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 H atoms for multiple conformations # These examples are from pdb and initially failed #----------------------------------------------------------------------------- def exercise(pdb_str, type_list_known): 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_para = 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_para) - h_para.count(None) assert (number_h_para == number_h), 'Not all H atoms are parameterized' for ih in h_distances: labels = atoms[ih].fetch_labels() assert (h_distances[ih] < 0.2), \ 'distance too large: %s atom: %s (%s) residue: %s ' \ % (h_para[ih].htype, atoms[ih].name, ih, labels.resseq.strip()) for type1, type2 in zip(type_list, type_list_known): assert (type1 == type2) #print "'%s'," % type1, # Several fragments from pdb with double conformations which caused crashes # There are 68 H atoms in the pdb_string, check if all of them are recognized # Note: one H atom (VAL 7 HA) is bound to two CA atoms at once pdb_str1 = """\ CRYST1 27.832 30.931 25.475 90.00 90.00 90.00 P 1 SCALE1 0.035930 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032330 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039254 0.00000 ATOM 1 CB SER A 1 10.278 16.843 12.582 1.00 6.41 C ANISOU 1 CB SER A 1 638 591 1207 -162 148 106 C ATOM 2 OG SER A 1 9.084 17.462 12.244 1.00 7.60 O ANISOU 2 OG SER A 1 680 955 1251 -244 -164 339 O ATOM 3 HB2 SER A 1 10.836 16.758 11.793 1.00 6.41 H ATOM 4 HB3 SER A 1 10.100 15.944 12.901 1.00 6.41 H ATOM 5 HG SER A 1 8.783 17.124 11.536 1.00 7.60 H ATOM 6 N ASER A 1 11.457 18.906 13.130 0.40 5.10 N ANISOU 6 N ASER A 1 500 632 808 -107 58 104 N ATOM 7 CA ASER A 1 11.030 17.638 13.665 0.40 5.95 C ANISOU 7 CA ASER A 1 582 671 1007 -168 135 158 C ATOM 8 C ASER A 1 12.200 16.876 14.296 0.40 5.79 C ANISOU 8 C ASER A 1 661 588 952 -116 206 135 C ATOM 9 O ASER A 1 12.094 16.315 15.382 0.40 6.83 O ANISOU 9 O ASER A 1 874 705 1015 -39 314 258 O ATOM 10 HA ASER A 1 10.350 17.812 14.335 0.40 5.95 H ATOM 11 N BSER A 1 11.557 18.906 13.130 0.60 5.10 N ANISOU 11 N BSER A 1 500 632 808 -107 58 104 N ATOM 12 CA BSER A 1 11.130 17.638 13.665 0.60 5.95 C ANISOU 12 CA BSER A 1 582 671 1007 -168 135 158 C ATOM 13 C BSER A 1 12.300 16.876 14.296 0.60 5.79 C ANISOU 13 C BSER A 1 661 588 952 -116 206 135 C ATOM 14 O BSER A 1 12.194 16.315 15.382 0.60 6.83 O ANISOU 14 O BSER A 1 874 705 1015 -39 314 258 O ATOM 15 HA BSER A 1 10.450 17.812 14.335 0.60 5.95 H ATOM 16 CA SER A 2 7.255 21.911 13.410 1.00 5.95 C ANISOU 16 CA SER A 2 582 671 1007 -168 135 158 C ATOM 17 OG SER A 2 