from __future__ import absolute_import, division, print_function import time import mmtbx.model import iotbx.pdb from libtbx.utils import null_out from six.moves import zip #----------------------------------------------------------------------------- # This test checks the parameterization of hydrogen atoms for nucleic acids # Steps: # 1) determine parameterization # 2) Compare calculated position of H from parameterization to input position # test fails if distance is > 0.001 A (= precision of coordinates) #----------------------------------------------------------------------------- def exercise(): pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) model.process(make_restraints=True) pdb_hierarchy = model.get_hierarchy() sites_cart = model.get_sites_cart() atoms = pdb_hierarchy.atoms() model.setup_riding_h_manager() riding_h_manager = model.get_riding_h_manager() h_parameterization = riding_h_manager.h_parameterization diagnostics = riding_h_manager.diagnostics( sites_cart = sites_cart, threshold = 0.05) h_distances = diagnostics.h_distances type_list = diagnostics.type_list number_h = model.get_hd_selection().count(True) number_h_para = len(h_parameterization) - h_parameterization.count(None) # There are 90 H atoms in pdb_string, check if all of them are recognized assert (number_h_para == number_h), 'Not all H atoms are parameterized' # For every H , check if distance between computed H and H in input model is # < 0.03 A for ih in h_distances: labels = atoms[ih].fetch_labels() assert (h_distances[ih] < 0.03), 'distance too large: %s atom: %s (%s) residue: %s ' \ % (h_parameterization[ih].htype, atoms[ih].name, ih, labels.resseq.strip()) # Check if parameterization types are correct for type1, type2 in zip(type_list, type_list_known): assert (type1 == type2) # DNA and RNA nucleic acids pdb_str = """\ 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 P DA A 1 4.321 6.421 9.951 1.00 76.88 P ATOM 2 OP1 DA A 1 3.975 5.004 10.200 1.00 78.59 O ATOM 3 OP2 DA A 1 3.621 7.495 10.691 1.00 75.20 O ATOM 4 O5' DA A 1 5.895 6.618 10.165 1.00 78.76 O ATOM 5 C5' DA A 1 6.704 5.513 10.551 1.00 77.93 C ATOM 6 C4' DA A 1 8.179 5.858 10.453 1.00 78.66 C ATOM 7 O4' DA A 1 8.521 6.124 9.066 1.00 79.49 O ATOM 8 C3' DA A 1 8.598 7.103 11.220 1.00 78.23 C ATOM 9 O3' DA A 1 8.961 6.778 12.559 1.00 77.17 O ATOM 10 