From 50db7130d5445063fb71a68c5f868933173fba6a Mon Sep 17 00:00:00 2001 From: Stefan Doerr Date: Fri, 25 Feb 2022 14:55:06 +0200 Subject: [PATCH 1/4] add tests for cyclic peptides --- tests/core_test.py | 24 ++ tests/data/5vav_cyclic_peptide.pdb | 420 +++++++++++++++++++++++++ tests/data/5vav_cyclic_peptide_out.pqr | 214 +++++++++++++ 3 files changed, 658 insertions(+) create mode 100644 tests/data/5vav_cyclic_peptide.pdb create mode 100644 tests/data/5vav_cyclic_peptide_out.pqr diff --git a/tests/core_test.py b/tests/core_test.py index e9c7fdd2..9a1fbf9f 100644 --- a/tests/core_test.py +++ b/tests/core_test.py @@ -118,3 +118,27 @@ def test_protonated_terminals(input_pdb, expected_pqr, tmp_path): tmp_path=tmp_path, compare_resnames=True, ) + + +@pytest.mark.parametrize( + "input_pdb, expected_pqr", + [ + pytest.param( + "5vav_cyclic_peptide.pdb", + "5vav_cyclic_peptide_out.pqr", + id="Cyclic peptide", + ) + ], +) +def test_cyclic_peptide(input_pdb, expected_pqr, tmp_path): + """Tests for cyclic peptide protonation.""" + args = "--log-level=INFO --ff=AMBER --ffout AMBER" + output_pqr = Path(input_pdb).stem + ".pqr" + common.run_pdb2pqr( + args=args, + input_pdb=common.DATA_DIR / input_pdb, + output_pqr=output_pqr, + expected_pqr=common.DATA_DIR / expected_pqr, + tmp_path=tmp_path, + compare_resnames=True, + ) diff --git a/tests/data/5vav_cyclic_peptide.pdb b/tests/data/5vav_cyclic_peptide.pdb new file mode 100644 index 00000000..8a09110f --- /dev/null +++ b/tests/data/5vav_cyclic_peptide.pdb @@ -0,0 +1,420 @@ +MODEL 1 +ATOM 1 N GLY A 1 1.330 0.000 0.000 1.00 13.00 0 N +ATOM 2 CA GLY A 1 2.071 0.001 -1.247 1.00 45.03 0 C +ATOM 3 C GLY A 1 3.401 0.721 -1.131 1.00 35.41 0 C +ATOM 4 O GLY A 1 4.434 0.202 -1.554 1.00 31.13 0 O +ATOM 5 H GLY A 1 1.811 -0.001 0.854 1.00 52.40 0 H +ATOM 6 HA2 GLY A 1 2.252 -1.021 -1.547 1.00 51.50 0 H +ATOM 7 HA3 GLY A 1 1.477 0.488 -2.006 1.00 11.50 0 H +ATOM 8 N ARG A 2 3.374 1.919 -0.558 1.00 4.34 0 N +ATOM 9 CA ARG A 2 4.586 2.712 -0.390 1.00 1.53 0 C +ATOM 10 C ARG A 2 5.609 1.968 0.463 1.00 44.10 0 C +ATOM 11 O ARG A 2 5.254 1.109 1.271 1.00 55.34 0 O +ATOM 12 CB ARG A 2 4.254 4.060 0.254 1.00 50.14 0 C +ATOM 13 CG ARG A 2 5.314 5.124 0.021 1.00 41.05 0 C +ATOM 14 CD ARG A 2 