from __future__ import absolute_import, division, print_function import time from tst_ncs_user_selections import get_ncs_groups # # Example of shortcoming of NCS verification procedure. The error is due to # exotic order of chains inside NCS groups. # # The failure shows that not something is broken, but is an example of the corner # case with which current code cannot deal with. # pdb_str=""" CRYST1 106.713 90.134 63.871 90.00 90.00 90.00 P 1 SCALE1 0.009371 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011095 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015657 0.00000 ATOM 1 N SER A 3 13.654 19.632 7.555 1.00 34.27 N ATOM 2 CA SER A 3 12.388 18.913 7.485 1.00 34.27 C ATOM 3 C SER A 3 12.618 17.449 7.145 1.00 34.27 C ATOM 4 O SER A 3 13.438 17.137 6.282 1.00 34.27 O ATOM 5 CB SER A 3 11.461 19.548 6.451 1.00 34.27 C ATOM 6 OG SER A 3 11.917 19.290 5.135 1.00 34.27 O ATOM 7 N PRO A 4 11.898 16.555 7.831 1.00 33.04 N ATOM 8 CA PRO A 4 12.068 15.118 7.555 1.00 33.04 C ATOM 9 C PRO A 4 11.762 14.729 6.120 1.00 33.04 C ATOM 10 O PRO A 4 12.428 13.841 5.571 1.00 33.04 O ATOM 11 CB PRO A 4 11.101 14.461 8.549 1.00 33.04 C ATOM 12 CG PRO A 4 10.135 15.537 8.917 1.00 33.04 C ATOM 13 CD PRO A 4 10.919 16.800 8.900 1.00 33.04 C TER ATOM 14 N SER B 3 49.210 85.134 17.642 1.00 20.33 N ATOM 15 CA SER B 3 48.236 84.429 18.467 1.00 20.33 C ATOM 16 C SER B 3 48.154 82.969 18.058 1.00 20.33 C ATOM 17 O SER B 3 48.185 82.668 16.869 1.00 20.33 O ATOM 18 CB SER B 3 46.860 85.086 18.357 1.00 20.33 C ATOM 19 OG SER B 3 45.877 84.345 19.060 1.00 20.33 O ATOM 20 N PRO B 4 48.033 82.073 19.053 1.00 17.85 N ATOM 21 CA PRO B 4 48.012 80.628 18.778 1.00 17.85 C ATOM 22 C PRO B 4 47.212 80.215 17.552 1.00 17.85 C ATOM 23 O PRO B 4 47.712 79.456 16.715 1.00 17.85 O ATOM 24 CB PRO B 4 47.390 80.040 20.052 1.00 17.85 C ATOM 25 CG PRO B 4 47.304 81.176 21.047 1.00 17.85 C ATOM 26 CD PRO B 4 48.041 82.344 20.496 1.00 17.85 C TER ATOM 27 N LEU C 27 5.385 30.101 36.788 1.00 41.94 N ATOM 28 CA LEU C 27 5.992 30.923 37.828 1.00 41.94 C ATOM 29 C LEU C 27 6.816 32.057 37.227 1.00 41.94 C ATOM 30 O LEU C 27 6.274 33.081 36.813 1.00 41.94 O ATOM 31 CB LEU C 27 6.870 30.069 38.742 1.00 41.94 C ATOM 32 CG LEU C 27 6.182 28.907 39.459 1.00 41.94 C ATOM 33 CD1 LEU C 27 7.173 28.162 40.339 1.00 41.94 C ATOM 34 CD2 LEU C 27 5.000 29.405 40.276 1.00 41.94 C ATOM 35 N LEU C 28 8.132 31.860 37.178 1.00 43.81 N ATOM 36 CA LEU C 28 9.055 32.874 36.690 1.00 43.81 C ATOM 37 C LEU C 28 10.305 32.191 36.157 1.00 43.81 C ATOM 38 O LEU C 28 