from __future__ import division from mmtbx.secondary_structure import sec_str_master_phil, manager from mmtbx.secondary_structure.base_pairing import pair_database from mmtbx.geometry_restraints import hbond from iotbx import file_reader import iotbx.pdb.hierarchy import libtbx.load_env import iotbx.pdb.secondary_structure as ioss from libtbx.utils import null_out import os def exercise_protein () : pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/1ywf.pdb", test=os.path.isfile) pdb_file_h = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/1ywf_h.pdb", test=os.path.isfile) if pdb_file is None : print "Skipping exercise(): input file not available." return False if pdb_file_h is None : print "Skipping exercise(): input file not available." return False run_ksdssp = True if (not libtbx.env.has_module(name="ksdssp")): print "Skipping KSDSSP tests: ksdssp module not available." run_ksdssp = False log = null_out() expected_distances = [2.9, 1.975] for k, file_name in enumerate([pdb_file, pdb_file_h]) : pdb_in = file_reader.any_file(file_name, force_type="pdb").file_object pdb_hierarchy = pdb_in.hierarchy sec_str_from_pdb_file = pdb_in.input.extract_secondary_structure() m = manager(pdb_hierarchy=pdb_hierarchy, sec_str_from_pdb_file=sec_str_from_pdb_file) m.find_automatically(log=log) m.params.h_bond_restraints.remove_outliers = False hbond_params = hbond.master_phil.extract() build_proxies = m.create_hbond_proxies(hbond_params=hbond_params, log=log) proxies = build_proxies.proxies assert (len(proxies) == len(build_proxies.exclude_nb_list) == 109) assert (type(proxies[0]).__name__ == "h_bond_simple_proxy") assert (proxies[0].distance_ideal == expected_distances[k]) (frac_alpha, frac_beta) = m.calculate_structure_content() assert ("%.3f" % frac_alpha == "0.643") assert ("%.3f" % frac_beta == "0.075") # Make sure the hydrogen auto-detection override is working m.params.h_bond_restraints.substitute_n_for_h = True build_proxies = m.create_hbond_proxies( log=log, as_python_objects=True) proxies = build_proxies.proxies atom_ids = [] for i_seq in proxies[0].i_seqs : atom_ids.append(pdb_hierarchy.atoms()[i_seq].id_str()) assert (atom_ids == ['pdb=" N ARG A 41 "', 'pdb=" O ASP A 37 "']) assert (proxies[0].distance_ideal == 2.9) if (run_ksdssp) : m = manager(pdb_hierarchy=pdb_hierarchy, sec_str_from_pdb_file=None) m.find_automatically(log=log) m.params.h_bond_restraints.remove_outliers = False hbond_params.restraint_type = "simple" build_proxies = m.create_hbond_proxies(hbond_params=hbond_params, log=log) assert (build_proxies.proxies.size() == 90) def exercise_nucleic_acids () : pdb_file_rna = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/1u8d.pdb", test=os.path.isfile) pdb_file_dna = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/dnatest.pdb", test=os.path.isfile) if (pdb_file_rna is None) : print "Skipping exercise_nucleic_acids(): input file not available." return False # Nucleic acids (requires REDUCE and PROBE) if (libtbx.env.has_module(name="reduce") and libtbx.env.has_module(name="probe")): pdb_in = file_reader.any_file(pdb_file_rna, force_type="pdb").file_object pdb_hierarchy = pdb_in.hierarchy sec_str_from_pdb_file = pdb_in.input.extract_secondary_structure() m = manager(pdb_hierarchy=pdb_hierarchy, sec_str_from_pdb_file=sec_str_from_pdb_file) log = null_out() m.find_automatically(log=log) build_proxies = m.create_hbond_proxies(log=log) assert (build_proxies.proxies.size() == 70) db = pair_database() assert (db.get_atoms("A-U", "WWT", True) == [('H61', 'O4'), ('N1', 'H3')]) assert (db.get_atoms("DA-DT", "WWT", False) == [('N6', 'O4'), ('N1', 'N3')]) assert (db.get_atoms("DT-DA", "WWT", False) == [('O4', 'N6'), ('N3', 'N1')]) assert (db.get_atoms("G-C", "WWT", False) == [('O6', 'N4'), ('N1', 'N3'), ('N2', 'O2')]) assert (db.get_atoms("C-G", "WWT", False) == [('N4', 'O6'), ('N3', 'N1'), ('O2', 'N2')]) assert db.get_pair_type("A-U", [('H61', 'O4'), ('N1', 'H3')], True) == "XX" assert db.get_pair_type("A-U", [('N1', 'H3'), ('H61', 'O4')], True) == "XX" assert db.get_pair_type("C-G", [('N4', 'O6'), ('N3', 'N1'), ('O2', 'N2')], False) == "XIX" # DNA pdb_in = file_reader.any_file(pdb_file_dna, force_type="pdb").file_object pdb_hierarchy = pdb_in.hierarchy sec_str_from_pdb_file = pdb_in.input.extract_secondary_structure() m = manager(pdb_hierarchy=pdb_hierarchy, sec_str_from_pdb_file=sec_str_from_pdb_file) log = null_out() m.find_automatically(log=log) assert (len(m.params.nucleic_acids.base_pair) == 4) else: print "Skipping base-pairing tests: reduce or probe module not available." pass def exercise_sheet_ends () : pdb_in = iotbx.pdb.hierarchy.input(pdb_string="""\ ATOM 1 N ALA A 37 27.738 -0.961 14.033 1.00 20.00 N ATOM 2 CA ALA A 37 27.940 0.419 14.337 1.00 20.00 C ATOM 3 C ALA A 37 26.683 0.986 14.948 1.00 20.00 C ATOM 4 O ALA A 37 26.735 1.984 15.528 1.00 20.00 O ATOM 5 CB ALA A 37 28.398 1.219 13.140 1.00 20.00 C ATOM 6 N ALA A 38 25.588 0.264 14.880 1.00 20.00 N ATOM 7 CA ALA A 38 24.384 0.731 15.506 1.00 20.00 C ATOM 8 C ALA A 38 23.201 0.011 14.926 1.00 20.00 C ATOM 9 O ALA A 38 23.327 -1.063 14.341 1.00 20.00 O ATOM 10 N ALA A 39 22.037 0.615 15.074 1.00 20.00 N ATOM 11 CA ALA A 39 20.822 -0.033 14.646 1.00 20.00 C ATOM 12 C ALA A 39 19.950 0.873 13.809 1.00 20.00 C ATOM 13 O ALA A 39 20.035 2.092 13.903 1.00 20.00 O ATOM 14 CB ALA A 39 20.054 -0.530 15.864 1.00 20.00 C ATOM 15 N ALA A 40 19.119 0.270 12.969 1.00 20.00 N ATOM 16 CA ALA A 40 18.164 1.039 12.204 1.00 20.00 C ATOM 17 C ALA A 40 16.761 0.571 12.489 1.00 20.00 C ATOM 18 O ALA A 40 16.444 -0.583 12.263 1.00 20.00 O ATOM 19 CB ALA A 40 18.436 0.930 10.717 1.00 20.00 C ATOM 20 N ALA A 41 15.938 1.493 12.973 1.00 20.00 N ATOM 21 CA ALA A 41 14.533 1.270 13.264 1.00 20.00 C ATOM 22 C ALA A 41 13.658 1.820 12.148 1.00 20.00 C ATOM 23 O ALA A 41 13.680 3.008 11.883 1.00 20.00 O ATOM 24 CB ALA A 41 14.135 1.952 14.582 1.00 20.00 C ATOM 25 N ALA A 42 12.897 0.961 11.489 1.00 20.00 N ATOM 26 CA ALA A 42 11.938 1.402 10.495 1.00 20.00 C ATOM 27 C ALA A 42 10.559 1.417 11.119 1.00 20.00 C ATOM 28 O ALA A 42 10.172 0.468 11.765 1.00 20.00 O ATOM 29 N ALA A 43 9.825 2.465 10.888 1.00 20.00 N ATOM 30 CA ALA A 43 8.546 2.641 11.492 1.00 20.00 C ATOM 31 C ALA A 43 7.468 3.106 10.585 1.00 20.00 C ATOM 32 O ALA A 43 7.710 3.854 9.738 1.00 20.00 O ATOM 33 CB ALA A 43 8.646 3.437 12.767 1.00 20.00 C ATOM 34 N ALA A 44 6.285 2.569 10.752 1.00 20.00 N ATOM 35 CA ALA A 44 5.209 2.771 9.823 1.00 20.00 C ATOM 36 C ALA A 44 3.822 2.663 10.467 1.00 20.00 C ATOM 37 O ALA A 44 3.610 1.972 11.406 1.00 20.00 O ATOM 38 CB ALA A 44 5.381 1.912 8.510 1.00 20.00 C ATOM 39 N ALA A 45 2.883 3.390 9.914 1.00 20.00 N ATOM 40 CA ALA A 45 1.539 3.355 10.375 1.00 20.00 C ATOM 41 C ALA A 45 0.845 2.276 9.614 1.00 20.00 C ATOM 42 O ALA A 45 1.284 1.970 8.558 1.00 20.00 O ATOM 43 CB ALA A 45 0.868 4.648 10.084 1.00 20.00 C ATOM 44 N ALA A 74 -2.478 6.652 17.490 1.00 20.00 N ATOM 45 CA ALA A 74 -2.170 5.880 16.289 1.00 20.00 C ATOM 46 C ALA A 74 -1.360 4.598 16.476 1.00 20.00 C ATOM 47 O ALA A 74 -0.341 4.581 17.153 1.00 20.00 O ATOM 48 CB ALA A 74 -1.405 6.748 15.290 1.00 20.00 C ATOM 49 N ALA A 75 -1.809 3.528 15.830 1.00 20.00 N ATOM 50 CA ALA A 75 -1.038 2.294 15.762 1.00 20.00 C ATOM 51 C ALA A 75 0.178 2.394 14.825 1.00 20.00 C ATOM 52 O ALA A 75 0.029 2.691 13.638 1.00 20.00 O ATOM 53 CB ALA A 75 -1.942 1.143 15.310 1.00 20.00 C ATOM 54 N ALA A 76 1.369 2.129 15.363 1.00 20.00 N ATOM 55 CA ALA A 76 2.612 2.062 14.578 1.00 20.00 C ATOM 56 C ALA A 76 3.222 0.655 14.618 1.00 20.00 C ATOM 57 O ALA A 76 3.065 -0.086 15.584 1.00 20.00 O ATOM 58 CB ALA A 76 3.655 3.064 15.089 1.00 20.00 C ATOM 59 N ALA A 77 3.933 0.308 13.558 1.00 20.00 N ATOM 60 CA ALA A 77 4.639 -0.950 13.487 1.00 20.00 C ATOM 61 C ALA A 77 6.146 -0.691 13.381 1.00 20.00 C ATOM 62 O ALA A 77 6.547 0.319 12.808 1.00 20.00 O ATOM 63 CB ALA A 77 4.125 -1.752 12.300 1.00 20.00 C ATOM 64 N ALA A 78 6.978 -1.586 13.921 1.00 20.00 N ATOM 65 CA ALA A 78 8.426 -1.349 13.964 1.00 20.00 C ATOM 66 C ALA A 78 9.300 -2.568 13.613 1.00 20.00 C ATOM 67 O ALA A 78 8.926 -3.706 13.886 1.00 20.00 O ATOM 68 CB ALA A 78 8.844 -0.866 15.364 1.00 20.00 C ATOM 69 N ALA A 79 10.475 -2.320 13.029 1.00 20.00 N ATOM 70 CA ALA A 79 11.544 -3.327 12.991 1.00 20.00 C ATOM 71 C ALA A 79 12.910 -2.716 13.258 1.00 20.00 C ATOM 72 O ALA A 79 13.172 -1.578 12.910 1.00 20.00 O ATOM 73 CB ALA A 79 11.648 -4.067 11.649 1.00 20.00 C ATOM 74 N ALA A 80 13.783 -3.507 13.858 1.00 20.00 N ATOM 75 CA ALA A 80 15.135 -3.088 14.163 1.00 20.00 C ATOM 76 C ALA A 80 16.153 -4.001 13.478 1.00 20.00 C ATOM 77 O ALA A 80 16.078 -5.224 13.575 1.00 20.00 O ATOM 78 CB ALA A 80 15.395 -3.117 15.671 1.00 20.00 