from __future__ import absolute_import, division, print_function import iotbx.pdb from scitbx.array_family import flex import time pdb_str=""" CRYST1 454.007 426.033 459.047 90.00 90.00 90.00 P 1 SCALE1 0.002203 0.000000 0.000000 0.00000 SCALE2 0.000000 0.002347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002178 0.00000 ATOM 1 CA VAL A1358 148.938 119.717 100.000 1.00 33.88 C ATOM 2 CA PRO A1359 149.108 116.282 101.953 1.00 31.91 C ATOM 3 CA PRO A1360 146.078 114.542 103.797 1.00 26.33 C ATOM 4 CA PRO A1361 145.621 112.862 107.337 1.00 18.42 C ATOM 5 CA THR A1362 145.081 109.243 108.683 1.00 21.37 C ATOM 6 CA ASP A1363 143.651 106.972 111.575 1.00 20.53 C ATOM 7 CA LEU A1364 140.301 108.604 112.732 1.00 13.10 C ATOM 8 CA ARG A1365 138.856 107.558 116.217 1.00 13.90 C ATOM 9 CA PHE A1366 136.295 108.604 118.951 1.00 12.59 C ATOM 10 CA THR A1367 136.338 108.844 122.851 1.00 18.27 C ATOM 11 CA ASN A1368 134.748 110.767 125.861 1.00 35.66 C ATOM 12 CA ILE A1369 131.093 110.630 124.665 1.00 20.50 C ATOM 13 CA GLY A1370 128.787 112.946 126.681 1.00 31.22 C ATOM 14 CA PRO A1371 125.231 114.133 125.725 1.00 30.22 C ATOM 15 CA ASP A1372 126.459 117.360 124.041 1.00 23.75 C ATOM 16 CA THR A1373 130.112 116.268 123.662 1.00 17.75 C ATOM 17 CA MET A1374 132.554 113.816 121.995 1.00 13.70 C ATOM 18 CA ARG A1375 136.395 113.642 121.605 1.00 12.83 C ATOM 19 CA VAL A1376 137.530 112.924 118.003 1.00 11.64 C ATOM 20 CA THR A1377 141.175 111.755 117.305 1.00 13.55 C ATOM 21 CA TRP A1378 143.436 111.275 114.163 1.00 10.25 C ATOM 22 CA ALA A1379 147.077 110.870 112.883 1.00 20.66 C ATOM 23 CA PRO A1380 148.832 113.776 110.968 1.00 25.69 C ATOM 24 CA PRO A1381 150.776 113.842 107.607 1.00 34.10 C ATOM 25 CA ASP A1385 154.007 122.439 109.035 1.00 55.68 C ATOM 26 CA LEU A1386 150.309 122.713 108.083 1.00 39.19 C ATOM 27 CA THR A1387 148.167 125.829 108.846 1.00 33.58 C ATOM 28 CA ASN A1388 144.910 123.873 109.428 1.00 18.33 C ATOM 29 CA PHE A1389 142.989 120.679 110.062 1.00 13.50 C ATOM 30 CA LEU A1390 139.443 121.388 108.928 1.00 14.05 C ATOM 31 CA VAL A1391 137.092 119.270 111.076 1.00 11.67 C ATOM 32 CA ARG A1392 133.729 119.258 109.231 1.00 12.02 C ATOM 33 CA TYR A1393 130.897 117.502 111.152 1.00 10.39 C ATOM 34 CA SER A1394 127.111 117.090 110.574 1.00 16.06 C ATOM 35 CA PRO A1395 124.173 114.979 111.936 1.00 17.95 C ATOM 36 CA VAL A1396 123.808 111.698 109.904 1.00 24.54 C ATOM 37 CA LYS A1397 120.134 112.689 109.250 1.00 44.54 C ATOM 38 CA ASN A1398 121.139 116.103 107.784 1.00 43.24 C ATOM 39 CA GLU A1399 124.609 115.685 106.151 1.00 54.32 C ATOM 40 CA GLU A1400 124.190 119.276 104.701 1.00 42.39 C ATOM 41 CA VAL A1402 128.032 120.991 108.262 1.00 34.73 C ATOM 42 CA ALA A1403 129.573 122.671 111.271 1.00 