from __future__ import absolute_import, division, print_function import iotbx.pdb from six.moves import cStringIO as StringIO pdb_str = """\ ATOM 1 C5' U 5 97.750 -47.885 -63.217 1.00 83.53 A16S C ATOM 2 O5' U 5 98.491 -48.524 -62.188 1.00 79.28 A16S O ATOM 3 C4' U 5 96.316 -48.337 -63.206 1.00 86.16 A16S C ATOM 4 O4' U 5 95.819 -48.280 -61.845 1.00 86.45 A16S O ATOM 5 C3' U 5 95.333 -47.485 -63.995 1.00 87.46 A16S C ATOM 6 O3' U 5 95.360 -47.739 -65.396 1.00 87.28 A16S O ATOM 7 C2' U 5 94.014 -47.773 -63.286 1.00 84.71 A16S C ATOM 8 O2' U 5 93.532 -49.058 -63.634 1.00 85.00 A16S O ATOM 9 C1' U 5 94.476 -47.853 -61.835 1.00 84.81 A16S C ATOM 10 N1 U 5 94.415 -46.549 -61.136 1.00 89.08 A16S N ATOM 11 C2 U 5 94.346 -46.619 -59.764 1.00 90.22 A16S C ATOM 12 O2 U 5 94.352 -47.676 -59.164 1.00 86.48 A16S O ATOM 13 N3 U 5 94.297 -45.413 -59.117 1.00 91.22 A16S N ATOM 14 C4 U 5 94.296 -44.164 -59.695 1.00 88.42 A16S C ATOM 15 O4 U 5 94.242 -43.169 -58.977 1.00 87.55 A16S O ATOM 16 C5 U 5 94.358 -44.166 -61.121 1.00 88.94 A16S C ATOM 17 C6 U 5 94.408 -45.329 -61.773 1.00 89.00 A16S C ATOM 99999 P C 172 78.677 39.674 -73.035 1.00136.18 B23S P ATOM 99999 C5' C 172 78.936 39.931 -75.628 1.00129.50 B23S C ATOM 99999 O5' C 172 78.085 39.757 -74.507 1.00131.05 B23S O ATOM 99999 C4' C 172 78.137 39.999 -76.900 1.00127.67 B23S C ATOM 99999 O4' C 172 77.604 38.690 -77.227 1.00128.58 B23S O ATOM 99999 C3' C 172 76.907 40.883 -76.846 1.00128.68 B23S C ATOM 99999 O3' C 172 77.201 42.258 -76.974 1.00129.72 B23S O ATOM 99999 C2' C 172 76.054 40.323 -77.972 1.00130.33 B23S C ATOM 99999 O2' C 172 76.544 40.754 -79.232 1.00129.46 B23S O ATOM 99999 C1' C 172 76.335 38.830 -77.835 1.00131.16 B23S C ATOM 99999 N1 C 172 75.328 38.158 -76.984 1.00132.38 B23S N ATOM 99999 C2 C 172 74.039 37.935 -77.483 1.00130.56 B23S C ATOM 99999 O2 C 172 73.763 38.302 -78.634 1.00128.13 B23S O ATOM 99999 N3 C 172 73.131 37.313 -76.697 1.00130.47 B23S N ATOM 99999 C4 C 172 73.464 36.923 -75.469 1.00131.73 B23S C ATOM 99999 N4 C 172 72.544 36.315 -74.719 1.00129.68 B23S N ATOM 99999 C5 C 172 74.765 37.140 -74.941 1.00132.57 B23S C ATOM 99999 C6 C 172 75.656 37.757 -75.722 1.00131.42 B23S C ATOM 99999 OP1 C 172 79.530 40.865 -72.814 1.00135.64 B23S O ATOM 99999 OP2 C 172 77.560 39.387 -72.106 1.00132.48 B23S O1- ATOM 99999 N PRO 44 38.238 25.445 -61.632 1.00 58.89 BL28 N ATOM 99999 CA PRO 44 38.138 24.574 -62.799 1.00 58.30 BL28 C ATOM 99999 C PRO 44 38.531 23.151 -62.439 1.00 58.13 BL28 C ATOM 99999 O PRO 44 38.794 22.820 -61.286 1.00 57.98 BL28 O ATOM 99999 CB PRO 44 39.136 25.191 -63.776 1.00 56.49 BL28 C ATOM 99999 CG PRO 44 40.143 25.804 -62.902 1.00 55.93 BL28 C ATOM 99999 CD PRO 44 39.395 26.345 -61.727 1.00 56.81 BL28 C """ def exercise(prefix="iotbx_tst_mmcif_segids"): """ Properly output segids when chain ids are empty. Case for Ribosome community. After making it work, it should be moved to cctbx_project/iotbx/regression. """ out = StringIO() pdb_inp = iotbx.pdb.input(lines=pdb_str, source_info=None) h = pdb_inp.construct_hierarchy() print("Original:") print(h.as_pdb_string()) assert len(h.only_model().chains()) == 3 assert [x.id for x in h.only_model().chains()] == [' ', ' ', ' '] assert [x.segid for x in h.atoms()] == ['A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'A16S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'B23S', 'BL28', 'BL28', 'BL28', 'BL28', 'BL28', 'BL28', 'BL28'] cif_block = h.as_cif_block() cif = iotbx.cif.model.cif() cif['test'] = cif_block cif.show(out=out, align_columns=True) lines = out.getvalue() assert " ATOM 20 OP2 . C B23S 172 ? 77.56000 39.38700 -72.10600 1.000 132.48000 O 1- B ? . 1" in lines if __name__ == "__main__": exercise()