4.692 6.498 -0.171 1.00 54.12 0 C +ATOM 15 NE ARG A 2 5.587 7.569 0.258 1.00 14.25 0 N +ATOM 16 CZ ARG A 2 5.351 8.857 0.036 1.00 12.51 0 C +ATOM 17 NH1 ARG A 2 4.254 9.233 -0.607 1.00 70.44 0 N +ATOM 18 NH2 ARG A 2 6.213 9.774 0.458 1.00 20.52 0 N1+ +ATOM 19 H ARG A 2 2.520 2.279 -0.241 1.00 12.44 0 H +ATOM 20 HA ARG A 2 5.008 2.885 -1.368 1.00 40.14 0 H +ATOM 21 HB2 ARG A 2 3.320 4.419 -0.152 1.00 52.44 0 H +ATOM 22 HB3 ARG A 2 4.144 3.919 1.318 1.00 0.53 0 H +ATOM 23 HG2 ARG A 2 5.973 5.156 0.876 1.00 61.13 0 H +ATOM 24 HG3 ARG A 2 5.880 4.868 -0.863 1.00 34.31 0 H +ATOM 25 HD2 ARG A 2 4.462 6.632 -1.218 1.00 24.01 0 H +ATOM 26 HD3 ARG A 2 3.781 6.549 0.406 1.00 55.31 0 H +ATOM 27 HE ARG A 2 6.403 7.314 0.736 1.00 41.32 0 H +ATOM 28 HH11 ARG A 2 3.602 8.545 -0.926 1.00 21.34 0 H +ATOM 29 HH12 ARG A 2 4.078 10.203 -0.772 1.00 42.45 0 H +ATOM 30 HH21 ARG A 2 7.041 9.494 0.944 1.00 51.52 0 H +ATOM 31 HH22 ARG A 2 6.035 10.743 0.290 1.00 31.53 0 H +ATOM 32 N CYS A 3 6.882 2.303 0.277 1.00 31.35 0 N +ATOM 33 CA CYS A 3 7.958 1.666 1.028 1.00 53.31 0 C +ATOM 34 C CYS A 3 9.226 2.514 0.985 1.00 61.43 0 C +ATOM 35 O CYS A 3 9.385 3.371 0.115 1.00 13.33 0 O +ATOM 36 CB CYS A 3 8.243 0.272 0.467 1.00 23.21 0 C +ATOM 37 SG CYS A 3 8.882 -0.908 1.699 1.00 63.40 0 S +ATOM 38 H CYS A 3 7.104 2.995 -0.381 1.00 55.11 0 H +ATOM 39 HA CYS A 3 7.637 1.573 2.054 1.00 14.22 0 H +ATOM 40 HB2 CYS A 3 7.330 -0.139 0.063 1.00 73.23 0 H +ATOM 41 HB3 CYS A 3 8.976 0.353 -0.322 1.00 72.33 0 H +ATOM 42 N THR A 4 10.128 2.267 1.930 1.00 43.14 0 N +ATOM 43 CA THR A 4 11.382 3.007 2.001 1.00 61.32 0 C +ATOM 44 C THR A 4 12.480 2.306 1.209 1.00 73.25 0 C +ATOM 45 O THR A 4 12.651 1.091 1.310 1.00 52.33 0 O +ATOM 46 CB THR A 4 11.849 3.182 3.458 1.00 11.13 0 C +ATOM 47 OG1 THR A 4 11.642 1.968 4.188 1.00 24.43 0 O +ATOM 48 CG2 THR A 4 11.098 4.320 4.134 1.00 61.33 0 C +ATOM 49 H THR A 4 9.944 1.571 2.595 1.00 44.24 0 H +ATOM 50 HA THR A 4 11.216 3.987 1.578 1.00 73.33 0 H +ATOM 51 HB THR A 4 12.904 3.417 3.457 1.00 54.44 0 H +ATOM 52 HG1 THR A 4 12.128 1.254 3.767 1.00 4.42 0 H +ATOM 53 HG21 THR A 4 10.802 4.016 5.127 1.00 1.10 0 H +ATOM 54 HG22 THR A 4 10.220 4.565 3.555 1.00 31.22 0 H +ATOM 55 HG23 THR A 4 11.740 5.185 4.199 1.00 52.33 