31.08 C ATOM 43 CA GLU A1404 133.269 123.451 110.546 1.00 18.73 C ATOM 44 CA LEU A1405 136.125 123.710 113.086 1.00 23.21 C ATOM 45 CA SER A1406 139.558 125.155 112.173 1.00 19.59 C ATOM 46 CA ILE A1407 141.752 123.692 114.833 1.00 22.08 C ATOM 47 CA SER A1408 145.018 126.033 115.249 1.00 33.50 C ATOM 48 CA PRO A1409 148.634 124.336 115.685 1.00 35.29 C ATOM 49 CA SER A1410 148.476 120.979 118.025 1.00 37.93 C ATOM 50 CA ASP A1411 145.131 118.710 118.597 1.00 27.98 C ATOM 51 CA ASN A1412 145.573 115.280 117.118 1.00 21.72 C ATOM 52 CA ALA A1413 142.225 115.275 119.063 1.00 16.22 C ATOM 53 CA VAL A1414 139.281 117.816 119.201 1.00 15.68 C ATOM 54 CA VAL A1415 136.371 117.803 121.698 1.00 15.31 C ATOM 55 CA LEU A1416 133.225 118.528 119.662 1.00 16.01 C ATOM 56 CA THR A1417 130.718 120.452 121.897 1.00 20.05 C ATOM 57 CA ASN A1418 127.070 121.739 121.572 1.00 32.11 C ATOM 58 CA LEU A1419 125.988 118.404 119.986 1.00 15.97 C ATOM 59 CA LEU A1420 122.395 117.086 119.982 1.00 22.66 C ATOM 60 CA PRO A1421 121.812 114.423 122.733 1.00 20.32 C ATOM 61 CA GLY A1422 121.263 110.823 121.509 1.00 23.77 C ATOM 62 CA THR A1423 122.224 111.850 117.885 1.00 18.46 C ATOM 63 CA GLU A1424 124.604 110.218 115.318 1.00 14.18 C ATOM 64 CA TYR A1425 127.176 112.502 113.569 1.00 13.02 C ATOM 65 CA VAL A1426 129.513 112.297 110.551 1.00 12.30 C ATOM 66 CA VAL A1427 132.997 113.789 111.143 1.00 12.16 C ATOM 67 CA SER A1428 135.627 114.576 108.470 1.00 11.24 C ATOM 68 CA VAL A1429 139.197 116.027 108.576 1.00 11.54 C ATOM 69 CA SER A1430 141.130 117.805 105.734 1.00 13.82 C ATOM 70 CA SER A1431 144.703 119.108 106.173 1.00 18.85 C ATOM 71 CA VAL A1432 145.115 122.769 105.027 1.00 24.56 C ATOM 72 CA TYR A1433 148.261 124.777 104.098 1.00 45.81 C ATOM 73 CA HIS A1436 144.719 125.120 100.347 1.00 55.81 C ATOM 74 CA GLU A1437 142.703 122.002 101.363 1.00 29.48 C ATOM 75 CA SER A1438 143.992 118.417 101.042 1.00 22.89 C ATOM 76 CA THR A1439 141.620 115.400 100.644 1.00 28.41 C ATOM 77 CA PRO A1440 139.399 114.638 103.739 1.00 17.14 C ATOM 78 CA LEU A1441 139.506 111.600 106.101 1.00 14.44 C ATOM 79 CA ARG A1442 135.936 110.522 107.346 1.00 14.35 C ATOM 80 CA GLY A1443 134.058 108.636 110.191 1.00 15.43 C ATOM 81 CA ARG A1444 130.819 108.445 112.368 1.00 11.66 C ATOM 82 CA GLN A1445 129.772 108.415 116.114 1.00 11.50 C ATOM 83 CA LYS A1446 126.623 108.803 118.415 1.00 16.19 C ATOM 84 CA THR A1447 126.219 111.062 121.551 1.00 17.99 C ATOM 85 CA GLY A1448 124.870 110.091 125.040 1.00 29.95 C ATOM 86 CA LEU A1449 121.592 110.926 126.887 1.00 22.66 C ATOM 87 CA ASP A1450 121.190 114.131 128.936 1.00 29.34 C ATOM 88 CA SER A1451 119.589 114.286 132.415 1.00 22.82 C ATOM 89 CA PRO A1452 116.259 115.773 133.432 1.00 20.71 C ATOM 90 CA THR