from __future__ import absolute_import, division, print_function import iotbx.ncs import iotbx.ncs as ncs from iotbx import pdb pdb_str_1="""\ CRYST1 421.520 421.520 421.520 90.00 90.00 90.00 P 1 SCALE1 0.002372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.002372 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002372 0.00000 00 20.00 O ATOM 20750 N GLN A3048 172.895 272.881 181.246 1.00 20.00 N ATOM 20751 CA GLN A3048 174.038 273.205 180.405 1.00 20.00 C ATOM 20752 C GLN A3048 174.922 274.193 181.146 1.00 20.00 C ATOM 20753 O GLN A3048 174.493 275.310 181.448 1.00 20.00 O ATOM 20754 CB GLN A3048 173.603 273.813 179.071 1.00 20.00 C ATOM 20755 CG GLN A3048 172.982 272.857 178.082 1.00 20.00 C ATOM 20756 CD GLN A3048 172.668 273.524 176.749 1.00 20.00 C ATOM 20757 OE1 GLN A3048 172.822 274.735 176.593 1.00 20.00 O ATOM 20758 NE2 GLN A3048 172.245 272.728 175.776 1.00 20.00 N ATOM 20759 N ARG A3049 176.156 273.792 181.437 1.00 20.00 N ATOM 20760 CA ARG A3049 177.074 274.640 182.189 1.00 20.00 C ATOM 20761 C ARG A3049 178.316 274.918 181.353 1.00 20.00 C ATOM 20762 O ARG A3049 179.235 274.074 181.309 1.00 20.00 O ATOM 20763 CB ARG A3049 177.431 274.001 183.534 1.00 20.00 C ATOM 20764 CG ARG A3049 178.396 274.815 184.382 1.00 20.00 C ATOM 20765 CD ARG A3049 177.873 276.220 184.584 1.00 20.00 C ATOM 20766 NE ARG A3049 176.541 276.220 185.179 1.00 20.00 N ATOM 20767 CZ ARG A3049 175.728 277.269 185.183 1.00 20.00 C ATOM 20768 NH1 ARG A3049 176.111 278.407 184.624 1.00 20.00 N ATOM 20769 NH2 ARG A3049 174.529 277.182 185.738 1.00 20.00 N ATOM 20770 N PRO A3050 178.391 276.070 180.668 1.00 20.00 N ATOM 20771 CA PRO A3050 179.609 276.516 179.987 1.00 20.00 C ATOM 20772 C PRO A3050 180.606 277.102 180.972 1.00 20.00 C ATOM 20773 O PRO A3050 180.209 277.351 182.108 1.00 20.00 O ATOM 20774 CB PRO A3050 179.099 277.587 179.023 1.00 20.00 C ATOM 20775 CG PRO A3050 177.888 278.128 179.689 1.00 20.00 C ATOM 20776 CD PRO A3050 177.254 276.969 180.399 1.00 20.00 C HETATM20777 C1' FMN A3994 169.244 267.550 126.473 1.00 20.00 C HETATM20778 C10 FMN A3994 168.218 265.806 127.908 1.00 20.00 C HETATM20779 C2 FMN A3994 168.985 263.559 127.660 1.00 20.00 C HETATM20780 C2' FMN A3994 168.655 267.365 125.077 1.00 20.00 C HETATM20781 C3' FMN A3994 169.586 267.961 124.044 1.00 20.00 C HETATM20782 C4 FMN A3994 167.291 264.058 129.235 1.00 20.00 C HETATM20783 C4' FMN A3994 169.743 269.452 124.272 1.00 20.00 C HETATM20784 C4A FMN A3994 167.336 265.394 128.881 1.00 20.00 C HETATM20785 C5' FMN A3994 170.460 270.146 123.129 1.00 20.00 C HETATM20786 C5A FMN A3994 166.562 267.625 129.128 1.00 20.00 C HETATM20787 C6 FMN A3994 165.727 268.539 129.744 1.00 20.00 C HETATM20788 C7 FMN A3994 165.784 269.873 129.378 1.00 20.00 