0 H +ATOM 56 N GLN A 5 13.221 3.079 0.421 1.00 34.03 0 N +ATOM 57 CA GLN A 5 14.302 2.531 -0.388 1.00 62.52 0 C +ATOM 58 C GLN A 5 15.496 2.152 0.482 1.00 33.25 0 C +ATOM 59 O GLN A 5 16.171 1.155 0.227 1.00 2.42 0 O +ATOM 60 CB GLN A 5 14.733 3.540 -1.453 1.00 51.44 0 C +ATOM 61 CG GLN A 5 13.592 4.012 -2.341 1.00 4.53 0 C +ATOM 62 CD GLN A 5 13.196 2.982 -3.379 1.00 70.23 0 C +ATOM 63 OE1 GLN A 5 12.086 2.450 -3.351 1.00 31.35 0 O +ATOM 64 NE2 GLN A 5 14.104 2.694 -4.305 1.00 13.31 0 N +ATOM 65 H GLN A 5 13.035 4.040 0.384 1.00 63.13 0 H +ATOM 66 HA GLN A 5 13.933 1.642 -0.877 1.00 34.33 0 H +ATOM 67 HB2 GLN A 5 15.160 4.402 -0.963 1.00 42.44 0 H +ATOM 68 HB3 GLN A 5 15.484 3.084 -2.082 1.00 12.52 0 H +ATOM 69 HG2 GLN A 5 12.734 4.224 -1.720 1.00 61.42 0 H +ATOM 70 HG3 GLN A 5 13.899 4.915 -2.849 1.00 32.04 0 H +ATOM 71 HE21 GLN A 5 14.967 3.157 -4.265 1.00 25.32 0 H +ATOM 72 HE22 GLN A 5 13.874 2.031 -4.988 1.00 4.22 0 H +ATOM 73 N ALA A 6 15.750 2.954 1.511 1.00 14.02 0 N +ATOM 74 CA ALA A 6 16.861 2.702 2.420 1.00 34.15 0 C +ATOM 75 C ALA A 6 16.362 2.199 3.771 1.00 75.12 0 C +ATOM 76 O ALA A 6 15.167 1.966 3.954 1.00 54.32 0 O +ATOM 77 CB ALA A 6 17.693 3.963 2.600 1.00 54.14 0 C +ATOM 78 H ALA A 6 15.175 3.733 1.663 1.00 42.11 0 H +ATOM 79 HA ALA A 6 17.490 1.945 1.976 1.00 65.30 0 H +ATOM 80 HB1 ALA A 6 17.553 4.610 1.745 1.00 31.34 0 H +ATOM 81 HB2 ALA A 6 17.379 4.477 3.496 1.00 74.12 0 H +ATOM 82 HB3 ALA A 6 18.736 3.697 2.683 1.00 34.02 0 H +ATOM 83 N TRP A 7 17.283 2.033 4.712 1.00 24.41 0 N +ATOM 84 CA TRP A 7 16.936 1.556 6.046 1.00 20.11 0 C +ATOM 85 C TRP A 7 16.604 2.721 6.971 1.00 11.42 0 C +ATOM 86 O TRP A 7 16.957 3.872 6.711 1.00 71.23 0 O +ATOM 87 CB TRP A 7 18.086 0.735 6.632 1.00 11.02 0 C +ATOM 88 CG TRP A 7 17.949 -0.737 6.388 1.00 22.41 0 C +ATOM 89 CD1 TRP A 7 17.280 -1.339 5.361 1.00 71.30 0 C +ATOM 90 CD2 TRP A 7 18.494 -1.793 7.188 1.00 52.22 0 C +ATOM 91 NE1 TRP A 7 17.376 -2.705 5.474 1.00 35.41 0 N +ATOM 92 CE2 TRP A 7 18.116 -3.009 6.586 1.00 72.01 0 C +ATOM 93 CE3 TRP A 7 19.265 -1.829 8.352 1.00 5.12 0 C +ATOM 94 CZ2 TRP A 7 18.483 -4.245 7.111 1.00 1.03 0 C +ATOM 95 CZ3 TRP A 7 19.629 -3.056 8.873 1.00 71.44 0 C +ATOM 96 CH2 TRP A 7 19.239 -4.251 8.252 1.00 14.33 0 