C ATOM 79 N ALA A 81 17.119 -3.408 12.798 1.00 20.00 N ATOM 80 CA ALA A 81 18.232 -4.178 12.289 1.00 20.00 C ATOM 81 C ALA A 81 19.542 -3.491 12.560 1.00 20.00 C ATOM 82 O ALA A 81 19.643 -2.276 12.472 1.00 20.00 O ATOM 83 CB ALA A 81 18.067 -4.425 10.802 1.00 20.00 C ATOM 84 N ALA A 82 20.541 -4.285 12.908 1.00 20.00 N ATOM 85 CA ALA A 82 21.892 -3.793 13.044 1.00 20.00 C ATOM 86 C ALA A 82 22.410 -3.375 11.697 1.00 20.00 C ATOM 87 O ALA A 82 21.897 -3.798 10.685 1.00 20.00 O ATOM 88 CB ALA A 82 22.786 -4.846 13.647 1.00 20.00 C ATOM 89 N ALA A 83 23.426 -2.532 11.679 1.00 20.00 N ATOM 90 CA ALA A 83 24.083 -2.208 10.429 1.00 20.00 C ATOM 91 C ALA A 83 25.543 -2.018 10.735 1.00 20.00 C ATOM 92 O ALA A 83 25.905 -1.692 11.853 1.00 20.00 O ATOM 93 CB ALA A 83 23.488 -0.951 9.765 1.00 20.00 C ATOM 94 N ALA A 84 26.388 -2.269 9.753 1.00 20.00 N ATOM 95 CA ALA A 84 27.766 -1.859 9.852 1.00 20.00 C ATOM 96 C ALA A 84 28.199 -1.539 8.456 1.00 20.00 C ATOM 97 O ALA A 84 27.350 -1.415 7.580 1.00 20.00 O ATOM 98 CB ALA A 84 28.646 -2.929 10.507 1.00 20.00 C ATOM 99 N ALA A 94 8.539 -8.036 13.764 1.00 20.00 N ATOM 100 CA ALA A 94 7.784 -6.815 13.849 1.00 20.00 C ATOM 101 C ALA A 94 7.141 -6.661 15.220 1.00 20.00 C ATOM 102 O ALA A 94 6.628 -7.611 15.776 1.00 20.00 O ATOM 103 CB ALA A 94 6.745 -6.817 12.744 1.00 20.00 C ATOM 104 N ALA A 95 7.188 -5.460 15.782 1.00 20.00 N ATOM 105 CA ALA A 95 6.447 -5.181 17.013 1.00 20.00 C ATOM 106 C ALA A 95 5.605 -3.906 16.830 1.00 20.00 C ATOM 107 O ALA A 95 5.855 -3.110 15.933 1.00 20.00 O ATOM 108 CB ALA A 95 7.387 -5.044 18.220 1.00 20.00 C ATOM 109 N ALA A 96 4.581 -3.743 17.658 1.00 20.00 N ATOM 110 CA ALA A 96 3.609 -2.664 17.488 1.00 20.00 C ATOM 111 C ALA A 96 3.285 -1.911 18.775 1.00 20.00 C ATOM 112 O ALA A 96 3.129 -2.501 19.839 1.00 20.00 O ATOM 113 CB ALA A 96 2.316 -3.219 16.906 1.00 20.00 C ATOM 114 N ALA A 97 3.188 -0.599 18.670 1.00 20.00 N ATOM 115 CA ALA A 97 2.653 0.184 19.763 1.00 20.00 C ATOM 116 C ALA A 97 1.705 1.289 19.259 1.00 20.00 C ATOM 117 O ALA A 97 1.820 1.731 18.115 1.00 20.00 O ATOM 118 CB ALA A 97 3.779 0.765 20.569 1.00 20.00 C ATOM 119 N ALA A 98 0.739 1.686 20.047 1.00 20.00 N ATOM 120 CA ALA A 98 -0.189 2.723 19.701 1.00 20.00 C ATOM 121 C ALA A 98 0.076 3.866 20.555 1.00 20.00 C ATOM 122 O ALA A 98 0.025 3.751 21.692 1.00 20.00 O ATOM 123 CB ALA A 98 -1.627 2.343 20.021 1.00 20.00 C """) pdb_hierarchy = pdb_in.hierarchy pdb_hierarchy.atoms().reset_i_seq() m = manager(pdb_hierarchy=pdb_hierarchy, sec_str_from_pdb_file=None) m.params.input.use_ksdssp = False m.find_automatically(log=null_out()) m.params.h_bond_restraints.remove_outliers = False hbond_params = hbond.master_phil.extract() build_proxies = m.create_hbond_proxies(hbond_params=hbond_params, log=null_out()) proxies = build_proxies.proxies assert len(proxies) == 12 def exercise_sheets_bonding_pattern(): pdb_apar_input = iotbx.pdb.hierarchy.input(pdb_string = """\ SCRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1 SCALE1 0.021524 0.012427 0.000000 0.00000 SCALE2 0.000000 0.024854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005176 0.00000 ATOM 1 N GLY A 1 28.066 -23.487 2.817 1.00 16.21 N ATOM 2 CA GLY A 1 27.219 -22.652 1.936 1.00 13.03 C ATOM 3 C GLY A 1 27.859 -21.336 1.546 1.00 9.56 C ATOM 4 O GLY A 1 28.868 -20.882 2.096 1.00 12.48 O ATOM 5 N TYR A 2 27.208 -20.701 0.590 1.00 7.29 N ATOM 6 CA TYR A 2 27.617 -19.424 0.052 1.00 7.96 C ATOM 7 C TYR A 2 26.483 -18.436 0.263 1.00 6.87 C ATOM 8 O TYR A 2 25.303 -18.771 0.249 1.00 6.97 O ATOM 9 CB TYR A 2 27.861 -19.541 -1.451 1.00 7.90 C ATOM 10 CG TYR A 2 28.902 -20.556 -1.857 1.00 9.09 C ATOM 11 CD1 TYR A 2 30.255 -20.336 -1.592 1.00 11.43 C ATOM 12 CD2 TYR A 2 28.566 -21.697 -2.545 1.00 10.59 C ATOM 13 CE1 TYR A 2 31.227 -21.244 -1.987 1.00 13.93 C ATOM 14 CE2 TYR A 2 29.518 -22.630 -2.915 1.00 11.76 C ATOM 15 CZ TYR A 2 30.847 -22.395 -2.659 1.00 13.67 C ATOM 16 OH TYR A 2 31.792 -23.309 -3.059 1.00 18.26 O ATOM 17 N SER A 3 26.854 -17.177 0.412 1.00 6.66 N ATOM 18 CA SER A 3 25.899 -16.083 0.383 0.53 6.83 C ATOM 20 C SER A 3 26.500 -14.946 -0.440 1.00 5.61 C ATOM 21 O SER A 3 27.729 -14.822 -0.565 1.00 8.14 O ATOM 22 CB SER A 3 25.569 -15.634 1.795 0.53 7.38 C ATOM 24 OG SER A 3 26.740 -15.136 2.390 0.53 9.79 O ATOM 26 N CYS A 4 25.627 -14.135 -0.995 1.00 5.11 N ATOM 27 CA CYS A 4 26.070 -13.062 -1.865 1.00 5.65 C ATOM 28 C CYS A 4 25.043 -11.934 -1.798 1.00 4.54 C ATOM 29 O CYS A 4 23.856 -12.180 -1.528 1.00 5.60 O ATOM 30 CB CYS A 4 26.253 -13.557 -3.295 1.00 7.00 C ATOM 31 SG CYS A 4 24.806 -14.269 -4.119 1.00 8.88 S ATOM 32 N ARG A 5 25.486 -10.691 -2.002 1.00 4.69 N ATOM 33 CA ARG A 5 24.558 -9.545 -2.064 1.00 4.87 C ATOM 34 C ARG A 5 25.196 -8.395 -2.796 1.00 4.57 C ATOM 35 O ARG A 5 26.416 -8.238 -2.793 1.00 5.50 O ATOM 36 CB ARG A 5 24.061 -9.108 -0.700 1.00 6.43 C ATOM 37 CG ARG A 5 25.121 -8.566 0.219 1.00 6.96 C ATOM 38 CD ARG A 5 24.461 -8.032 1.494 1.00 7.25 C ATOM 39 NE ARG A 5 25.452 -7.547 2.440 1.00 7.63 N ATOM 40 CZ ARG A 5 26.107 -8.341 3.280 1.00 9.10 C ATOM 41 NH1 ARG A 5 25.867 -9.642 3.297 1.00 9.68 N ATOM 42 NH2 ARG A 5 26.974 -7.836 4.146 1.00 10.30 N ATOM 43 N ALA A 6 24.325 -7.563 -3.358 1.00 4.39 N ATOM 44 CA ALA A 6 24.723 -6.362 -4.067 1.00 4.73 C ATOM 45 C ALA A 6 23.693 -5.275 -3.769 1.00 4.15 C ATOM 46 O ALA A 6 22.482 -5.458 -3.987 1.00 4.96 O ATOM 47 CB ALA A 6 24.831 -6.626 -5.558 1.00 5.96 C ATOM 48 N VAL A 7 24.165 -4.139 -3.284 1.00 4.97 N ATOM 49 CA VAL A 7 23.374 -2.917 -3.085 1.00 4.42 C ATOM 50 C VAL A 7 23.482 -2.046 -4.325 1.00 4.45 C ATOM 51 O VAL A 7 24.589 -1.663 -4.717 1.00 5.55 O ATOM 52 CB VAL A 7 23.830 -2.159 -1.806 1.00 5.09 C ATOM 53 CG1 VAL A 7 23.111 -0.842 -1.686 1.00 5.65 C ATOM 54 CG2 VAL A 7 23.612 -2.998 -0.570 1.00 6.88 C ATOM 204 N MET A 31 18.177 -3.966 -4.656 1.00 4.72 N ATOM 205 CA MET A 31 18.833 -4.887 -3.744 1.00 5.29 C ATOM 206 C MET A 31 18.765 -6.294 -4.322 1.00 4.60 C ATOM 207 O MET A 31 17.661 -6.738 -4.657 1.00 4.98 O ATOM 208 CB MET A 31 18.097 -4.868 -2.387 1.00 6.39 C ATOM 209 CG MET A 31 18.723 -5.755 -1.334 1.00 8.61 C ATOM 210 SD MET A 31 20.248 -5.074 -0.655 1.00 11.04 S ATOM 211 CE MET A 31 21.358 -6.427 -0.777 1.00 8.94 C ATOM 212 N ALA A 32 19.899 -6.986 -4.412 1.00 3.90 N ATOM 213 CA ALA A 32 19.934 -8.380 -4.864 1.00 3.55 C ATOM 214 C ALA A 32 20.720 -9.194 -3.858 1.00 3.90 C ATOM 215 O ALA A 32 21.762 -8.763 -3.393 1.00 5.01 O ATOM 216 CB ALA A 32 20.552 -8.500 -6.255 1.00 4.55 C ATOM 217 N SER A 33 20.230 -10.407 -3.567 1.00 4.02 N ATOM 218 CA SER A 33 20.980 -11.288 -2.645 1.00 3.79 C ATOM 219 C SER A 33 20.591 -12.727 -2.850 1.00 4.33 C ATOM 220 O SER A 33 19.532 -13.045 -3.412 1.00 4.84 O ATOM 221 CB SER A 33 20.830 -10.880 -1.167 1.00 4.55 C ATOM 222 OG SER A 33 19.498 -11.105 -0.710 1.00 5.25 O ATOM 223 N GLY A 34 21.415 -13.600 -2.283 1.00 4.96 N ATOM 224 CA GLY A 34 21.104 -14.997 -2.335 1.00 4.50 C ATOM 225 C GLY A 34 21.914 -15.837 -1.397 1.00 4.64 C ATOM 226 O GLY A 34 22.836 -15.343 -0.732 1.00 4.96 O ATOM 227 N THR A 35 21.521 -17.105 -1.329 1.00 4.35 N ATOM 228 CA THR A 35 22.277 -18.138 -0.654 1.00 4.02 C ATOM 229 C THR A 35 22.226 -19.392 -1.495 1.00 4.55 C ATOM 230 O THR A 35 21.221 -19.652 -2.170 1.00 4.35 O ATOM 231 CB THR A 35 21.715 -18.436 0.762 1.00 5.12 C ATOM 232 OG1 THR A 35 20.356 -18.929 0.668 1.00 5.51 O ATOM 233 CG2 THR A 35 21.733 -17.222 1.670 1.00 5.97 C ATOM 234 N SER A 36 23.294 -20.178 -1.426 1.00 4.63 N ATOM 235 CA SER A 36 23.402 -21.406 -2.221 1.00 4.58 C ATOM 236 C SER A 36 24.387 -22.368 -1.553 1.00 5.05 C ATOM 237 O SER A 36 24.929 -22.095 -0.497 1.00 6.22 O ATOM 238 CB SER A 36 23.881 -21.071 -3.639 1.00 5.69 C ATOM 239 OG SER A 36 25.213 -20.561 -3.633 1.00 7.12 O """) pdb_par_input = iotbx.pdb.hierarchy.input(pdb_string = """\ CRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1 SCALE1 0.021524 0.012427 0.000000 0.00000 SCALE2 0.000000 0.024854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005176 0.00000 ATOM 67 N ALA A 15 5.011 -5.031 -8.967 1.00 5.73 N ATOM 68 CA ALA A 15 4.943 -6.455 -9.287 1.00 6.16 C ATOM 69 C ALA A 15 5.610 -7.252 -8.166 1.00 6.39 C ATOM 70 O ALA A 15 6.751 -7.007 -7.857 1.00 9.87 O ATOM 71 CB ALA A 15 5.684 -6.739 -10.604 1.00 7.46 C ATOM 72 N THR A 16 4.929 -8.263 -7.636 1.00 5.49 N ATOM 73 C THR A 16 5.316 -10.600 -7.084 1.00 5.07 C ATOM 74 O THR A 16 4.214 -11.002 -7.422 1.00 6.51 O ATOM 75 CA THR A 16 5.513 -9.172 -6.657 1.00 5.70 C ATOM 76 CB THR A 16 4.864 -9.001 -5.276 1.00 8.31 C ATOM 77 N GLY A 17 6.393 -11.375 -7.067 1.00 4.56 N ATOM 78 CA GLY A 17 6.325 -12.770 -7.439 1.00 4.26 C ATOM 79 C GLY A 17 7.219 -13.654 -6.621 1.00 4.41 C ATOM 80 O GLY A 17 8.263 -13.233 -6.114 1.00 5.01 O ATOM 