from __future__ import absolute_import, division, print_function from mmtbx.secondary_structure import sec_str_master_phil_str, manager from cctbx import geometry_restraints from iotbx import file_reader import iotbx.pdb import libtbx.load_env import iotbx.pdb.secondary_structure as ioss from libtbx.utils import null_out from libtbx.test_utils import approx_equal 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() import sys log = sys.stdout 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.params.secondary_structure.protein.remove_outliers = False proxies, hb_angles = m.create_protein_hbond_proxies( annotation=None, log=log) print(proxies.size(), hb_angles.size()) assert proxies.size() == 109 assert hb_angles.size() == 294+27, hb_angles.size() # helix+sheet angles assert isinstance(proxies, geometry_restraints.shared_bond_simple_proxy) (frac_alpha, frac_beta) = m.calculate_structure_content() assert approx_equal(frac_alpha, 0.643, eps=1e-3) assert approx_equal(frac_beta, 0.0539, eps=1e-3) # Make sure the hydrogen auto-detection override is working # Functionality is disabled # m.params.secondary_structure.protein.substitute_n_for_h = True # build_proxies = m.create_hbond_proxies( # log=log, # as_python_objects=True, # as_regular_bond_proxies=False) # proxies = build_proxies.proxies # atom_ids = [] # for i_seq in proxies[0].i_seqs : # atom_ids.append(pdb_hierarchy.atoms()[i_seq].id_str()) # print atom_ids # 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.params.secondary_structure.protein.remove_outliers = False proxies, angle_p = m.create_protein_hbond_proxies( annotation=None, log=log) assert proxies.size() == 90 assert angle_p.size() == 243+18, angle_p.size() def exercise_sheet_ends(): pdb_in = iotbx.pdb.input(source_info=None, lines="""\ SHEET 1 A 3 ALA A 38 ALA A 44 0 SHEET 2 A 3 ALA A 76 ALA A 83 -1 N ALA A 83 O ALA A 38 SHEET 3 A 3 ALA A 95 ALA A 97 -1 N ALA A 97 O ALA A 76 ATOM 1 N ALA A 37 27.792 -1.121 13.875 1.00 20.00 N ATOM 2 CA ALA A 37 28.151 0.253 14.202 1.00 20.00 C ATOM 3 C ALA A 37 26.961 1.003 14.792 1.00 20.00 C ATOM 4 O ALA A 37 27.129 2.000 15.494 1.00 20.00 O ATOM 5 CB ALA A 37 28.674 0.973 12.969 1.00 20.00 C ATOM 6 N ALA A 38 25.758 0.515 14.502 1.00 20.00 N ATOM 7 CA ALA A 38 24.529 1.125 14.995 1.00 20.00 C ATOM 8 C ALA A 38 23.363 0.264 14.524 1.00 20.00 C ATOM 9 O ALA A 38 23.538 -0.687 13.756 1.00 20.00 O ATOM 10 N ALA A 39 22.168 0.611 14.996 1.00 20.00 N ATOM 11 CA ALA A 39 20.950 -0.103 14.648 1.00 20.00 C ATOM 12 C ALA A 39 19.925 0.874 14.089 1.00 20.00 C ATOM 13 O ALA A 39 19.845 2.028 14.517 1.00 20.00 O ATOM 14 CB ALA A 39 20.363 -0.841 15.859 1.00 20.00 C ATOM 15 N ALA A 40 19.142 0.396 13.127 1.00 20.00 N ATOM 16 CA ALA A 40 18.108 1.191 12.480 1.00 20.00 C ATOM 17 C ALA A 40 16.741 0.588 12.768 1.00 20.00 C ATOM 18 O ALA A 40 16.573 -0.635 12.745 1.00 20.00 O ATOM 19 CB ALA A 40 18.337 1.274 10.967 1.00 20.00 C ATOM 20 N ALA A 41 15.767 1.453 13.040 1.00 20.00 N ATOM 21 CA ALA A 41 14.401 1.043 13.338 1.00 20.00 C ATOM 22 C ALA A 41 13.470 1.644 12.296 1.00 20.00 C ATOM 23 O ALA A 41 13.452 2.865 12.106 1.00 20.00 O ATOM 24 CB ALA A 41 13.989 1.477 14.746 1.00 20.00 C ATOM 25 N ALA A 42 12.701 0.790 11.627 1.00 20.00 N ATOM 26 CA ALA A 42 11.760 1.215 10.599 1.00 20.00 C ATOM 27 C ALA A 42 10.357 1.223 11.194 1.00 20.00 C ATOM 28 O ALA A 42 9.857 0.180 11.630 1.00 20.00 O ATOM 29 N ALA A 43 9.727 2.394 11.209 1.00 20.00 N ATOM 30 CA ALA A 43 8.385 2.564 11.743 1.00 20.00 C ATOM 31 C ALA A 43 7.444 3.011 10.634 1.00 20.00 C ATOM 32 O ALA A 43 7.806 3.844 9.796 1.00 20.00 O ATOM 33 CB ALA A 43 8.367 3.583 12.887 1.00 20.00 C ATOM 34 N ALA A 44 6.235 2.453 10.633 1.00 20.00 N ATOM 35 CA ALA A 44 5.236 2.788 9.630 1.00 20.00 C ATOM 36 C ALA A 44 3.852 2.693 10.255 1.00 20.00 C ATOM 37 O ALA A 44 3.636 1.941 11.209 1.00 20.00 O ATOM 38 CB ALA A 44 5.332 1.870 8.406 1.00 20.00 C ATOM 39 N ALA A 45 2.919 3.463 9.705 1.00 20.00 N ATOM 40 CA ALA A 45 1.548 3.476 10.200 1.00 20.00 C ATOM 41 C ALA A 45 0.715 2.390 9.527 1.00 20.00 C ATOM 42 O ALA A 45 1.135 1.800 8.531 1.00 20.00 O ATOM 43 CB ALA A 45 0.917 4.842 9.979 1.00 20.00 C ATOM 44 N ALA A 74 -2.563 6.328 17.723 1.00 20.00 N ATOM 45 CA ALA A 74 -2.435 5.677 16.425 1.00 20.00 C ATOM 46 C ALA A 74 -1.470 4.499 16.498 1.00 20.00 C ATOM 47 O ALA A 74 -0.401 