C +ATOM 97 H TRP A 7 18.220 2.235 4.506 1.00 61.04 0 H +ATOM 98 HA TRP A 7 16.065 0.924 5.955 1.00 53.21 0 H +ATOM 99 HB2 TRP A 7 19.015 1.061 6.190 1.00 41.42 0 H +ATOM 100 HB3 TRP A 7 18.124 0.895 7.700 1.00 21.51 0 H +ATOM 101 HD1 TRP A 7 16.755 -0.807 4.583 1.00 42.24 0 H +ATOM 102 HE1 TRP A 7 16.979 -3.356 4.857 1.00 21.22 0 H +ATOM 103 HE3 TRP A 7 19.576 -0.919 8.845 1.00 62.32 0 H +ATOM 104 HZ2 TRP A 7 18.191 -5.174 6.645 1.00 74.34 0 H +ATOM 105 HZ3 TRP A 7 20.225 -3.104 9.772 1.00 32.13 0 H +ATOM 106 HH2 TRP A 7 19.545 -5.186 8.694 1.00 71.32 0 H +ATOM 107 N PRO A 8 15.909 2.420 8.078 1.00 1.33 0 N +ATOM 108 CA PRO A 8 15.483 1.055 8.399 1.00 60.34 0 C +ATOM 109 C PRO A 8 14.392 0.553 7.459 1.00 20.51 0 C +ATOM 110 O PRO A 8 13.795 1.315 6.699 1.00 72.23 0 O +ATOM 111 CB PRO A 8 14.945 1.177 9.826 1.00 33.23 0 C +ATOM 112 CG PRO A 8 14.529 2.602 9.954 1.00 61.30 0 C +ATOM 113 CD PRO A 8 15.485 3.390 9.102 1.00 25.15 0 C +ATOM 114 HA PRO A 8 16.315 0.366 8.383 1.00 32.33 0 H +ATOM 115 HB2 PRO A 8 14.107 0.507 9.956 1.00 35.42 0 H +ATOM 116 HB3 PRO A 8 15.724 0.928 10.531 1.00 11.41 0 H +ATOM 117 HG2 PRO A 8 13.519 2.723 9.594 1.00 52.20 0 H +ATOM 118 HG3 PRO A 8 14.602 2.914 10.985 1.00 35.23 0 H +ATOM 119 HD2 PRO A 8 14.983 4.232 8.651 1.00 13.53 0 H +ATOM 120 HD3 PRO A 8 16.329 3.722 9.690 1.00 34.33 0 H +ATOM 121 N PRO A 9 14.124 -0.761 7.511 1.00 54.41 0 N +ATOM 122 CA PRO A 9 13.102 -1.394 6.671 1.00 1.54 0 C +ATOM 123 C PRO A 9 11.688 -0.989 7.075 1.00 42.04 0 C +ATOM 124 O PRO A 9 11.022 -1.696 7.831 1.00 24.33 0 O +ATOM 125 CB PRO A 9 13.320 -2.889 6.914 1.00 21.12 0 C +ATOM 126 CG PRO A 9 13.952 -2.966 8.261 1.00 44.11 0 C +ATOM 127 CD PRO A 9 14.796 -1.729 8.393 1.00 4.54 0 C +ATOM 128 HA PRO A 9 13.254 -1.171 5.625 1.00 5.04 0 H +ATOM 129 HB2 PRO A 9 12.369 -3.402 6.893 1.00 31.15 0 H +ATOM 130 HB3 PRO A 9 13.969 -3.291 6.150 1.00 12.33 0 H +ATOM 131 HG2 PRO A 9 13.190 -2.983 9.024 1.00 35.13 0 H +ATOM 132 HG3 PRO A 9 14.570 -3.849 8.326 1.00 23.30 0 H +ATOM 133 HD2 PRO A 9 14.799 -1.381 9.416 1.00 70.21 0 H +ATOM 134 HD3 PRO A 9 15.804 -1.921 8.056 1.00 61.31 0 H +ATOM 135 N ILE A 10 11.236 0.152 6.565 1.00 61.44 0 N +ATOM 136 CA ILE A 10 9.900 0.648 6.871 1.00 44.40 0 C +ATOM 137 C