from __future__ import division import iotbx.pdb from cctbx.array_family import flex from cctbx import adp_restraints # import dependency from mmtbx.torsion_restraints import torsion_ncs, utils import cStringIO pdb_str_1 = """ CRYST1 46.053 9.561 20.871 90.00 97.43 90.00 C 1 2 1 8 ATOM 1 N LYS A 1 8.669 0.060 3.795 1.00 12.85 N ATOM 2 CA LYS A 1 7.501 -0.641 4.336 1.00 11.37 C ATOM 3 C LYS A 1 6.186 0.030 3.984 1.00 11.88 C ATOM 4 O LYS A 1 6.176 1.208 3.641 1.00 11.02 O ATOM 5 CB LYS A 1 7.606 -0.792 5.871 1.00 15.61 C ATOM 6 CG LYS A 1 7.543 0.531 6.652 1.00 23.32 C ATOM 7 CD LYS A 1 8.894 0.917 7.175 1.00 22.74 C ATOM 8 CE LYS A 1 8.851 2.260 7.839 1.00 22.96 C ATOM 9 NZ LYS A 1 10.091 2.510 8.611 1.00 18.89 N ATOM 10 N LEU A 2 5.063 -0.702 4.139 1.00 8.33 N ATOM 11 CA LEU A 2 3.720 -0.164 3.917 1.00 8.69 C ATOM 12 C LEU A 2 2.701 -0.803 4.885 1.00 9.37 C ATOM 13 O LEU A 2 2.675 -2.017 5.019 1.00 8.16 O ATOM 14 CB LEU A 2 3.331 -0.407 2.441 1.00 9.53 C ATOM 15 CG LEU A 2 1.966 0.033 1.872 1.00 16.06 C ATOM 16 CD1 LEU A 2 0.773 -0.824 2.351 1.00 15.86 C ATOM 17 CD2 LEU A 2 1.747 1.479 1.927 1.00 17.67 C ATOM 18 N VAL A 3 1.856 0.019 5.527 1.00 6.29 N ATOM 19 CA VAL A 3 0.748 -0.404 6.386 1.00 6.45 C ATOM 20 C VAL A 3 -0.501 0.203 5.783 1.00 11.86 C ATOM 21 O VAL A 3 -0.569 1.425 5.609 1.00 10.67 O ATOM 22 CB VAL A 3 0.865 0.064 7.854 1.00 10.59 C ATOM 23 CG1 VAL A 3 -0.285 -0.493 8.710 1.00 10.71 C ATOM 24 CG2 VAL A 3 2.219 -0.288 8.450 1.00 10.64 C ATOM 25 N PHE A 4 -1.510 -0.637 5.537 1.00 8.41 N ATOM 26 CA PHE A 4 -2.797 -0.223 4.998 1.00 8.51 C ATOM 27 C PHE A 4 -3.900 -0.807 5.880 1.00 11.98 C ATOM 28 O PHE A 4 -3.871 -2.003 6.216 1.00 10.68 O ATOM 29 CB PHE A 4 -2.954 -0.769 3.564 1.00 9.14 C ATOM 30 CG PHE A 4 -4.317 -0.526 2.953 1.00 9.69 C ATOM 31 CD1 PHE A 4 -4.536 0.563 2.127 1.00 10.70 C ATOM 32 CD2 PHE A 4 -5.362 -1.422 3.159 1.00 12.10 C ATOM 33 CE1 PHE A 4 -5.787 0.791 1.562 1.00 11.47 C ATOM 34 CE2 PHE A 4 -6.618 -1.195 2.592 1.00 15.42 C ATOM 35 CZ PHE A 4 -6.815 -0.096 1.778 1.00 13.27 C ATOM 36 N PHE A 5 -4.902 0.009 6.183 1.00 8.96 N ATOM 37 CA PHE A 5 -6.081 -0.452 6.908 1.00 9.67 C ATOM 38 C PHE A 5 -7.304 0.208 6.324 1.00 13.65 C ATOM 39 O PHE A 5 -7.349 1.428 6.235 1.00 10.13 O ATOM 40 CB PHE A 5 -5.986 -0.239 8.445 1.00 11.19 C ATOM 41 CG PHE A 5 -7.306 -0.481 9.152 1.00 12.79 C ATOM 42 CD1 PHE A 5 -7.716 -1.766 9.473 1.00 16.12 C ATOM 43 CD2 PHE A 5 -8.156 0.580 9.457 1.00 15.48 C ATOM 44 CE1 PHE A 5 -8.953 -1.987 10.088 1.00 17.28 C ATOM 45 CE2 PHE A 5 -9.379 0.359 10.098 1.00 18.56 C ATOM 46 CZ PHE A 5 -9.771 -0.922 10.402 1.00 15.89 C ATOM 47 N ALA A 6 -8.282 -0.608 5.899 1.00 12.21 N ATOM 48 CA ALA A 6 -9.570 -0.134 5.389 1.00 15.49 C ATOM 49 C ALA A 6 -10.647 -0.909 6.127 1.00 31.54 C ATOM 50 O ALA A 6 -10.637 -2.159 6.058 1.00 33.30 O ATOM 51 CB ALA A 6 -9.677 -0.381 3.898 1.00 16.16 C ATOM 52 OXT ALA A 6 -11.417 -0.275 6.874 1.00 51.39 O TER 53 ALA A 6 ATOM 54 N LYS B 1 -10.065 -4.813 6.193 1.00 12.06 N ATOM 55 CA LYS B 1 -8.858 -5.207 5.451 