C2' DA A 1 9.776 7.622 10.408 1.00 79.34 C ATOM 11 C1' DA A 1 9.411 7.226 8.980 1.00 78.22 C ATOM 12 N9 DA A 1 8.758 8.292 8.225 1.00 20.00 N ATOM 13 C8 DA A 1 7.414 8.503 8.091 1.00 20.00 C ATOM 14 N7 DA A 1 7.112 9.543 7.350 1.00 20.00 N ATOM 15 C5 DA A 1 8.344 10.050 6.971 1.00 20.00 C ATOM 16 C6 DA A 1 8.713 11.153 6.176 1.00 20.00 C ATOM 17 N6 DA A 1 7.829 11.974 5.600 1.00 20.00 N ATOM 18 N1 DA A 1 10.031 11.381 5.996 1.00 20.00 N ATOM 19 C2 DA A 1 10.913 10.557 6.575 1.00 20.00 C ATOM 20 N3 DA A 1 10.687 9.491 7.341 1.00 20.00 N ATOM 21 C4 DA A 1 9.369 9.291 7.502 1.00 20.00 C ATOM 22 H5' DA A 1 6.514 4.760 9.969 1.00 77.93 H ATOM 23 H5'' DA A 1 6.494 5.269 11.466 1.00 77.93 H ATOM 24 H4' DA A 1 8.701 5.104 10.767 1.00 78.66 H ATOM 25 H3' DA A 1 7.879 7.754 11.217 1.00 78.23 H ATOM 26 H2' DA A 1 9.849 8.586 10.488 1.00 79.34 H ATOM 27 H2'' DA A 1 10.599 7.190 10.683 1.00 79.34 H ATOM 28 H1' DA A 1 10.214 6.951 8.511 1.00 78.22 H ATOM 29 H8 DA A 1 6.772 7.960 8.488 1.00 20.00 H ATOM 30 H61 DA A 1 8.103 12.635 5.123 1.00 20.00 H ATOM 31 H62 DA A 1 6.986 11.841 5.706 1.00 20.00 H ATOM 32 H2 DA A 1 11.808 10.757 6.421 1.00 20.00 H ATOM 33 P DC A 2 8.575 7.768 13.765 1.00 76.88 P ATOM 34 OP1 DC A 2 8.992 7.120 15.028 1.00 78.59 O ATOM 35 OP2 DC A 2 7.165 8.176 13.578 1.00 75.20 O ATOM 36 O5' DC A 2 9.494 9.054 13.516 1.00 78.76 O ATOM 37 C5' DC A 2 10.911 8.922 13.497 1.00 77.93 C ATOM 38 C4' DC A 2 11.571 10.212 13.045 1.00 78.66 C ATOM 39 O4' DC A 2 11.202 10.488 11.669 1.00 79.49 O ATOM 40 C3' DC A 2 11.163 11.450 13.828 1.00 78.23 C ATOM 41 O3' DC A 2 11.993 11.627 14.972 1.00 77.17 O ATOM 42 C2' DC A 2 11.332 12.566 12.806 1.00 79.34 C ATOM 43 C1' DC A 2 10.997 11.881 11.483 1.00 78.22 C ATOM 44 N1 DC A 2 9.591 12.099 11.036 1.00 20.00 N ATOM 45 C2 DC A 2 9.254 13.276 10.359 1.00 20.00 C ATOM 46 O2 DC A 2 10.133 14.120 10.143 1.00 20.00 O ATOM 47 N3 DC A 2 7.972 13.459 9.959 1.00 20.00 N ATOM 48 C4 DC A 2 7.054 12.524 10.212 1.00 20.00 C ATOM 49 N4 DC A 2 5.802 12.749 9.798 1.00 20.00 N ATOM 50 C5 DC A 2 7.378 11.318 10.900 1.00 20.00 C ATOM 51 C6 DC A 2 8.646 11.149 11.290 1.00 20.00 C ATOM 52 H5' DC A 2 11.156 8.208 12.888 1.00 77.93 H ATOM 53 H5'' DC A 2 11.222 8.701 14.389 1.00 77.93 H ATOM 54 H4' DC A 2 12.534 10.109 13.099 1.00 78.66 H ATOM 55 H3' DC A 2 10.233 11.382 14.095 1.00 78.23 H ATOM 