4.596 17.100 1.00 20.00 O ATOM 48 CB ALA A 74 -1.975 6.676 15.374 1.00 20.00 C ATOM 49 N ALA A 75 -1.856 3.385 15.882 1.00 20.00 N ATOM 50 CA ALA A 75 -1.023 2.191 15.881 1.00 20.00 C ATOM 51 C ALA A 75 0.069 2.303 14.825 1.00 20.00 C ATOM 52 O ALA A 75 -0.171 2.768 13.707 1.00 20.00 O ATOM 53 CB ALA A 75 -1.873 0.946 15.627 1.00 20.00 C ATOM 54 N ALA A 76 1.275 1.871 15.189 1.00 20.00 N ATOM 55 CA ALA A 76 2.411 1.917 14.283 1.00 20.00 C ATOM 56 C ALA A 76 3.331 0.742 14.576 1.00 20.00 C ATOM 57 O ALA A 76 3.469 0.314 15.726 1.00 20.00 O ATOM 58 CB ALA A 76 3.180 3.238 14.405 1.00 20.00 C ATOM 59 N ALA A 77 3.957 0.225 13.525 1.00 20.00 N ATOM 60 CA ALA A 77 4.871 -0.901 13.624 1.00 20.00 C ATOM 61 C ALA A 77 6.309 -0.431 13.446 1.00 20.00 C ATOM 62 O ALA A 77 6.578 0.615 12.849 1.00 20.00 O ATOM 63 CB ALA A 77 4.537 -1.975 12.583 1.00 20.00 C ATOM 64 N ALA A 78 7.237 -1.225 13.977 1.00 20.00 N ATOM 65 CA ALA A 78 8.654 -0.911 13.889 1.00 20.00 C ATOM 66 C ALA A 78 9.447 -2.207 13.806 1.00 20.00 C ATOM 67 O ALA A 78 8.994 -3.266 14.248 1.00 20.00 O ATOM 68 CB ALA A 78 9.122 -0.070 15.082 1.00 20.00 C ATOM 69 N ALA A 79 10.643 -2.108 13.230 1.00 20.00 N ATOM 70 CA ALA A 79 11.528 -3.254 13.071 1.00 20.00 C ATOM 71 C ALA A 79 12.965 -2.807 13.282 1.00 20.00 C ATOM 72 O ALA A 79 13.402 -1.815 12.692 1.00 20.00 O ATOM 73 CB ALA A 79 11.368 -3.894 11.687 1.00 20.00 C ATOM 74 N ALA A 80 13.693 -3.538 14.121 1.00 20.00 N ATOM 75 CA ALA A 80 15.083 -3.235 14.423 1.00 20.00 C ATOM 76 C ALA A 80 16.005 -4.091 13.566 1.00 20.00 C ATOM 77 O ALA A 80 15.755 -5.284 13.366 1.00 20.00 O ATOM 78 CB ALA A 80 15.383 -3.466 15.905 1.00 20.00 C ATOM 79 N ALA A 81 17.071 -3.475 13.060 1.00 20.00 N ATOM 80 CA ALA A 81 18.037 -4.171 12.222 1.00 20.00 C ATOM 81 C ALA A 81 19.414 -3.568 12.449 1.00 20.00 C ATOM 82 O ALA A 81 19.590 -2.353 12.320 1.00 20.00 O ATOM 83 CB ALA A 81 17.653 -4.084 10.741 1.00 20.00 C ATOM 84 N ALA A 82 20.381 -4.417 12.785 1.00 20.00 N ATOM 85 CA ALA A 82 21.741 -3.960 13.029 1.00 20.00 C ATOM 86 C ALA A 82 22.475 -3.742 11.713 1.00 20.00 C ATOM 87 O ALA A 82 22.392 -4.561 10.793 1.00 20.00 O ATOM 88 CB ALA A 82 22.499 -4.970 13.891 1.00 20.00 C ATOM 89 N ALA A 83 23.197 -2.628 11.628 1.00 20.00 N ATOM 90 CA ALA A 83 23.957 -2.270 10.443 1.00 20.00 C ATOM 91 C ALA A 83 25.415 -2.029 10.812 1.00 20.00 C ATOM 92 O ALA A 83 25.748 -1.734 11.963 1.00 20.00 O ATOM 93 CB ALA A 83 23.375 -1.024 9.761 1.00 20.00 C ATOM 94 N ALA A 84 26.284 -2.160 9.815 1.00 20.00 N ATOM 95 CA ALA A 84 27.714 -1.960 10.014 1.00 20.00 C ATOM 96 C ALA A 84 28.356 -1.340 8.778 1.00 20.00 C ATOM 97 O ALA A 84 27.800 -1.400 7.681 1.00 20.00 O ATOM 98 CB ALA A 84 28.391 -3.277 10.360 1.00 20.00 C ATOM 99 N ALA A 94 8.798 -7.831 13.977 1.00 20.00 N ATOM 100 CA ALA A 94 8.087 -6.560 13.921 1.00 20.00 C ATOM 101 C ALA A 94 7.265 -6.339 15.186 1.00 20.00 C ATOM 102 O ALA A 94 6.554 -7.235 15.641 1.00 20.00 O ATOM 103 CB ALA A 94 7.193 -6.507 12.691 1.00 20.00 C ATOM 104 N ALA A 95 7.368 -5.139 15.750 1.00 20.00 N ATOM 105 CA ALA A 95 6.649 -4.772 16.959 1.00 20.00 C ATOM 106 C ALA A 95 5.563 -3.754 16.637 1.00 20.00 C ATOM 107 O ALA A 95 5.679 -2.974 15.687 1.00 20.00 O ATOM 108 CB ALA A 95 7.601 -4.200 18.015 1.00 20.00 C ATOM 109 N ALA A 96 4.502 -3.771 17.439 1.00 20.00 N ATOM 110 CA ALA A 96 3.371 -2.869 17.277 1.00 20.00 C ATOM 111 C ALA A 96 3.194 -2.052 18.548 1.00 20.00 C ATOM 112 O ALA A 96 3.221 -2.603 19.654 1.00 20.00 O ATOM 113 CB ALA A 96 2.088 -3.642 16.958 1.00 20.00 C ATOM 114 N ALA A 97 3.014 -0.743 18.388 1.00 20.00 N ATOM 115 CA ALA A 97 2.831 0.162 19.512 1.00 20.00 C ATOM 116 C ALA A 97 1.807 1.223 19.144 1.00 20.00 C ATOM 117 O ALA A 97 1.829 1.760 18.033 1.00 20.00 O ATOM 118 CB ALA A 97 4.153 0.825 19.921 1.00 20.00 C ATOM 119 N ALA A 98 0.913 1.521 20.082 1.00 20.00 N ATOM 120 CA ALA A 98 -0.125 2.521 19.861 1.00 20.00 C ATOM 121 C ALA A 98 0.164 3.791 20.655 1.00 20.00 C ATOM 122 O ALA A 98 0.052 3.806 21.881 1.00 20.00 O ATOM 123 CB ALA A 98 -1.489 1.961 20.232 1.00 20.00 C TER END """) pdb_hierarchy = pdb_in.construct_hierarchy() pdb_hierarchy.atoms().reset_i_seq() ss_from_file = pdb_in.extract_secondary_structure() if not libtbx.env.has_module(name="ksdssp"): print("Skipping KSDSSP tests: ksdssp module not available.") return m = manager(pdb_hierarchy=pdb_hierarchy, sec_str_from_pdb_file=None) # m.params.secondary_structure.use_ksdssp = False m.params.secondary_structure.protein.remove_outliers = False log = open("exercise_sheet_ends.log", "w") proxies, hb_angles = m.create_protein_hbond_proxies(annotation=ss_from_file, log=log) log.close() # probably the determination of SS by ksdssp is not stable. assert proxies.size() == 12, proxies.size() assert hb_angles.size() == 27, hb_angles.size() def exercise_helix_bonding_pattern(): alpha_h1_simple = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 N ALA 1 1.643 -2.366 -1.408 1.00 0.00 N ATOM 2 CA ALA 1 1.280 -3.608 -2.069 1.00 0.00 C ATOM 3 C ALA 1 -0.114 -3.466 -2.684 1.00 0.00 C ATOM 4 O ALA 1 -0.327 -3.827 -3.840 1.00 0.00 O ATOM 5 CB ALA 1 1.361 -4.762 -1.068 1.00 0.00 C ATOM 6 N ALA 2 -1.028 -2.938 -1.882 1.00 0.00 N ATOM 7 CA ALA 2 -2.395 -2.743 -2.332 1.00 0.00 C ATOM 8 C ALA 2 -2.396 -1.855 -3.579 1.00 0.00 C ATOM 9 O ALA 2 -3.059 -2.167 -4.567 1.00 0.00 O ATOM 10 CB ALA 2 -3.228 -2.150 -1.194 1.00 0.00 C ATOM 11 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N ATOM 12 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C ATOM 13 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C ATOM 14 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O ATOM 15 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C ATOM 16 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N ATOM 17 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C ATOM 18 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C ATOM 19 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O ATOM 20 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C ATOM 21 N ALA 5 -1.184 -3.711 -6.463 1.00 0.00 N ATOM 22 CA ALA 5 -2.231 -4.619 -6.901 1.00 0.00 C ATOM 23 C ALA 5 -3.253 -3.847 -7.737 1.00 0.00 C ATOM 24 O ALA 5 -3.647 -4.296 -8.813 1.00 0.00 O ATOM 25 CB ALA 5 -2.864 -5.294 -5.683 1.00 0.00 C ATOM 26 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N ATOM 27 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C ATOM 28 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C ATOM 29 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O ATOM 30 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C ATOM 31 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N ATOM 32 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C ATOM 33 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C ATOM 34 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O ATOM 35 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C ATOM 36 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N ATOM 37 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C ATOM 38 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C ATOM 39 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O ATOM 40 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C ATOM 41 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N ATOM 42 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C ATOM 43 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C ATOM 44 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O ATOM 45 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C ATOM 46 N ALA 10 -5.617 -2.338 -12.812 1.00 0.00 N ATOM 47 CA ALA 10 -5.879 -1.301 -13.795 1.00 0.00 C ATOM 48 C ALA 10 -5.242 -1.695 -15.130 1.00 0.00 C ATOM 49 O ALA 10 -5.880 -1.605 -16.177 1.00 0.00 O ATOM 50 CB ALA 10 -5.358 0.040 -13.274 1.00 0.00 C TER """).construct_hierarchy() alpha_h1_1ac = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 N AALA 1 1.643 -2.366 -1.408 0.50 0.00 N ATOM 2 CA AALA 1 1.280 -3.608 -2.069 0.50 0.00 C ATOM 3 C AALA 1 -0.114 -3.466 -2.684 0.50 0.00 C ATOM 4 O AALA 1 -0.327 -3.827 -3.840 0.50 0.00 O ATOM 5 CB AALA 1 1.361 -4.762 -1.068 0.50 0.00 C ATOM 6 N BALA 1 1.743 -2.366 -1.408 0.50 0.00 N ATOM 7 CA BALA 1 1.380 -3.608 -2.069 0.50 0.00 C ATOM 8 C BALA 1 -0.014 -3.466 -2.684 0.50 0.00 C ATOM 9 O BALA 1 -0.227 -3.827 -3.840 0.50 0.00 O ATOM 10 CB BALA 1 1.461 -4.762 -1.068 0.50 0.00 C ATOM 11 N ALA 2 -1.028 -2.938 -1.882 1.00 0.00 N ATOM 12 CA ALA 2 -2.395 -2.743 -2.332 1.00 0.00 C ATOM 13 C ALA 2 -2.396 -1.855 -3.579 1.00 0.00 C ATOM 14 O ALA 2 -3.059 -2.167 -4.567 1.00 0.00 O ATOM 15 CB ALA 2 -3.228 -2.150 -1.194 1.00 0.00 C ATOM 16 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N ATOM 17 