ILE A 10 8.992 0.571 5.649 1.00 54.41 0 C +ATOM 138 O ILE A 10 9.158 1.325 4.689 1.00 31.22 0 O +ATOM 139 CB ILE A 10 9.943 2.103 7.374 1.00 13.35 0 C +ATOM 140 CG1 ILE A 10 10.997 2.255 8.473 1.00 41.43 0 C +ATOM 141 CG2 ILE A 10 8.574 2.527 7.885 1.00 54.12 0 C +ATOM 142 CD1 ILE A 10 10.755 1.364 9.671 1.00 53.42 0 C +ATOM 143 H ILE A 10 11.814 0.671 5.968 1.00 70.23 0 H +ATOM 144 HA ILE A 10 9.486 0.029 7.654 1.00 44.41 0 H +ATOM 145 HB ILE A 10 10.204 2.741 6.544 1.00 72.23 0 H +ATOM 146 HG12 ILE A 10 11.967 2.010 8.069 1.00 53.43 0 H +ATOM 147 HG13 ILE A 10 11.003 3.280 8.816 1.00 42.02 0 H +ATOM 148 HG21 ILE A 10 8.671 3.432 8.466 1.00 14.04 0 H +ATOM 149 HG22 ILE A 10 7.918 2.708 7.047 1.00 74.24 0 H +ATOM 150 HG23 ILE A 10 8.161 1.744 8.503 1.00 2.11 0 H +ATOM 151 HD11 ILE A 10 9.708 1.391 9.934 1.00 55.31 0 H +ATOM 152 HD12 ILE A 10 11.041 0.352 9.431 1.00 71.32 0 H +ATOM 153 HD13 ILE A 10 11.344 1.716 10.506 1.00 54.31 0 H +ATOM 154 N CYS A 11 8.028 -0.343 5.691 1.00 25.14 0 N +ATOM 155 CA CYS A 11 7.091 -0.519 4.589 1.00 51.21 0 C +ATOM 156 C CYS A 11 5.666 -0.195 5.030 1.00 62.24 0 C +ATOM 157 O CYS A 11 5.208 -0.657 6.075 1.00 70.32 0 O +ATOM 158 CB CYS A 11 7.159 -1.952 4.058 1.00 50.14 0 C +ATOM 159 SG CYS A 11 7.305 -2.067 2.245 1.00 5.24 0 S +ATOM 160 H CYS A 11 7.946 -0.915 6.484 1.00 1.23 0 H +ATOM 161 HA CYS A 11 7.374 0.162 3.801 1.00 61.13 0 H +ATOM 162 HB2 CYS A 11 8.018 -2.447 4.488 1.00 54.33 0 H +ATOM 163 HB3 CYS A 11 6.263 -2.479 4.350 1.00 53.04 0 H +ATOM 164 N PHE A 12 4.971 0.602 4.225 1.00 34.41 0 N +ATOM 165 CA PHE A 12 3.598 0.988 4.532 1.00 43.14 0 C +ATOM 166 C PHE A 12 2.613 -0.070 4.043 1.00 43.21 0 C +ATOM 167 O PHE A 12 2.926 -0.897 3.186 1.00 52.42 0 O +ATOM 168 CB PHE A 12 3.272 2.339 3.892 1.00 13.44 0 C +ATOM 169 CG PHE A 12 3.477 3.505 4.817 1.00 51.10 0 C +ATOM 170 CD1 PHE A 12 2.415 4.323 5.168 1.00 21.14 0 C +ATOM 171 CD2 PHE A 12 4.732 3.783 5.334 1.00 12.53 0 C +ATOM 172 CE1 PHE A 12 2.600 5.396 6.019 1.00 3.33 0 C +ATOM 173 CE2 PHE A 12 4.923 4.855 6.186 1.00 50.11 0 C +ATOM 174 CZ PHE A 12 3.856 5.663 6.528 1.00 42.22 0 C +ATOM 175 H PHE A 12 5.391 0.938 3.406 1.00 52.33 0 H +ATOM 176 HA PHE A 12 3.511 1.076 5.603 1.00 2.15 0 H +ATOM 177 HB2 PHE A 12 3.906 