from __future__ import absolute_import, division, print_function import time, sys, os from six.moves import cStringIO as StringIO import libtbx.load_env import mmtbx.model import iotbx.pdb from mmtbx.monomer_library import pdb_interpretation from cctbx.array_family import flex def run(): verbose = "--verbose" in sys.argv[1:] exercise_00(verbose=verbose) exercise_01(verbose=verbose) exercise_02(verbose=verbose) exercise_03(verbose=verbose) def get_model(file_name, log, pdb_str=None, make_restraints=True): pdb_interpretation_params = iotbx.phil.parse( input_string=pdb_interpretation.grand_master_phil_str, process_includes=True).extract() pdb_interpretation_params.pdb_interpretation.sort_atoms=False if not pdb_str: pdb_inp = iotbx.pdb.input(file_name=file_name) else: pdb_inp = iotbx.pdb.input(lines=pdb_str, source_info=None) model = mmtbx.model.manager( model_input = pdb_inp, stop_for_unknowns = False, log=log) model.process(pdb_interpretation_params=pdb_interpretation_params, make_restraints = make_restraints) return model def setup_riding(model): model.setup_riding_h_manager(ignore_h_with_dof = True) riding_h_manager = model.get_riding_h_manager() h_para = riding_h_manager.h_parameterization sel_h = model.get_hd_selection() sel_h_in_para = flex.bool( [bool(x) for x in riding_h_manager.h_parameterization]) sel_h_not_in_para = sel_h_in_para.exclusive_or(sel_h) return(list(sel_h_not_in_para.iselection())) def exercise_00(verbose): if (verbose): log = sys.stdout else: log = StringIO() model = get_model(file_name = None, log = log, pdb_str = pdb_str_1) rotatable_hd_sel = model.rotatable_hd_selection(use_shortcut = True) list_sel_h_not_in_para = setup_riding(model = model) s1 = set(list(rotatable_hd_sel)) s2 = set(list_sel_h_not_in_para) assert(s1 == s2) ph = model.get_hierarchy() atoms = ph.atoms() def exercise_01(verbose): if (verbose): log = sys.stdout else: log = StringIO() pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/ala_hd.pdb", test=os.path.isfile) model = get_model(pdb_file, log) # gives wrong result here: ignores D1,D2,D3 #rotatable_hd_sel = model.rotatable_hd_selection(use_shortcut = True) list_sel_h_not_in_para = setup_riding(model = model) s1 = set([5, 6, 7, 9, 10, 11, 12, 13, 14]) s2 = set(list_sel_h_not_in_para) assert(s1 == s2) def exercise_02(verbose): if (verbose): log = sys.stdout else: log = StringIO() pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/ala_lys_arg_ser_tyr_neutron_hd.pdb", test=os.path.isfile) model = get_model(pdb_file, log) # here rotatable has 6,7,8 twice in the selection??? rotatable_hd_sel = model.rotatable_hd_selection(use_shortcut = True) list_sel_h_not_in_para = setup_riding(model = model) s1 = set(list(rotatable_hd_sel)) s2 = set(list_sel_h_not_in_para) assert(s1 == s2) def exercise_03(verbose): """ Check incomplete propellers in H/D exchanged sites """ if (verbose): log = sys.stdout else: log = StringIO() model = get_model(file_name = None, log = log, pdb_str = pdb_str_2) rotatable_hd_sel = model.rotatable_hd_selection(use_shortcut = True) list_sel_h_not_in_para = setup_riding(model = model) #s1 = set(list(rotatable_hd_sel)) s1 = set([12, 13, 14, 15, 18, 19, 20, 21, 31, 34, 41, 51]) s2 = set(list_sel_h_not_in_para) #print(list(rotatable_hd_sel)) #print(list_sel_h_not_in_para) assert(s1 == s2) ph = model.get_hierarchy() atoms = ph.atoms() #ph = model.get_hierarchy() #atoms = ph.atoms() #for bla in list_sel_h_not_in_para: # print(atoms[bla].id_str()) # Ideal amino acids pdb_str_1 = """\ CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 SCALE1 0.033333 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033333 0.00000 ATOM 1 N ARG A 2 3.050 19.481 25.856 1.00 0.00 N ATOM 2 CA ARG A 2 3.759 20.265 24.852 1.00 0.00 C ATOM 3 C ARG A 2 5.253 20.304 25.155 1.00 0.00 C ATOM 4 O ARG A 2 5.659 20.516 26.298 1.00 0.00 O ATOM 5 CB ARG A 2 3.197 21.687 24.787 1.00 0.00 C ATOM 6 CG ARG A 2 3.800 22.542 23.684 1.00 0.00 C ATOM 7 CD ARG A 2 3.128 23.904 23.607 1.00 0.00 C ATOM 8 NE ARG A 2 3.721 24.751 22.576 1.00 0.00 N ATOM 9 CZ ARG A 2 3.311 25.983 22.290 1.00 0.00 C ATOM 10 NH1 ARG A 2 2.301 26.525 22.957 1.00 0.00 N1+ ATOM 11 NH2 ARG A 2 3.914 26.676 21.334 1.00 0.00 N ATOM 12 HA ARG A 2 3.638 19.852 23.983 1.00 0.00 H ATOM 13 HB2 ARG A 2 2.240 21.637 24.633 1.00 0.00 H ATOM 14 HB3 ARG A 2 3.370 22.129 25.633 1.00 0.00 H ATOM 15 HG2 ARG A 2 4.743 22.680 23.864 1.00 0.00 H ATOM 16 HG3 ARG A 2 3.682 22.096 22.831 1.00 0.00 H ATOM 17 HD2 ARG A 2 2.189 23.783 23.396 1.00 0.00 H ATOM 18 HD3 ARG A 2 3.224 24.355 24.460 1.00 0.00 H ATOM 19 HE ARG A 2 4.380 24.432 22.124 1.00 0.00 H ATOM 20 HH11 ARG A 2 1.905 26.082 23.579 1.00 0.00 H ATOM 21 HH12 ARG A 2 2.041 27.322 22.767 1.00 0.00 H ATOM 22 HH21 ARG A 2 4.569 26.329 20.898 1.00 0.00 H ATOM 23 HH22 ARG A 2 3.649 27.473 21.149 1.00 0.00 H ATOM 24 N HIS A 3 6.067 20.098 24.123 1.00 0.00 N ATOM 25 CA HIS A 3 7.516 20.107 24.260 1.00 0.00 C ATOM 26 C HIS A 3 8.133 20.732 23.018 1.00 0.00 C ATOM 27 O HIS A 3 7.638 20.536 21.904 1.00 0.00 O ATOM 28 CB HIS A 3 8.069 18.691 24.464 1.00 0.00 C ATOM 29 CG HIS A 3 7.630 18.050 25.743 1.00 0.00 C ATOM 30 ND1 HIS A 3 8.154 18.399 26.969 1.00 0.00 N ATOM 31 CD2 HIS A 3 6.716 17.080 25.988 1.00 0.00 C ATOM 32 CE1 HIS A 3 7.582 17.674 27.913 1.00 0.00 C ATOM 33 NE2 HIS A 3 6.706 16.865 27.344 1.00 0.00 N ATOM 34 H HIS A 3 5.797 19.948 23.320 1.00 0.00 H ATOM 35 HA HIS A 3 7.764 20.646 25.027 1.00 0.00 H ATOM 36 HB2 HIS A 3 7.768 18.129 23.732 1.00 0.00 H ATOM 37 HB3 HIS A 3 9.038 18.731 24.470 1.00 0.00 H ATOM 38 HD2 HIS A 3 6.194 16.642 25.355 1.00 0.00 H ATOM 39 HE1 HIS A 3 7.765 17.723 28.824 1.00 0.00 H ATOM 40 N LYS A 4 9.213 21.483 23.217 1.00 0.00 N ATOM 41 CA LYS A 4 9.902 22.139 22.116 1.00 0.00 C ATOM 42 C LYS A 4 11.340 22.409 22.530 1.00 0.00 C ATOM 43 O LYS A 4 11.602 22.774 23.678 1.00 0.00 O ATOM 44 CB LYS A 4 9.205 23.447 21.722 1.00 0.00 C ATOM 45 