note salva This script below does what you have asked for. It uses [mod://Math::Vector::Real::kdTree] for fast lookups. <readmore> <c> #!/usr/bin/perl use strict; use warnings; my $line = <<EOL; ATOM CA GLY A 84 -3.901 9.352 -1.557 ATOM CA GLY A 85 -6.632 8.551 -2.508 ATOM CA GLY A 86 -9.362 7.750 -3.459 ATOM CA GLY A 87 -12.092 6.950 -4.409 ATOM CA GLY A 88 -14.823 6.149 -5.360 ATOM CA GLY A 89 -17.553 5.348 -6.311 ATOM CA GLY A 90 -20.283 4.547 -7.262 ATOM CA GLY A 91 -23.014 3.746 -8.212 ATOM CA GLY A 92 -25.744 2.945 -9.163 ATOM CA GLY A 93 -28.474 2.145 -10.114 ATOM CA GLY A 94 -31.205 1.344 -11.065 ATOM CA GLY A 95 -33.935 0.543 -12.015 ATOM CA GLY A 96 -36.666 -0.258 -12.966 ATOM CA GLY A 97 -39.396 -1.059 -13.917 ATOM CA GLY A 98 -42.126 -1.859 -14.867 ATOM CA GLY A 99 -44.857 -2.660 -15.818 ATOM CA GLY A 100 -47.587 -3.461 -16.769 ATOM CA GLY A 101 -50.317 -4.262 -17.720 EOL my $points = <<EOP; ATOM 183 N MET B 25 -18.731 -0.135 -11.272 ATOM 184 CA MET B 25 -19.287 -1.473 -11.499 ATOM 185 C MET B 25 -20.545 -1.396 -12.335 ATOM 186 O MET B 25 -21.421 -0.553 -12.114 ATOM 187 CB MET B 25 -19.594 -2.172 -10.170 ATOM 188 CG MET B 25 -18.388 -2.409 -9.308 ATOM 189 SD MET B 25 -18.784 -3.016 -7.671 ATOM 190 CE MET B 25 -17.107 -3.128 -6.966 ATOM 191 N PRO B 26 -20.681 -2.300 -13.307 ATOM 192 CA PRO B 26 -21.870 -2.245 -14.145 ATOM 193 C PRO B 26 -23.239 -2.337 -13.447 ATOM 194 O PRO B 26 -24.201 -1.730 -13.882 ATOM 195 CB PRO B 26 -21.604 -3.351 -15.184 ATOM 196 CG PRO B 26 -20.782 -4.304 -14.461 ATOM 197 CD PRO B 26 -19.827 -3.453 -13.654 ATOM 198 N GLU B 27 -23.296 -3.065 -12.345 ATOM 199 CA GLU B 27 -24.545 -3.199 -11.624 ATOM 200 C GLU B 27 -24.971 -1.907 -10.917 ATOM 201 O GLU B 27 -26.155 -1.714 -10.652 ATOM 202 CB GLU B 27 -24.417 -4.262 -10.541 ATOM 203 CG GLU B 27 -24.206 -5.670 -11.059 ATOM 204 CD GLU B 27 -22.756 -6.001 -11.359 ATOM 205 OE1 GLU B 27 -21.843 -5.132 -11.182 ATOM 206 OE2 GLU B 27 -22.549 -7.164 -11.773 ATOM 340 N VAL B 44 -28.758 -0.366 -7.293 ATOM 341 CA VAL B 44 -28.277 -1.382 -8.227 ATOM 342 C VAL B 44 -29.430 -2.020 -8.991 ATOM 343 O VAL B 44 -30.583 -2.037 -8.548 ATOM 344 CB VAL B 44 -27.545 -2.528 -7.509 ATOM 345 CG1 VAL B 44 -26.301 -2.027 -6.834 ATOM 346 CG2 VAL B 44 -28.453 -3.165 -6.499 ATOM 347 N GLU B 45 -29.101 -2.474 -10.197 ATOM 348 CA GLU B 45 -30.032 -3.224 -11.040 ATOM 349 C GLU B 45 -29.268 -4.484 -11.492 ATOM 350 O GLU B 45 -28.116 -4.412 -11.942 ATOM 351 CB GLU B 45 -30.496 -2.378 -12.258 ATOM 352 CG GLU B 45 -31.341 -1.173 -11.858 ATOM 353 CD GLU B 45 -31.677 -0.230 -13.021 ATOM 354 OE1 GLU B 45 -30.974 -0.274 -14.048 ATOM 355 OE2 GLU B 45 -32.633 0.552 -12.884 ATOM 356 N THR B 46 -29.918 -5.632 -11.352 ATOM 357 CA THR B 46 -29.341 -6.925 -11.736 ATOM 358 C THR B 46 -30.384 -7.735 -12.500 ATOM 359 O THR B 46 -31.579 -7.459 -12.407 ATOM 360 CB THR B 46 -28.853 -7.732 -10.500 ATOM 361 OG1 THR B 46 -29.953 -8.003 -9.622 ATOM 362 CG2 THR B 46 -27.735 -6.958 -9.755 ATOM 363 N ASP B 47 -29.939 -8.747 -13.241 ATOM 364 CA ASP B 47 -30.878 -9.551 -14.011 ATOM 365 C ASP B 47 -31.833 -10.352 -13.136 ATOM 366 O ASP B 47 -33.036 -10.461 -13.408 ATOM 367 CB ASP B 47 -30.088 -10.510 -14.903 ATOM 368 CG ASP B 47 -29.320 -9.797 -15.991 ATOM 369 OD1 ASP B 47 -29.582 -8.595 -16.229 ATOM 370 OD2 ASP B 47 -28.457 -10.451 -16.622 ATOM 371 N THR B 48 -31.275 -10.936 -12.094 ATOM 372 CA THR B 48 -31.996 -11.805 -11.190 ATOM 373 C THR B 48 -31.636 -11.519 -9.746 ATOM 374 O THR B 48 -30.654 -10.802 -9.448 ATOM 375 CB THR B 48 -31.599 -13.294 -11.440 ATOM 376 OG1 THR B 48 -30.210 -13.487 -11.070 ATOM 377 CG2 THR B 48 -31.741 -13.642 -12.949 ATOM 378 N LEU B 49 -32.428 -12.075 -8.840 ATOM 379 CA LEU B 49 -32.135 -11.978 -7.411 ATOM 380 C LEU B 49 -30.851 -12.716 -7.074 ATOM 381 O LEU B 49 -30.080 -12.298 -6.199 ATOM 382 CB LEU B 49 -33.281 -12.532 -6.554 ATOM 383 CG LEU B 49 -34.391 -11.563 -6.233 ATOM 384 CD1 LEU B 49 -35.291 -12.246 -5.196 ATOM 385 CD2 LEU B 49 -33.834 -10.232 -5.630 ATOM 386 N LYS B 50 -30.598 -13.835 -7.746 ATOM 387 CA LYS B 50 -29.385 -14.574 -7.494 ATOM 388 C LYS B 50 -28.185 -13.675 -7.804 ATOM 389 O LYS B 50 -27.196 -13.667 -7.069 ATOM 390 CB LYS B 50 -29.374 -15.839 -8.366 ATOM 391 CG LYS B 50 -28.083 -16.600 -8.281 ATOM 392 CD LYS B 50 -28.213 -17.957 -8.920 ATOM 393 CE LYS B 50 -26.851 -18.613 -9.055 ATOM 394 NZ LYS B 50 -26.976 -20.031 -9.478 ATOM 395 N ASP B 51 -28.281 -12.904 -8.884 ATOM 396 CA ASP B 51 -27.192 -11.993 -9.228 ATOM 397 C ASP B 51 -27.020 -10.918 -8.147 ATOM 398 O ASP B 51 -25.897 -10.550 -7.798 ATOM 399 CB ASP B 51 -27.447 -11.319 -10.586 ATOM 400 CG ASP B 51 -27.316 -12.286 -11.759 ATOM 401 OD1 ASP B 51 -26.408 -13.135 -11.716 ATOM 402 OD2 ASP B 51 -28.108 -12.169 -12.711 ATOM 403 N LEU B 52 -28.126 -10.396 -7.647 ATOM 404 CA LEU B 52 -28.039 -9.393 -6.586 ATOM 405 C LEU B 52 -27.400 -9.998 -5.331 ATOM 406 O LEU B 52 -26.592 -9.339 -4.682 ATOM 407 CB LEU B 52 -29.432 -8.849 -6.290 ATOM 408 CG LEU B 52 -29.515 -7.909 -5.079 ATOM 409 CD1 LEU B 52 -28.622 -6.677 -5.324 ATOM 410 CD2 LEU B 52 -30.990 -7.549 -4.806 ATOM 411 N ASP B 53 -27.788 -11.220 -4.974 ATOM 412 CA ASP B 53 -27.250 -11.886 -3.803 ATOM 413 C ASP B 53 -25.745 -12.043 -3.924 ATOM 414 O ASP B 53 -25.000 -11.783 -2.971 ATOM 415 CB ASP B 53 -27.931 -13.252 -3.645 ATOM 416 CG ASP B 53 -27.790 -13.802 -2.257 ATOM 417 OD1 ASP B 53 -27.786 -13.011 -1.288 ATOM 418 OD2 ASP B 53 -27.688 -15.033 -2.135 ATOM 419 N GLN B 54 -25.280 -12.456 -5.100 ATOM 420 CA GLN B 54 -23.859 -12.616 -5.309 ATOM 421 C GLN B 54 -23.145 -11.284 -5.250 ATOM 422 O GLN B 54 -22.033 -11.206 -4.727 ATOM 423 CB GLN B 54 -23.597 -13.346 -6.625 ATOM 424 CG GLN B 54 -24.127 -14.755 -6.529 ATOM 425 CD GLN B 54 -23.878 -15.578 -7.770 ATOM 426 OE1 GLN B 54 -23.247 -15.119 -8.724 ATOM 427 NE2 GLN B 54 -24.368 -16.813 -7.760 ATOM 428 N PHE B 55 -23.758 -10.226 -5.757 ATOM 429 CA PHE B 55 -23.128 -8.913 -5.673 ATOM 430 C PHE B 55 -22.938 -8.514 -4.211 ATOM 431 O PHE B 55 -21.864 -8.030 -3.828 ATOM 432 CB PHE B 55 -24.018 -7.892 -6.380 ATOM 433 CG PHE B 55 -23.448 -6.509 -6.415 ATOM 434 CD1 PHE B 55 -22.595 -6.140 -7.449 ATOM 435 CD2 PHE B 55 -23.733 -5.581 -5.409 ATOM 436 CE1 PHE B 55 -22.035 -4.860 -7.485 ATOM 437 CE2 PHE B 55 -23.167 -4.280 -5.431 ATOM 438 CZ PHE B 55 -22.322 -3.934 -6.480 ATOM 439 N ILE B 56 -23.984 -8.686 -3.405 ATOM 440 CA ILE B 56 -23.948 -8.313 -2.000 ATOM 441 C ILE B 56 -22.987 -9.148 -1.168 ATOM 442 O ILE B 56 -22.261 -8.598 -0.347 ATOM 443 CB ILE B 56 -25.376 -8.459 -1.390 ATOM 444 CG1 ILE B 56 -26.289 -7.371 -1.967 ATOM 445 CG2 ILE B 56 -25.329 -8.392 0.151 ATOM 446 CD1 ILE B 56 -27.739 -7.521 -1.574 ATOM 447 N THR B 57 -22.959 -10.461 -1.364 ATOM 448 CA THR B 57 -22.088 -11.246 -0.490 ATOM 449 C THR B 57 -20.683 -11.497 -1.042 ATOM 450 O THR B 57 -19.718 -11.631 -0.257 ATOM 451 CB THR B 57 -22.774 -12.556 -0.095 ATOM 452 OG1 THR B 57 -22.821 -13.385 -1.247 ATOM 453 CG2 THR B 57 -24.225 -12.310 0.420 ATOM 454 N GLU B 58 -20.531 -11.490 -2.358 ATOM 455 CA GLU B 58 -19.203 -11.666 -2.942 ATOM 456 C GLU B 58 -18.510 -10.387 -3.385 ATOM 457 O GLU B 58 -17.411 -10.096 -2.922 ATOM 458 CB GLU B 58 -19.234 -12.599 -4.139 ATOM 459 CG GLU B 58 -19.923 -13.930 -3.875 ATOM 460 CD GLU B 58 -19.918 -14.829 -5.113 ATOM 461 OE1 GLU B 58 -20.834 -15.660 -5.290 ATOM 462 OE2 GLU B 58 -18.981 -14.717 -5.920 EOP my $ends = <<EOE; ATOM 39 N ILE A 6 -28.498 -0.713 -1.733 0.03 ATOM 40 CA ILE A 6 -27.704 -1.211 -0.641 0.03 ATOM 41 C ILE A 6 -27.201 -0.065 0.236 0.03 ATOM 42 O ILE A 6 -26.458 0.817 -0.235 0.03 ATOM 43 CB ILE A 6 -26.486 -1.991 -1.182 0.03 ATOM 44 CG1 ILE A 6 -26.936 -3.007 -2.231 0.03 ATOM 45 CG2 ILE A 6 -25.762 -2.672 -0.060 0.03 ATOM 46 CD1 ILE A 6 -25.781 -3.823 -2.789 0.03 ATOM 47 N LEU A 7 -27.587 -0.085 1.510 0.02 ATOM 