from __future__ import absolute_import, division, print_function from mmtbx.validation.molprobity import mp_geo from iotbx import pdb import time pdb_str_1 = """ ATOM 60 N GLU A 9 7.757 9.623 27.829 1.00 12.74 N ATOM 61 CA GLU A 9 7.695 10.769 26.927 1.00 12.72 C ATOM 62 C GLU A 9 7.351 12.056 27.684 1.00 12.59 C ATOM 63 O GLU A 9 6.321 12.134 28.348 1.00 14.32 O ATOM 64 CB GLU A 9 6.633 10.459 25.859 1.00 13.52 C ATOM 65 CG GLU A 9 6.323 11.587 24.899 1.00 15.93 C ATOM 66 CD GLU A 9 7.533 12.006 24.105 1.00 16.48 C ATOM 67 OE1 GLU A 9 8.059 11.171 23.337 1.00 19.96 O ATOM 68 OE2 GLU A 9 7.960 13.164 24.257 1.00 18.90 O ATOM 69 N ASP A 10 8.216 13.062 27.589 1.00 14.68 N ATOM 70 CA ASP A 10 7.992 14.328 28.283 1.00 15.47 C ATOM 71 C ASP A 10 6.987 15.255 27.598 1.00 15.82 C ATOM 72 O ASP A 10 6.315 16.049 28.258 1.00 15.43 O ATOM 73 CB ASP A 10 9.322 15.075 28.453 1.00 16.97 C ATOM 74 CG AASP A 10 9.139 16.482 28.993 0.50 16.48 C ATOM 75 CG BASP A 10 9.941 15.472 27.128 0.50 17.05 C ATOM 76 OD1AASP A 10 9.189 17.442 28.197 0.50 17.34 O ATOM 77 OD1BASP A 10 11.349 14.573 26.359 0.50 18.03 O ATOM 78 OD2AASP A 10 8.934 16.630 30.215 0.50 17.88 O ATOM 79 OD2BASP A 10 10.016 16.689 26.852 0.50 20.20 O """ pdb_str_2 = """ ATOM 516 P C B 115 25.417 97.388 92.531 1.00161.67 P ATOM 517 OP1 C B 115 25.620 96.786 93.873 1.00161.61 O ATOM 518 OP2 C B 115 26.429 97.148 91.471 1.00157.52 O ATOM 519 O5' C B 115 23.989 96.929 91.981 1.00165.73 O ATOM 520 C5' C B 115 22.830 97.049 92.795 1.00166.81 C ATOM 521 C4' C B 115 21.568 96.608 92.088 1.00164.72 C ATOM 522 O4' C B 115 21.307 97.449 90.932 1.00165.07 O ATOM 523 C3' C B 115 21.553 95.203 91.511 1.00161.21 C ATOM 524 O3' C B 115 21.376 94.188 92.483 1.00162.42 O ATOM 525 C2' C B 115 20.419 95.291 90.500 1.00160.96 C ATOM 526 O2' C B 115 19.151 95.246 91.141 1.00163.14 O ATOM 527 C1' C B 115 20.634 96.695 89.939 1.00161.73 C ATOM 528 N1 C B 115 21.449 96.670 88.703 1.00156.58 N ATOM 529 C2 C B 115 20.847 96.216 87.521 1.00153.43 C ATOM 530 O2 C B 115 19.660 95.854 87.547 1.00152.48 O ATOM 531 N3 C B 115 21.572 96.181 86.379 1.00150.07 N ATOM 532 C4 C B 115 22.845 96.576 86.385 1.00149.02 C ATOM 533 N4 C B 115 23.520 96.526 85.235 1.00146.94 N ATOM 534 C5 C B 115 23.484 97.040 87.572 1.00150.48 C ATOM 535 C6 C B 115 22.758 97.069 88.698 1.00153.67 C ATOM 547 P A A B 116 21.844 92.681 92.170 0.51179.08 P ATOM 548 OP1A A B 116 21.573 91.863 93.379 0.51179.56 O ATOM 549 OP2A A B 116 23.220 92.732 91.614 0.51177.92 O ATOM 550 O5'A A B 116 20.860 92.191 91.014 0.51167.56 O ATOM 551 C5'A A B 116 19.551 91.726 91.313 0.51164.82 C ATOM 552 C4'A A B 116 18.742 91.493 90.060 0.51155.92 C ATOM 553 O4'A A B 116 18.898 92.626 89.165 0.51149.57 O ATOM 554 C3'A A B 116 19.141 90.293 89.209 0.51151.37 C ATOM 555 O3'A A B 116 18.607 89.067 89.684 0.51153.31 O ATOM 556 C2'A A B 116 18.628 90.683 87.831 