CG LYS A 4 9.799 24.121 20.495 1.00 0.00 C ATOM 46 CD LYS A 4 9.008 25.357 20.102 1.00 0.00 C ATOM 47 CE LYS A 4 9.606 26.035 18.880 1.00 0.00 C ATOM 48 NZ LYS A 4 8.842 27.250 18.484 1.00 0.00 N1+ ATOM 49 H LYS A 4 9.568 21.628 23.987 1.00 0.00 H ATOM 50 HA LYS A 4 9.909 21.551 21.344 1.00 0.00 H ATOM 51 HB2 LYS A 4 8.272 23.258 21.533 1.00 0.00 H ATOM 52 HB3 LYS A 4 9.270 24.070 22.462 1.00 0.00 H ATOM 53 HG2 LYS A 4 10.710 24.392 20.688 1.00 0.00 H ATOM 54 HG3 LYS A 4 9.784 23.500 19.750 1.00 0.00 H ATOM 55 HD2 LYS A 4 8.096 25.101 19.892 1.00 0.00 H ATOM 56 HD3 LYS A 4 9.018 25.991 20.837 1.00 0.00 H ATOM 57 HE2 LYS A 4 10.517 26.302 19.078 1.00 0.00 H ATOM 58 HE3 LYS A 4 9.594 25.415 18.135 1.00 0.00 H ATOM 59 HZ1 LYS A 4 9.215 27.624 17.768 1.00 0.00 H ATOM 60 HZ2 LYS A 4 8.001 27.031 18.292 1.00 0.00 H ATOM 61 HZ3 LYS A 4 8.842 27.840 19.151 1.00 0.00 H ATOM 62 N ASP A 5 12.263 22.226 21.588 1.00 0.00 N ATOM 63 CA ASP A 5 13.678 22.447 21.845 1.00 0.00 C ATOM 64 C ASP A 5 14.374 22.763 20.531 1.00 0.00 C ATOM 65 O ASP A 5 14.035 22.197 19.489 1.00 0.00 O ATOM 66 CB ASP A 5 14.324 21.224 22.508 1.00 0.00 C ATOM 67 CG ASP A 5 15.729 21.504 23.005 1.00 0.00 C ATOM 68 OD1 ASP A 5 16.213 22.640 22.819 1.00 0.00 O ATOM 69 OD2 ASP A 5 16.350 20.587 23.582 1.00 0.00 O1- ATOM 70 H ASP A 5 12.091 21.972 20.785 1.00 0.00 H ATOM 71 HA ASP A 5 13.783 23.208 22.438 1.00 0.00 H ATOM 72 HB2 ASP A 5 13.785 20.954 23.267 1.00 0.00 H ATOM 73 HB3 ASP A 5 14.372 20.503 21.861 1.00 0.00 H ATOM 74 N GLU A 6 15.346 23.668 20.589 1.00 0.00 N ATOM 75 CA GLU A 6 16.096 24.064 19.403 1.00 0.00 C ATOM 76 C GLU A 6 17.433 24.684 19.794 1.00 0.00 C ATOM 77 O GLU A 6 17.829 24.647 20.959 1.00 0.00 O ATOM 78 CB GLU A 6 15.283 25.051 18.561 1.00 0.00 C ATOM 79 CG GLU A 6 15.942 25.433 17.245 1.00 0.00 C ATOM 80 CD GLU A 6 15.076 26.352 16.405 1.00 0.00 C ATOM 81 OE1 GLU A 6 13.969 26.708 16.861 1.00 0.00 O ATOM 82 OE2 GLU A 6 15.503 26.718 15.290 1.00 0.00 O1- ATOM 83 H GLU A 6 15.592 24.070 21.309 1.00 0.00 H ATOM 84 HA GLU A 6 16.273 23.279 18.862 1.00 0.00 H ATOM 85 HB2 GLU A 6 14.424 24.651 18.356 1.00 0.00 H ATOM 86 HB3 GLU A 6 15.153 25.864 19.073 1.00 0.00 H ATOM 87 HG2 GLU A 6 16.776 25.893 17.428 1.00 0.00 H ATOM 88 HG3 GLU A 6 16.112 24.628 16.730 1.00 0.00 H TER ATOM 89 N SER B 2 10.846 4.462 24.534 1.00 0.00 N ATOM 90 CA SER B 2 11.518 5.747 24.391 1.00 0.00 C ATOM 91 C SER B 2 13.032 5.575 24.457 1.00 0.00 C ATOM 92 O SER B 2 13.532 4.595 25.009 1.00 0.00 O ATOM 93 CB SER B 2 11.052 6.719 25.477 1.00 0.00 C ATOM 94 OG SER B 2 11.455 6.279 26.762 1.00 0.00 O ATOM 95 HA SER B 2 11.295 6.129 23.528 1.00 0.00 H ATOM 96 HB2 SER B 2 11.440 7.591 25.307 1.00 0.00 H ATOM 97 HB3 SER B 2 10.084 6.777 25.453 1.00 0.00 H ATOM 98 HG SER B 2 11.125 5.523 26.924 1.00 0.00 H ATOM 99 N THR B 3 13.758 6.536 23.889 1.00 0.00 N ATOM 100 CA THR B 3 15.212 6.498 23.880 1.00 0.00 C ATOM 101 C THR B 3 15.741 7.920 23.778 1.00 0.00 C