48 CA LEU A 7 -27.153 0.909 2.483 0.02 ATOM 49 C LEU A 7 -25.832 0.351 2.982 0.02 ATOM 50 O LEU A 7 -25.725 -0.855 3.179 0.02 ATOM 51 CB LEU A 7 -28.150 0.965 3.635 0.02 ATOM 52 CG LEU A 7 -29.480 1.674 3.398 0.02 ATOM 53 CD1 LEU A 7 -30.088 1.292 2.072 0.02 ATOM 54 CD2 LEU A 7 -30.441 1.320 4.561 0.02 ATOM 55 N MET A 8 -24.844 1.208 3.209 0.02 ATOM 56 CA MET A 8 -23.528 0.721 3.622 0.02 ATOM 57 C MET A 8 -22.874 1.588 4.663 0.02 ATOM 58 O MET A 8 -23.051 2.789 4.654 0.02 ATOM 59 CB MET A 8 -22.538 0.723 2.437 0.02 ATOM 60 CG MET A 8 -22.909 -0.149 1.303 0.02 ATOM 61 SD MET A 8 -21.700 0.110 -0.066 0.02 ATOM 62 CE MET A 8 -22.383 -1.085 -1.224 0.02 ATOM 63 N VAL A 9 -22.103 0.946 5.551 0.04 ATOM 64 CA VAL A 9 -21.251 1.656 6.509 0.04 ATOM 65 C VAL A 9 -19.827 1.350 6.024 0.04 ATOM 66 O VAL A 9 -19.506 0.197 5.667 0.04 ATOM 67 CB VAL A 9 -21.425 1.146 7.936 0.04 ATOM 68 CG1 VAL A 9 -20.279 1.661 8.813 0.04 ATOM 69 CG2 VAL A 9 -22.738 1.625 8.459 0.04 ATOM 70 N THR A 10 -18.983 2.377 5.928 0.09 ATOM 71 CA THR A 10 -17.612 2.153 5.477 0.09 ATOM 72 C THR A 10 -16.618 2.492 6.565 0.09 ATOM 73 O THR A 10 -16.966 3.024 7.616 0.09 ATOM 74 CB THR A 10 -17.207 3.026 4.219 0.09 ATOM 75 OG1 THR A 10 -17.096 4.420 4.591 0.09 ATOM 76 CG2 THR A 10 -18.220 2.859 3.097 0.09 ATOM 77 N ALA A 11 -15.364 2.173 6.285 0.10 ATOM 78 CA ALA A 11 -14.313 2.532 7.215 0.10 ATOM 79 C ALA A 11 -14.258 4.060 7.162 0.10 ATOM 80 O ALA A 11 -14.598 4.689 6.142 0.10 ATOM 81 CB ALA A 11 -12.997 1.943 6.763 0.10 ATOM 82 N ALA A 12 -13.817 4.657 8.263 0.10 ATOM 83 CA ALA A 12 -13.702 6.102 8.382 0.10 ATOM 84 C ALA A 12 -12.862 6.679 7.260 0.10 ATOM 85 O ALA A 12 -11.763 6.198 6.975 0.10 ATOM 86 CB ALA A 12 -13.038 6.467 9.721 0.10 ATOM 87 N GLY A 13 -13.401 7.713 6.625 0.10 ATOM 88 CA GLY A 13 -12.709 8.403 5.560 0.10 ATOM 89 C GLY A 13 -12.679 7.741 4.199 0.10 ATOM 90 O GLY A 13 -12.124 8.301 3.256 0.10 ATOM 91 N LYS A 14 -13.292 6.567 4.099 0.10 ATOM 92 CA LYS A 14 -13.296 5.834 2.836 0.10 ATOM 93 C LYS A 14 -14.613 5.968 2.067 0.10 ATOM 94 O LYS A 14 -14.816 5.265 1.073 0.10 ATOM 95 CB LYS A 14 -13.052 4.340 3.097 0.10 ATOM 96 CG LYS A 14 -11.847 4.006 3.973 0.10 ATOM 97 CD LYS A 14 -10.669 3.514 3.192 0.10 ATOM 98 CE LYS A 14 -9.425 3.504 4.096 0.10 ATOM 99 NZ LYS A 14 -8.294 2.793 3.470 0.10 ATOM 100 N GLU A 15 -15.515 6.845 2.506 0.10 ATOM 101 CA GLU A 15 -16.819 6.965 1.812 0.10 ATOM 102 C GLU A 15 -16.734 7.312 0.338 0.10 ATOM 103 O GLU A 15 -17.331 6.638 -0.490 0.10 ATOM 104 CB GLU A 15 -17.727 8.003 2.502 0.10 ATOM 105 CG GLU A 15 -18.061 7.715 3.976 0.10 ATOM 106 CD GLU A 