0.51140.91 C ATOM 557 O2'A A B 116 17.227 90.473 87.724 0.51147.22 O ATOM 558 C1'A A B 116 18.903 92.185 87.824 0.51133.46 C ATOM 559 N9 A A B 116 20.215 92.506 87.229 0.51115.10 N ATOM 560 C8 A A B 116 21.352 92.925 87.874 0.51103.22 C ATOM 561 N7 A A B 116 22.369 93.136 87.075 0.51 94.11 N ATOM 562 C5 A A B 116 21.867 92.833 85.817 0.51 93.20 C ATOM 563 C6 A A B 116 22.449 92.855 84.538 0.51 84.33 C ATOM 564 N6 A A B 116 23.716 93.210 84.308 0.51 83.97 N ATOM 565 N1 A A B 116 21.676 92.496 83.490 0.51 83.45 N ATOM 566 C2 A A B 116 20.406 92.141 83.722 0.51 89.16 C ATOM 567 N3 A A B 116 19.746 92.081 84.877 0.51100.01 N ATOM 568 C4 A A B 116 20.543 92.444 85.897 0.51106.03 C ATOM 580 P B A B 116 21.673 92.654 92.107 0.49176.43 P ATOM 581 OP1B A B 116 22.052 91.946 93.355 0.49179.31 O ATOM 582 OP2B A B 116 22.589 92.619 90.939 0.49177.26 O ATOM 583 O5'B A B 116 20.256 92.106 91.631 0.49166.83 O ATOM 584 C5'B A B 116 20.155 90.953 90.811 0.49162.34 C ATOM 585 C4'B A B 116 18.753 90.785 90.285 0.49156.23 C ATOM 586 O4'B A B 116 18.380 91.954 89.503 0.49153.24 O ATOM 587 C3'B A B 116 18.530 89.625 89.328 0.49153.93 C ATOM 588 O3'B A B 116 18.398 88.370 89.971 0.49155.29 O ATOM 589 C2'B A B 116 17.290 90.074 88.574 0.49152.57 C ATOM 590 O2'B A B 116 16.122 89.934 89.370 0.49160.43 O ATOM 591 C1'B A B 116 17.592 91.558 88.399 0.49146.63 C ATOM 592 N9 B A B 116 18.368 91.795 87.168 0.49131.17 N ATOM 593 C8 B A B 116 19.613 92.360 87.046 0.49119.64 C ATOM 594 N7 B A B 116 20.046 92.418 85.809 0.49108.75 N ATOM 595 C5 B A B 116 19.018 91.847 85.070 0.49102.94 C ATOM 596 C6 B A B 116 18.857 91.610 83.694 0.49 95.23 C ATOM 597 N6 B A B 116 19.769 91.933 82.774 0.49 88.20 N ATOM 598 N1 B A B 116 17.711 91.021 83.287 0.49 91.58 N ATOM 599 C2 B A B 116 16.795 90.696 84.207 0.49 93.21 C ATOM 600 N3 B A B 116 16.833 90.868 85.525 0.49101.29 N ATOM 601 C4 B A B 116 17.982 91.457 85.895 0.49111.07 C ATOM 613 C4' G B 117 18.093 86.821 85.795 1.00149.42 C ATOM 614 O4' G B 117 18.411 88.142 85.277 1.00150.38 O ATOM 615 C3' G B 117 19.188 85.938 85.221 1.00152.20 C ATOM 616 O3' G B 117 18.860 84.561 85.207 1.00157.98 O ATOM 617 C2' G B 117 19.390 86.537 83.840 1.00148.15 C ATOM 618 O2' G B 117 18.348 86.156 82.953 1.00150.85 O ATOM 619 C1' G B 117 19.255 88.022 84.148 1.00142.90 C ATOM 620 N9 G B 117 20.565 88.616 84.472 1.00129.09 N ATOM 621 C8 G B 117 21.040 88.952 85.716 1.00125.15 C ATOM 622 N7 G B 117 22.244 89.453 85.691 1.00119.89 N ATOM 623 C5 G B 117 22.593 89.440 84.347 1.00115.13 C ATOM 624 C6 G B 117 23.787 89.862 83.702 1.00106.78 C ATOM 625 O6 G B 117 24.807 90.345 84.211 1.00103.03 O ATOM 626 N1 G B 117 23.723 89.674 82.323 1.00103.58 N ATOM 627 C2 G B 117 22.649 89.144 81.651 1.00105.31 C ATOM 628 N2 G B 117 22.777 89.041 80.320 1.00103.13 N ATOM 629 N3 G B 117 21.530 88.746 82.240 1.00112.17 N ATOM 630 C4 G B 117 21.569 88.921 