ATOM 102 O THR B 3 15.212 8.733 23.015 1.00 0.00 O ATOM 103 CB THR B 3 15.746 5.652 22.717 1.00 0.00 C ATOM 104 OG1 THR B 3 15.230 4.319 22.813 1.00 0.00 O ATOM 105 CG2 THR B 3 17.268 5.606 22.740 1.00 0.00 C ATOM 106 H THR B 3 13.425 7.226 23.499 1.00 0.00 H ATOM 107 HA THR B 3 15.530 6.111 24.711 1.00 0.00 H ATOM 108 HB THR B 3 15.465 6.046 21.876 1.00 0.00 H ATOM 109 HG1 THR B 3 15.519 3.852 22.178 1.00 0.00 H ATOM 110 HG21 THR B 3 17.587 4.933 22.118 1.00 0.00 H ATOM 111 HG22 THR B 3 17.633 6.467 22.484 1.00 0.00 H ATOM 112 HG23 THR B 3 17.580 5.381 23.631 1.00 0.00 H ATOM 113 N ASN B 4 16.785 8.212 24.552 1.00 0.00 N ATOM 114 CA ASN B 4 17.402 9.533 24.564 1.00 0.00 C ATOM 115 C ASN B 4 18.904 9.364 24.725 1.00 0.00 C ATOM 116 O ASN B 4 19.359 8.747 25.692 1.00 0.00 O ATOM 117 CB ASN B 4 16.835 10.400 25.693 1.00 0.00 C ATOM 118 CG ASN B 4 15.357 10.690 25.518 1.00 0.00 C ATOM 119 OD1 ASN B 4 14.528 10.254 26.317 1.00 0.00 O ATOM 120 ND2 ASN B 4 15.019 11.430 24.468 1.00 0.00 N ATOM 121 H ASN B 4 17.158 7.651 25.086 1.00 0.00 H ATOM 122 HA ASN B 4 17.232 9.979 23.719 1.00 0.00 H ATOM 123 HB2 ASN B 4 16.953 9.937 26.537 1.00 0.00 H ATOM 124 HB3 ASN B 4 17.307 11.247 25.709 1.00 0.00 H ATOM 125 HD21 ASN B 4 14.193 11.622 24.326 1.00 0.00 H ATOM 126 HD22 ASN B 4 15.626 11.717 23.931 1.00 0.00 H ATOM 127 N GLN B 5 19.666 9.908 23.781 1.00 0.00 N ATOM 128 CA GLN B 5 21.121 9.817 23.821 1.00 0.00 C ATOM 129 C GLN B 5 21.756 11.122 23.352 1.00 0.00 C ATOM 130 O GLN B 5 21.299 11.734 22.387 1.00 0.00 O ATOM 131 CB GLN B 5 21.610 8.654 22.957 1.00 0.00 C ATOM 132 CG GLN B 5 21.217 7.283 23.483 1.00 0.00 C ATOM 133 CD GLN B 5 21.709 6.155 22.598 1.00 0.00 C ATOM 134 OE1 GLN B 5 22.296 6.391 21.542 1.00 0.00 O ATOM 135 NE2 GLN B 5 21.472 4.920 23.025 1.00 0.00 N ATOM 136 H GLN B 5 19.362 10.339 23.102 1.00 0.00 H ATOM 137 HA GLN B 5 21.406 9.656 24.734 1.00 0.00 H ATOM 138 HB2 GLN B 5 21.235 8.747 22.067 1.00 0.00 H ATOM 139 HB3 GLN B 5 22.578 8.686 22.909 1.00 0.00 H ATOM 140 HG2 GLN B 5 21.600 7.161 24.366 1.00 0.00 H ATOM 141 HG3 GLN B 5 20.250 7.227 23.530 1.00 0.00 H ATOM 142 HE21 GLN B 5 21.732 4.246 22.559 1.00 0.00 H ATOM 143 HE22 GLN B 5 21.059 4.795 23.769 1.00 0.00 H TER ATOM 144 N CYS C 2 14.789 22.141 7.021 1.00 0.00 N ATOM 145 CA CYS C 2 15.170 23.547 7.063 1.00 0.00 C ATOM 146 C CYS C 2 16.660 23.696 7.350 1.00 0.00 C ATOM 147 O CYS C 2 17.074 23.780 8.506 1.00 0.00 O ATOM 148 CB CYS C 2 14.354 24.292 8.122 1.00 0.00 C ATOM 149 SG CYS C 2 14.698 26.064 8.213 1.00 0.00 S ATOM 150 HA CYS C 2 14.987 23.952 6.201 1.00 0.00 H ATOM 151 HB2 CYS C 2 13.411 24.185 7.920 1.00 0.00 H ATOM 152 HB3 CYS C 2 14.548 23.908 8.991 1.00 0.00 H ATOM 153 HG CYS C 2 14.012 26.553 9.067 1.00 0.00 H ATOM 154 N GLY C 3 17.463 23.727 6.287 1.00 0.00 N ATOM 155 CA GLY C 3 18.892 23.864 6.428 1.00 0.00 C ATOM 156 C GLY C 3 19.301 25.288 6.737 1.00 0.00 C ATOM 157 O GLY C 3 18.476 26.206 6.840 1.00 0.00 O ATOM 158 