A1453 116.918 119.260 134.966 1.00 21.30 C ATOM 91 CA GLY A1454 115.025 121.690 137.311 1.00 40.30 C ATOM 92 CA ILE A1455 113.515 119.461 140.065 1.00 15.59 C ATOM 93 CA ASP A1456 110.666 121.305 141.864 1.00 20.21 C ATOM 94 CA PHE A1457 108.039 120.443 144.565 1.00 13.19 C ATOM 95 CA SER A1458 104.364 121.636 144.401 1.00 31.40 C ATOM 96 CA ASP A1459 100.972 120.385 145.865 1.00 30.41 C ATOM 97 CA ILE A1460 102.658 120.059 149.305 1.00 24.94 C ATOM 98 CA THR A1461 100.000 118.617 151.677 1.00 48.83 C ATOM 99 CA ASN A1463 100.070 113.301 152.758 1.00 22.51 C ATOM 100 CA SER A1464 101.256 114.201 149.190 1.00 18.68 C ATOM 101 CA PHE A1465 103.502 116.463 147.133 1.00 13.23 C ATOM 102 CA THR A1466 103.878 116.832 143.319 1.00 15.46 C ATOM 103 CA VAL A1467 107.394 116.566 141.859 1.00 13.69 C ATOM 104 CA HIS A1468 108.182 118.418 138.594 1.00 14.58 C ATOM 105 CA TRP A1469 111.247 118.176 136.299 1.00 10.82 C ATOM 106 CA ILE A1470 112.365 119.716 132.973 1.00 19.51 C ATOM 107 CA ALA A1471 112.613 117.148 130.133 1.00 23.06 C ATOM 108 CA PRO A1472 116.007 116.133 128.576 1.00 26.02 C ATOM 109 CA ARG A1473 116.707 117.205 124.930 1.00 24.80 C ATOM 110 CA ALA A1474 117.405 113.548 123.992 1.00 30.93 C ATOM 111 CA THR A1475 114.556 111.456 122.577 1.00 27.61 C ATOM 112 CA ILE A1476 113.479 109.292 125.565 1.00 20.47 C ATOM 113 CA THR A1477 111.104 106.367 126.245 1.00 20.70 C ATOM 114 CA GLY A1478 110.236 107.515 129.830 1.00 17.71 C ATOM 115 CA TYR A1479 111.339 108.336 133.412 1.00 11.13 C ATOM 116 CA ARG A1480 112.030 106.377 136.642 1.00 11.29 C ATOM 117 CA ILE A1481 111.354 108.176 139.957 1.00 11.59 C ATOM 118 CA ARG A1482 112.549 106.852 143.378 1.00 11.91 C ATOM 119 CA HIS A1483 111.280 108.193 146.740 1.00 12.39 C ATOM 120 CA HIS A1484 111.933 107.485 150.478 1.00 13.07 C ATOM 121 CA PRO A1485 111.962 109.317 153.882 1.00 16.85 C ATOM 122 CA GLU A1486 115.450 110.852 154.527 1.00 35.55 C ATOM 123 CA HIS A1487 116.161 108.541 157.533 1.00 37.44 C ATOM 124 CA PHE A1488 114.775 105.425 155.653 1.00 55.77 C ATOM 125 CA GLY A1490 114.925 100.391 153.173 1.00 51.28 C ATOM 126 CA ARG A1491 114.526 100.000 149.373 1.00 35.07 C ATOM 127 CA PRO A1492 113.029 103.299 147.995 1.00 34.67 C ATOM 128 CA ARG A1493 109.580 103.211 146.323 1.00 19.34 C ATOM 129 CA GLU A1494 110.097 103.197 142.505 1.00 17.33 C ATOM 130 CA ASP A1495 107.545 104.782 140.129 1.00 18.92 C ATOM 131 CA ARG A1496 107.622 104.735 136.272 1.00 14.77 C ATOM 132 CA VAL A1497 106.408 107.703 134.219 1.00 18.52 C ATOM 133 CA PRO A1498 105.929 107.937 130.379 1.00 22.40 C ATOM 134 CA HIS A1499 108.129 110.340 128.324 1.00 27.21 C ATOM 135 CA SER A1500 104.897 112.436 127.939 1.00 31.96 C ATOM 136 CA ARG A1501 104.944 113.394 131.694 1.00 25.65 C ATOM 