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C ATOM 18 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C ATOM 19 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O ATOM 20 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C ATOM 21 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N ATOM 22 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C ATOM 23 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C ATOM 24 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O ATOM 25 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C ATOM 26 N ALA 5 -1.184 -3.711 -6.463 1.00 0.00 N ATOM 27 CA ALA 5 -2.231 -4.619 -6.901 1.00 0.00 C ATOM 28 C ALA 5 -3.253 -3.847 -7.737 1.00 0.00 C ATOM 29 O ALA 5 -3.647 -4.296 -8.813 1.00 0.00 O ATOM 30 CB ALA 5 -2.864 -5.294 -5.683 1.00 0.00 C ATOM 31 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N ATOM 32 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C ATOM 33 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C ATOM 34 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O ATOM 35 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C ATOM 36 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N ATOM 37 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C ATOM 38 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C ATOM 39 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O ATOM 40 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C ATOM 41 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N ATOM 42 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C ATOM 43 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C ATOM 44 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O ATOM 45 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C ATOM 46 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N ATOM 47 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C ATOM 48 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C ATOM 49 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O ATOM 50 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C ATOM 51 N ALA 10 -5.617 -2.338 -12.812 1.00 0.00 N ATOM 52 CA ALA 10 -5.879 -1.301 -13.795 1.00 0.00 C ATOM 53 C ALA 10 -5.242 -1.695 -15.130 1.00 0.00 C ATOM 54 O ALA 10 -5.880 -1.605 -16.177 1.00 0.00 O ATOM 55 CB ALA 10 -5.358 0.040 -13.274 1.00 0.00 C TER 56 ALA 10 END """).construct_hierarchy() alpha_h1_1_10ac = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 N AALA 1 1.643 -2.366 -1.408 0.50 0.00 N ATOM 2 CA AALA 1 1.280 -3.608 -2.069 0.50 0.00 C ATOM 3 C AALA 1 -0.114 -3.466 -2.684 0.50 0.00 C ATOM 4 O AALA 1 -0.327 -3.827 -3.840 0.50 0.00 O ATOM 5 CB AALA 1 1.361 -4.762 -1.068 0.50 0.00 C ATOM 6 N BALA 1 1.743 -2.366 -1.408 0.50 0.00 N ATOM 7 CA BALA 1 1.380 -3.608 -2.069 0.50 0.00 C ATOM 8 C BALA 1 -0.014 -3.466 -2.684 0.50 0.00 C ATOM 9 O BALA 1 -0.227 -3.827 -3.840 0.50 0.00 O ATOM 10 CB BALA 1 1.461 -4.762 -1.068 0.50 0.00 C ATOM 11 N ALA 2 -1.028 -2.938 -1.882 1.00 0.00 N ATOM 12 CA ALA 2 -2.395 -2.743 -2.332 1.00 0.00 C ATOM 13 C ALA 2 -2.396 -1.855 -3.579 1.00 0.00 C ATOM 14 O ALA 2 -3.059 -2.167 -4.567 1.00 0.00 O ATOM 15 CB ALA 2 -3.228 -2.150 -1.194 1.00 0.00 C ATOM 16 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N ATOM 17 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C ATOM 18 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C ATOM 19 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O ATOM 20 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C ATOM 21 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N ATOM 22 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C ATOM 23 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C ATOM 24 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O ATOM 25 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C ATOM 26 N ALA 5 -1.184 -3.711 -6.463 1.00 0.00 N ATOM 27 CA ALA 5 -2.231 -4.619 -6.901 1.00 0.00 C ATOM 28 C ALA 5 -3.253 -3.847 -7.737 1.00 0.00 C ATOM 29 O ALA 5 -3.647 -4.296 -8.813 1.00 0.00 O ATOM 30 CB ALA 5 -2.864 -5.294 -5.683 1.00 0.00 C ATOM 31 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N ATOM 32 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C ATOM 33 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C ATOM 34 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O ATOM 35 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C