5.325 21.752 11.965 1.00 7.60 O ANISOU 17 OG SER A 2 680 955 1251 -244 -164 339 O ATOM 18 HA SER A 2 6.575 22.085 14.080 1.00 5.95 H ATOM 19 HG SER A 2 5.027 21.411 11.258 1.00 7.60 H ATOM 20 N ASER A 2 7.582 23.179 12.875 0.40 5.10 N ANISOU 20 N ASER A 2 500 632 808 -107 58 104 N ATOM 21 C ASER A 2 8.325 21.149 14.041 0.40 5.79 C ANISOU 21 C ASER A 2 661 588 952 -116 206 135 C ATOM 22 O ASER A 2 8.219 20.588 15.127 0.40 6.83 O ANISOU 22 O ASER A 2 874 705 1015 -39 314 258 O ATOM 23 CB ASER A 2 6.403 21.116 12.327 0.40 6.41 C ANISOU 23 CB ASER A 2 638 591 1207 -162 148 106 C ATOM 24 HB2ASER A 2 6.961 21.031 11.538 0.40 6.41 H ATOM 25 HB3ASER A 2 6.225 20.217 12.646 0.40 6.41 H ATOM 26 N BSER A 2 7.682 23.179 12.875 0.60 5.10 N ANISOU 26 N BSER A 2 500 632 808 -107 58 104 N ATOM 27 C BSER A 2 8.425 21.149 14.041 0.60 5.79 C ANISOU 27 C BSER A 2 661 588 952 -116 206 135 C ATOM 28 O BSER A 2 8.319 20.588 15.127 0.60 6.83 O ANISOU 28 O BSER A 2 874 705 1015 -39 314 258 O ATOM 29 CB BSER A 2 6.503 21.116 12.327 0.60 6.41 C ANISOU 29 CB BSER A 2 638 591 1207 -162 148 106 C ATOM 30 HB2BSER A 2 7.070 21.011 11.547 0.60 6.41 H ATOM 31 HB3BSER A 2 6.305 20.224 12.655 0.60 6.41 H ATOM 32 OG SER A 3 8.348 24.487 15.352 1.00 7.60 O ANISOU 32 OG SER A 3 680 955 1251 -244 -164 339 O ATOM 33 HG SER A 3 8.047 24.149 14.644 1.00 7.60 H ATOM 34 N ASER A 3 10.721 25.931 16.238 0.40 5.10 N ANISOU 34 N ASER A 3 500 632 808 -107 58 104 N ATOM 35 CA ASER A 3 10.294 24.663 16.773 0.40 5.95 C ANISOU 35 CA ASER A 3 582 671 1007 -168 135 158 C ATOM 36 C ASER A 3 11.464 23.901 17.404 0.40 5.79 C ANISOU 36 C ASER A 3 661 588 952 -116 206 135 C ATOM 37 O ASER A 3 11.358 23.340 18.490 0.40 6.83 O ANISOU 37 O ASER A 3 874 705 1015 -39 314 258 O ATOM 38 CB ASER A 3 9.542 23.868 15.690 0.40 6.41 C ANISOU 38 CB ASER A 3 638 591 1207 -162 148 106 C ATOM 39 HA ASER A 3 9.614 24.837 17.443 0.40 5.95 H ATOM 40 HB2ASER A 3 10.100 23.783 14.901 0.40 6.41 H ATOM 41 HB3ASER A 3 9.364 22.969 16.009 0.40 6.41 H ATOM 42 N BSER A 3 10.821 25.931 16.238 0.60 5.10 N ANISOU 42 N BSER A 3 500 632 808 -107 58 104 N ATOM 43 CA BSER A 3 10.394 24.663 16.773 0.60 5.95 C ANISOU 43 CA BSER A 3 582 671 1007 -168 135 158 C ATOM 44 C BSER A 3 11.564 23.901 17.404 0.60 5.79 C ANISOU 44 C BSER A 3 661 588 952 -116 206 135 C ATOM 45 O BSER A 3 11.458 23.340 18.490 0.60 6.83 O ANISOU 45 O BSER A 3 874 705 1015 -39 314 258 O ATOM 46 CB BSER A 3 9.642 23.868 15.690 0.60 6.41 C ANISOU 46 CB BSER A 3 638 591 1207 -162 148 106 C ATOM 47 HA BSER A 3 9.714 24.837 17.443 0.60 5.95 H ATOM 48 HB2BSER A 3 10.209 