81 N SER A 18 6.827 -14.921 -6.561 1.00 4.24 N ATOM 82 CA SER A 18 7.657 -15.945 -5.959 1.00 4.02 C ATOM 83 C SER A 18 7.539 -17.244 -6.724 1.00 3.64 C ATOM 84 O SER A 18 6.482 -17.526 -7.331 1.00 4.07 O ATOM 85 CB SER A 18 7.335 -16.157 -4.481 1.00 5.86 C ATOM 86 N ALA A 19 8.573 -18.049 -6.627 1.00 3.19 N ATOM 87 CA ALA A 19 8.578 -19.414 -7.195 1.00 3.31 C ATOM 88 C ALA A 19 9.370 -20.307 -6.238 1.00 3.20 C ATOM 89 O ALA A 19 10.484 -19.956 -5.817 1.00 4.21 O ATOM 90 CB ALA A 19 9.235 -19.415 -8.574 1.00 3.85 C ATOM 91 N THR A 20 8.825 -21.476 -5.940 1.00 3.77 N ATOM 92 CA THR A 20 9.478 -22.432 -5.047 1.00 3.70 C ATOM 93 C THR A 20 9.444 -23.827 -5.640 1.00 3.56 C ATOM 94 O THR A 20 8.383 -24.281 -6.108 1.00 4.14 O ATOM 95 CB THR A 20 8.787 -22.430 -3.673 1.00 4.76 C ATOM 96 N THR A 21 10.560 -24.542 -5.569 1.00 4.00 N ATOM 97 CA THR A 21 10.597 -25.962 -5.876 1.00 4.05 C ATOM 98 C THR A 21 10.984 -26.770 -4.636 1.00 4.53 C ATOM 99 O THR A 21 11.770 -26.361 -3.802 1.00 5.04 O ATOM 100 CB THR A 21 11.488 -26.293 -7.083 1.00 4.38 C ATOM 189 N GLN A 40 0.280 -6.099 -9.049 1.00 6.35 N ATOM 190 CA GLN A 40 0.087 -7.454 -9.580 1.00 6.35 C ATOM 191 C GLN A 40 0.964 -8.417 -8.788 1.00 6.09 C ATOM 192 O GLN A 40 2.080 -8.093 -8.393 1.00 6.87 O ATOM 193 CB GLN A 40 0.461 -7.523 -11.060 1.00 7.52 C ATOM 194 N THR A 41 0.419 -9.596 -8.544 1.00 6.66 N ATOM 195 CA THR A 41 1.108 -10.640 -7.800 1.00 6.93 C ATOM 196 C THR A 41 0.932 -12.005 -8.414 1.00 6.82 C ATOM 197 O THR A 41 -0.069 -12.258 -9.104 1.00 8.79 O ATOM 198 CB THR A 41 0.633 -10.636 -6.352 1.00 10.84 C ATOM 199 N ALA A 42 1.951 -12.847 -8.263 1.00 6.44 N ATOM 200 CA ALA A 42 1.923 -14.209 -8.797 1.00 6.59 C ATOM 201 C ALA A 42 2.829 -15.117 -7.992 1.00 5.51 C ATOM 202 O ALA A 42 3.835 -14.684 -7.420 1.00 5.94 O ATOM 203 CB ALA A 42 2.327 -14.218 -10.264 1.00 9.02 C ATOM 204 N LYS A 43 2.479 -16.398 -7.978 1.00 6.26 N ATOM 205 CA LYS A 43 3.247 -17.395 -7.256 1.00 6.48 C ATOM 206 C LYS A 43 3.186 -18.741 -7.955 1.00 5.78 C ATOM 207 O LYS A 43 2.206 -19.041 -8.623 1.00 9.40 O ATOM 208 CB LYS A 43 2.727 -17.535 -5.836 1.00 8.81 C ATOM 209 N SER A 44 4.243 -19.534 -7.818 1.00 4.43 N ATOM 210 CA SER A 44 4.241 -20.890 -8.325 1.00 4.28 C ATOM 211 C SER A 44 4.998 -21.811 -7.358 1.00 4.09 C ATOM 212 O SER A 44 5.865 -21.377 -6.584 1.00 4.53 O ATOM 213 CB SER A 44 4.831 -20.949 -9.731 1.00 5.33 C ATOM 214 N PHE A 45 4.660 -23.091 -7.444 1.00 4.39 N ATOM 215 CA PHE A 45 5.198 -24.135 -6.576 1.00 4.44 C ATOM 216 C PHE A 45 5.222 -25.415 -7.389 1.00 4.16 C ATOM 217 O PHE A 45 4.183 -25.754 -7.979 1.00 5.11 O ATOM 218 CB PHE A 45 4.254 -24.281 -5.370 1.00 5.22 C ATOM 219 N ALA A 46 6.347 -26.119 -7.403 1.00 3.62 N ATOM 220 CA ALA A 46 6.443 -27.338 -8.202 1.00 3.99 C ATOM 221 C ALA A 46 7.579 -28.205 -7.717 1.00 4.57 C ATOM 222 O ALA A 46 8.479 -27.750 -7.000 1.00 4.79 O ATOM 223 CB ALA A 46 6.607 -27.026 -9.678 1.00 4.52 C TER END """) pdb_apar2_input = iotbx.pdb.hierarchy.input(pdb_string = """\ CRYST1 172.640 172.640 172.640 90.00 90.00 90.00 P 1 ATOM 2094 C ASP N 271 109.854 129.638 88.152 1.00 0.00 C ATOM 2095 CA ASP N 271 108.849 130.718 87.818 1.00 0.00 C ATOM 2096 CB ASP N 271 109.517 131.848 87.048 1.00 0.00 C ATOM 2097 CG ASP N 271 108.534 132.901 86.590 1.00 0.00 C ATOM 2098 N ASP N 271 108.279 131.208 89.060 1.00 0.00 N ATOM 2099 O ASP N 271 110.669 129.804 89.047 1.00 0.00 O ATOM 2100 OD1 ASP N 271 107.322 132.611 86.550 1.00 0.00 O ATOM 2101 OD2 ASP N 271 108.973 134.031 86.298 1.00 0.00 O ATOM 2102 C LYS N 272 111.760 127.262 86.697 1.00 0.00 C ATOM 2103 CA LYS N 272 110.671 127.408 87.746 1.00 0.00 C ATOM 2104 CB LYS N 272 109.854 126.123 87.810 1.00 0.00 C ATOM 2105 CD LYS N 272 108.904 126.401 90.106 1.00 0.00 C ATOM 2106 CE LYS N 272 107.623 126.322 90.905 1.00 0.00 C ATOM 2107 CG LYS N 272 108.611 126.182 88.660 1.00 0.00 C ATOM 2108 N LYS N 272 109.816 128.535 87.424 1.00 0.00 N ATOM 2109 NZ LYS N 272 107.845 126.530 92.350 1.00 0.00 N ATOM 2110 O LYS N 272 111.665 126.402 85.830 1.00 0.00 O ATOM 2111 C ILE N 273 114.616 126.730 85.969 1.00 0.00 C ATOM 2112 CA ILE N 273 113.831 127.992 85.732 1.00 0.00 C ATOM 2113 CB ILE N 273 114.800 129.181 85.738 1.00 0.00 C ATOM 2114 CD1 ILE N 273 116.646 130.274 87.071 1.00 0.00 C ATOM 2115 CG1 ILE N 273 115.554 129.250 87.064 1.00 0.00 C ATOM 2116 CG2 ILE N 273 114.064 130.470 