations that overlap") print("First annotation") print(annotation.as_pdb_str()) print("Overlapping annotation") print(overlapping_annotation.as_pdb_str()) merged=overlapping_annotation.combine_annotations(other=annotation, hierarchy=hierarchy) print("\nMerged: ") print(merged.as_pdb_str()) assert merged.is_same_as(other=annotation) def tst_15(): import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(multi_copy_text) ).construct_hierarchy() annotation_std=find_secondary_structure( hierarchy=hierarchy,ss_by_chain=False,use_representative_chains=False,out=null_out()).get_annotation() annotation_chains=find_secondary_structure( hierarchy=hierarchy,ss_by_chain=True,use_representative_chains=False,out=null_out()).get_annotation() annotation_chains_rep=find_secondary_structure( hierarchy=hierarchy,ss_by_chain=True,use_representative_chains=True,out=null_out()).get_annotation() print(annotation_std) assert annotation_std.is_same_as(other=annotation_chains) assert annotation_std.is_same_as(other=annotation_chains_rep) print("OK") def tst_16(): print("Checking missing atoms...", end=' ') import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(strands_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) expected_text=""" Model 1 N: 6 Start: 23 End: 28 Class: Beta strand N: 6 Start: 23 End: 28 Rise: 3.42 A Dot: 0.97 Model 2 N: 6 Start: 31 End: 36 Class: Beta strand N: 6 Start: 31 End: 36 Rise: 3.54 A Dot: 0.98 Model 3 N: 6 Start: 23 End: 28 Class: Beta strand N: 6 Start: 23 End: 28 Rise: 3.44 A Dot: 0.96 Model 4 N: 6 Start: 31 End: 36 Class: Beta strand N: 6 Start: 31 End: 36 Rise: 3.56 A Dot: 0.98 FINAL PDB RECORDS: SHEET 1 1 2 GLY B 23 ASN B 28 0 SHEET 2 1 2 GLY B 31 ALA B 36 -1 N ALA B 35 O PHE B 24 SHEET 1 2 2 GLY D 23 ASN D 28 0 SHEET 2 2 2 GLY D 31 ALA D 36 -1 N ALA D 35 O PHE D 24 FINAL PDB selections: "(chain 'B' and resid 23 through 28 ) or (chain 'B' and resid 31 through 36 ) or (chain 'D' and resid 23 through 28 ) or (chain 'D' and resid 31 through 36 )" """ f=StringIO() fss.show_summary(out=f,verbose=True) found_text=f.getvalue() #assert not test_utils.show_diff(found_text, expected_text) 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_17(): print("Checking missing atoms part 2...", end=' ') import iotbx.pdb from cctbx.array_family import flex hierarchy=iotbx.pdb.input(source_info='text', lines=flex.split_lines(strands_add_o_text)).construct_hierarchy() fss=find_secondary_structure(hierarchy=hierarchy,ss_by_chain=False,out=null_out()) expected_text=""" Model 1 N: 6 Start: 23 End: 28 Class: Beta strand N: 6 Start: 23 End: 28 Rise: 3.42 A Dot: 0.97 Model 2 N: 6 Start: 31 End: 36 Class: Beta strand N: 6 Start: 31 End: 36 Rise: 3.54 A Dot: 0.98 Model 3 N: 6 Start: 23 End: 28 Class: Beta strand N: 6 Start: 23 End: 28 Rise: 3.44 A Dot: 0.96 Model 4 N: 6 Start: 31 End: 36 Class: Beta strand N: 6 Start: 31 End: 36 Rise: 3.56 A Dot: 0.98 FINAL PDB RECORDS: SHEET 1 1 2 GLY B 23 ASN B 28 0 SHEET 2 1 2 GLY B 31 ALA B 36 -1 N ALA B 35 O PHE B 24 SHEET 1 2 2 GLY D 23 ASN D 28 0 SHEET 2 2 2 GLY D 31 ALA D 36 -1 N ALA D 35 O PHE D 24 FINAL PDB selections: "(chain 'B' and resid 23 through 28 ) or (chain 'B' and resid 31 through 36 ) or (chain 'D' and resid 23 through 28 ) or (chain 'D' and resid 31 through 36 )" """ f=StringIO() fss.show_summary(out=f,verbose=True) found_text=f.getvalue() #assert not test_utils.show_diff(found_text, expected_text) 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") if __name__=="__main__": import sys tst_00() tst_01() tst_02() tst_03() tst_04() tst_05() tst_06() tst_07() tst_08() tst_09() tst_10() tst_11() tst_12() tst_13() tst_14() tst_15() tst_16() tst_17() print("OK")