ATOM 36 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N ATOM 37 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C ATOM 38 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C ATOM 39 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O ATOM 40 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C ATOM 41 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N ATOM 42 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C ATOM 43 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C ATOM 44 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O ATOM 45 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C ATOM 46 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N ATOM 47 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C ATOM 48 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C ATOM 49 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O ATOM 50 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C ATOM 51 N AALA 10 -5.617 -2.338 -12.812 0.50 0.00 N ATOM 52 CA AALA 10 -5.879 -1.301 -13.795 0.50 0.00 C ATOM 53 C AALA 10 -5.242 -1.695 -15.130 0.50 0.00 C ATOM 54 O AALA 10 -5.880 -1.605 -16.177 0.50 0.00 O ATOM 55 CB AALA 10 -5.358 0.040 -13.274 0.50 0.00 C ATOM 57 N BALA 10 -5.517 -2.338 -12.812 0.50 0.00 N ATOM 58 CA BALA 10 -5.779 -1.301 -13.795 0.50 0.00 C ATOM 59 C BALA 10 -5.142 -1.695 -15.130 0.50 0.00 C ATOM 60 O BALA 10 -5.780 -1.605 -16.177 0.50 0.00 O ATOM 61 CB BALA 10 -5.258 0.040 -13.274 0.50 0.00 C END """).construct_hierarchy() alpha_h1_1_5_10ac = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 N AALA 1 1.643 -2.366 -1.408 0.50 0.00 N ATOM 2 CA AALA 1 1.280 -3.608 -2.069 0.50 0.00 C ATOM 3 C AALA 1 -0.114 -3.466 -2.684 0.50 0.00 C ATOM 4 O AALA 1 -0.327 -3.827 -3.840 0.50 0.00 O ATOM 5 CB AALA 1 1.361 -4.762 -1.068 0.50 0.00 C ATOM 6 N BALA 1 1.743 -2.366 -1.408 0.50 0.00 N ATOM 7 CA BALA 1 1.380 -3.608 -2.069 0.50 0.00 C ATOM 8 C BALA 1 -0.014 -3.466 -2.684 0.50 0.00 C ATOM 9 O BALA 1 -0.227 -3.827 -3.840 0.50 0.00 O ATOM 10 CB BALA 1 1.461 -4.762 -1.068 0.50 0.00 C ATOM 11 N ALA 2 -1.028 -2.938 -1.882 1.00 0.00 N ATOM 12 CA ALA 2 -2.395 -2.743 -2.332 1.00 0.00 C ATOM 13 C ALA 2 -2.396 -1.855 -3.579 1.00 0.00 C ATOM 14 O ALA 2 -3.059 -2.167 -4.567 1.00 0.00 O ATOM 15 CB ALA 2 -3.228 -2.150 -1.194 1.00 0.00 C ATOM 16 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N ATOM 17 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C ATOM 18 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C ATOM 19 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O ATOM 20 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C ATOM 21 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N ATOM 22 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C ATOM 23 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C ATOM 24 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O ATOM 25 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C ATOM 26 N AALA 5 -1.184 -3.711 -6.463 0.50 0.00 N ATOM 27 CA AALA 5 -2.231 -4.619 -6.901 0.50 0.00 C ATOM 28 C AALA 5 -3.253 -3.847 -7.737 0.50 0.00 C ATOM 29 O AALA 5 -3.647 -4.296 -8.813 0.50 0.00 O ATOM 30 CB AALA 5 -2.864 -5.294 -5.683 0.50 0.00 C ATOM 31 N BALA 5 -1.084 -3.711 -6.463 0.50 0.00 N ATOM 32 CA BALA 5 -2.131 -4.619 -6.901 0.50 0.00 C ATOM 33 C BALA 5 -3.153 -3.847 -7.737 0.50 0.00 C ATOM 34 O BALA 5 -3.547 -4.296 -8.813 0.50 0.00 O ATOM 35 CB BALA 5 -2.764 -5.294 -5.683 0.50 0.00 C ATOM 36 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N ATOM 37 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C ATOM 38 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C ATOM 39 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O ATOM 40 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C ATOM 41 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N ATOM 42 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C ATOM 43 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C ATOM 44 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O ATOM 45 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C ATOM 46 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N ATOM 47 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C ATOM 48 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C ATOM 49 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O ATOM 50 