85.480 1.00 0.00 C ATOM 2117 N ILE N 273 112.790 128.090 86.749 1.00 0.00 N ATOM 2118 O ILE N 273 114.607 126.208 87.067 1.00 0.00 O ATOM 2119 C SER N 274 117.460 125.414 84.290 1.00 0.00 C ATOM 2120 CA SER N 274 116.236 125.152 85.140 1.00 0.00 C ATOM 2121 CB SER N 274 115.642 123.795 84.795 1.00 0.00 C ATOM 2122 N SER N 274 115.266 126.216 84.935 1.00 0.00 N ATOM 2123 O SER N 274 117.336 125.793 83.133 1.00 0.00 O ATOM 2124 OG SER N 274 115.345 123.724 83.415 1.00 0.00 O ATOM 2125 C PHE N 275 120.234 124.460 83.057 1.00 0.00 C ATOM 2126 CA PHE N 275 119.856 125.505 84.086 1.00 0.00 C ATOM 2127 CB PHE N 275 121.036 125.723 85.016 1.00 0.00 C ATOM 2128 CD1 PHE N 275 120.424 128.127 85.038 1.00 0.00 C ATOM 2129 CD2 PHE N 275 121.668 127.271 86.864 1.00 0.00 C ATOM 2130 CE1 PHE N 275 120.431 129.366 85.608 1.00 0.00 C ATOM 2131 CE2 PHE N 275 121.671 128.508 87.443 1.00 0.00 C ATOM 2132 CG PHE N 275 121.048 127.068 85.652 1.00 0.00 C ATOM 2133 CZ PHE N 275 121.052 129.559 86.815 1.00 0.00 C ATOM 2134 N PHE N 275 118.643 125.218 84.853 1.00 0.00 N ATOM 2135 O PHE N 275 119.942 123.279 83.207 1.00 0.00 O ATOM 2136 C ALA N 276 122.598 123.230 81.591 1.00 0.00 C ATOM 2137 CA ALA N 276 121.463 124.047 80.996 1.00 0.00 C ATOM 2138 CB ALA N 276 121.959 124.853 79.811 1.00 0.00 C ATOM 2139 N ALA N 276 120.896 124.925 82.004 1.00 0.00 N ATOM 2140 O ALA N 276 123.300 123.693 82.488 1.00 0.00 O ATOM 2141 C GLY N 277 123.870 120.733 82.942 1.00 0.00 C ATOM 2142 CA GLY N 277 123.899 121.188 81.499 1.00 0.00 C ATOM 2143 N GLY N 277 122.761 122.003 81.113 1.00 0.00 N ATOM 2144 O GLY N 277 123.935 119.542 83.232 1.00 0.00 O ATOM 2145 C VAL N 278 122.701 120.500 85.709 1.00 0.00 C ATOM 2146 CA VAL N 278 123.826 121.425 85.269 1.00 0.00 C ATOM 2147 CB VAL N 278 123.748 122.729 86.052 1.00 0.00 C ATOM 2148 CG1 VAL N 278 123.758 122.461 87.531 1.00 0.00 C ATOM 2149 CG2 VAL N 278 124.889 123.634 85.653 1.00 0.00 C ATOM 2150 N VAL N 278 123.766 121.693 83.847 1.00 0.00 N ATOM 2151 O VAL N 278 121.576 120.625 85.240 1.00 0.00 O ATOM 2152 C LYS N 279 122.293 118.200 88.623 1.00 0.00 C ATOM 2153 CA LYS N 279 122.266 118.434 87.093 1.00 0.00 C ATOM 2154 CB LYS N 279 122.696 117.173 86.350 1.00 0.00 C ATOM 2155 CD LYS N 279 122.717 115.904 84.174 1.00 0.00 C ATOM 2156 CE LYS N 279 121.718 114.856 84.636 1.00 0.00 C ATOM 2157 CG LYS N 279 122.463 117.242 84.850 1.00 0.00 C ATOM 2158 N LYS N 279 123.053 119.597 86.639 1.00 0.00 N ATOM 2159 NZ LYS N 279 121.960 113.522 84.020 1.00 0.00 N ATOM 2160 O LYS N 279 123.105 118.821 89.310 1.00 0.00 O ATOM 2161 C PHE N 280 122.110 115.862 91.064 1.00 0.00 C ATOM 2162 CA PHE N 280 121.227 117.043 90.584 1.00 0.00 C ATOM 2163 CB PHE N 280 119.768 116.778 90.931 1.00 0.00 C ATOM 2164 CD1 PHE N 280 118.146 118.596 91.497 1.00 0.00 C ATOM 2165 CD2 PHE N 280 118.685 118.230 89.208 1.00 0.00 C ATOM 2166 CE1 PHE N 280 117.295 119.619 91.132 1.00 0.00 C ATOM 2167 CE2 PHE N 280 117.837 119.253 88.835 1.00 0.00 C ATOM 2168 CG PHE N 280 118.845 117.889 90.538 1.00 0.00 C ATOM 2169 CZ PHE N 280 117.141 119.950 89.799 1.00 0.00 C ATOM 2170 N PHE N 280 121.378 117.359 89.139 1.00 0.00 N ATOM 2171 O PHE N 280 122.105 114.774 90.467 1.00 0.00 O ATOM 2602 C ALA N 339 120.464 128.840 79.943 1.00 0.00 C ATOM 2603 CA ALA N 339 121.554 129.338 79.013 1.00 0.00 C ATOM 2604 CB ALA N 339 121.199 129.029 77.578 1.00 0.00 C ATOM 2605 N ALA N 339 122.841 128.757 79.352 1.00 0.00 N ATOM 2606 O ALA N 339 120.396 127.658 80.263 1.00 0.00 O ATOM 2607 C VAL N 340 117.492 128.599 80.322 1.00 0.00 C ATOM 2608 CA VAL N 340 118.447 129.411 81.169 1.00 0.00 C ATOM 2609 CB VAL N 340 117.734 130.666 81.702 1.00 0.00 C ATOM 2610 CG1 VAL N 340 116.444 130.309 82.399 1.00 0.00 C ATOM 2611 CG2 VAL N 340 118.643 131.413 82.642 1.00 0.00 C ATOM 2612 N VAL N 340 119.609 129.757 80.376 1.00 0.00 N ATOM 2613 O VAL N 340 117.373 128.821 79.119 1.00 0.00 O ATOM 2614 C ASN N 341 114.499 127.022 81.166 1.00 0.00 C ATOM 2615 CA ASN N 341 115.761 126.908 80.322 1.00 0.00 C ATOM 2616 CB ASN N 341 116.146 125.449 80.130 1.00 0.00 C ATOM 2617 CG ASN N 341 115.213 124.731 79.202 1.00 0.00 C ATOM 2618 N ASN N 341 116.838 127.636 80.954 1.00 0.00 N ATOM 2619 ND2 ASN N 341 114.996 123.450 79.455 1.00 0.00 N ATOM 2620 O ASN N 341 114.354 126.315 82.161 1.00 0.00 O ATOM 2621 OD1 ASN N 341 114.676 125.323 78.268 1.00 0.00 O ATOM 2622 C