56 H2' DC A 2 10.711 13.290 12.984 1.00 79.34 H ATOM 57 H2'' DC A 2 12.247 12.890 12.802 1.00 79.34 H ATOM 58 H1' DC A 2 11.602 12.202 10.797 1.00 78.22 H ATOM 59 H41 DC A 2 5.188 12.166 9.949 1.00 20.00 H ATOM 60 H42 DC A 2 5.612 13.476 9.380 1.00 20.00 H ATOM 61 H5 DC A 2 6.731 10.673 11.071 1.00 20.00 H ATOM 62 H6 DC A 2 8.886 10.372 11.740 1.00 20.00 H ATOM 63 P DG A 3 11.380 12.226 16.332 1.00 76.88 P ATOM 64 OP1 DG A 3 12.439 12.169 17.364 1.00 78.59 O ATOM 65 OP2 DG A 3 10.081 11.560 16.572 1.00 75.20 O ATOM 66 O5' DG A 3 11.087 13.759 15.979 1.00 78.76 O ATOM 67 C5' DG A 3 12.153 14.613 15.582 1.00 77.93 C ATOM 68 C4' DG A 3 11.625 15.948 15.088 1.00 78.66 C ATOM 69 O4' DG A 3 10.821 15.738 13.897 1.00 79.49 O ATOM 70 C3' DG A 3 10.718 16.679 16.065 1.00 78.23 C ATOM 71 O3' DG A 3 11.476 17.512 16.939 1.00 77.17 O ATOM 72 C2' DG A 3 9.805 17.477 15.146 1.00 79.34 C ATOM 73 C1' DG A 3 9.678 16.578 13.920 1.00 78.22 C ATOM 74 N9 DG A 3 8.483 15.738 13.931 1.00 20.00 N ATOM 75 C8 DG A 3 8.377 14.458 14.419 1.00 20.00 C ATOM 76 N7 DG A 3 7.181 13.952 14.294 1.00 20.00 N ATOM 77 C5 DG A 3 6.447 14.961 13.684 1.00 20.00 C ATOM 78 C6 DG A 3 5.086 14.991 13.297 1.00 20.00 C ATOM 79 O6 DG A 3 4.233 14.102 13.422 1.00 20.00 O ATOM 80 N1 DG A 3 4.744 16.208 12.711 1.00 20.00 N ATOM 81 C2 DG A 3 5.609 17.261 12.523 1.00 20.00 C ATOM 82 N2 DG A 3 5.096 18.354 11.940 1.00 20.00 N ATOM 83 N3 DG A 3 6.886 17.245 12.881 1.00 20.00 N ATOM 84 C4 DG A 3 7.234 16.067 13.454 1.00 20.00 C ATOM 85 H5' DG A 3 12.655 14.186 14.870 1.00 77.93 H ATOM 86 H5'' DG A 3 12.740 14.763 16.340 1.00 77.93 H ATOM 87 H4' DG A 3 12.376 16.521 14.865 1.00 78.66 H ATOM 88 H3' DG A 3 10.199 16.041 16.579 1.00 78.23 H ATOM 89 H2' DG A 3 8.938 17.616 15.561 1.00 79.34 H ATOM 90 H2'' DG A 3 10.213 18.325 14.909 1.00 79.34 H ATOM 91 H1' DG A 3 9.672 17.129 13.121 1.00 78.22 H ATOM 92 H8 DG A 3 9.088 13.997 14.801 1.00 20.00 H ATOM 93 H1 DG A 3 3.932 16.308 12.447 1.00 20.00 H ATOM 94 H21 DG A 3 5.594 19.042 11.803 1.00 20.00 H ATOM 95 H22 DG A 3 4.269 18.367 11.703 1.00 20.00 H ATOM 96 P DT A 4 11.038 17.682 18.476 1.00 76.88 P ATOM 97 OP1 DT A 4 12.063 18.517 19.142 1.00 78.59 O ATOM 98 OP2 DT A 4 10.727 16.337 19.007 1.00 75.20 O ATOM 99 O5' DT A 4 9.670 18.508 18.398 1.00 78.76 O ATOM 100 C5' DT A 4 9.648 19.790 17.782 1.00 77.93 C ATOM 101 