10.553 31.011 36.416 1.00 43.81 O ATOM 39 CB LEU C 28 9.439 33.868 37.792 1.00 43.81 C ATOM 40 CG LEU C 28 8.481 35.000 38.154 1.00 43.81 C ATOM 41 CD1 LEU C 28 8.934 35.675 39.438 1.00 43.81 C ATOM 42 CD2 LEU C 28 8.405 36.006 37.021 1.00 43.81 C TER ATOM 43 O5' DA K 1 24.122 38.760 12.604 1.00 49.90 O ATOM 44 C5' DA K 1 24.158 37.777 11.573 1.00 49.90 C ATOM 45 C4' DA K 1 24.551 38.399 10.243 1.00 49.90 C ATOM 46 O4' DA K 1 23.742 39.580 10.004 1.00 49.90 O ATOM 47 C3' DA K 1 26.001 38.862 10.146 1.00 49.90 C ATOM 48 O3' DA K 1 26.480 38.693 8.827 1.00 49.90 O ATOM 49 C2' DA K 1 25.908 40.332 10.513 1.00 49.90 C ATOM 50 C1' DA K 1 24.571 40.717 9.897 1.00 49.90 C ATOM 51 N9 DA K 1 23.923 41.829 10.585 1.00 49.90 N ATOM 52 C8 DA K 1 23.464 41.847 11.872 1.00 49.90 C ATOM 53 N7 DA K 1 22.930 42.991 12.226 1.00 49.90 N ATOM 54 C5 DA K 1 23.050 43.778 11.094 1.00 49.90 C ATOM 55 C6 DA K 1 22.670 45.105 10.816 1.00 49.90 C ATOM 56 N6 DA K 1 22.070 45.899 11.707 1.00 49.90 N ATOM 57 N1 DA K 1 22.933 45.584 9.582 1.00 49.90 N ATOM 58 C2 DA K 1 23.533 44.785 8.693 1.00 49.90 C ATOM 59 N3 DA K 1 23.936 43.525 8.839 1.00 49.90 N ATOM 60 C4 DA K 1 23.656 43.076 10.072 1.00 49.90 C TER ATOM 61 O5' DG L 2 76.950 13.593 57.985 1.00 91.25 O ATOM 62 C5' DG L 2 76.703 14.675 58.871 1.00 91.25 C ATOM 63 C4' DG L 2 76.734 16.000 58.130 1.00 91.25 C ATOM 64 O4' DG L 2 77.717 15.944 57.064 1.00 91.25 O ATOM 65 C3' DG L 2 75.435 16.402 57.445 1.00 91.25 C ATOM 66 O3' DG L 2 75.390 17.820 57.381 1.00 91.25 O ATOM 67 C2' DG L 2 75.629 15.800 56.050 1.00 91.25 C ATOM 68 C1' DG L 2 77.071 16.215 55.835 1.00 91.25 C ATOM 69 N9 DG L 2 77.814 15.539 54.772 1.00 91.25 N ATOM 70 C8 DG L 2 77.703 14.240 54.328 1.00 91.25 C ATOM 71 N7 DG L 2 78.562 13.946 53.377 1.00 91.25 N ATOM 72 C5 DG L 2 79.288 15.124 53.202 1.00 91.25 C ATOM 73 C6 DG L 2 80.359 15.443 52.317 1.00 91.25 C ATOM 74 O6 DG L 2 80.916 14.723 51.477 1.00 91.25 O ATOM 75 N1 DG L 2 80.789 16.763 52.490 1.00 91.25 N ATOM 76 C2 DG L 2 80.253 17.654 53.392 1.00 91.25 C ATOM 77 N2 DG L 2 80.791 18.886 53.421 1.00 91.25 N ATOM 78 N3 DG L 2 79.264 17.365 54.210 1.00 91.25 N ATOM 79 C4 DG L 2 78.835 16.097 54.062 1.00 91.25 C TER ATOM 80 N SER D 3 93.227 70.323 7.415 1.00 34.27 N ATOM 81 CA SER D 3 94.496 71.037 7.347 1.00 34.27 C ATOM 82 C SER D 3 94.273 72.500 6.999 1.00 34.27 C ATOM 83 O SER D 3 93.457 72.811 6.131 1.00 34.27 O ATOM 84 CB SER D 3 95.425 70.394 6.319 1.00 34.27 C ATOM 85 OG SER D 3 94.975 70.647 5.000 1.00 34.27 O ATOM 86 N PRO D 4 94.993 73.395 7.684 1.00 