15 -17.016 8.228 4.947 0.10 ATOM 107 OE1 GLU A 15 -15.892 8.584 4.527 0.10 ATOM 108 OE2 GLU A 15 -17.340 8.275 6.164 0.10 ATOM 109 N ARG A 16 -15.982 8.340 -0.017 0.10 ATOM 110 CA ARG A 16 -15.900 8.706 -1.430 0.10 ATOM 111 C ARG A 16 -15.152 7.639 -2.208 0.10 ATOM 112 O ARG A 16 -15.500 7.374 -3.355 0.10 ATOM 113 CB ARG A 16 -15.213 10.071 -1.614 0.10 ATOM 114 CG ARG A 16 -15.066 10.477 -3.074 0.10 ATOM 115 CD ARG A 16 -14.327 11.819 -3.243 0.10 ATOM 116 NE ARG A 16 -13.901 11.961 -4.661 0.10 ATOM 117 CZ ARG A 16 -12.676 12.396 -4.952 0.10 ATOM 118 NH1 ARG A 16 -11.841 12.690 -3.980 0.10 ATOM 119 NH2 ARG A 16 -12.324 12.531 -6.223 0.10 ATOM 120 N GLU A 17 -14.127 7.041 -1.600 0.10 ATOM 121 CA GLU A 17 -13.340 5.994 -2.257 0.10 ATOM 122 C GLU A 17 -14.268 4.836 -2.644 0.10 ATOM 123 O GLU A 17 -14.220 4.331 -3.769 0.10 ATOM 124 CB GLU A 17 -12.243 5.483 -1.324 0.10 ATOM 125 CG GLU A 17 -11.398 4.389 -1.922 0.10 ATOM 126 CD GLU A 17 -10.374 3.854 -0.952 0.10 ATOM 127 OE1 GLU A 17 -9.787 4.637 -0.182 0.10 ATOM 128 OE2 GLU A 17 -10.145 2.634 -0.974 0.10 ATOM 129 N VAL A 18 -15.088 4.417 -1.687 0.05 ATOM 130 CA VAL A 18 -16.032 3.353 -1.954 0.05 ATOM 131 C VAL A 18 -17.052 3.764 -3.010 0.05 ATOM 132 O VAL A 18 -17.362 2.988 -3.934 0.05 ATOM 133 CB VAL A 18 -16.728 2.910 -0.642 0.05 ATOM 134 CG1 VAL A 18 -17.948 1.984 -0.944 0.05 ATOM 135 CG2 VAL A 18 -15.732 2.187 0.235 0.05 ATOM 136 N MET A 19 -17.576 4.985 -2.896 0.07 ATOM 137 CA MET A 19 -18.546 5.491 -3.868 0.07 ATOM 138 C MET A 19 -17.983 5.393 -5.290 0.07 ATOM 139 O MET A 19 -18.674 4.895 -6.177 0.07 ATOM 140 CB MET A 19 -18.893 6.968 -3.577 0.07 ATOM 141 CG MET A 19 -20.080 7.412 -4.413 0.07 ATOM 142 SD MET A 19 -20.383 9.219 -4.338 0.07 ATOM 143 CE MET A 19 -19.063 9.830 -5.317 0.07 ATOM 144 N GLU A 20 -16.756 5.884 -5.511 0.09 ATOM 145 CA GLU A 20 -16.196 5.861 -6.857 0.09 ATOM 146 C GLU A 20 -15.772 4.495 -7.343 0.09 ATOM 147 O GLU A 20 -15.901 4.220 -8.534 0.09 ATOM 148 CB GLU A 20 -15.044 6.862 -6.987 0.09 ATOM 149 CG GLU A 20 -15.543 8.306 -6.956 0.09 ATOM 150 CD GLU A 20 -16.363 8.708 -8.202 0.09 ATOM 151 OE1 GLU A 20 -16.970 9.796 -8.155 0.09 ATOM 152 OE2 GLU A 20 -16.379 7.971 -9.220 0.09 ATOM 153 N LYS A 21 -15.252 3.643 -6.462 0.10 ATOM 154 CA LYS A 21 -14.915 2.272 -6.858 0.10 ATOM 155 C LYS A 21 -16.180 1.564 -7.282 0.10 ATOM 156 O LYS A 21 -16.169 0.784 -8.252 0.10 ATOM 157 CB LYS A 21 -14.303 1.491 -5.708 0.10 ATOM 158 CG LYS A 21 -12.832 1.764 -5.525 0.10 ATOM 159 CD LYS A 21 -12.327 1.210 -4.178 0.10 ATOM 160 CE LYS A 21 -10.801 1.122 -4.130 0.10 ATOM 161 NZ LYS A 21 -10.349 