H GLY C 3 17.194 23.670 5.472 1.00 0.00 H ATOM 159 HA2 GLY C 3 19.202 23.291 7.146 1.00 0.00 H ATOM 160 HA3 GLY C 3 19.325 23.590 5.604 1.00 0.00 H ATOM 161 N PRO C 4 20.618 25.490 6.891 1.00 0.00 N ATOM 162 CA PRO C 4 21.173 26.813 7.198 1.00 0.00 C ATOM 163 C PRO C 4 21.113 27.768 6.010 1.00 0.00 C ATOM 164 O PRO C 4 21.345 27.333 4.882 1.00 0.00 O ATOM 165 CB PRO C 4 22.622 26.503 7.578 1.00 0.00 C ATOM 166 CG PRO C 4 22.943 25.252 6.843 1.00 0.00 C ATOM 167 CD PRO C 4 21.667 24.460 6.790 1.00 0.00 C ATOM 168 HA PRO C 4 20.715 27.207 7.957 1.00 0.00 H ATOM 169 HB2 PRO C 4 23.199 27.228 7.291 1.00 0.00 H ATOM 170 HB3 PRO C 4 22.689 26.366 8.536 1.00 0.00 H ATOM 171 HG2 PRO C 4 23.244 25.471 5.947 1.00 0.00 H ATOM 172 HG3 PRO C 4 23.628 24.761 7.322 1.00 0.00 H ATOM 173 HD2 PRO C 4 21.599 23.988 5.945 1.00 0.00 H ATOM 174 HD3 PRO C 4 21.617 23.851 7.543 1.00 0.00 H TER ATOM 175 N ALA D 2 2.619 6.211 7.571 1.00 0.00 N ATOM 176 CA ALA D 2 3.623 7.047 8.219 1.00 0.00 C ATOM 177 C ALA D 2 4.961 6.321 8.294 1.00 0.00 C ATOM 178 O ALA D 2 5.056 5.233 8.863 1.00 0.00 O ATOM 179 CB ALA D 2 3.159 7.450 9.610 1.00 0.00 C ATOM 180 HA ALA D 2 3.748 7.855 7.697 1.00 0.00 H ATOM 181 HB1 ALA D 2 3.840 8.005 10.021 1.00 0.00 H ATOM 182 HB2 ALA D 2 2.329 7.947 9.534 1.00 0.00 H ATOM 183 HB3 ALA D 2 3.018 6.650 10.139 1.00 0.00 H ATOM 184 N LEU D 3 6.002 6.934 7.712 1.00 0.00 N ATOM 185 CA LEU D 3 7.348 6.371 7.695 1.00 0.00 C ATOM 186 C LEU D 3 8.344 7.510 7.935 1.00 0.00 C ATOM 187 O LEU D 3 9.150 7.868 7.078 1.00 0.00 O ATOM 188 CB LEU D 3 7.634 5.644 6.379 1.00 0.00 C ATOM 189 CG LEU D 3 6.792 4.396 6.105 1.00 0.00 C ATOM 190 CD1 LEU D 3 7.036 3.888 4.692 1.00 0.00 C ATOM 191 CD2 LEU D 3 7.088 3.307 7.125 1.00 0.00 C ATOM 192 H LEU D 3 5.945 7.694 7.313 1.00 0.00 H ATOM 193 HA LEU D 3 7.438 5.734 8.421 1.00 0.00 H ATOM 194 HB2 LEU D 3 7.479 6.264 5.649 1.00 0.00 H ATOM 195 HB3 LEU D 3 8.565 5.371 6.377 1.00 0.00 H ATOM 196 HG LEU D 3 5.853 4.628 6.180 1.00 0.00 H ATOM 197 HD11 LEU D 3 6.493 3.099 4.543 1.00 0.00 H ATOM 198 HD12 LEU D 3 6.791 4.583 4.061 1.00 0.00 H ATOM 199 HD13 LEU D 3 7.975 3.668 4.594 1.00 0.00 H ATOM 200 HD21 LEU D 3 6.619 2.498 6.867 1.00 0.00 H ATOM 201 HD22 LEU D 3 8.044 3.144 7.143 1.00 0.00 H ATOM 202 HD23 LEU D 3 6.785 3.600 7.998 1.00 0.00 H ATOM 203 N ILE D 4 8.286 8.091 9.130 1.00 0.00 N ATOM 204 CA ILE D 4 9.174 9.189 9.499 1.00 0.00 C ATOM 205 C ILE D 4 10.531 8.595 9.863 1.00 0.00 C ATOM 206 O ILE D 4 10.691 7.990 10.926 1.00 0.00 O ATOM 207 CB ILE D 4 8.599 10.013 10.657 1.00 0.00 C ATOM 208 CG1 ILE D 4 7.284 10.674 10.236 1.00 0.00 C ATOM 209 CG2 ILE D 4 9.604 11.067 11.108 1.00 0.00 C ATOM 210 CD1 ILE D 4 6.474 11.224 11.392 1.00 0.00 C ATOM 211 H ILE D 4 7.736 7.865 9.751 1.00 0.00 H ATOM 212 HA ILE D 4 9.293 9.777 8.736 1.00 0.00 H ATOM 213 HB ILE D 4 8.421 9.417 11.401 1.00 0.00 H ATOM 214 HG12 ILE D 4 7.482 11.410 9.637 1.00 0.00 H ATOM 215 HG13 ILE D 4 6.734 10.018 9.778 