33.04 N ATOM 87 CA PRO D 4 94.830 74.831 7.400 1.00 33.04 C ATOM 88 C PRO D 4 95.143 75.212 5.965 1.00 33.04 C ATOM 89 O PRO D 4 94.482 76.100 5.409 1.00 33.04 O ATOM 90 CB PRO D 4 95.795 75.489 8.395 1.00 33.04 C ATOM 91 CG PRO D 4 96.756 74.411 8.772 1.00 33.04 C ATOM 92 CD PRO D 4 95.967 73.151 8.758 1.00 33.04 C TER ATOM 93 N SER E 3 57.388 5.000 17.660 1.00 20.33 N ATOM 94 CA SER E 3 58.361 5.705 18.486 1.00 20.33 C ATOM 95 C SER E 3 58.450 7.163 18.071 1.00 20.33 C ATOM 96 O SER E 3 58.425 7.459 16.880 1.00 20.33 O ATOM 97 CB SER E 3 59.735 5.043 18.385 1.00 20.33 C ATOM 98 OG SER E 3 60.718 5.783 19.088 1.00 20.33 O ATOM 99 N PRO E 4 58.571 8.063 19.062 1.00 17.85 N ATOM 100 CA PRO E 4 58.598 9.507 18.780 1.00 17.85 C ATOM 101 C PRO E 4 59.405 9.911 17.556 1.00 17.85 C ATOM 102 O PRO E 4 58.911 10.668 16.713 1.00 17.85 O ATOM 103 CB PRO E 4 59.217 10.098 20.054 1.00 17.85 C ATOM 104 CG PRO E 4 59.295 8.967 21.055 1.00 17.85 C ATOM 105 CD PRO E 4 58.556 7.799 20.506 1.00 17.85 C TER ATOM 106 N LEU F 27 101.339 59.959 36.729 1.00 41.94 N ATOM 107 CA LEU F 27 100.725 59.144 37.770 1.00 41.94 C ATOM 108 C LEU F 27 99.899 58.010 37.171 1.00 41.94 C ATOM 109 O LEU F 27 100.439 56.983 36.764 1.00 41.94 O ATOM 110 CB LEU F 27 99.847 60.006 38.677 1.00 41.94 C ATOM 111 CG LEU F 27 100.536 61.168 39.391 1.00 41.94 C ATOM 112 CD1 LEU F 27 99.544 61.921 40.264 1.00 41.94 C ATOM 113 CD2 LEU F 27 101.713 60.670 40.215 1.00 41.94 C ATOM 114 N LEU F 28 98.584 58.212 37.116 1.00 43.81 N ATOM 115 CA LEU F 28 97.659 57.199 36.629 1.00 43.81 C ATOM 116 C LEU F 28 96.414 57.884 36.088 1.00 43.81 C ATOM 117 O LEU F 28 96.169 59.066 36.340 1.00 43.81 O ATOM 118 CB LEU F 28 97.267 56.212 37.734 1.00 43.81 C ATOM 119 CG LEU F 28 98.220 55.078 38.105 1.00 43.81 C ATOM 120 CD1 LEU F 28 97.759 54.411 39.390 1.00 43.81 C ATOM 121 CD2 LEU F 28 98.296 54.066 36.977 1.00 43.81 C TER ATOM 122 O5' DA I 1 82.668 51.257 12.510 1.00 49.90 O ATOM 123 C5' DA I 1 82.640 52.236 11.474 1.00 49.90 C ATOM 124 C4' DA I 1 82.250 51.609 10.145 1.00 49.90 C ATOM 125 O4' DA I 1 83.055 50.424 9.915 1.00 49.90 O ATOM 126 C3' DA I 1 80.798 51.151 10.045 1.00 49.90 C ATOM 127 O3' DA I 1 80.325 51.316 8.723 1.00 49.90 O ATOM 128 C2' DA I 1 80.885 49.682 10.419 1.00 49.90 C ATOM 129 C1' DA I 1 82.223 49.289 9.810 1.00 49.90 C ATOM 130 N9 DA I 1 82.864 48.178 10.506 1.00 49.90 N ATOM 131 C8 DA I 1 83.317 48.165 11.795 1.00 49.90 C ATOM 132 N7 DA I 1 83.846 47.020 12.156 1.00 49.90 N ATOM 133 C5 DA I 1 83.727 46.228 11.027 1.00 49.90 C ATOM 134 