C4' DT A 4 8.226 20.307 17.653 1.00 78.66 C ATOM 102 O4' DT A 4 7.471 19.434 16.774 1.00 79.49 O ATOM 103 C3' DT A 4 7.437 20.345 18.951 1.00 78.23 C ATOM 104 O3' DT A 4 7.650 21.574 19.642 1.00 77.17 O ATOM 105 C2' DT A 4 5.998 20.186 18.477 1.00 79.34 C ATOM 106 C1' DT A 4 6.134 19.307 17.235 1.00 78.22 C ATOM 107 N1 DT A 4 5.854 17.865 17.489 1.00 20.00 N ATOM 108 C2 DT A 4 4.559 17.407 17.408 1.00 20.00 C ATOM 109 O2 DT A 4 3.613 18.124 17.136 1.00 20.00 O ATOM 110 N3 DT A 4 4.408 16.069 17.658 1.00 20.00 N ATOM 111 C4 DT A 4 5.402 15.162 17.975 1.00 20.00 C ATOM 112 O4 DT A 4 5.166 13.976 18.183 1.00 20.00 O ATOM 113 C5 DT A 4 6.738 15.708 18.044 1.00 20.00 C ATOM 114 C7 DT A 4 7.899 14.820 18.380 1.00 20.00 C ATOM 115 C6 DT A 4 6.898 17.018 17.800 1.00 20.00 C ATOM 116 H5' DT A 4 10.044 19.726 16.899 1.00 77.93 H ATOM 117 H5'' DT A 4 10.164 20.411 18.319 1.00 77.93 H ATOM 118 H4' DT A 4 8.247 21.198 17.270 1.00 78.66 H ATOM 119 H3' DT A 4 7.687 19.597 19.515 1.00 78.23 H ATOM 120 HO3' DT A 4 7.975 21.569 20.416 1.00 77.17 H ATOM 121 H2' DT A 4 5.463 19.742 19.153 1.00 79.34 H ATOM 122 H2'' DT A 4 5.617 21.047 18.247 1.00 79.34 H ATOM 123 H1' DT A 4 5.530 19.632 16.549 1.00 78.22 H ATOM 124 H3 DT A 4 3.607 15.760 17.614 1.00 20.00 H ATOM 125 H71 DT A 4 8.506 14.781 17.623 1.00 20.00 H ATOM 126 H72 DT A 4 8.367 15.177 19.151 1.00 20.00 H ATOM 127 H73 DT A 4 7.577 13.927 18.582 1.00 20.00 H ATOM 128 H6 DT A 4 7.756 17.372 17.844 1.00 20.00 H TER ATOM 129 P A B 1 18.553 9.499 13.673 1.00 76.88 P ATOM 130 OP1 A B 1 18.244 8.077 13.965 1.00 78.59 O ATOM 131 OP2 A B 1 18.063 10.559 14.590 1.00 75.20 O ATOM 132 O5' A B 1 20.135 9.645 13.551 1.00 78.76 O ATOM 133 C5' A B 1 20.984 8.516 13.690 1.00 77.93 C ATOM 134 C4' A B 1 22.397 8.832 13.268 1.00 78.66 C ATOM 135 O4' A B 1 22.420 9.197 11.863 1.00 79.49 O ATOM 136 C3' A B 1 23.053 10.012 13.969 1.00 78.23 C ATOM 137 O3' A B 1 23.578 9.678 15.242 1.00 77.17 O ATOM 138 C2' A B 1 24.112 10.447 12.965 1.00 79.34 C ATOM 139 O2' A B 1 25.261 9.616 13.036 1.00 79.34 O ATOM 140 C1' A B 1 23.396 10.192 11.639 1.00 78.22 C ATOM 141 N9 A B 1 22.725 11.403 11.128 1.00 20.00 N ATOM 142 C8 A B 1 21.387 11.706 11.176 1.00 20.00 C ATOM 143 N7 A B 1 21.088 12.863 10.637 1.00 20.00 N ATOM 144 C5 A B 1 22.312 13.355 10.204 1.00 20.00 C ATOM 145 C6 A B 1 22.676 14.544 9.548 