23.763 14.910 0.60 6.41 H ATOM 49 HB3BSER A 3 9.444 22.976 16.018 0.60 6.41 H ATOM 50 CA TYR A 4 22.290 10.873 7.693 1.00 13.00 C ANISOU 50 CA TYR A 4 2514 1244 1180 -28 116 139 C ATOM 51 C TYR A 4 22.074 9.526 7.008 1.00 11.81 C ANISOU 51 C TYR A 4 2332 1026 1130 -105 88 190 C ATOM 52 O TYR A 4 21.538 8.599 7.605 1.00 12.59 O ANISOU 52 O TYR A 4 2489 1154 1140 -72 111 219 O ATOM 53 N VAL A 5 22.517 9.437 5.761 1.00 10.80 N ANISOU 53 N VAL A 5 2053 884 1167 -29 80 167 N ATOM 54 H VAL A 5 22.832 10.103 5.318 1.00 12.96 H ATOM 55 CA AVAL A 5 22.516 8.185 5.022 0.40 10.37 C ANISOU 55 CA AVAL A 5 1783 902 1255 67 -148 -14 C ATOM 56 CA BVAL A 5 22.616 8.185 5.022 0.60 10.37 C ANISOU 56 CA BVAL A 5 1783 902 1255 67 -148 -14 C ATOM 57 N SER A 6 17.758 20.026 12.546 1.00 4.20 N ANISOU 57 N SER A 6 578 469 547 -59 10 -119 N ATOM 58 CA SER A 6 17.692 20.410 11.150 1.00 4.34 C ANISOU 58 CA SER A 6 576 472 600 -2 0 0 C ATOM 59 C SER A 6 18.920 19.904 10.378 1.00 3.90 C ANISOU 59 C SER A 6 554 387 543 -50 -15 -34 C ATOM 60 O SER A 6 18.798 19.501 9.222 1.00 4.24 O ANISOU 60 O SER A 6 634 443 534 -77 -67 -59 O ATOM 62 HA SER A 6 16.905 19.937 10.839 1.00 4.34 H ATOM 63 CB ASER A 6 17.651 21.951 11.144 0.60 5.87 C ANISOU 63 CB ASER A 6 843 568 821 229 -39 -32 C ATOM 64 OG ASER A 6 17.494 22.382 9.839 0.60 6.95 O ANISOU 64 OG ASER A 6 1107 702 833 257 200 132 O ATOM 65 HB2ASER A 6 16.919 22.271 11.695 0.60 4.80 H ATOM 66 HB3ASER A 6 18.469 22.311 11.522 0.60 4.80 H ATOM 67 HG ASER A 6 16.967 23.036 9.821 0.60 4.95 H ATOM 68 CB BSER A 6 17.234 21.814 10.776 0.20 4.89 C ANISOU 68 CB BSER A 6 429 509 922 98 134 102 C ATOM 69 OG BSER A 6 18.212 22.672 11.327 0.20 5.81 O ANISOU 69 OG BSER A 6 757 477 971 72 15 -142 O ATOM 70 HB2BSER A 6 17.175 21.920 9.814 0.20 4.80 H ATOM 71 HB3BSER A 6 16.354 22.005 11.137 0.20 4.80 H ATOM 72 HG BSER A 6 18.020 23.469 11.146 0.20 4.95 H ATOM 73 CB CSER A 6 17.677 21.930 10.974 0.20 4.80 C ANISOU 73 CB CSER A 6 432 322 1070 -132 173 4 C ATOM 74 OG CSER A 6 16.492 22.377 11.598 0.20 4.95 O ANISOU 74 OG CSER A 6 511 563 806 114 -22 -75 O ATOM 75 HB2CSER A 6 18.459 22.335 11.381 0.20 4.80 H ATOM 76 HB3CSER A 6 17.688 22.172 10.035 0.20 4.80 H ATOM 77 HG CSER A 6 16.620 22.446 12.425 0.20 4.95 H ATOM 78 N VAL A 7 17.941 13.419 15.481 1.00 10.80 N ANISOU 78 N VAL A 7 2053 884 1167 -29 80 167 N ATOM 79 C VAL A 7 19.247 12.139 13.940 1.00 9.56 C ANISOU 79 C VAL A 7 1874 685 1073 3 -185 85 C ATOM 80 O VAL A 7 19.671 13.155 13.422 1.00 10.25 O ANISOU 80 O VAL A 7 2013 634 1247 25 7 95 O ATOM 81 HA VAL A 7 17.920 11.415 15.343 0.44 