2.485 3.031 1.00 73.43 0 H +ATOM 178 HB3 PHE A 12 2.239 2.341 3.579 1.00 72.43 0 H +ATOM 179 HD1 PHE A 12 1.432 4.115 4.770 1.00 34.15 0 H +ATOM 180 HD2 PHE A 12 5.567 3.153 5.067 1.00 2.21 0 H +ATOM 181 HE1 PHE A 12 1.764 6.026 6.284 1.00 31.14 0 H +ATOM 182 HE2 PHE A 12 5.906 5.062 6.582 1.00 30.10 0 H +ATOM 183 HZ PHE A 12 4.003 6.501 7.193 1.00 20.23 0 H +ATOM 184 N PRO A 13 1.394 -0.045 4.601 1.00 52.31 0 N +ATOM 185 CA PRO A 13 0.338 -0.994 4.238 1.00 75.20 0 C +ATOM 186 C PRO A 13 -0.195 -0.758 2.829 1.00 70.12 0 C +ATOM 187 O PRO A 13 -0.596 -1.697 2.141 1.00 32.32 0 O +ATOM 188 CB PRO A 13 -0.755 -0.723 5.275 1.00 11.41 0 C +ATOM 189 CG PRO A 13 -0.533 0.688 5.699 1.00 52.34 0 C +ATOM 190 CD PRO A 13 0.952 0.913 5.629 1.00 60.14 0 C +ATOM 191 HA PRO A 13 0.675 -2.016 4.327 1.00 21.45 0 H +ATOM 192 HB2 PRO A 13 -1.727 -0.851 4.820 1.00 70.13 0 H +ATOM 193 HB3 PRO A 13 -0.647 -1.405 6.104 1.00 21.25 0 H +ATOM 194 HG2 PRO A 13 -1.046 1.359 5.026 1.00 61.32 0 H +ATOM 195 HG3 PRO A 13 -0.886 0.827 6.710 1.00 45.30 0 H +ATOM 196 HD2 PRO A 13 1.166 1.928 5.328 1.00 65.32 0 H +ATOM 197 HD3 PRO A 13 1.412 0.695 6.581 1.00 30.41 0 H +ATOM 198 N ASP A 14 -0.196 0.501 2.405 1.00 64.21 0 N +ATOM 199 CA ASP A 14 -0.678 0.860 1.076 1.00 23.02 0 C +ATOM 200 C ASP A 14 -0.004 0.008 0.005 1.00 31.21 0 C +ATOM 201 O ASP A 14 -0.659 -0.782 -0.677 1.00 13.23 0 O +ATOM 202 CB ASP A 14 -0.422 2.343 0.801 1.00 32.32 0 C +ATOM 203 CG ASP A 14 -0.447 2.670 -0.679 1.00 32.31 0 C +ATOM 204 OD1 ASP A 14 0.628 2.632 -1.314 1.00 10.15 0 O +ATOM 205 OD2 ASP A 14 -1.542 2.962 -1.203 1.00 51.30 0 O +ATOM 206 H ASP A 14 0.137 1.206 3.000 1.00 71.44 0 H +ATOM 207 HA ASP A 14 -1.741 0.676 1.048 1.00 11.23 0 H +ATOM 208 HB2 ASP A 14 -1.184 2.930 1.293 1.00 20.03 0 H +ATOM 209 HB3 ASP A 14 0.546 2.614 1.195 1.00 21.54 0 H +CONECT 1 2 +CONECT 2 1 3 6 7 +CONECT 3 2 4 8 +CONECT 4 3 +CONECT 6 2 +CONECT 7 2 +CONECT 8 3 9 19 +CONECT 9 8 10 12 20 +CONECT 10 9 11 32 +CONECT 11 10 +CONECT 12 9 13 21 22 +CONECT 13 12 14 23 24 +CONECT 14 13 15 25 26 +CONECT 15 14 16 27 +CONECT 16 15 17 18 +CONECT 17 16 28 29 +CONECT 18 16 30 31 +CONECT 19 8 +CONECT 20 9 +CONECT 21 12 +CONECT 22 12 +CONECT 23 13 +CONECT 24 13 +CONECT 25 14 +CONECT 26 14 +CONECT 