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C ATOM 51 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N ATOM 52 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C ATOM 53 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C ATOM 54 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O ATOM 55 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C ATOM 56 N AALA 10 -5.617 -2.338 -12.812 0.50 0.00 N ATOM 57 CA AALA 10 -5.879 -1.301 -13.795 0.50 0.00 C ATOM 58 C AALA 10 -5.242 -1.695 -15.130 0.50 0.00 C ATOM 59 O AALA 10 -5.880 -1.605 -16.177 0.50 0.00 O ATOM 60 CB AALA 10 -5.358 0.040 -13.274 0.50 0.00 C ATOM 62 N BALA 10 -5.517 -2.338 -12.812 0.50 0.00 N ATOM 63 CA BALA 10 -5.779 -1.301 -13.795 0.50 0.00 C ATOM 64 C BALA 10 -5.142 -1.695 -15.130 0.50 0.00 C ATOM 65 O BALA 10 -5.780 -1.605 -16.177 0.50 0.00 O ATOM 66 CB BALA 10 -5.258 0.040 -13.274 0.50 0.00 C END """).construct_hierarchy() alpha_h1_1_5_10ac_insertions = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 N AALA 1 1.643 -2.366 -1.408 0.50 0.00 N ATOM 2 CA AALA 1 1.280 -3.608 -2.069 0.50 0.00 C ATOM 3 C AALA 1 -0.114 -3.466 -2.684 0.50 0.00 C ATOM 4 O AALA 1 -0.327 -3.827 -3.840 0.50 0.00 O ATOM 5 CB AALA 1 1.361 -4.762 -1.068 0.50 0.00 C ATOM 6 N BALA 1 1.743 -2.366 -1.408 0.50 0.00 N ATOM 7 CA BALA 1 1.380 -3.608 -2.069 0.50 0.00 C ATOM 8 C BALA 1 -0.014 -3.466 -2.684 0.50 0.00 C ATOM 9 O BALA 1 -0.227 -3.827 -3.840 0.50 0.00 O ATOM 10 CB BALA 1 1.461 -4.762 -1.068 0.50 0.00 C ATOM 11 N ALA 2 -1.028 -2.938 -1.882 1.00 0.00 N ATOM 12 CA ALA 2 -2.395 -2.743 -2.332 1.00 0.00 C ATOM 13 C ALA 2 -2.396 -1.855 -3.579 1.00 0.00 C ATOM 14 O ALA 2 -3.059 -2.167 -4.567 1.00 0.00 O ATOM 15 CB ALA 2 -3.228 -2.150 -1.194 1.00 0.00 C ATOM 16 N ALA 2A -1.646 -0.767 -3.491 1.00 0.00 N ATOM 17 CA ALA 2A -1.551 0.168 -4.599 1.00 0.00 C ATOM 18 C ALA 2A -1.044 -0.568 -5.841 1.00 0.00 C ATOM 19 O ALA 2A -1.601 -0.419 -6.927 1.00 0.00 O ATOM 20 CB ALA 2A -0.646 1.337 -4.205 1.00 0.00 C ATOM 21 N ALA 2B 0.008 -1.348 -5.639 1.00 0.00 N ATOM 22 CA ALA 2B 0.597 -2.109 -6.728 1.00 0.00 C ATOM 23 C ALA 2B -0.466 -3.023 -7.340 1.00 0.00 C ATOM 24 O ALA 2B -0.611 -3.085 -8.559 1.00 0.00 O ATOM 25 CB ALA 2B 1.808 -2.887 -6.211 1.00 0.00 C ATOM 26 N AALA 2C -1.184 -3.711 -6.463 0.50 0.00 N ATOM 27 CA AALA 2C -2.231 -4.619 -6.901 0.50 0.00 C ATOM 28 C AALA 2C -3.253 -3.847 -7.737 0.50 0.00 C ATOM 29 O AALA 2C -3.647 -4.296 -8.813 0.50 0.00 O ATOM 30 CB AALA 2C -2.864 -5.294 -5.683 0.50 0.00 C ATOM 31 N BALA 2C -1.084 -3.711 -6.463 0.50 0.00 N ATOM 32 CA BALA 2C -2.131 -4.619 -6.901 0.50 0.00 C ATOM 33 C BALA 2C -3.153 -3.847 -7.737 0.50 0.00 C ATOM 34 O BALA 2C -3.547 -4.296 -8.813 0.50 0.00 O ATOM 35 CB BALA 2C -2.764 -5.294 -5.683 0.50 0.00 C ATOM 36 N ALA 2D -3.654 -2.699 -7.211 1.00 0.00 N ATOM 37 CA ALA 2D -4.623 -1.860 -7.896 1.00 0.00 C ATOM 38 C ALA 2D -4.090 -1.499 -9.284 1.00 0.00 C ATOM 39 O ALA 2D -4.809 -1.602 -10.276 1.00 0.00 O ATOM 40 CB ALA 2D -4.919 -0.623 -7.045 1.00 0.00 C ATOM 41 N ALA 3 -2.831 -1.084 -9.309 1.00 0.00 N ATOM 42 CA ALA 3 -2.192 -0.708 -10.559 1.00 0.00 C ATOM 43 C ALA 3 -2.243 -1.890 -11.529 1.00 0.00 C ATOM 44 O ALA 3 -2.600 -1.727 -12.695 1.00 0.00 O ATOM 45 CB ALA 3 -0.761 -0.243 -10.281 1.00 0.00 C ATOM 46 N ALA 4 -1.881 -3.055 -11.012 1.00 0.00 N ATOM 47 CA ALA 4 -1.882 -4.264 -11.817 1.00 0.00 C ATOM 48 C ALA 4 -3.285 -4.496 -12.382 1.00 0.00 C ATOM 49 O ALA 4 -3.442 -4.772 -13.570 1.00 0.00 O ATOM 50 CB ALA 4 -1.391 -5.441 -10.972 1.00 0.00 C ATOM 51 N ALA 5 -4.269 -4.376 -11.503 1.00 0.00 N ATOM 52 CA ALA 5 -5.653 -4.568 -11.898 1.00 0.00 C ATOM 53 C ALA 5 -6.000 -3.590 -13.022 1.00 0.00 C ATOM 54 O ALA 5 -6.590 -3.978 -14.029 1.00 0.00 O ATOM 55 CB ALA 5 -6.561 -4.400 -10.678 1.00 0.00 C ATOM 56 N AALA 6 -5.617 -2.338 -12.812 0.50 0.00 N ATOM 57 CA AALA 6 -5.879 -1.301 -13.795 0.50 0.00 C ATOM 58 C AALA 6 -5.242 -1.695 -15.130 0.50 0.00 C ATOM 59 O AALA 6 -5.880 -1.605 -16.177 0.50 0.00 O ATOM 60 CB AALA 6 -5.358 0.040 -13.274 0.50 0.00 C ATOM 62 N BALA 6 -5.517 -2.338 -12.812 0.50 0.00 N ATOM 63 CA BALA 6 -5.779 -1.301 -13.795 0.50 0.00 C ATOM 64 C BALA 6 -5.142 -1.695 -15.130 0.50 0.00 C ATOM 65 O BALA 6 -5.780 -1.605 -16.177 0.50 0.00 O ATOM 66 CB BALA 6 -5.258 0.040 -13.274 0.50 0.00 C END """).construct_hierarchy() alpha_annot_1 = """\ HELIX 1 1 ALA 1 ALA 10 1 10 """ alpha_annot_2 = """\ HELIX 1 1 ALA 2 ALA 5 1 10 """ log = null_out() n_hbonds = [] n_hangles = [] for pdb_h, recs in [ (alpha_h1_simple, alpha_annot_1), (alpha_h1_1ac, alpha_annot_1), (alpha_h1_1_10ac, alpha_annot_1), (alpha_h1_1_5_10ac, alpha_annot_1), (alpha_h1_1_5_10ac_insertions, alpha_annot_1), (alpha_h1_1_5_10ac_insertions, alpha_annot_2), ]: ioss_annotation = ioss.annotation.from_records(records = recs.split('\n')) ann = ioss_annotation.as_restraint_groups(prefix_scope="secondary_structure") defpars = iotbx.phil.parse(sec_str_master_phil_str) custom_pars = defpars.fetch(iotbx.phil.parse(ann)) custom_pars_ex = custom_pars.extract() ss_manager = manager( pdb_h, sec_str_from_pdb_file=None, params=custom_pars_ex.secondary_structure, verbose=-1) proxies_for_grm, angle_p = ss_manager.create_protein_hbond_proxies( annotation= None, log = log) pdb_h.write_pdb_file(file_name="alpha_h1_1_5_10ac.pdb") # print proxies_for_grm.as_pymol_dashes(pdb_inp.hierarchy) # print angle_p.as_pymol_dashes(pdb_hierarchy=pdb_inp.hierarchy) # print "hbonds, hangles:", proxies_for_grm.size(), angle_p.size() # STOP() n_hbonds.append(proxies_for_grm.size()) n_hangles.append(angle_p.size()) print(n_hbonds, n_hangles) assert n_hbonds == [ 6, 7, 8, 9, 9, 5] assert n_hangles == [18, 21, 24, 28, 28, 16] def exercise_sheets_bonding_pattern(): pdb_apar_h = iotbx.pdb.input(source_info=None, lines = """\ 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 """).construct_hierarchy() pdb_par_h = iotbx.pdb.input(source_info=None, lines = """\ 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 """).construct_hierarchy() pdb_par_ac_h = iotbx.pdb.input(source_info=None, lines = """\ 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 1 N AALA A 15 5.011 -5.031 -8.967 0.50 5.73 N ATOM 2 CA AALA A 15 4.943 -6.455 -9.287 0.50 6.16 C ATOM 3 C AALA A 15 5.610 -7.252 -8.166 0.50 6.39 C ATOM 4 O AALA A 15 6.751 -7.007 -7.857 0.50 9.87 O ATOM 5 CB AALA A 15 5.684 -6.739 -10.604 0.50 7.46 C ATOM 6 N BALA A 15 5.111 -5.031 -8.967 0.50 5.73 N ATOM 7 CA BALA A 15 5.043 -6.455 -9.287 0.50 6.16 C ATOM 8 C BALA A 15 5.710 -7.252 -8.166 0.50 6.39 C ATOM 9 O BALA A 15 6.851 -7.007 -7.857 0.50 9.87 O ATOM 10 CB BALA A 15 5.784 -6.739 -10.604 0.50 7.46 C ATOM 11 N ATHR A 16 4.929 -8.263 -7.636 0.50 5.49 N ATOM 12 C ATHR A 16 5.316 -10.600 -7.084 0.50 5.07 C ATOM 13 O ATHR A 16 4.214 -11.002 -7.422 0.50 6.51 O ATOM 14 CA ATHR A 16 5.513 -9.172 -6.657 0.50 5.70 C ATOM 15 CB ATHR A 16 4.864 -9.001 -5.276 0.50 8.31 C ATOM 16 N BTHR A 16 5.029 -8.263 -7.636 0.50 5.49 N ATOM 17 C BTHR A 16 5.416 -10.600 -7.084 0.50 5.07 C ATOM 18 O BTHR A 16 4.314 -11.002 -7.422 0.50 6.51 O ATOM 19 CA BTHR A 16 5.613 -9.172 -6.657 0.50 5.70 C ATOM 20 CB BTHR A 16 4.964 -9.001 -5.276 0.50 8.31 C ATOM 21 N GLY A 17 6.393 -11.375 -7.067 1.00 4.56 N ATOM 22 CA GLY A 17 6.325 -12.770 -7.439 1.00 4.26 C ATOM 23 C GLY A 17 7.219 -13.654 -6.621 1.00 4.41 C ATOM 24 O GLY A 17 8.263 -13.233 -6.114 1.00 5.01 O ATOM 25 N SER A 18 6.827 -14.921 -6.561 1.00 4.24 N ATOM 26 CA SER A 18 7.657 -15.945 -5.959 1.00 4.02 C ATOM 27 C SER A 18 7.539 -17.244 -6.724 1.00 3.64 C ATOM 28 O SER A 18 6.482 -17.526 -7.331 1.00 4.07 O ATOM 29 CB SER A 18 7.335 -16.157 -4.481 1.00 5.86 C ATOM 30 N ALA A 19 8.573 -18.049 -6.627 1.00 3.19 N ATOM 31 CA ALA A 19 8.578 -19.414 -7.195 1.00 3.31 C ATOM 32 C ALA A 19 9.370 -20.307 -6.238 1.00 3.20 C ATOM 33 O ALA A 19 10.484 -19.956 -5.817 1.00 4.21 O ATOM 34 CB ALA A 19 9.235 -19.415 -8.574 1.00 3.85 C ATOM 35 N THR A 20 8.825 -21.476 -5.940 1.00 3.77 N ATOM 36 CA THR A 20 9.478 -22.432 -5.047 1.00 3.70 C ATOM 37 C THR A 20 9.444 -23.827 -5.640 1.00 3.56 C ATOM 38 O THR A 20 8.383 -24.281 -6.108 1.00 4.14 O ATOM 39 CB THR A 20 8.787 -22.430 -3.673 1.00 4.76 C ATOM 40 N THR A 21 10.560 -24.542 -5.569 1.00 4.00 N ATOM 41 CA THR A 21 10.597 -25.962 -5.876 1.00 4.05 C ATOM 42 C THR A 21 10.984 -26.770 -4.636 1.00 4.53 C ATOM 43 O THR A 21 11.770 -26.361 -3.802 1.00 5.04 O ATOM 44 CB THR A 21 11.488 -26.293 -7.083 1.00 4.38 C ATOM 45 N GLN A 40 0.280 -6.099 -9.049 1.00 6.35 N ATOM 46 CA GLN A 40 0.087 -7.454 -9.580 1.00 6.35 C ATOM 47 C GLN A 40 0.964 -8.417 -8.788 1.00 6.09 C ATOM 48 O GLN A 40 2.080 -8.093 -8.393 1.00 6.87 O ATOM 49 CB GLN A 40 0.461 -7.523 -11.060 1.00 7.52 C ATOM 50 N THR A 41 0.419 -9.596 -8.544 1.00 