C6 DA I 1 84.104 44.899 10.757 1.00 49.90 C ATOM 135 N6 DA I 1 84.697 44.107 11.654 1.00 49.90 N ATOM 136 N1 DA I 1 83.844 44.415 9.524 1.00 49.90 N ATOM 137 C2 DA I 1 83.250 45.212 8.629 1.00 49.90 C ATOM 138 N3 DA I 1 82.851 46.474 8.768 1.00 49.90 N ATOM 139 C4 DA I 1 83.128 46.928 10.000 1.00 49.90 C TER ATOM 140 O5' DG J 2 29.751 76.829 57.560 1.00 91.25 O ATOM 141 C5' DG J 2 29.991 75.750 58.452 1.00 91.25 C ATOM 142 C4' DG J 2 29.958 74.422 57.717 1.00 91.25 C ATOM 143 O4' DG J 2 28.979 74.477 56.647 1.00 91.25 O ATOM 144 C3' DG J 2 31.258 74.012 57.039 1.00 91.25 C ATOM 145 O3' DG J 2 31.298 72.594 56.982 1.00 91.25 O ATOM 146 C2' DG J 2 31.072 74.608 55.640 1.00 91.25 C ATOM 147 C1' DG J 2 29.629 74.198 55.422 1.00 91.25 C ATOM 148 N9 DG J 2 28.893 74.871 54.352 1.00 91.25 N ATOM 149 C8 DG J 2 29.010 76.168 53.903 1.00 91.25 C ATOM 150 N7 DG J 2 28.156 76.461 52.947 1.00 91.25 N ATOM 151 C5 DG J 2 27.427 75.285 52.775 1.00 91.25 C ATOM 152 C6 DG J 2 26.358 74.965 51.887 1.00 91.25 C ATOM 153 O6 DG J 2 25.807 75.684 51.041 1.00 91.25 O ATOM 154 N1 DG J 2 25.923 73.648 52.064 1.00 91.25 N ATOM 155 C2 DG J 2 26.452 72.759 52.972 1.00 91.25 C ATOM 156 N2 DG J 2 25.909 71.529 53.005 1.00 91.25 N ATOM 157 N3 DG J 2 27.438 73.048 53.793 1.00 91.25 N ATOM 158 C4 DG J 2 27.873 74.314 53.641 1.00 91.25 C TER END """ def exercise_1(): """ The desired outcome of the ncs_search procedure is that user's selections are fully preserved. The current procedure results in dropping chains I,J and K,L from selections. Chains match as following: A <--> D B <--> E C <--> F I <--> K J <--> L The reason for this is that in input pdb the chains order require the procedure to do the match: m m m m m (master) A-B-C-K-L-D-E-F-I-J c c c c c (copy) where in master chains I,J are following protein ABC and in copy chains K,L are preceding protein DEF. """ phil_str=""" ncs_group { reference = chain A or chain B or chain C or chain I or chain J selection = chain F or chain D or chain E or chain K or chain L } """ ncs_groups = get_ncs_groups(phil_str, pdb_str) # import iotbx.pdb # h = iotbx.pdb.input(source_info=None, lines=pdb_str).construct_hierarchy() # ncs_groups._show(hierarchy=h, brief=False) assert len(ncs_groups) == 1 assert ncs_groups[0].master_str_selection == "chain A or chain B or chain C or chain I or chain J" assert ncs_groups[0].copies[0].str_selection == "chain F or chain D or chain E or chain K or chain L" if (__name__ == "__main__"): t0=time.time() exercise_1() print("Time: %6.4f"%(time.time()-t0)) print("OK")