C HETATM20789 C7M FMN A3994 164.880 270.860 130.041 1.00 20.00 C HETATM20790 C8 FMN A3994 166.673 270.291 128.396 1.00 20.00 C HETATM20791 C8M FMN A3994 166.765 271.726 127.976 1.00 20.00 C HETATM20792 C9 FMN A3994 167.504 269.374 127.783 1.00 20.00 C HETATM20793 C9A FMN A3994 167.449 268.040 128.146 1.00 20.00 C HETATM20794 N1 FMN A3994 169.038 264.885 127.302 1.00 20.00 N HETATM20795 N10 FMN A3994 168.274 267.125 127.533 1.00 20.00 N HETATM20796 N3 FMN A3994 168.110 263.141 128.630 1.00 20.00 N HETATM20797 N5 FMN A3994 166.508 266.302 129.495 1.00 20.00 N HETATM20798 O1P FMN A3994 168.602 272.266 122.870 1.00 20.00 O HETATM20799 O2 FMN A3994 169.722 262.750 127.115 1.00 20.00 O HETATM20800 O2' FMN A3994 168.523 265.992 124.811 1.00 20.00 O HETATM20801 O2P FMN A3994 170.055 273.770 124.179 1.00 20.00 O HETATM20802 O3' FMN A3994 170.842 267.349 124.198 1.00 20.00 O HETATM20803 O3P FMN A3994 170.661 273.201 121.851 1.00 20.00 O HETATM20804 O4 FMN A3994 166.516 263.678 130.091 1.00 20.00 O HETATM20805 O4' FMN A3994 168.489 270.061 124.431 1.00 20.00 O HETATM20806 O5' FMN A3994 170.809 271.411 123.629 1.00 20.00 O HETATM20807 P FMN A3994 170.022 272.701 123.117 1.00 20.00 P TER ATOM 41557 N GLN B3048 175.987 146.935 181.245 1.00 20.00 N ATOM 41558 CA GLN B3048 175.135 147.763 180.404 1.00 20.00 C ATOM 41559 C GLN B3048 173.837 148.035 181.145 1.00 20.00 C ATOM 41560 O GLN B3048 173.084 147.105 181.447 1.00 20.00 O ATOM 41561 CB GLN B3048 174.825 147.082 179.070 1.00 20.00 C ATOM 41562 CG GLN B3048 175.963 147.022 178.081 1.00 20.00 C ATOM 41563 CD GLN B3048 175.543 146.417 176.748 1.00 20.00 C ATOM 41564 OE1 GLN B3048 174.417 145.945 176.592 1.00 20.00 O ATOM 41565 NE2 GLN B3048 176.443 146.448 175.775 1.00 20.00 N ATOM 41566 N ARG B3049 173.568 149.304 181.436 1.00 20.00 N ATOM 41567 CA ARG B3049 172.374 149.675 182.188 1.00 20.00 C ATOM 41568 C ARG B3049 171.513 150.612 181.352 1.00 20.00 C ATOM 41569 O ARG B3049 171.784 151.830 181.308 1.00 20.00 O ATOM 41570 CB ARG B3049 172.750 150.304 183.533 1.00 20.00 C ATOM 41571 CG ARG B3049 171.562 150.733 184.381 1.00 20.00 C ATOM 41572 CD ARG B3049 170.607 149.578 184.583 1.00 20.00 C ATOM 41573 NE ARG B3049 171.273 148.424 185.178 1.00 20.00 N ATOM 41574 CZ ARG B3049 170.770 147.196 185.182 1.00 20.00 C ATOM 41575 NH1 ARG B3049 169.593 146.958 184.623 1.00 20.00 N ATOM 41576 NH2 ARG B3049 171.445 146.201 185.737 1.00 20.00 N ATOM 41577 N PRO B3050 170.477 150.101 180.667 1.00 20.00 N ATOM 41578 CA PRO B3050 169.482 150.933 179.986 1.00 20.00 C ATOM 41579 C PRO B3050 168.476 151.504 180.972 1.00 20.00 C ATOM 41580 O PRO B3050 168.459 151.036 182.108 1.00 20.00 O ATOM 41581 CB PRO B3050 168.809 149.956 179.023 1.00 20.00 C ATOM 41582 CG PRO B3050 