1.00 0.00 H ATOM 216 HG21 ILE D 4 9.158 11.702 11.690 1.00 0.00 H ATOM 217 HG22 ILE D 4 10.326 10.633 11.590 1.00 0.00 H ATOM 218 HG23 ILE D 4 9.953 11.525 10.328 1.00 0.00 H ATOM 219 HD11 ILE D 4 5.603 11.498 11.065 1.00 0.00 H ATOM 220 HD12 ILE D 4 6.373 10.531 12.063 1.00 0.00 H ATOM 221 HD13 ILE D 4 6.939 11.986 11.771 1.00 0.00 H ATOM 222 N MET D 5 11.514 8.768 8.978 1.00 0.00 N ATOM 223 CA MET D 5 12.863 8.258 9.192 1.00 0.00 C ATOM 224 C MET D 5 13.872 9.277 8.657 1.00 0.00 C ATOM 225 O MET D 5 14.680 9.000 7.775 1.00 0.00 O ATOM 226 CB MET D 5 13.042 6.896 8.525 1.00 0.00 C ATOM 227 CG MET D 5 12.226 5.783 9.162 1.00 0.00 C ATOM 228 SD MET D 5 12.466 4.191 8.350 1.00 0.00 S ATOM 229 CE MET D 5 11.320 3.166 9.268 1.00 0.00 C ATOM 230 H MET D 5 11.418 9.186 8.232 1.00 0.00 H ATOM 231 HA MET D 5 13.009 8.144 10.144 1.00 0.00 H ATOM 232 HB2 MET D 5 12.772 6.965 7.596 1.00 0.00 H ATOM 233 HB3 MET D 5 13.977 6.644 8.577 1.00 0.00 H ATOM 234 HG2 MET D 5 12.490 5.689 10.091 1.00 0.00 H ATOM 235 HG3 MET D 5 11.284 6.009 9.107 1.00 0.00 H ATOM 236 HE1 MET D 5 11.356 2.262 8.918 1.00 0.00 H ATOM 237 HE2 MET D 5 11.574 3.169 10.204 1.00 0.00 H ATOM 238 HE3 MET D 5 10.425 3.525 9.167 1.00 0.00 H ATOM 239 N PHE D 6 13.825 10.488 9.205 1.00 0.00 N ATOM 240 CA PHE D 6 14.731 11.547 8.787 1.00 0.00 C ATOM 241 C PHE D 6 16.111 11.331 9.393 1.00 0.00 C ATOM 242 O PHE D 6 16.244 10.831 10.514 1.00 0.00 O ATOM 243 CB PHE D 6 14.186 12.914 9.206 1.00 0.00 C ATOM 244 CG PHE D 6 12.873 13.276 8.562 1.00 0.00 C ATOM 245 CD1 PHE D 6 12.416 12.605 7.437 1.00 0.00 C ATOM 246 CD2 PHE D 6 12.093 14.294 9.087 1.00 0.00 C ATOM 247 CE1 PHE D 6 11.210 12.943 6.852 1.00 0.00 C ATOM 248 CE2 PHE D 6 10.887 14.635 8.506 1.00 0.00 C ATOM 249 CZ PHE D 6 10.445 13.959 7.388 1.00 0.00 C ATOM 250 H PHE D 6 13.274 10.720 9.823 1.00 0.00 H ATOM 251 HA PHE D 6 14.827 11.530 7.822 1.00 0.00 H ATOM 252 HB2 PHE D 6 14.055 12.916 10.167 1.00 0.00 H ATOM 253 HB3 PHE D 6 14.833 13.595 8.962 1.00 0.00 H ATOM 254 HD1 PHE D 6 12.924 11.919 7.069 1.00 0.00 H ATOM 255 HD2 PHE D 6 12.386 14.753 9.841 1.00 0.00 H ATOM 256 HE1 PHE D 6 10.914 12.486 6.099 1.00 0.00 H ATOM 257 HE2 PHE D 6 10.373 15.320 8.869 1.00 0.00 H ATOM 258 HZ PHE D 6 9.634 14.188 6.995 1.00 0.00 H ATOM 259 N TRP D 7 17.142 11.711 8.641 1.00 0.00 N ATOM 260 CA TRP D 7 18.523 11.570 9.084 1.00 0.00 C ATOM 261 C TRP D 7 19.334 12.742 8.558 1.00 0.00 C ATOM 262 O TRP D 7 19.223 13.098 7.381 1.00 0.00 O ATOM 263 CB TRP D 7 19.129 10.247 8.600 1.00 0.00 C ATOM 264 CG TRP D 7 18.518 9.038 9.242 1.00 0.00 C ATOM 265 CD1 TRP D 7 17.534 8.246 8.727 1.00 0.00 C ATOM 266 CD2 TRP D 7 18.852 8.483 10.520 1.00 0.00 C ATOM 267 NE1 TRP D 7 17.234 7.232 9.605 1.00 0.00 N ATOM 268 CE2 TRP D 7 18.030 7.356 10.713 1.00 0.00 C ATOM 269 CE3 TRP D 7 19.767 8.831 11.519 1.00 0.00 C ATOM 270 CZ2 TRP D 7 18.095 6.573 11.864 1.00 0.00 C ATOM 271 CZ3 TRP D 7 19.829 8.053 12.661 1.00 0.00 C ATOM 272 CH2 