from __future__ import absolute_import, division, print_function from mmtbx.command_line.fix_rotamer_outliers import run import iotbx.pdb import mmtbx.model pdb_str_1 = """\ CRYST1 18.486 29.189 16.919 90.00 90.00 90.00 P 1 ATOM 1 N TYR A 58 6.848 19.603 11.185 1.00 7.73 N ATOM 2 CA TYR A 58 7.439 18.674 10.233 1.00 8.65 C ATOM 3 C TYR A 58 7.228 17.251 10.706 1.00 9.84 C ATOM 4 O TYR A 58 7.212 16.994 11.919 1.00 8.58 O ATOM 5 CB TYR A 58 8.929 18.959 10.045 1.00 20.00 C ATOM 6 CG TYR A 58 9.344 20.355 10.457 1.00 20.00 C ATOM 7 CD1 TYR A 58 8.393 21.339 10.700 1.00 20.00 C ATOM 8 CD2 TYR A 58 10.683 20.685 10.603 1.00 20.00 C ATOM 9 CE1 TYR A 58 8.768 22.614 11.076 1.00 20.00 C ATOM 10 CE2 TYR A 58 11.068 21.959 10.980 1.00 20.00 C ATOM 11 CZ TYR A 58 10.107 22.918 11.215 1.00 20.00 C ATOM 12 OH TYR A 58 10.483 24.189 11.588 1.00 20.00 O ATOM 13 N SER A 59 7.076 16.327 9.756 1.00 9.65 N ATOM 14 CA SER A 59 6.909 14.912 10.080 1.00 5.80 C ATOM 15 C SER A 59 7.795 14.069 9.169 1.00 10.35 C ATOM 16 O SER A 59 8.161 14.502 8.075 1.00 10.56 O ATOM 17 CB SER A 59 5.446 14.487 9.943 1.00 20.00 C ATOM 18 OG SER A 59 5.000 14.619 8.604 1.00 20.00 O """ pdb_str_2 = """\ CRYST1 130.848 130.848 149.639 90.00 90.00 120.00 P 64 2 2 12 ATOM 95 N ARG A 30 -18.833 17.433 -14.879 1.00191.24 N ATOM 96 CA ARG A 30 -18.615 17.619 -16.290 1.00191.04 C ATOM 97 C ARG A 30 -18.032 19.002 -16.408 1.00190.51 C ATOM 98 O ARG A 30 -18.720 19.978 -16.161 1.00190.07 O ATOM 99 CB ARG A 30 -19.941 17.558 -17.076 1.00191.84 C ATOM 100 CG ARG A 30 -20.909 16.521 -16.584 1.00192.91 C ATOM 101 CD ARG A 30 -22.176 16.530 -17.408 1.00193.90 C ATOM 102 NE ARG A 30 -23.271 15.875 -16.703 1.00195.21 N ATOM 103 CZ ARG A 30 -24.498 15.744 -17.196 1.00195.78 C ATOM 104 NH1 ARG A 30 -24.776 16.224 -18.399 1.00196.03 N ATOM 105 NH2 ARG A 30 -25.449 15.149 -16.488 1.00195.90 N ATOM 106 N LYS A 31 -16.776 19.084 -16.815 1.00190.39 N ATOM 107 CA LYS A 31 -16.164 20.381 -17.016 1.00190.65 C ATOM 108 C LYS A 31 -17.139 21.024 -18.016 1.00191.02 C ATOM 109 O LYS A 31 -17.240 22.238 -18.137 1.00190.75 O ATOM 110 CB LYS A 31 -14.782 20.200 -17.673 1.00190.39 C ATOM 111 CG LYS A 31 -13.794 21.338 -17.444 1.00189.92 C ATOM 112 CD LYS A 31 -12.448 20.983 -18.063 1.00189.44 C ATOM 113 CE LYS A 31 -11.369 21.951 -17.632 1.00189.51 C ATOM 114 NZ LYS A 31 -10.046 21.567 -18.180 1.00189.58 N ATOM 115 N ASP A 32 -17.885 20.148 -18.681 1.00192.02 N ATOM 116 CA ASP A 32 -18.842 20.462 -19.742 1.00192.58 C ATOM 117 C ASP A 32 -19.950 21.497 -19.544 1.00191.35 C ATOM 118 O ASP A 32 -20.097 22.367 -20.384 1.00191.52 O ATOM 119 CB ASP A 32 -19.488 19.164 -20.226 1.00195.14 C ATOM 120 CG ASP A 32 -18.506 17.994 -20.259 1.00197.19 C ATOM 121 OD1 ASP A 32 -18.792 16.987 -20.944 1.00197.86 O ATOM 122 OD2 ASP A 32 -17.446 18.072 -19.596 1.00198.95 O ATOM 123 N ILE A 33 -20.744 21.422 -18.481 1.00189.52 N ATOM 124 CA ILE A 33 -21.803 22.408 -18.347 1.00187.36 C ATOM 125 C ILE A 33 -21.351 23.724 -17.684 1.00186.08 C ATOM 126 O ILE A 33 -22.173 24.531 -17.271 1.00185.90 O ATOM 127 CB ILE A 33 -23.073 21.768 -17.669 1.00186.97 C ATOM 128 CG1 ILE A 33 -22.681 20.853 -16.498 1.00186.29 C ATOM 129 CG2 ILE A 33 -23.832 20.928 -18.700 1.00186.44 C ATOM 130 CD1 ILE A 33 -23.867 20.142 -15.833 1.00184.51 C ATOM 131 N SER A 34 -20.030 23.933 -17.618 1.00184.40 N ATOM 132 CA SER A 34 -19.424 25.157 -17.069 1.00182.95 C ATOM 133 C SER A 34 -19.038 25.962 -18.306 1.00182.29 