168.946 148.637 179.689 1.00 20.00 C ATOM 41583 CD PRO B3050 170.267 148.667 180.398 1.00 20.00 C HETATM41584 C1' FMN B3994 182.422 146.436 126.471 1.00 20.00 C HETATM41585 C10 FMN B3994 184.446 146.419 127.906 1.00 20.00 C HETATM41586 C2 FMN B3994 186.008 148.207 127.657 1.00 20.00 C HETATM41587 C2' FMN B3994 182.877 146.019 125.075 1.00 20.00 C HETATM41588 C3' FMN B3994 181.895 146.527 124.042 1.00 20.00 C HETATM41589 C4 FMN B3994 186.423 146.490 129.232 1.00 20.00 C HETATM41590 C4' FMN B3994 180.525 145.918 124.270 1.00 20.00 C HETATM41591 C4A FMN B3994 185.243 145.861 128.879 1.00 20.00 C HETATM41592 C5' FMN B3994 179.565 146.192 123.127 1.00 20.00 C HETATM41593 C5A FMN B3994 183.698 144.076 129.126 1.00 20.00 C HETATM41594 C6 FMN B3994 183.324 142.896 129.742 1.00 20.00 C HETATM41595 C7 FMN B3994 182.140 142.279 129.376 1.00 20.00 C HETATM41596 C7M FMN B3994 181.737 141.002 130.039 1.00 20.00 C HETATM41597 C8 FMN B3994 181.333 142.840 128.394 1.00 20.00 C HETATM41598 C8M FMN B3994 180.044 142.202 127.974 1.00 20.00 C HETATM41599 C9 FMN B3994 181.712 144.018 127.781 1.00 20.00 C HETATM41600 C9A FMN B3994 182.895 144.637 128.144 1.00 20.00 C HETATM41601 N1 FMN B3994 184.833 147.590 127.300 1.00 20.00 N HETATM41602 N10 FMN B3994 183.275 145.809 127.531 1.00 20.00 N HETATM41603 N3 FMN B3994 186.808 147.658 128.627 1.00 20.00 N HETATM41604 N5 FMN B3994 184.871 144.690 129.493 1.00 20.00 N HETATM41605 O1P FMN B3994 178.658 143.523 122.868 1.00 20.00 O HETATM41606 O2 FMN B3994 186.341 149.249 127.112 1.00 20.00 O HETATM41607 O2' FMN B3994 184.132 146.591 124.809 1.00 20.00 O HETATM41608 O2P FMN B3994 176.629 144.030 124.178 1.00 20.00 O HETATM41609 O3' FMN B3994 181.797 147.921 124.196 1.00 20.00 O HETATM41610 O3P FMN B3994 176.819 144.839 121.850 1.00 20.00 O HETATM41611 O4 FMN B3994 187.140 146.009 130.088 1.00 20.00 O HETATM41612 O4' FMN B3994 180.624 144.527 124.429 1.00 20.00 O HETATM41613 O5' FMN B3994 178.295 145.862 123.627 1.00 20.00 O HETATM41614 P FMN B3994 177.571 144.536 123.116 1.00 20.00 P TER END """ def exercise_00(): """ Verify that ligand is properly included by default """ pdb_inp = iotbx.pdb.input(lines=pdb_str_1,source_info=None) hierarchy = pdb_inp.construct_hierarchy() asc = hierarchy.atom_selection_cache() ncs_inp = iotbx.ncs.input(hierarchy = hierarchy) ncs_groups = ncs_inp.get_ncs_restraints_group_list() assert len(ncs_groups) == 1 assert len(ncs_groups[0].copies) == 1, len(ncs_groups[0].copies) # print list(ncs_groups[0].master_iselection) assert ncs_groups[0].master_iselection.size() == 58 # all chain # print hierarchy.select(asc.selection("chain A")).atoms_size() assert ncs_groups[0].copies[0].iselection.size() == 58 # all chain if(__name__=='__main__'): exercise_00()