1.00 20.00 C ATOM 146 N6 A B 1 21.805 15.494 9.199 1.00 20.00 N ATOM 147 N1 A B 1 23.983 14.727 9.259 1.00 20.00 N ATOM 148 C2 A B 1 24.857 13.775 9.609 1.00 20.00 C ATOM 149 N3 A B 1 24.636 12.617 10.227 1.00 20.00 N ATOM 150 C4 A B 1 23.329 12.466 10.500 1.00 20.00 C ATOM 151 H5' A B 1 20.643 7.794 13.139 1.00 77.93 H ATOM 152 H5'' A B 1 20.986 8.233 14.618 1.00 77.93 H ATOM 153 H4' A B 1 22.948 8.043 13.397 1.00 78.66 H ATOM 154 H3' A B 1 22.401 10.723 14.070 1.00 78.23 H ATOM 155 H2' A B 1 24.339 11.384 13.071 1.00 79.34 H ATOM 156 HO2' A B 1 25.651 9.749 13.767 1.00 79.34 H ATOM 157 H1' A B 1 24.035 9.875 10.982 1.00 78.22 H ATOM 158 H8 A B 1 20.752 11.143 11.556 1.00 20.00 H ATOM 159 H61 A B 1 22.081 16.203 8.797 1.00 20.00 H ATOM 160 H62 A B 1 20.969 15.398 9.376 1.00 20.00 H ATOM 161 H2 A B 1 25.744 13.946 9.388 1.00 20.00 H ATOM 162 P C B 2 23.325 10.645 16.500 1.00 76.88 P ATOM 163 OP1 C B 2 23.900 9.992 17.704 1.00 78.59 O ATOM 164 OP2 C B 2 21.895 11.044 16.495 1.00 75.20 O ATOM 165 O5' C B 2 24.199 11.937 16.177 1.00 78.76 O ATOM 166 C5' C B 2 25.609 11.848 16.041 1.00 77.93 C ATOM 167 C4' C B 2 26.197 13.135 15.518 1.00 78.66 C ATOM 168 O4' C B 2 25.672 13.412 14.193 1.00 79.49 O ATOM 169 C3' C B 2 25.871 14.389 16.315 1.00 78.23 C ATOM 170 O3' C B 2 26.696 14.550 17.457 1.00 77.17 O ATOM 171 C2' C B 2 26.036 15.493 15.280 1.00 79.34 C ATOM 172 O2' C B 2 27.405 15.824 15.094 1.00 79.34 O ATOM 173 C1' C B 2 25.517 14.805 14.017 1.00 78.22 C ATOM 174 N1 C B 2 24.086 15.094 13.772 1.00 20.00 N ATOM 175 C2 C B 2 23.736 16.306 13.170 1.00 20.00 C ATOM 176 O2 C B 2 24.634 17.102 12.859 1.00 20.00 O ATOM 177 N3 C B 2 22.430 16.578 12.942 1.00 20.00 N ATOM 178 C4 C B 2 21.494 15.695 13.292 1.00 20.00 C ATOM 179 N4 C B 2 20.218 16.005 13.048 1.00 20.00 N ATOM 180 C5 C B 2 21.823 14.452 13.907 1.00 20.00 C ATOM 181 C6 C B 2 23.119 14.195 14.126 1.00 20.00 C ATOM 182 H5' C B 2 25.824 11.130 15.426 1.00 77.93 H ATOM 183 H5'' C B 2 25.999 11.651 16.907 1.00 77.93 H ATOM 184 H4' C B 2 27.161 13.040 15.462 1.00 78.66 H ATOM 185 H3' C B 2 24.943 14.354 16.595 1.00 78.23 H ATOM 186 H2' C B 2 25.505 16.273 15.503 1.00 79.34 H ATOM 187 HO2' C B 2 27.694 16.194 15.791 1.00 79.34 H ATOM 188 H1' C B 2 26.041 15.093 13.253 1.00 78.22 H ATOM 189 H41 C B 2 19.593 15.456 13.265 1.00 20.00 H ATOM 190 H42 C B 2 20.022 