0.604 -2.784 0.10 ATOM 162 N LEU A 22 -17.288 1.806 -6.579 0.11 ATOM 163 CA LEU A 22 -18.534 1.162 -6.994 0.11 ATOM 164 C LEU A 22 -19.072 1.736 -8.301 0.11 ATOM 165 O LEU A 22 -19.512 0.989 -9.171 0.11 ATOM 166 CB LEU A 22 -19.598 1.245 -5.873 0.11 ATOM 167 CG LEU A 22 -19.223 0.453 -4.620 0.11 ATOM 168 CD1 LEU A 22 -20.205 0.865 -3.502 0.11 ATOM 169 CD2 LEU A 22 -19.288 -1.055 -4.861 0.11 ATOM 223 N GLU A 30 -26.173 4.298 -9.604 0.06 ATOM 224 CA GLU A 30 -26.154 5.548 -8.818 0.06 ATOM 225 C GLU A 30 -25.520 5.244 -7.485 0.06 ATOM 226 O GLU A 30 -25.520 4.099 -7.058 0.06 ATOM 227 CB GLU A 30 -27.568 6.089 -8.553 0.06 ATOM 228 CG GLU A 30 -28.375 6.303 -9.811 0.06 ATOM 229 CD GLU A 30 -29.809 6.722 -9.535 0.06 ATOM 230 OE1 GLU A 30 -30.598 6.782 -10.509 0.06 ATOM 231 OE2 GLU A 30 -30.165 6.966 -8.358 0.06 ATOM 232 N ALA A 31 -24.951 6.248 -6.833 0.05 ATOM 233 CA ALA A 31 -24.363 6.006 -5.506 0.05 ATOM 234 C ALA A 31 -24.301 7.338 -4.796 0.05 ATOM 235 O ALA A 31 -24.077 8.365 -5.437 0.05 ATOM 236 CB ALA A 31 -22.978 5.359 -5.608 0.05 ATOM 237 N TYR A 32 -24.572 7.316 -3.488 0.04 ATOM 238 CA TYR A 32 -24.652 8.533 -2.696 0.04 ATOM 239 C TYR A 32 -23.980 8.358 -1.362 0.04 ATOM 240 O TYR A 32 -24.240 7.361 -0.691 0.04 ATOM 241 CB TYR A 32 -26.131 8.855 -2.372 0.04 ATOM 242 CG TYR A 32 -27.052 8.910 -3.572 0.04 ATOM 243 CD1 TYR A 32 -27.483 10.132 -4.088 0.04 ATOM 244 CD2 TYR A 32 -27.498 7.734 -4.193 0.04 ATOM 245 CE1 TYR A 32 -28.332 10.204 -5.226 0.04 ATOM 246 CE2 TYR A 32 -28.364 7.805 -5.341 0.04 ATOM 247 CZ TYR A 32 -28.750 9.031 -5.829 0.04 ATOM 248 OH TYR A 32 -29.576 9.155 -6.940 0.04 ATOM 249 N VAL A 33 -23.111 9.305 -0.989 0.05 ATOM 250 CA VAL A 33 -22.554 9.322 0.369 0.05 ATOM 251 C VAL A 33 -23.675 10.096 1.073 0.05 ATOM 252 O VAL A 33 -24.156 11.136 0.594 0.05 ATOM 253 CB VAL A 33 -21.220 10.083 0.445 0.05 ATOM 254 CG1 VAL A 33 -20.755 10.141 1.920 0.05 ATOM 255 CG2 VAL A 33 -20.178 9.346 -0.413 0.05 ATOM 256 N VAL A 34 -24.084 9.606 2.238 0.04 ATOM 257 CA VAL A 34 -25.214 10.222 2.922 0.04 ATOM 258 C VAL A 34 -24.914 10.490 4.371 0.04 ATOM 259 O VAL A 34 -23.962 9.945 4.913 0.04 ATOM 260 CB VAL A 34 -26.489 9.301 2.849 0.04 ATOM 261 CG1 VAL A 34 -26.909 9.102 1.409 0.04 ATOM 262 CG2 VAL A 34 -26.195 7.910 3.440 0.04 ATOM 263 N TYR A 35 -25.732 11.375 4.933 0.04 ATOM 264 CA TYR A 35 -25.675 11.728 6.350 0.04 ATOM 265 C TYR A 35 -26.947 11.098 6.898 0.04 ATOM 266 O TYR A 35 -28.070 11.485 6.523 0.04 ATOM 267 CB TYR A 35 -25.713 13.247 6.505 0.04 ATOM 268 CG TYR A 35 -25.506 13.693 7.918 0.04 ATOM 269 CD1 TYR A 35 -24.229 13.810 8.453 0.04 