1.00 12.29 C ATOM 56 C LYS B 1 -7.574 -4.609 6.062 1.00 12.37 C ATOM 57 O LYS B 1 -7.486 -3.387 6.205 1.00 7.97 O ATOM 58 CB LYS B 1 -8.985 -4.776 3.968 1.00 15.40 C ATOM 59 CG LYS B 1 -7.989 -5.451 3.027 1.00 27.98 C ATOM 60 CD LYS B 1 -8.475 -5.495 1.572 1.00 36.65 C ATOM 61 CE LYS B 1 -8.321 -4.183 0.829 1.00 51.92 C ATOM 62 NZ LYS B 1 -9.598 -3.419 0.783 1.00 65.39 N ATOM 63 N LEU B 2 -6.567 -5.463 6.352 1.00 8.53 N ATOM 64 CA LEU B 2 -5.275 -5.044 6.904 1.00 8.19 C ATOM 65 C LEU B 2 -4.174 -5.652 6.041 1.00 9.32 C ATOM 66 O LEU B 2 -4.161 -6.876 5.835 1.00 8.36 O ATOM 67 CB LEU B 2 -5.179 -5.546 8.364 1.00 9.24 C ATOM 68 CG LEU B 2 -4.127 -5.040 9.352 1.00 14.56 C ATOM 69 CD1 LEU B 2 -2.893 -5.867 9.314 1.00 16.64 C ATOM 70 CD2 LEU B 2 -3.873 -3.540 9.265 1.00 13.86 C ATOM 71 N VAL B 3 -3.293 -4.804 5.481 1.00 5.98 N ATOM 72 CA VAL B 3 -2.164 -5.264 4.671 1.00 4.31 C ATOM 73 C VAL B 3 -0.910 -4.581 5.178 1.00 8.02 C ATOM 74 O VAL B 3 -0.872 -3.349 5.309 1.00 7.46 O ATOM 75 CB VAL B 3 -2.312 -5.033 3.142 1.00 6.99 C ATOM 76 CG1 VAL B 3 -1.206 -5.781 2.368 1.00 6.50 C ATOM 77 CG2 VAL B 3 -3.696 -5.419 2.642 1.00 7.17 C ATOM 78 N PHE B 4 0.131 -5.371 5.389 1.00 4.71 N ATOM 79 CA PHE B 4 1.445 -4.868 5.777 1.00 5.68 C ATOM 80 C PHE B 4 2.526 -5.586 4.957 1.00 9.59 C ATOM 81 O PHE B 4 2.440 -6.805 4.790 1.00 9.76 O ATOM 82 CB PHE B 4 1.661 -5.087 7.288 1.00 7.35 C ATOM 83 CG PHE B 4 3.098 -5.169 7.735 1.00 10.11 C ATOM 84 CD1 PHE B 4 3.900 -4.033 7.765 1.00 14.40 C ATOM 85 CD2 PHE B 4 3.655 -6.388 8.121 1.00 13.08 C ATOM 86 CE1 PHE B 4 5.239 -4.115 8.153 1.00 16.51 C ATOM 87 CE2 PHE B 4 4.988 -6.466 8.532 1.00 17.07 C ATOM 88 CZ PHE B 4 5.770 -5.324 8.557 1.00 16.28 C ATOM 89 N PHE B 5 3.546 -4.840 4.448 1.00 7.84 N ATOM 90 CA PHE B 5 4.703 -5.447 3.782 1.00 6.46 C ATOM 91 C PHE B 5 5.938 -4.609 3.941 1.00 10.69 C ATOM 92 O PHE B 5 5.830 -3.420 4.235 1.00 8.77 O ATOM 93 CB PHE B 5 4.457 -5.846 2.320 1.00 8.36 C ATOM 94 CG PHE B 5 3.975 -4.763 1.395 1.00 8.12 C ATOM 95 CD1 PHE B 5 4.873 -3.877 0.812 1.00 10.77 C ATOM 96 CD2 PHE B 5 2.629 -4.640 1.092 1.00 8.53 C ATOM 97 CE1 PHE B 5 4.421 -2.862 -0.036 1.00 11.77 C ATOM 98 CE2 PHE B 5 2.170 -3.607 0.275 1.00 11.24 C ATOM 99 CZ PHE B 5 3.073 -2.744 -0.307 1.00 10.01 C ATOM 100 N ALA B 6 7.120 -5.247 3.770 1.00 10.09 N ATOM 101 CA ALA B 6 8.448 -4.651 3.900 1.00 12.61 C ATOM 102 C ALA B 6 9.483 -5.594 3.319 1.00 36.73 C ATOM 103 O ALA B 6 9.457 -6.801 3.661 1.00 40.97 O ATOM 104 CB ALA B 6 8.760 -4.382 5.366 1.00 13.92 C ATOM 105 OXT ALA B 6 10.304 -5.128 2.503 1.00 60.32 O TER 106 ALA B 6 """ def exercise_1(): log = cStringIO.StringIO() dihedral_proxies = utils.get_complete_dihedral_proxies( raw_records=pdb_str_1) assert len(dihedral_proxies) == 54 pdb_hierarchy = iotbx.pdb.input( source_info=None, lines=flex.split_lines(pdb_str_1)).construct_hierarchy() ncs_manager = torsion_ncs.torsion_ncs( pdb_hierarchy=pdb_hierarchy, log=log) assert len(ncs_manager.ncs_dihedral_proxies) == 46 if (__name__ == "__main__") : exercise_1() print "OK"