16.754 12.674 1.00 20.00 H ATOM 191 H5 C B 2 21.163 13.843 14.147 1.00 20.00 H ATOM 192 H6 C B 2 23.364 13.393 14.526 1.00 20.00 H ATOM 193 P G B 3 26.058 15.013 18.858 1.00 76.88 P ATOM 194 OP1 G B 3 27.123 14.941 19.891 1.00 78.59 O ATOM 195 OP2 G B 3 24.791 14.266 19.059 1.00 75.20 O ATOM 196 O5' G B 3 25.696 16.547 18.630 1.00 78.76 O ATOM 197 C5' G B 3 26.713 17.507 18.380 1.00 77.93 C ATOM 198 C4' G B 3 26.131 18.843 17.993 1.00 78.66 C ATOM 199 O4' G B 3 25.392 18.715 16.750 1.00 79.49 O ATOM 200 C3' G B 3 25.121 19.437 18.964 1.00 78.23 C ATOM 201 O3' G B 3 25.730 20.093 20.063 1.00 77.17 O ATOM 202 C2' G B 3 24.308 20.364 18.072 1.00 79.34 C ATOM 203 O2' G B 3 24.988 21.590 17.846 1.00 79.34 O ATOM 204 C1' G B 3 24.268 19.570 16.766 1.00 78.22 C ATOM 205 N9 G B 3 23.049 18.747 16.654 1.00 20.00 N ATOM 206 C8 G B 3 22.948 17.389 16.836 1.00 20.00 C ATOM 207 N7 G B 3 21.735 16.938 16.671 1.00 20.00 N ATOM 208 C5 G B 3 20.988 18.066 16.360 1.00 20.00 C ATOM 209 C6 G B 3 19.605 18.202 16.074 1.00 20.00 C ATOM 210 O6 G B 3 18.735 17.324 16.037 1.00 20.00 O ATOM 211 N1 G B 3 19.265 19.526 15.812 1.00 20.00 N ATOM 212 C2 G B 3 20.142 20.583 15.823 1.00 20.00 C ATOM 213 N2 G B 3 19.620 21.786 15.544 1.00 20.00 N ATOM 214 N3 G B 3 21.433 20.469 16.088 1.00 20.00 N ATOM 215 C4 G B 3 21.785 19.192 16.345 1.00 20.00 C ATOM 216 H5' G B 3 27.279 17.188 17.659 1.00 77.93 H ATOM 217 H5'' G B 3 27.250 17.615 19.180 1.00 77.93 H ATOM 218 H4' G B 3 26.854 19.476 17.865 1.00 78.66 H ATOM 219 H3' G B 3 24.546 18.729 19.295 1.00 78.23 H ATOM 220 H2' G B 3 23.416 20.507 18.427 1.00 79.34 H ATOM 221 HO2' G B 3 25.624 21.654 18.390 1.00 79.34 H ATOM 222 H1' G B 3 24.316 20.182 16.014 1.00 78.22 H ATOM 223 H8 G B 3 23.671 16.847 17.056 1.00 20.00 H ATOM 224 H1 G B 3 18.442 19.695 15.629 1.00 20.00 H ATOM 225 H21 G B 3 18.776 21.865 15.394 1.00 20.00 H ATOM 226 H22 G B 3 20.128 22.479 15.515 1.00 20.00 H ATOM 227 P U B 4 25.038 20.052 21.513 1.00 76.88 P ATOM 228 OP1 U B 4 25.946 20.728 22.475 1.00 78.59 O ATOM 229 OP2 U B 4 24.599 18.658 21.776 1.00 75.20 O ATOM 230 O5' U B 4 23.737 20.955 21.346 1.00 78.76 O ATOM 231 C5' U B 4 23.842 22.322 20.974 1.00 77.93 C ATOM 232 C4' U B 4 22.492 22.914 20.655 1.00 78.66 C ATOM 233 O4' U B 4 21.908 22.220 19.522 1.00 79.49 O ATOM 234 C3' U B 4 21.438 22.796 21.745 1.00 78.23 C