83.580 1.00119.07 C ATOM 640 P A G B 117 19.377 87.681 89.414 0.57155.42 P ATOM 641 OP1A G B 117 18.636 86.602 90.115 0.57154.98 O ATOM 642 OP2A G B 117 20.818 87.886 89.703 0.57156.38 O ATOM 643 O5'A G B 117 19.216 87.435 87.847 0.57148.01 O ATOM 644 C5'A G B 117 18.022 86.888 87.300 0.57148.38 C ATOM 647 P B G B 117 19.331 87.141 89.518 0.43155.13 P ATOM 648 OP1B G B 117 18.722 85.885 90.026 0.43152.30 O ATOM 649 OP2B G B 117 20.734 87.474 89.871 0.43155.64 O ATOM 650 O5'B G B 117 19.213 87.135 87.929 0.43147.38 O ATOM 651 C5'B G B 117 17.973 86.851 87.299 0.43148.35 C ATOM 654 P C B 118 20.023 83.460 85.359 1.00146.31 P ATOM 655 OP1 C B 118 19.377 82.123 85.410 1.00144.77 O ATOM 656 OP2 C B 118 20.921 83.881 86.465 1.00146.69 O ATOM 657 O5' C B 118 20.835 83.565 83.989 1.00123.79 O ATOM 658 C5' C B 118 20.203 83.271 82.751 1.00120.61 C ATOM 659 C4' C B 118 20.991 83.775 81.563 1.00114.71 C ATOM 660 O4' C B 118 21.385 85.159 81.765 1.00115.11 O ATOM 661 C3' C B 118 22.301 83.069 81.260 1.00107.01 C ATOM 662 O3' C B 118 22.124 81.826 80.602 1.00104.55 O ATOM 663 C2' C B 118 23.035 84.105 80.419 1.00107.93 C ATOM 664 O2' C B 118 22.544 84.120 79.087 1.00108.92 O ATOM 665 C1' C B 118 22.610 85.406 81.104 1.00111.02 C ATOM 666 N1 C B 118 23.615 85.886 82.083 1.00107.14 N ATOM 667 C2 C B 118 24.827 86.373 81.586 1.00106.46 C ATOM 668 O2 C B 118 25.014 86.373 80.361 1.00109.38 O ATOM 669 N3 C B 118 25.774 86.826 82.437 1.00103.02 N ATOM 670 C4 C B 118 25.543 86.811 83.747 1.00103.40 C ATOM 671 N4 C B 118 26.507 87.269 84.549 1.00103.30 N ATOM 672 C5 C B 118 24.316 86.326 84.289 1.00103.70 C ATOM 673 C6 C B 118 23.387 85.879 83.432 1.00104.01 C """ def exercise_mp_geo(): with open('mp_geo.pdb', 'w') as f: f.write(pdb_str_1) args = ['pdb=mp_geo.pdb', 'out_file=mp_geo.out', 'outliers_only=False', 'bonds_and_angles=True'] mp_geo.run(args) f = open('mp_geo.out', 'r') # Strip out newline and carriage return chars to # prevent platform-specific errors. lines = [i.rstrip('\n\r') for i in f.readlines()] assert 'mp_geo.pdb: A: 10: :B:ASP:CG--OD1:1.839:31.054:PROTEIN' in lines assert \ 'mp_geo.pdb: A: 10: :B:ASP:OD1-CG-OD2:109.733:5.486:PROTEIN' in lines f.close() with open('mp_geo.pdb', 'w') as f: f.write(pdb_str_2) args = ['pdb=mp_geo.pdb', 'out_file=mp_geo.out', 'rna_backbone=True'] mp_geo.run(args) f = open('mp_geo.out', 'r') lines = [i.rstrip('\n\r') for i in f.readlines()] f.close() assert lines[0] == \ ' :1: B: 115: : : C:__?__:178.072:55.525:76.414:-158.236:-67.172' assert lines[1] == \ ' :1: B: 116: :A: A:-80.906:172.347:71.412:81.732:-151.720:-70.053' assert lines[2] == \ ' :1: B: 117: :A: G:-80.508:177.077:61.989:80.676:-149.321:-69.591' assert lines[3] == \ ' :1: B: 118: : : C:-62.565:164.517:69.624:78.058:__?__:__?__' if (__name__ == "__main__"): t0 = time.time() exercise_mp_geo() print("OK. Time: %8.3f"%(time.time()-t0))