ATOM 270 CD2 TYR A 35 -26.602 14.002 8.703 0.04 ATOM 271 CE1 TYR A 35 -24.064 14.240 9.769 0.04 ATOM 272 CE2 TYR A 35 -26.438 14.440 10.025 0.04 ATOM 273 CZ TYR A 35 -25.179 14.547 10.528 0.04 ATOM 274 OH TYR A 35 -25.061 15.008 11.825 0.04 ATOM 275 N GLY A 36 -26.755 10.167 7.815 0.05 ATOM 276 CA GLY A 36 -27.878 9.430 8.387 0.05 ATOM 277 C GLY A 36 -27.317 8.205 9.102 0.05 ATOM 278 O GLY A 36 -26.136 8.180 9.497 0.05 ATOM 279 N GLU A 37 -28.152 7.181 9.241 0.06 ATOM 280 CA GLU A 37 -27.716 5.986 9.945 0.06 ATOM 281 C GLU A 37 -26.676 5.184 9.210 0.06 ATOM 282 O GLU A 37 -25.909 4.448 9.828 0.06 ATOM 283 CB GLU A 37 -28.913 5.123 10.324 0.06 ATOM 284 CG GLU A 37 -29.626 5.662 11.596 0.06 ATOM 285 CD GLU A 37 -28.641 5.978 12.759 0.06 ATOM 286 OE1 GLU A 37 -28.100 7.102 12.829 0.06 ATOM 287 OE2 GLU A 37 -28.369 5.099 13.599 0.06 ATOM 288 N TYR A 38 -26.637 5.312 7.885 0.06 ATOM 289 CA TYR A 38 -25.628 4.630 7.088 0.06 ATOM 290 C TYR A 38 -24.754 5.692 6.410 0.06 ATOM 291 O TYR A 38 -25.087 6.891 6.460 0.06 ATOM 292 CB TYR A 38 -26.302 3.702 6.043 0.06 ATOM 293 CG TYR A 38 -26.774 2.386 6.623 0.06 ATOM 294 CD1 TYR A 38 -25.935 1.280 6.620 0.06 ATOM 295 CD2 TYR A 38 -28.064 2.253 7.172 0.06 ATOM 296 CE1 TYR A 38 -26.345 0.074 7.134 0.06 ATOM 297 CE2 TYR A 38 -28.480 1.039 7.696 0.06 ATOM 298 CZ TYR A 38 -27.612 -0.032 7.671 0.06 ATOM 299 OH TYR A 38 -27.972 -1.249 8.206 0.06 ATOM 300 N ASP A 39 -23.666 5.240 5.773 0.07 ATOM 301 CA ASP A 39 -22.715 6.122 5.095 0.07 ATOM 302 C ASP A 39 -22.972 6.280 3.599 0.07 ATOM 303 O ASP A 39 -22.630 7.313 3.035 0.07 ATOM 304 CB ASP A 39 -21.268 5.626 5.263 0.07 ATOM 305 CG ASP A 39 -20.814 5.604 6.699 0.07 ATOM 306 OD1 ASP A 39 -21.158 6.535 7.462 0.07 ATOM 307 OD2 ASP A 39 -20.061 4.677 7.044 0.07 ATOM 308 N LEU A 40 -23.514 5.243 2.964 0.05 ATOM 309 CA LEU A 40 -23.828 5.322 1.528 0.05 ATOM 310 C LEU A 40 -25.104 4.579 1.239 0.05 ATOM 311 O LEU A 40 -25.514 3.699 1.976 0.05 ATOM 312 CB LEU A 40 -22.778 4.630 0.631 0.05 ATOM 313 CG LEU A 40 -21.479 5.351 0.353 0.05 ATOM 314 CD1 LEU A 40 -20.465 4.981 1.407 0.05 ATOM 315 CD2 LEU A 40 -21.005 4.968 -1.063 0.05 ATOM 316 N ILE A 41 -25.715 4.944 0.130 0.04 ATOM 317 CA ILE A 41 -26.837 4.195 -0.420 0.04 ATOM 318 C ILE A 41 -26.429 4.027 -1.883 0.04 ATOM 319 O ILE A 41 -26.037 4.995 -2.562 0.04 ATOM 320 CB ILE A 41 -28.223 4.858 -0.239 0.04 ATOM 321 CG1 ILE A 41 -29.288 3.916 -0.824 0.04 ATOM 322 CG2 ILE A 41 -28.325 6.173 -0.938 0.04 ATOM 323 CD1 ILE A 41 -30.749 4.243 -0.427 0.04 ATOM 541 N MET A 68 -20.563 -2.717 6.892 0.13 ATOM 542 CA MET A 68 -21.918 -3.188 7.191 