TRP D 7 18.998 6.937 12.824 1.00 0.00 C ATOM 273 H TRP D 7 17.064 12.059 7.859 1.00 0.00 H ATOM 274 HA TRP D 7 18.555 11.585 10.053 1.00 0.00 H ATOM 275 HB2 TRP D 7 18.996 10.173 7.642 1.00 0.00 H ATOM 276 HB3 TRP D 7 20.077 10.244 8.803 1.00 0.00 H ATOM 277 HD1 TRP D 7 17.125 8.373 7.901 1.00 0.00 H ATOM 278 HE1 TRP D 7 16.644 6.620 9.479 1.00 0.00 H ATOM 279 HE3 TRP D 7 20.322 9.570 11.418 1.00 0.00 H ATOM 280 HZ2 TRP D 7 17.544 5.832 11.976 1.00 0.00 H ATOM 281 HZ3 TRP D 7 20.434 8.274 13.332 1.00 0.00 H ATOM 282 HH2 TRP D 7 19.063 6.433 13.603 1.00 0.00 H ATOM 283 N TYR D 8 20.146 13.338 9.431 1.00 0.00 N ATOM 284 CA TYR D 8 20.988 14.478 9.066 1.00 0.00 C ATOM 285 C TYR D 8 22.308 14.337 9.818 1.00 0.00 C ATOM 286 O TYR D 8 22.402 14.703 10.993 1.00 0.00 O ATOM 287 CB TYR D 8 20.302 15.800 9.392 1.00 0.00 C ATOM 288 CG TYR D 8 19.076 16.075 8.551 1.00 0.00 C ATOM 289 CD1 TYR D 8 19.192 16.579 7.263 1.00 0.00 C ATOM 290 CD2 TYR D 8 17.801 15.832 9.046 1.00 0.00 C ATOM 291 CE1 TYR D 8 18.075 16.832 6.490 1.00 0.00 C ATOM 292 CE2 TYR D 8 16.678 16.082 8.282 1.00 0.00 C ATOM 293 CZ TYR D 8 16.820 16.582 7.005 1.00 0.00 C ATOM 294 OH TYR D 8 15.704 16.833 6.240 1.00 0.00 O ATOM 295 H TYR D 8 20.228 13.097 10.252 1.00 0.00 H ATOM 296 HA TYR D 8 21.173 14.454 8.115 1.00 0.00 H ATOM 297 HB2 TYR D 8 20.027 15.788 10.322 1.00 0.00 H ATOM 298 HB3 TYR D 8 20.931 16.523 9.244 1.00 0.00 H ATOM 299 HD1 TYR D 8 20.037 16.749 6.913 1.00 0.00 H ATOM 300 HD2 TYR D 8 17.703 15.494 9.907 1.00 0.00 H ATOM 301 HE1 TYR D 8 18.168 17.170 5.629 1.00 0.00 H ATOM 302 HE2 TYR D 8 15.831 15.914 8.626 1.00 0.00 H ATOM 303 HH TYR D 8 15.010 16.638 6.671 1.00 0.00 H ATOM 304 N VAL D 9 23.320 13.807 9.139 1.00 0.00 N ATOM 305 CA VAL D 9 24.632 13.618 9.743 1.00 0.00 C ATOM 306 C VAL D 9 25.377 14.947 9.786 1.00 0.00 C ATOM 307 O VAL D 9 25.756 15.491 8.749 1.00 0.00 O ATOM 308 CB VAL D 9 25.449 12.559 8.980 1.00 0.00 C ATOM 309 CG1 VAL D 9 26.843 12.427 9.578 1.00 0.00 C ATOM 310 CG2 VAL D 9 24.726 11.220 8.995 1.00 0.00 C ATOM 311 H VAL D 9 23.271 13.548 8.320 1.00 0.00 H ATOM 312 HA VAL D 9 24.518 13.309 10.655 1.00 0.00 H ATOM 313 HB VAL D 9 25.544 12.838 8.056 1.00 0.00 H ATOM 314 HG11 VAL D 9 27.251 11.612 9.245 1.00 0.00 H ATOM 315 HG12 VAL D 9 27.376 13.193 9.316 1.00 0.00 H ATOM 316 HG13 VAL D 9 26.769 12.386 10.544 1.00 0.00 H ATOM 317 HG21 VAL D 9 25.275 10.560 8.542 1.00 0.00 H ATOM 318 HG22 VAL D 9 24.578 10.952 9.915 1.00 0.00 H ATOM 319 HG23 VAL D 9 23.876 11.314 8.536 1.00 0.00 H TER END """ pdb_str_2 = """ CRYST1 43.705 48.284 96.292 90.00 90.00 90.00 P 1 SCALE1 0.022881 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010385 0.00000 ATOM 37 N LEU A 3 23.374 -21.865 -28.222 1.00 15.90 N ATOM 38 CA LEU A 3 23.342 -21.224 -29.530 1.00 15.47 C ATOM 39 C LEU A 3 23.637 -19.727 -29.491 1.00 18.18 C ATOM 40 O LEU A 3 24.174 -19.175 -30.462 1.00 20.24 O ATOM 41 CB LEU A 3 22.021 -21.521 -30.238 1.00 15.76 C ATOM 