ILE N 342 111.425 126.940 81.377 1.00 0.00 C ATOM 2623 CA ILE N 342 112.363 128.130 81.513 1.00 0.00 C ATOM 2624 CB ILE N 342 111.639 129.408 81.044 1.00 0.00 C ATOM 2625 CD1 ILE N 342 111.812 131.926 81.022 1.00 0.00 C ATOM 2626 CG1 ILE N 342 112.389 130.643 81.531 1.00 0.00 C ATOM 2627 CG2 ILE N 342 110.218 129.459 81.550 1.00 0.00 C ATOM 2628 N ILE N 342 113.615 127.943 80.794 1.00 0.00 N ATOM 2629 O ILE N 342 111.219 126.417 80.289 1.00 0.00 O ATOM 2630 C LEU N 343 108.457 125.498 82.528 1.00 0.00 C ATOM 2631 CA LEU N 343 109.977 125.339 82.513 1.00 0.00 C ATOM 2632 CB LEU N 343 110.373 124.459 83.691 1.00 0.00 C ATOM 2633 CD1 LEU N 343 112.060 123.086 84.901 1.00 0.00 C ATOM 2634 CD2 LEU N 343 111.765 122.813 82.425 1.00 0.00 C ATOM 2635 CG LEU N 343 111.736 123.787 83.591 1.00 0.00 C ATOM 2636 N LEU N 343 110.810 126.539 82.484 1.00 0.00 N ATOM 2637 O LEU N 343 107.761 124.516 82.764 1.00 0.00 O END """) s_apar_records1 = """\ SHEET 1 A 2 TYR A 2 VAL A 7 0 SHEET 2 A 2 MET A 31 SER A 36 -1 O ALA A 36 N ALA A 2 """ s_apar_records2 = """\ SHEET 1 A 2 TYR A 2 VAL A 7 0 SHEET 2 A 2 MET A 31 SER A 36 -1 O ALA A 32 N ALA A 6 """ s_par_records1 = """\ SHEET 1 B 2 ALA A 15 THR A 21 0 SHEET 2 B 2 GLN A 40 ALA A 46 1 O GLN A 40 N THR A 16 """ s_par_records2 = """\ SHEET 1 B 2 ALA A 15 THR A 21 0 SHEET 2 B 2 GLN A 40 ALA A 46 1 O GLN A 44 N THR A 20 """ s_par_records3 = """\ SHEET 1 B 2 ALA A 15 THR A 21 0 SHEET 2 B 2 GLN A 40 ALA A 46 1 N GLN A 42 O THR A 16 """ s_par_records4 = """\ SHEET 1 B 2 ALA A 15 THR A 21 0 SHEET 2 B 2 GLN A 40 ALA A 46 1 N GLN A 46 O THR A 20 """ s_par_records5 = """\ SHEET 1 B 2 GLN A 40 ALA A 46 0 SHEET 2 B 2 ALA A 15 THR A 21 1 O THR A 20 N ALA A 46 """ s_par_records6 = """\ SHEET 1 B 2 GLN A 40 ALA A 46 0 SHEET 2 B 2 ALA A 15 THR A 21 1 N THR A 20 O ALA A 44 """ s_par_records7 = """\ SHEET 1 B 2 GLN A 40 ALA A 46 0 SHEET 2 B 2 ALA A 15 THR A 21 1 N THR A 16 O GLN A 40 """ s_par_records8 = """\ SHEET 1 B 2 GLN A 40 ALA A 46 0 SHEET 2 B 2 ALA A 15 THR A 21 1 O THR A 16 N ALA A 42 """ s_apar_records3 = """\ SHEET 1 D 2 LYS N 272 LYS N 279 0 SHEET 2 D 2 VAL N 340 ILE N 342 -1 N ASN N 341 O SER N 274 """ s_par_records9 = """\ SHEET 1 B 2 SER A 44 ALA A 46 0 SHEET 2 B 2 ALA A 15 THR A 21 1 N THR A 20 O SER A 44 """ s_par_records10 = """\ SHEET 1 B 2 GLN A 40 ALA A 46 0 SHEET 2 B 2 SER A 18 THR A 21 1 N THR A 20 O SER A 44 """ s_par_records11 = """\ SHEET 1 B 2 GLN A 40 ALA A 46 0 SHEET 2 B 2 ALA A 19 THR A 21 1 N THR A 20 O SER A 44 """ s_par_records12 = """\ SHEET 1 B 2 GLN A 40 ALA A 46 0 SHEET 2 B 2 THR A 20 THR A 21 1 O THR A 20 N ALA A 46 """ log = null_out() defpars = sec_str_master_phil.fetch() n_hbonds = [] for pdb_inp, recs in [(pdb_apar_input, s_apar_records1), (pdb_apar_input, s_apar_records2), (pdb_par_input, s_par_records1), (pdb_par_input, s_par_records2), (pdb_par_input, s_par_records3), (pdb_par_input, s_par_records4), (pdb_par_input, s_par_records5), (pdb_par_input, s_par_records6), (pdb_par_input, s_par_records7), (pdb_par_input, s_par_records8), (pdb_apar2_input, s_apar_records3), (pdb_par_input, s_par_records9), (pdb_par_input, s_par_records10), (pdb_par_input, s_par_records11), (pdb_par_input, s_par_records12), ]: ioss_annotation = ioss.annotation(records = recs.split('\n')) ann = ioss_annotation.as_restraint_groups() custom_pars = defpars.fetch(source = iotbx.phil.parse(ann)) ss_manager = manager( pdb_inp.hierarchy, sec_str_from_pdb_file=None, params=custom_pars.extract(), assume_hydrogens_all_missing=None, tmp_dir=None, verbose=-1) proxies_for_grm = ss_manager.create_hbond_proxies( log = log, as_python_objects = True) n_hbonds.append(len(proxies_for_grm.proxies)) #print n_hbonds assert n_hbonds == [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 3, 4, 2, 2] def exercise_segid(): if (not libtbx.env.has_module(name="ksdssp")): print "KSDSSP not available, skipping exercise_segid()" return pdb_par_segid_input = iotbx.pdb.hierarchy.input(pdb_string = """\ CRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1 SCALE1 0.021524 0.012427 0.000000 0.00000 SCALE2 0.000000 0.024854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005176 0.00000 ATOM 67 N ALA A 15 5.011 -5.031 -8.967 1.00 5.73 N ATOM 68 CA ALA A 15 4.943 -6.455 -9.287 1.00 6.16 C ATOM 69 C ALA A 15 5.610 -7.252 -8.166 1.00 6.39 C ATOM 70 O ALA A 15 6.751 -7.007 -7.857 1.00 