0.13 ATOM 543 C MET A 68 -22.777 -2.880 5.974 0.13 ATOM 544 O MET A 68 -22.516 -1.911 5.266 0.13 ATOM 545 CB MET A 68 -22.532 -2.425 8.376 0.13 ATOM 546 CG MET A 68 -21.642 -2.257 9.591 0.13 ATOM 547 SD MET A 68 -22.647 -1.596 10.958 0.13 ATOM 548 CE MET A 68 -21.570 -1.866 12.362 0.13 ATOM 549 N THR A 69 -23.759 -3.734 5.714 0.14 ATOM 550 CA THR A 69 -24.695 -3.461 4.626 0.14 ATOM 551 C THR A 69 -26.114 -3.843 5.016 0.14 ATOM 552 O THR A 69 -26.355 -4.624 5.935 0.14 ATOM 553 CB THR A 69 -24.373 -4.249 3.311 0.14 ATOM 554 OG1 THR A 69 -24.469 -5.672 3.533 0.14 ATOM 555 CG2 THR A 69 -22.981 -3.930 2.810 0.14 ATOM 556 N SER A 70 -27.059 -3.260 4.303 0.20 ATOM 557 CA SER A 70 -28.483 -3.591 4.459 0.20 ATOM 558 C SER A 70 -28.977 -3.509 3.019 0.20 ATOM 559 O SER A 70 -28.971 -2.437 2.406 0.20 ATOM 560 CB SER A 70 -29.213 -2.581 5.344 0.20 ATOM 561 OG SER A 70 -30.606 -2.925 5.446 0.20 ATOM 562 N THR A 71 -29.427 -4.639 2.480 0.40 ATOM 563 CA THR A 71 -29.837 -4.738 1.093 0.40 ATOM 564 C THR A 71 -31.352 -4.814 0.899 0.40 ATOM 565 O THR A 71 -32.039 -5.562 1.600 0.40 ATOM 566 CB THR A 71 -29.178 -5.970 0.493 0.40 ATOM 567 OG1 THR A 71 -27.743 -5.825 0.591 0.40 ATOM 568 CG2 THR A 71 -29.593 -6.126 -0.957 0.40 EOE use Math::Vector::Real; use Math::Vector::Real::kdTree; my $epsilon = 0.15; my $deg2rad = 3.141592653589793 / 180; my @line = split /\s*\n/, $line; my @points = split /\s*\n/, $points; my @ends = split /\s*\n/, $ends; my (@vl, @vp, @ve); push @vl, V((split /\s+/)[5, 6, 7]) for @line; push @vp, V((split /\s+/)[6, 7, 8]) for @points; push @ve, V((split /\s+/)[6, 7, 8]) for @ends; my $vl0 = $vl[0]; my $vl = $vl[-1] - $vl0; my @vpo = map { $_ - $vl0 } @vp; my @veo = map { $_ - $vl0 } @ve; my $tree = Math::Vector::Real::kdTree->new(@veo); my $divisions = 360; for my $angle_ix (0 .. $divisions - 1) { my $angle = $angle_ix * 360 / $divisions; my @ro = $vl->rotate_3d($deg2rad * $angle, @vpo); for my $rix (0..$#ro) { my ($eix, $d) = $tree->find_nearest_neighbor($ro[$rix], $epsilon); if (defined $eix) { my $r = $ro[$rix] + $vl0; print("point $rix ($vp[$rix]) touchs end point $eix ($ve[$eix]) ", "after rotating it $angle deg ($r), distance is $d\n"); # last } } } </c> </readmore> <p>But anyway, I am not sure that this is really what you need. If by doing 1deg rotation you are trying to simulate a continuous rotation, 1deg may be not fine enough. Even going for 0.1deg may not be fine enough and the computational cost grows exponentially with the precision. <p>If you are on the continuous simulation problem there are better ways to do it... 978485 979082