6.66 N ATOM 51 CA THR A 41 1.108 -10.640 -7.800 1.00 6.93 C ATOM 52 C THR A 41 0.932 -12.005 -8.414 1.00 6.82 C ATOM 53 O THR A 41 -0.069 -12.258 -9.104 1.00 8.79 O ATOM 54 CB THR A 41 0.633 -10.636 -6.352 1.00 10.84 C ATOM 55 N ALA A 42 1.951 -12.847 -8.263 1.00 6.44 N ATOM 56 CA ALA A 42 1.923 -14.209 -8.797 1.00 6.59 C ATOM 57 C ALA A 42 2.829 -15.117 -7.992 1.00 5.51 C ATOM 58 O ALA A 42 3.835 -14.684 -7.420 1.00 5.94 O ATOM 59 CB ALA A 42 2.327 -14.218 -10.264 1.00 9.02 C ATOM 60 N LYS A 43 2.479 -16.398 -7.978 1.00 6.26 N ATOM 61 CA LYS A 43 3.247 -17.395 -7.256 1.00 6.48 C ATOM 62 C LYS A 43 3.186 -18.741 -7.955 1.00 5.78 C ATOM 63 O LYS A 43 2.206 -19.041 -8.623 1.00 9.40 O ATOM 64 CB LYS A 43 2.727 -17.535 -5.836 1.00 8.81 C ATOM 65 N SER A 44 4.243 -19.534 -7.818 1.00 4.43 N ATOM 66 CA SER A 44 4.241 -20.890 -8.325 1.00 4.28 C ATOM 67 C SER A 44 4.998 -21.811 -7.358 1.00 4.09 C ATOM 68 O SER A 44 5.865 -21.377 -6.584 1.00 4.53 O ATOM 69 CB SER A 44 4.831 -20.949 -9.731 1.00 5.33 C ATOM 70 N PHE A 45 4.660 -23.091 -7.444 1.00 4.39 N ATOM 71 CA PHE A 45 5.198 -24.135 -6.576 1.00 4.44 C ATOM 72 C PHE A 45 5.222 -25.415 -7.389 1.00 4.16 C ATOM 73 O PHE A 45 4.183 -25.754 -7.979 1.00 5.11 O ATOM 74 CB PHE A 45 4.254 -24.281 -5.370 1.00 5.22 C ATOM 75 N ALA A 46 6.347 -26.119 -7.403 1.00 3.62 N ATOM 76 CA ALA A 46 6.443 -27.338 -8.202 1.00 3.99 C ATOM 77 C ALA A 46 7.579 -28.205 -7.717 1.00 4.57 C ATOM 78 O ALA A 46 8.479 -27.750 -7.000 1.00 4.79 O ATOM 79 CB ALA A 46 6.607 -27.026 -9.678 1.00 4.52 C TER 80 ALA A 46 END """).construct_hierarchy() pdb_apar2_h = iotbx.pdb.input(source_info=None, lines = """\ 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 """).construct_hierarchy() 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 n_hbonds = [] n_hangles = [] for pdb_h, recs in [ (pdb_apar_h, s_apar_records1), (pdb_apar_h, s_apar_records2), (pdb_par_h, s_par_records1), (pdb_par_h, s_par_records2), (pdb_par_h, s_par_records3), (pdb_par_h, s_par_records4), (pdb_par_h, s_par_records5), (pdb_par_h, s_par_records6), (pdb_par_h, s_par_records7), (pdb_par_h, s_par_records8), (pdb_apar2_h, s_apar_records3), (pdb_par_h, s_par_records9), (pdb_par_h, s_par_records10), (pdb_par_h, s_par_records11), (pdb_par_h, s_par_records12), (pdb_par_ac_h, s_par_records1), # 8 hbonds ]: ioss_annotation = ioss.annotation.from_records(records = recs.split('\n')) ann = ioss_annotation.as_restraint_groups(prefix_scope="secondary_structure") defpars = iotbx.phil.parse(sec_str_master_phil_str) custom_pars = defpars.fetch(iotbx.phil.parse(ann)) custom_pars_ex = custom_pars.extract() ss_manager = manager( pdb_h, sec_str_from_pdb_file=None, params=custom_pars_ex.secondary_structure, verbose=-1) proxies_for_grm, h_angles = ss_manager.create_protein_hbond_proxies( annotation= None, log = log) # print proxies_for_grm.size() n_hbonds.append(proxies_for_grm.size()) n_hangles.append(h_angles.size()) print(n_hbonds, n_hangles) assert n_hbonds == [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 3, 4, 2, 2, 8] assert n_hangles ==[15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 9, 6, 3, 24] def exercise_segid(): if (not libtbx.env.has_module(name="ksdssp")): print("KSDSSP not available, skipping exercise_segid()") return pdb_par_segid_h = iotbx.pdb.input(source_info=None, lines = """\ 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 """).construct_hierarchy() log = null_out() defpars = iotbx.phil.parse(sec_str_master_phil_str) custom_pars = defpars.extract() custom_pars.secondary_structure.enabled=True # custom_pars = defpars.fetch(iotbx.phil.parse("secondary_structure_restraints=True")) ss_manager = manager( pdb_par_segid_h, sec_str_from_pdb_file=None, params=custom_pars.secondary_structure, verbose=-1) ss_manager.initialize() proxies_for_grm, h_angles = ss_manager.create_protein_hbond_proxies( annotation = None, log = log) assert proxies_for_grm.size() == 4 assert h_angles.size() == 12 def exercise_phil_generation(): log = null_out() defpars = sec_str_master_phil.fetch() if __name__ == "__main__" : exercise_protein() exercise_sheet_ends() exercise_helix_bonding_pattern() exercise_sheets_bonding_pattern() # exercise_segid() # appeared to be nonvalid test... now when we don't ignore # segid in SS, we cannot construct SHEET situated in two different segids... print("OK")