12.11 H ATOM 82 CA AVAL A 7 17.940 12.167 14.742 0.44 10.37 C ANISOU 82 CA AVAL A 7 1783 902 1255 67 -148 -14 C ATOM 83 CB AVAL A 7 16.693 12.086 13.853 0.44 11.26 C ANISOU 83 CB AVAL A 7 1571 963 1743 96 -176 62 C ATOM 84 CG1AVAL A 7 16.690 13.235 12.923 0.44 11.06 C ANISOU 84 CG1AVAL A 7 1704 1072 1425 125 -105 37 C ATOM 85 CG2AVAL A 7 16.608 10.757 13.097 0.44 10.02 C ANISOU 85 CG2AVAL A 7 1510 782 1516 -92 19 232 C ATOM 86 HB AVAL A 7 15.905 12.157 14.414 0.44 13.51 H ATOM 87 HG11AVAL A 7 16.677 14.057 13.438 0.44 13.27 H ATOM 88 HG12AVAL A 7 15.902 13.184 12.361 0.44 13.27 H ATOM 89 HG13AVAL A 7 17.490 13.200 12.376 0.44 13.27 H ATOM 90 HG21AVAL A 7 15.789 10.303 13.349 0.44 12.03 H ATOM 91 HG22AVAL A 7 17.375 10.211 13.331 0.44 12.03 H ATOM 92 HG23AVAL A 7 16.608 10.936 12.143 0.44 12.03 H ATOM 93 CA BVAL A 7 17.935 12.170 14.724 0.56 10.10 C ANISOU 93 CA BVAL A 7 1914 779 1143 -16 5 185 C ATOM 94 CB BVAL A 7 16.746 12.075 13.715 0.56 11.08 C ANISOU 94 CB BVAL A 7 1662 1363 1184 84 -25 58 C ATOM 95 CG1BVAL A 7 16.699 10.688 13.068 0.56 12.75 C ANISOU 95 CG1BVAL A 7 1479 1600 1766 255 -607 -238 C ATOM 96 CG2BVAL A 7 15.398 12.392 14.382 0.56 11.66 C ANISOU 96 CG2BVAL A 7 1508 1829 1094 214 -319 28 C ATOM 97 HB BVAL A 7 16.885 12.725 13.009 0.56 13.29 H ATOM 98 HG11BVAL A 7 17.532 10.533 12.595 0.56 15.30 H ATOM 99 HG12BVAL A 7 15.954 10.654 12.448 0.56 15.30 H ATOM 100 HG13BVAL A 7 16.583 10.020 13.762 0.56 15.30 H ATOM 101 HG21BVAL A 7 14.999 13.157 13.939 0.56 13.99 H ATOM 102 HG22BVAL A 7 15.550 12.594 15.318 0.56 13.99 H ATOM 103 HG23BVAL A 7 14.817 11.620 14.299 0.56 13.99 H ATOM 104 N SER A 8 14.526 19.060 18.223 1.00 5.10 N ANISOU 104 N SER A 8 500 632 808 -107 58 104 N ATOM 105 CA SER A 8 14.099 17.792 18.758 1.00 5.95 C ANISOU 105 CA SER A 8 582 671 1007 -168 135 158 C ATOM 106 C SER A 8 15.269 17.030 19.389 1.00 5.79 C ANISOU 106 C SER A 8 661 588 952 -116 206 135 C ATOM 107 O SER A 8 15.163 16.469 20.475 1.00 6.83 O ANISOU 107 O SER A 8 874 705 1015 -39 314 258 O ATOM 108 HA SER A 8 13.419 17.966 19.428 1.00 5.95 H ATOM 109 CB ASER A 8 13.570 16.905 17.583 0.52 10.56 C ANISOU 109 CB ASER A 8 1137 993 1883 -635 -478 170 C ATOM 110 OG ASER A 8 13.140 15.675 18.052 0.52 13.20 O ANISOU 110 OG ASER A 8 1612 1164 2238 -898 145 -29 O ATOM 111 HB2ASER A 8 12.840 17.358 17.133 0.52 6.41 H ATOM 112 HB3ASER A 8 14.272 16.778 16.926 0.52 6.41 H ATOM 113 HG ASER A 8 12.347 15.739 18.322 0.52 7.60 H ATOM 114 CB BSER A 8 13.347 16.997 17.675 0.47 6.41 C ANISOU 114 CB BSER A 8 638 591 1207 -162 148 106 C ATOM 115 OG BSER A 8 12.153 17.616 