C ATOM 134 O SER A 34 -18.590 25.403 -19.300 1.00182.43 O ATOM 135 CB SER A 34 -18.199 24.839 -16.225 1.00182.36 C ATOM 136 OG SER A 34 -16.990 25.070 -16.946 1.00182.11 O ATOM 137 N GLU A 35 -19.219 27.269 -18.236 1.00181.35 N ATOM 138 CA GLU A 35 -19.013 28.138 -19.394 1.00180.75 C ATOM 139 C GLU A 35 -17.702 28.735 -19.927 1.00179.75 C ATOM 140 O GLU A 35 -16.588 28.226 -19.772 1.00178.29 O ATOM 141 CB GLU A 35 -19.990 29.296 -19.259 1.00181.98 C ATOM 142 CG GLU A 35 -21.338 29.024 -19.904 1.00183.50 C ATOM 143 CD GLU A 35 -21.656 27.558 -20.136 1.00184.28 C ATOM 144 OE1 GLU A 35 -21.062 26.961 -21.059 1.00183.95 O ATOM 145 OE2 GLU A 35 -22.521 27.021 -19.411 1.00185.10 O ATOM 146 N ASN A 36 -17.914 29.823 -20.663 1.00179.92 N ATOM 147 CA ASN A 36 -16.844 30.610 -21.229 1.00180.62 C ATOM 148 C ASN A 36 -16.281 31.058 -19.926 1.00181.23 C ATOM 149 O ASN A 36 -15.103 31.341 -19.819 1.00181.62 O ATOM 150 CB ASN A 36 -17.388 31.832 -21.941 1.00180.82 C ATOM 151 CG ASN A 36 -17.645 31.611 -23.392 1.00182.08 C ATOM 152 OD1 ASN A 36 -16.729 31.377 -24.171 1.00182.92 O ATOM 153 ND2 ASN A 36 -18.907 31.705 -23.778 1.00183.27 N ATOM 154 N ALA A 37 -17.158 31.116 -18.928 1.00181.85 N ATOM 155 CA ALA A 37 -16.773 31.516 -17.583 1.00182.29 C ATOM 156 C ALA A 37 -15.531 30.754 -17.159 1.00182.76 C ATOM 157 O ALA A 37 -14.583 31.328 -16.615 1.00182.32 O ATOM 158 CB ALA A 37 -17.923 31.251 -16.606 1.00181.85 C ATOM 159 N LEU A 38 -15.547 29.456 -17.435 1.00183.67 N ATOM 160 CA LEU A 38 -14.427 28.579 -17.111 1.00184.12 C ATOM 161 C LEU A 38 -13.148 29.073 -17.763 1.00184.05 C ATOM 162 O LEU A 38 -12.040 28.809 -17.283 1.00183.42 O ATOM 163 CB LEU A 38 -14.738 27.147 -17.572 1.00184.55 C ATOM 164 CG LEU A 38 -13.625 26.095 -17.588 1.00184.94 C ATOM 165 CD1 LEU A 38 -14.247 24.709 -17.608 1.00185.45 C ATOM 166 CD2 LEU A 38 -12.721 26.297 -18.797 1.00184.46 C ATOM 167 N LYS A 39 -13.327 29.801 -18.859 1.00184.14 N ATOM 168 CA LYS A 39 -12.226 30.363 -19.628 1.00183.59 C ATOM 169 C LYS A 39 -11.302 31.159 -18.711 1.00182.98 C ATOM 170 O LYS A 39 -10.093 30.912 -18.655 1.00183.18 O ATOM 171 CB LYS A 39 -12.790 31.263 -20.749 1.00183.64 C ATOM 172 CG LYS A 39 -11.851 31.587 -21.912 1.00184.17 C ATOM 173 CD LYS A 39 -12.620 32.210 -23.080 1.00184.66 C ATOM 174 CE LYS A 39 -11.678 32.675 -24.183 1.00185.01 C ATOM 175 NZ LYS A 39 -12.408 33.271 -25.337 1.00185.25 N """ def get_necessary_inputs(pdb_str): pdb_inp = iotbx.pdb.input(lines=pdb_str, source_info=None) model = mmtbx.model.manager(model_input = pdb_inp) model.process(make_restraints=True) return model def exercise_1(): """ 58 is outlier """ model = get_necessary_inputs(pdb_str_1) # pdb_h.write_pdb_file("fix_rot_out_ex1_start.pdb") model = run( args=[], model=model) rotamers = [] # pdb_h.write_pdb_file("fix_rot_out_ex1_end.pdb") for res in model.get_hierarchy().only_chain().only_conformer().residues(): rotamers.append(model.get_rotamer_manager().evaluate_residue(res)) # print rotamers assert rotamers == ['m-80', 'p'], rotamers def exercise_2(): model = get_necessary_inputs(pdb_str_2) model = run( args=[], model = model) rotamers = [] for res in model.get_hierarchy().only_chain().only_conformer().residues(): rotamers.append(model.get_rotamer_manager().evaluate_residue(res)) assert rotamers == ['mtt180', 'tttt', 'm-30', 'pt', 'p', 'mm-30', 'm-40', 'EXCEPTION', 'tt', 'tttt'], rotamers if (__name__ == "__main__"): exercise_1() exercise_2() print("OK")