137 CA ASN A1502 107.309 115.925 133.305 1.00 18.08 C ATOM 138 CA SER A1503 105.596 115.470 136.749 1.00 13.26 C ATOM 139 CA ILE A1504 104.291 113.003 139.407 1.00 11.86 C ATOM 140 CA THR A1505 102.098 113.449 142.526 1.00 12.54 C ATOM 141 CA LEU A1506 103.719 111.288 145.225 1.00 13.17 C ATOM 142 CA THR A1507 100.924 110.090 147.581 1.00 17.45 C ATOM 143 CA ASN A1508 100.502 108.068 150.815 1.00 21.22 C ATOM 144 CA LEU A1509 103.276 110.082 152.508 1.00 15.59 C ATOM 145 CA THR A1510 103.316 110.677 156.334 1.00 27.65 C ATOM 146 CA PRO A1511 102.558 114.210 157.787 1.00 40.50 C ATOM 147 CA GLY A1512 105.530 116.313 159.047 1.00 44.65 C ATOM 148 CA THR A1513 108.047 113.929 157.313 1.00 22.55 C ATOM 149 CA GLU A1514 110.992 114.686 154.966 1.00 21.10 C ATOM 150 CA TYR A1515 111.497 112.635 151.738 1.00 12.67 C ATOM 151 CA VAL A1516 114.448 112.279 149.296 1.00 13.40 C ATOM 152 CA VAL A1517 113.412 111.940 145.595 1.00 11.78 C ATOM 153 CA SER A1518 115.583 110.904 142.590 1.00 12.34 C ATOM 154 CA ILE A1519 114.725 110.895 138.832 1.00 11.14 C ATOM 155 CA VAL A1520 116.321 109.121 135.793 1.00 12.44 C ATOM 156 CA ALA A1521 115.462 109.388 132.060 1.00 14.96 C ATOM 157 CA LEU A1522 115.507 106.239 129.850 1.00 16.54 C ATOM 158 CA ASN A1523 116.032 105.607 126.094 1.00 25.63 C ATOM 159 CA GLY A1524 115.153 101.870 125.768 1.00 29.20 C ATOM 160 CA ARG A1525 118.103 100.567 127.906 1.00 25.61 C ATOM 161 CA GLU A1526 120.342 103.685 128.085 1.00 26.12 C ATOM 162 CA GLU A1527 119.837 105.577 131.422 1.00 19.28 C ATOM 163 CA SER A1528 120.671 109.264 132.149 1.00 21.68 C ATOM 164 CA PRO A1529 122.567 110.558 135.203 1.00 26.78 C ATOM 165 CA LEU A1530 120.377 111.168 138.317 1.00 17.50 C ATOM 166 CA LEU A1531 118.417 114.337 139.198 1.00 14.81 C ATOM 167 CA ILE A1532 117.866 114.501 143.053 1.00 15.20 C ATOM 168 CA GLY A1533 115.890 116.681 145.574 1.00 19.48 C ATOM 169 CA GLN A1534 114.319 116.753 149.115 1.00 13.66 C ATOM 170 CA GLN A1535 110.796 117.747 150.352 1.00 14.79 C ATOM 171 CA SER A1536 108.762 117.751 153.634 1.00 21.12 C ATOM 172 CA THR A1537 104.992 117.146 154.169 1.00 27.76 C TER END """ def rf(a,b): a=abs(a).data() b=abs(b).data() sc = flex.sum(a*b)/flex.sum(b*b) b = b*sc return flex.sum(flex.abs(a-b))/flex.sum(a+b)*2*100. def run(): p = iotbx.pdb.input(source_info=None, lines=pdb_str) h = p.construct_hierarchy() x = h.extract_xray_structure(crystal_symmetry=p.crystal_symmetry()) for d_min in [8,9,10,15,20,25,30,35,40,45, 50,55,60,65,70,75,80,85,90,95,100,200]: t0=time.time() fc_f = x.structure_factors(d_min=d_min, algorithm="fft").f_calc() t = time.time()-t0 fc_d = x.structure_factors(d_min=d_min, algorithm="direct").f_calc() r = rf(fc_f, fc_d) assert r<0.6, r if (__name__ == "__main__"): run()