17.337 0.47 7.60 O ANISOU 115 OG BSER A 8 680 955 1251 -244 -164 339 O ATOM 116 HB2BSER A 8 13.905 16.912 16.886 0.47 6.41 H ATOM 117 HB3BSER A 8 13.169 16.098 17.994 0.47 6.41 H ATOM 118 HG BSER A 8 11.852 17.278 16.629 0.47 7.60 H ATOM 119 C AASN A 9 19.204 6.973 12.924 0.46 10.01 C ANISOU 119 C AASN A 9 1311 1084 1408 -15 -324 -40 C ATOM 120 C BASN A 9 19.123 6.961 12.995 0.54 9.67 C ANISOU 120 C BASN A 9 1289 1143 1241 -122 -106 160 C ATOM 121 N SER A 10 19.921 6.127 13.648 1.00 9.28 N ANISOU 121 N SER A 10 1274 902 1350 -21 -87 -74 N ATOM 122 H SER A 10 20.776 6.182 13.716 1.00 11.14 H ATOM 123 CA ASER A 10 19.327 5.020 14.363 0.63 9.94 C ANISOU 123 CA ASER A 10 1406 774 1598 87 -335 -196 C ATOM 124 CA BSER A 10 19.344 5.000 14.369 0.37 9.47 C ANISOU 124 CA BSER A 10 1420 764 1413 89 320 -137 C ATOM 125 N TYR A 11 9.640 8.356 6.598 1.00 15.00 N ATOM 126 C TYR A 11 11.549 9.847 6.197 1.00 15.00 C ATOM 127 O TYR A 11 11.823 9.939 5.000 1.00 15.00 O ATOM 128 HA TYR A 11 9.553 10.281 6.071 1.00 15.00 H ATOM 129 CA ATYR A 11 10.100 9.738 6.660 0.50 15.00 C ATOM 130 CB ATYR A 11 9.960 10.286 8.081 0.50 15.00 C ATOM 131 CG ATYR A 11 8.637 9.956 8.735 0.50 15.00 C ATOM 132 CD1ATYR A 11 7.436 10.254 8.105 0.50 15.00 C ATOM 133 CD2ATYR A 11 8.589 9.348 9.982 0.50 15.00 C ATOM 134 CE1ATYR A 11 6.224 9.955 8.699 0.50 15.00 C ATOM 135 CE2ATYR A 11 7.383 9.044 10.584 0.50 15.00 C ATOM 136 CZ ATYR A 11 6.203 9.350 9.938 0.50 15.00 C ATOM 137 OH ATYR A 11 5.000 9.050 10.533 0.50 15.00 O ATOM 138 HB2ATYR A 11 10.664 9.911 8.632 0.50 15.00 H ATOM 139 HB3ATYR A 11 10.044 11.252 8.053 0.50 15.00 H ATOM 140 HD1ATYR A 11 7.446 10.662 7.270 0.50 15.00 H ATOM 141 HD2ATYR A 11 9.383 9.140 10.420 0.50 15.00 H ATOM 142 HE1ATYR A 11 5.427 10.160 8.265 0.50 15.00 H ATOM 143 HE2ATYR A 11 7.366 8.637 11.419 0.50 15.00 H ATOM 144 HH ATYR A 11 5.131 8.687 11.279 0.50 15.00 H ATOM 145 CA BTYR A 11 10.100 9.738 6.660 0.50 15.00 C ATOM 146 CB BTYR A 11 9.960 10.286 8.081 0.50 15.00 C ATOM 147 CG BTYR A 11 10.474 11.698 8.244 0.50 15.00 C ATOM 148 CD1BTYR A 11 9.764 12.780 7.741 0.50 15.00 C ATOM 149 CD2BTYR A 11 11.671 11.950 8.902 0.50 15.00 C ATOM 150 CE1BTYR A 11 10.230 14.072 7.888 0.50 15.00 C ATOM 151 CE2BTYR A 11 12.146 13.239 9.053 0.50 15.00 C ATOM 152 CZ BTYR A 11 11.422 14.296 8.545 0.50 15.00 C ATOM 153 OH BTYR A 11 11.890 15.582 8.693 0.50 15.00 O ATOM 154 HB2BTYR A 11 9.021 10.283 8.326 0.50 15.00 H ATOM 155 HB3BTYR A 11 10.459 9.717 8.687 0.50 15.00 H ATOM 156 HD1BTYR A 11 8.960 12.632 7.297 0.50 15.00 H ATOM 157 HD2BTYR A 11 12.162 11.239 9.246 0.50 