9.87 O ATOM 71 CB ALA A 15 5.684 -6.739 -10.604 1.00 7.46 C ATOM 72 N THR A 16 4.929 -8.263 -7.636 1.00 5.49 N ATOM 73 C THR A 16 5.316 -10.600 -7.084 1.00 5.07 C ATOM 74 O THR A 16 4.214 -11.002 -7.422 1.00 6.51 O ATOM 75 CA THR A 16 5.513 -9.172 -6.657 1.00 5.70 C ATOM 76 CB THR A 16 4.864 -9.001 -5.276 1.00 8.31 C ATOM 77 N GLY A 17 6.393 -11.375 -7.067 1.00 4.56 N ATOM 78 CA GLY A 17 6.325 -12.770 -7.439 1.00 4.26 C ATOM 79 C GLY A 17 7.219 -13.654 -6.621 1.00 4.41 C ATOM 80 O GLY A 17 8.263 -13.233 -6.114 1.00 5.01 O ATOM 81 N SER A 18 6.827 -14.921 -6.561 1.00 4.24 N ATOM 82 CA SER A 18 7.657 -15.945 -5.959 1.00 4.02 C ATOM 83 C SER A 18 7.539 -17.244 -6.724 1.00 3.64 C ATOM 84 O SER A 18 6.482 -17.526 -7.331 1.00 4.07 O ATOM 85 CB SER A 18 7.335 -16.157 -4.481 1.00 5.86 C ATOM 86 N ALA A 19 8.573 -18.049 -6.627 1.00 3.19 N ATOM 87 CA ALA A 19 8.578 -19.414 -7.195 1.00 3.31 C ATOM 88 C ALA A 19 9.370 -20.307 -6.238 1.00 3.20 C ATOM 89 O ALA A 19 10.484 -19.956 -5.817 1.00 4.21 O ATOM 90 CB ALA A 19 9.235 -19.415 -8.574 1.00 3.85 seg C ATOM 91 N THR A 20 8.825 -21.476 -5.940 1.00 3.77 seg N ATOM 92 CA THR A 20 9.478 -22.432 -5.047 1.00 3.70 seg C ATOM 93 C THR A 20 9.444 -23.827 -5.640 1.00 3.56 seg C ATOM 94 O THR A 20 8.383 -24.281 -6.108 1.00 4.14 seg O ATOM 95 CB THR A 20 8.787 -22.430 -3.673 1.00 4.76 seg C ATOM 96 N THR A 21 10.560 -24.542 -5.569 1.00 4.00 seg N ATOM 97 CA THR A 21 10.597 -25.962 -5.876 1.00 4.05 seg C ATOM 98 C THR A 21 10.984 -26.770 -4.636 1.00 4.53 seg C ATOM 99 O THR A 21 11.770 -26.361 -3.802 1.00 5.04 seg O ATOM 100 CB THR A 21 11.488 -26.293 -7.083 1.00 4.38 seg C ATOM 189 N GLN A 40 0.280 -6.099 -9.049 1.00 6.35 seg N ATOM 190 CA GLN A 40 0.087 -7.454 -9.580 1.00 6.35 seg C ATOM 191 C GLN A 40 0.964 -8.417 -8.788 1.00 6.09 seg C ATOM 192 O GLN A 40 2.080 -8.093 -8.393 1.00 6.87 seg O ATOM 193 CB GLN A 40 0.461 -7.523 -11.060 1.00 7.52 seg C ATOM 194 N THR A 41 0.419 -9.596 -8.544 1.00 6.66 seg N ATOM 195 CA THR A 41 1.108 -10.640 -7.800 1.00 6.93 seg C ATOM 196 C THR A 41 0.932 -12.005 -8.414 1.00 6.82 seg C ATOM 197 O THR A 41 -0.069 -12.258 -9.104 1.00 8.79 seg O ATOM 198 CB THR A 41 0.633 -10.636 -6.352 1.00 10.84 seg C ATOM 199 N ALA A 42 1.951 -12.847 -8.263 1.00 6.44 seg N ATOM 200 CA ALA A 42 1.923 -14.209 -8.797 1.00 6.59 seg C ATOM 201 C ALA A 42 2.829 -15.117 -7.992 1.00 5.51 seg C ATOM 202 O ALA A 42 3.835 -14.684 -7.420 1.00 5.94 seg O ATOM 203 CB ALA A 42 2.327 -14.218 -10.264 1.00 9.02 seg C ATOM 204 N LYS A 43 2.479 -16.398 -7.978 1.00 6.26 seg N ATOM 205 CA LYS A 43 3.247 -17.395 -7.256 1.00 6.48 seg C ATOM 206 C LYS A 43 3.186 -18.741 -7.955 1.00 5.78 seg C ATOM 207 O LYS A 43 2.206 -19.041 -8.623 1.00 9.40 seg O ATOM 208 CB LYS A 43 2.727 -17.535 -5.836 1.00 8.81 seg C ATOM 209 N SER A 44 4.243 -19.534 -7.818 1.00 4.43 seg N ATOM 210 CA SER A 44 4.241 -20.890 -8.325 1.00 4.28 seg C ATOM 211 C SER A 44 4.998 -21.811 -7.358 1.00 4.09 seg C ATOM 212 O SER A 44 5.865 -21.377 -6.584 1.00 4.53 seg O ATOM 213 CB SER A 44 4.831 -20.949 -9.731 1.00 5.33 seg C ATOM 214 N PHE A 45 4.660 -23.091 -7.444 1.00 4.39 seg N ATOM 215 CA PHE A 45 5.198 -24.135 -6.576 1.00 4.44 seg C ATOM 216 C PHE A 45 5.222 -25.415 -7.389 1.00 4.16 seg C ATOM 217 O PHE A 45 4.183 -25.754 -7.979 1.00 5.11 seg O ATOM 218 CB PHE A 45 4.254 -24.281 -5.370 1.00 5.22 seg C ATOM 219 N ALA A 46 6.347 -26.119 -7.403 1.00 3.62 seg N ATOM 220 CA ALA A 46 6.443 -27.338 -8.202 1.00 3.99 seg C ATOM 221 C ALA A 46 7.579 -28.205 -7.717 1.00 4.57 seg C ATOM 222 O ALA A 46 8.479 -27.750 -7.000 1.00 4.79 seg O ATOM 223 CB ALA A 46 6.607 -27.026 -9.678 1.00 4.52 seg C TER END """) log = null_out() defpars = sec_str_master_phil.fetch() custom_pars = defpars.fetch(source=iotbx.phil.parse("secondary_structure_restraints=True")) ss_manager = manager( pdb_par_segid_input.hierarchy, sec_str_from_pdb_file=None, params=custom_pars.extract(), assume_hydrogens_all_missing=None, tmp_dir=None, verbose=-1) ss_manager.initialize() proxies_for_grm = ss_manager.create_hbond_proxies( log = log, as_python_objects = True) assert len(proxies_for_grm.proxies) == 4 def exercise_phil_generation(): log = null_out() defpars = sec_str_master_phil.fetch() if __name__ == "__main__" : exercise_protein() exercise_sheet_ends() exercise_nucleic_acids() exercise_sheets_bonding_pattern() exercise_segid() print "OK"