ATOM 235 O3' U B 4 21.564 23.790 22.747 1.00 77.17 O ATOM 236 C2' U B 4 20.136 22.882 20.959 1.00 79.34 C ATOM 237 O2' U B 4 19.818 24.228 20.636 1.00 79.34 O ATOM 238 C1' U B 4 20.506 22.137 19.676 1.00 78.22 C ATOM 239 N1 U B 4 20.119 20.709 19.729 1.00 20.00 N ATOM 240 C2 U B 4 18.803 20.391 19.462 1.00 20.00 C ATOM 241 O2 U B 4 17.962 21.229 19.188 1.00 20.00 O ATOM 242 N3 U B 4 18.508 19.052 19.527 1.00 20.00 N ATOM 243 C4 U B 4 19.379 18.023 19.826 1.00 20.00 C ATOM 244 O4 U B 4 18.961 16.865 19.845 1.00 20.00 O ATOM 245 C5 U B 4 20.725 18.433 20.091 1.00 20.00 C ATOM 246 C6 U B 4 21.037 19.732 20.034 1.00 20.00 C ATOM 247 H5' U B 4 24.413 22.395 20.194 1.00 77.93 H ATOM 248 H5'' U B 4 24.240 22.819 21.706 1.00 77.93 H ATOM 249 H4' U B 4 22.605 23.850 20.427 1.00 78.66 H ATOM 250 H3' U B 4 21.503 21.920 22.156 1.00 78.23 H ATOM 251 HO3' U B 4 20.932 24.324 22.892 1.00 77.17 H ATOM 252 H2' U B 4 19.409 22.442 21.427 1.00 79.34 H ATOM 253 HO2' U B 4 19.611 24.636 21.340 1.00 79.34 H ATOM 254 H1' U B 4 20.072 22.562 18.920 1.00 78.22 H ATOM 255 H5 U B 4 21.375 17.802 20.301 1.00 20.00 H ATOM 256 H3 U B 4 17.694 18.830 19.364 1.00 20.00 H ATOM 257 H6 U B 4 21.915 19.985 20.208 1.00 20.00 H TER END """ type_list_known = ['2tetra', '2tetra', '3neigbs', '3neigbs', '2tetra', '2tetra', '3neigbs', 'flat_2neigbs', 'alg1a', 'alg1a', 'flat_2neigbs', '2tetra', '2tetra', '3neigbs', '3neigbs', '2tetra', '2tetra', '3neigbs', 'alg1a', 'alg1a', 'flat_2neigbs', 'flat_2neigbs', '2tetra', '2tetra', '3neigbs', '3neigbs', '2tetra', '2tetra', '3neigbs', 'flat_2neigbs', 'flat_2neigbs', 'alg1a', 'alg1a', '2tetra', '2tetra', '3neigbs', '3neigbs', 'alg1b', '2tetra', '2tetra', '3neigbs', 'flat_2neigbs', 'prop', 'prop', 'prop', 'flat_2neigbs', '2tetra', '2tetra', '3neigbs', '3neigbs', '3neigbs', 'alg1b', '3neigbs', 'flat_2neigbs', 'alg1a', 'alg1a', 'flat_2neigbs', '2tetra', '2tetra', '3neigbs', '3neigbs', '3neigbs', 'alg1b', '3neigbs', 'alg1a', 'alg1a', 'flat_2neigbs', 'flat_2neigbs', '2tetra', '2tetra', '3neigbs', '3neigbs', '3neigbs', 'alg1b', '3neigbs', 'flat_2neigbs', 'flat_2neigbs', 'alg1a', 'alg1a', '2tetra', '2tetra', '3neigbs', '3neigbs', 'alg1b', '3neigbs', 'alg1b', '3neigbs', 'flat_2neigbs', 'flat_2neigbs', 'flat_2neigbs'] if (__name__ == "__main__"): t0 = time.time() exercise() print("OK. Time: %8.3f"%(time.time()-t0))