15.00 H ATOM 158 HE1BTYR A 11 9.744 14.787 7.545 0.50 15.00 H ATOM 159 HE2BTYR A 11 12.949 13.393 9.496 0.50 15.00 H ATOM 160 HH BTYR A 11 12.620 15.575 9.109 0.50 15.00 H TER END """ type_list_known1 = ['2tetra', '2tetra', 'alg1b', '3neigbs', '3neigbs', '3neigbs', 'alg1b', '2tetra', '2tetra', '2tetra', '2tetra', 'alg1b', '3neigbs', '2tetra', '2tetra', '3neigbs', '2tetra', '2tetra', 'flat_2neigbs', '3neigbs', '2tetra', '2tetra', 'alg1b', '2tetra', '2tetra', 'alg1b', '2tetra', '2tetra', 'alg1b', '3neigbs', '3neigbs', 'prop', 'prop', 'prop', 'prop', 'prop', 'prop', '3neigbs', 'prop', 'prop', 'prop', 'prop', 'prop', 'prop', '3neigbs', '2tetra', '2tetra', 'alg1b', '2tetra', '2tetra', 'alg1b', 'flat_2neigbs', '3neigbs', '2tetra', '2tetra', 'flat_2neigbs', 'flat_2neigbs', 'flat_2neigbs', 'flat_2neigbs', 'alg1b', '2tetra', '2tetra', 'flat_2neigbs', 'flat_2neigbs', 'flat_2neigbs', 'flat_2neigbs', 'alg1b'] pdb_str2 = """ CRYST1 13.142 13.841 12.524 90.00 90.00 90.00 P 1 SCALE1 0.076092 0.000000 0.000000 0.00000 SCALE2 0.000000 0.072249 0.000000 0.00000 SCALE3 0.000000 0.000000 0.079847 0.00000 ATOM 285 CB ALA A 25 21.105 -3.928 25.422 1.00 11.78 C ATOM 286 N AALA A 25 18.694 -4.221 25.276 0.50 9.87 N ATOM 287 CA AALA A 25 19.812 -3.247 25.214 0.50 10.86 C ATOM 288 C AALA A 25 19.902 -2.496 23.898 0.50 9.98 C ATOM 289 O AALA A 25 20.720 -1.565 23.768 0.50 7.99 O ATOM 291 HA AALA A 25 19.625 -2.606 25.918 0.50 11.03 H ATOM 292 HB1AALA A 25 21.824 -3.278 25.378 0.50 11.78 H ATOM 293 HB2AALA A 25 21.109 -4.356 26.292 0.50 11.78 H ATOM 294 HB3AALA A 25 21.233 -4.598 24.732 0.50 11.78 H ATOM 295 N BALA A 25 18.682 -4.224 25.328 0.50 10.05 N ATOM 296 CA BALA A 25 19.756 -3.242 25.276 0.50 11.02 C ATOM 297 C BALA A 25 19.678 -2.389 23.992 0.50 9.97 C ATOM 298 O BALA A 25 20.024 -1.203 24.029 0.50 11.29 O ATOM 300 HA BALA A 25 19.650 -2.631 26.022 0.50 11.03 H ATOM 301 HB1BALA A 25 21.811 -3.264 25.386 0.50 11.78 H ATOM 302 HB2BALA A 25 21.142 -4.393 26.273 0.50 11.78 H ATOM 303 HB3BALA A 25 21.224 -4.566 24.701 0.50 11.78 H """ type_list_known2 = ['3neigbs', 'prop', 'prop', 'prop', '3neigbs', 'prop', 'prop', 'prop'] # This fragment is from PDB model 1qjh # A residue (Arg 71 in 1qjh) is close to its symmetry mate. # The geo file lists two asu bond restraints for atom HH22 (there should be # only one, IMHO!). # The fact that HH22 has no simple bond proxy, but angle proxies, caused # an error (asu covalent bond restraints are currently ignored). pdb_str3 = """ CRYST1 49.701 49.701 73.255 90.00 90.00 90.00 P 42 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020120 