42 CG LEU A 3 21.790 -23.005 -30.533 1.00 19.30 C ATOM 43 CD1 LEU A 3 20.460 -23.197 -31.290 1.00 20.74 C ATOM 44 CD2 LEU A 3 22.957 -23.627 -31.336 1.00 17.02 C ATOM 45 DA LEU A 3 24.132 -21.653 -30.101 1.00 12.76 D ATOM 46 DB3 LEU A 3 21.233 -21.196 -29.610 1.00 17.93 D ATOM 48 DB2ALEU A 3 21.964 -20.976 -31.155 0.67 16.51 D ATOM 49 DG ALEU A 3 21.719 -23.530 -29.581 0.68 18.31 D REMARK ATOM 50 DD11ALEU A 3 19.620 -22.925 -30.652 0.74 20.52 D ATOM 51 DD12ALEU A 3 20.364 -24.239 -31.597 0.77 19.78 D ATOM 52 DD13ALEU A 3 20.458 -22.568 -32.171 0.49 20.26 D ATOM 53 DD21ALEU A 3 23.466 -22.855 -31.890 0.40 16.87 D REMARK ATOM 54 DD22ALEU A 3 22.563 -24.357 -32.028 0.00 16.68 D ATOM 55 DD23ALEU A 3 23.653 -24.109 -30.673 0.89 14.39 D ATOM 57 HB2BLEU A 3 21.964 -20.976 -31.155 0.33 14.51 H ATOM 58 HG BLEU A 3 21.719 -23.530 -29.581 0.32 18.31 H ATOM 59 HD11BLEU A 3 19.620 -22.925 -30.652 0.26 20.52 H ATOM 60 HD12BLEU A 3 20.364 -24.239 -31.597 0.23 19.78 H REMARK ATOM 61 HD13BLEU A 3 20.458 -22.568 -32.171 0.51 20.26 H REMARK ATOM 62 HD21BLEU A 3 23.466 -22.855 -31.890 0.60 16.87 H ATOM 63 HD22BLEU A 3 22.563 -24.357 -32.028 0.58 16.68 H ATOM 64 HD23BLEU A 3 23.653 -24.109 -30.673 0.11 14.39 H ATOM 65 N SER A 4 9.243 -32.509 -36.471 1.00 38.02 N ATOM 66 CA SER A 4 10.063 -33.604 -36.981 1.00 39.55 C ATOM 67 C SER A 4 11.459 -33.153 -37.367 1.00 37.45 C ATOM 68 O SER A 4 11.633 -32.304 -38.239 1.00 38.82 O ATOM 69 CB SER A 4 9.384 -34.279 -38.180 1.00 41.66 C ATOM 70 OG SER A 4 8.375 -35.181 -37.753 1.00 44.91 O ATOM 71 DA SER A 4 10.165 -34.324 -36.187 1.00 38.72 D ATOM 73 DB2ASER A 4 10.116 -34.818 -38.774 0.63 41.36 D ATOM 74 DB3ASER A 4 8.918 -33.518 -38.793 0.36 41.73 D ATOM 75 DG ASER A 4 8.699 -36.084 -37.842 0.36 43.61 D ATOM 77 HB2BSER A 4 8.918 -33.518 -38.793 0.64 41.73 H ATOM 78 HB3BSER A 4 10.116 -34.818 -38.774 0.37 41.36 H ATOM 79 HG BSER A 4 8.699 -36.084 -37.842 0.64 43.61 H ATOM 80 N SER A 5 26.478 -19.398 45.776 1.00 19.78 N ATOM 81 C SER A 5 27.940 -19.562 43.818 1.00 21.99 C ATOM 82 O SER A 5 29.005 -19.770 43.306 1.00 21.20 O ATOM 83 CA ASER A 5 27.849 -19.441 45.318 0.64 18.99 C ATOM 84 CB ASER A 5 28.611 -20.590 45.987 0.64 21.66 C ATOM 85 OG ASER A 5 28.819 -20.337 47.363 0.64 23.21 O ATOM 86 DG ASER A 5 29.639 -20.155 47.499 0.64 22.10 D ATOM 88 HA ASER A 5 28.296 -18.610 45.561 0.64 20.89 H ATOM 89 HB2ASER A 5 28.094 -21.408 45.903 0.00 22.17 H ATOM 90 HB3ASER A 5 29.468 -20.686 45.544 0.64 22.38 H ATOM 91 CA BSER A 5 27.851 -19.476 45.322 0.36 19.02 C ATOM 92 CB BSER A 5 28.561 -20.680 45.932 0.36 21.98 C ATOM 93 OG BSER A 5 28.005 -21.879 45.425 0.36 25.40 O ATOM 95 HA BSER A 5 28.327 -18.675 45.599 0.36 21.03 H ATOM 96 HB2BSER A 5 29.498 -20.638 45.691 0.36 22.55 H ATOM 97 HB3BSER A 5 28.462 -20.665 46.898 0.36 23.83 H ATOM 98 HG BSER A 5 27.486 -22.196 46.000 0.36 22.10 H TER """ if (__name__ == "__main__"): t0 = time.time() run() print("OK. Time: %8.3f"%(time.time()-t0))