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013651 0.00000 ATOM 575 N ARG A 71 4.405 19.140 21.765 1.00 56.18 N ATOM 576 CA ARG A 71 4.384 20.597 21.643 1.00 50.81 C ATOM 577 C ARG A 71 5.782 21.217 21.647 1.00 45.46 C ATOM 578 O ARG A 71 5.933 22.440 21.582 1.00 46.55 O ATOM 579 CB ARG A 71 3.558 21.214 22.773 1.00 51.01 C ATOM 580 CG ARG A 71 2.166 20.635 22.956 1.00 52.13 C ATOM 581 CD ARG A 71 1.358 20.625 21.661 1.00 60.92 C ATOM 582 NE ARG A 71 1.134 21.965 21.122 1.00 63.41 N ATOM 583 CZ ARG A 71 0.470 22.927 21.755 1.00 62.11 C ATOM 584 NH1 ARG A 71 -0.038 22.699 22.955 1.00 60.26 N ATOM 585 NH2 ARG A 71 0.310 24.119 21.188 1.00 62.26 N ATOM 0 HA ARG A 71 3.979 20.793 20.783 1.00 50.81 H ATOM 0 HB2 ARG A 71 4.047 21.109 23.604 1.00 51.01 H ATOM 0 HB3 ARG A 71 3.476 22.167 22.610 1.00 51.01 H ATOM 0 HG2 ARG A 71 2.238 19.729 23.295 1.00 52.13 H ATOM 0 HG3 ARG A 71 1.690 21.151 23.626 1.00 52.13 H ATOM 0 HD2 ARG A 71 1.822 20.088 20.999 1.00 60.92 H ATOM 0 HD3 ARG A 71 0.502 20.199 21.822 1.00 60.92 H ATOM 0 HE ARG A 71 1.453 22.143 20.343 1.00 63.41 H ATOM 0 HH11 ARG A 71 0.062 21.929 23.325 1.00 60.26 H ATOM 0 HH12 ARG A 71 -0.468 23.321 23.365 1.00 60.26 H ATOM 0 HH21 ARG A 71 0.637 24.271 20.407 1.00 62.26 H ATOM 0 HH22 ARG A 71 -0.120 24.738 21.602 1.00 62.26 H """ type_list_known3 = ['3neigbs', '2tetra', '2tetra', '2tetra', '2tetra', '2tetra', '2tetra', 'flat_2neigbs', 'alg1a', 'alg1a'] def exercise3(pdb_str, type_list_known): pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None) params = mmtbx.model.manager.get_default_pdb_interpretation_scope().extract() params.pdb_interpretation.allow_polymer_cross_special_position=True model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) model.process(pdb_interpretation_params=params, 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_para = 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_para) - h_para.count(None) assert (number_h_para == number_h-2), 'Not all H atoms are parameterized' for ih in h_distances: labels = atoms[ih].fetch_labels() assert (h_distances[ih] < 0.2), \ 'distance too large: %s atom: %s (%s) residue: %s ' \ % (h_para[ih].htype, atoms[ih].name, ih, labels.resseq.strip()) for type1, type2 in zip(type_list, type_list_known): assert (type1 == type2) if (__name__ == "__main__"): t0 = time.time() exercise(pdb_str = pdb_str1, type_list_known = type_list_known1) exercise(pdb_str = pdb_str2, type_list_known = type_list_known2) exercise3(pdb_str = pdb_str3, type_list_known = type_list_known3) print("OK. Time: %8.3f"%(time.time()-t0))