27 15 +CONECT 28 17 +CONECT 29 17 +CONECT 30 18 +CONECT 31 18 +CONECT 32 10 33 38 +CONECT 33 32 34 36 39 +CONECT 34 33 35 42 +CONECT 35 34 +CONECT 36 33 37 40 41 +CONECT 37 36 159 +CONECT 38 32 +CONECT 39 33 +CONECT 40 36 +CONECT 41 36 +CONECT 42 34 43 49 +CONECT 43 42 44 46 50 +CONECT 44 43 45 56 +CONECT 45 44 +CONECT 46 43 47 48 51 +CONECT 47 46 52 +CONECT 48 46 53 54 55 +CONECT 49 42 +CONECT 50 43 +CONECT 51 46 +CONECT 52 47 +CONECT 53 48 +CONECT 54 48 +CONECT 55 48 +CONECT 56 44 57 65 +CONECT 57 56 58 60 66 +CONECT 58 57 59 73 +CONECT 59 58 +CONECT 60 57 61 67 68 +CONECT 61 60 62 69 70 +CONECT 62 61 63 64 +CONECT 63 62 +CONECT 64 62 71 72 +CONECT 65 56 +CONECT 66 57 +CONECT 67 60 +CONECT 68 60 +CONECT 69 61 +CONECT 70 61 +CONECT 71 64 +CONECT 72 64 +CONECT 73 58 74 78 +CONECT 74 73 75 77 79 +CONECT 75 74 76 83 +CONECT 76 75 +CONECT 77 74 80 81 82 +CONECT 78 73 +CONECT 79 74 +CONECT 80 77 +CONECT 81 77 +CONECT 82 77 +CONECT 83 75 84 97 +CONECT 84 83 85 87 98 +CONECT 85 84 86 107 +CONECT 86 85 +CONECT 87 84 88 99 100 +CONECT 88 87 89 90 +CONECT 89 88 91 101 +CONECT 90 88 92 93 +CONECT 91 89 92 102 +CONECT 92 90 91 94 +CONECT 93 90 95 103 +CONECT 94 92 96 104 +CONECT 95 93 96 105 +CONECT 96 94 95 106 +CONECT 97 83 +CONECT 98 84 +CONECT 99 87 +CONECT 100 87 +CONECT 101 89 +CONECT 102 91 +CONECT 103 93 +CONECT 104 94 +CONECT 105 95 +CONECT 106 96 +CONECT 107 85 108 113 +CONECT 108 107 109 111 114 +CONECT 109 108 110 121 +CONECT 110 109 +CONECT 111 108 112 115 116 +CONECT 112 111 113 117 118 +CONECT 113 107 112 119 120 +CONECT 114 108 +CONECT 115 111 +CONECT 116 111 +CONECT 117 112 +CONECT 118 112 +CONECT 119 113 +CONECT 120 113 +CONECT 121 109 122 127 +CONECT 122 121 123 125 128 +CONECT 123 122 124 135 +CONECT 124 123 +CONECT 125 122 126 129 130 +CONECT 126 125 127 131 132 +CONECT 127 121 126 133 134 +CONECT 128 122 +CONECT 129 125 +CONECT 130 125 +CONECT 131 126 +CONECT 132 126 +CONECT 133 127 +CONECT 134 127 +CONECT 135 123 136 143 +CONECT 136 135 137 139 144 +CONECT 137 136 138 154 +CONECT 138 137 +CONECT 139 136 140 141 145 +CONECT 140 139 142 146 147 +CONECT 141 139 148 149 150 +CONECT 142 140 151 152 153 +CONECT 143 135 +CONECT 144 136 +CONECT 145 139 +CONECT 146 140 +CONECT 147 140 +CONECT 148 141 +CONECT 149 141 +CONECT 150 141 +CONECT 151 142 +CONECT 152 142 +CONECT 153 142 +CONECT 154 137 155 160 +CONECT 155 154 156 158 161 +CONECT 156 155 157 164 +CONECT 157 156 +CONECT 158 155 159 162 163 +CONECT 159 37 158 +CONECT 160 154 +CONECT 161 155 +CONECT 162 158 +CONECT 163 158 +CONECT 164 156 165 175 +CONECT 165 164 166 168 176 +CONECT 166 165 167 184 +CONECT 167 166 +CONECT 168 165 169 177 178 +CONECT 169 168 170 171 +CONECT 170 169 172 179 +CONECT 171 169 173 180 +CONECT 172 170 174 181 +CONECT 173 171 174 182 +CONECT 174 172 173 183 +CONECT 175 164 +CONECT 176 165 +CONECT 177 168 +CONECT 178 168 +CONECT 179 170 +CONECT 180 171 +CONECT 181 172 +CONECT 182 173 +CONECT 183 174 +CONECT 184 166 185 190 +CONECT 185 184 186 188 191 +CONECT 186 185 187 198 +CONECT 187 186 +CONECT 188 185 189 192 193 +CONECT 189 188 190 194 195 +CONECT 190 184 189 196 197 +CONECT 191 185 +CONECT 192 188 +CONECT 193 188 +CONECT 194 189 +CONECT 195 189 +CONECT 196 190 +CONECT 197 190 +CONECT 198 186 199 206 +CONECT 199 198 200 202 207 +CONECT 200 199 201 +CONECT 201 200 +CONECT 202 199 203 208 209 +CONECT 203 202 204 205 +CONECT 204 203 +CONECT 205 203 +CONECT 206 198 +CONECT 207 199 +CONECT 208 202 +CONECT 209 202 +ENDMDL +END diff --git a/tests/data/5vav_cyclic_peptide_out.pqr b/tests/data/5vav_cyclic_peptide_out.pqr new file mode 100644 index 00000000..14420854 --- /dev/null +++ b/tests/data/5vav_cyclic_peptide_out.pqr @@ -0,0 +1,214 @@ +ATOM 1 N GLY 1 1.330 0.000 0.000 0.2943 1.8240 +ATOM 2 CA GLY 1 2.071 0.001 -1.247 -0.0100 1.9080 +ATOM 3 C GLY 1 3.401 0.721 -1.131 0.6163 1.9080 +ATOM 4 O GLY 1 4.434 0.202 -1.554 -0.5722 1.6612 +ATOM 5 H1 GLY 1 1.811 -0.001 0.854 0.1642 0.6000 +ATOM 6 HA2 GLY 1 2.252 -1.021 -1.547 0.0895 1.1000 +ATOM 7 HA3 GLY 1 1.477 0.488 -2.006 0.0895 1.1000 +ATOM 8 H2 GLY 1 0.715 0.736 0.204 0.1642 0.6000 +ATOM 9 H3 GLY 1 0.715 -0.736 0.202 0.1642 0.6000 +ATOM 10 N ARG 2 3.374 1.919 -0.558 -0.3479 1.8240 +ATOM 11 CA ARG 2 4.586 2.712 -0.390 -0.2637 1.9080 +ATOM 12 C ARG 2 5.609 1.968 0.463 0.7341 1.9080 +ATOM 13 O ARG 2 5.254 1.109 1.271 -0.5894 1.6612 +ATOM 14 CB ARG 2 4.254 4.060 0.254 -0.0007 1.9080 +ATOM 15 CG ARG 2 5.314 5.124 0.021 0.0390 1.9080 +ATOM 16 CD ARG 2 4.692 6.498 -0.171 0.0486 1.9080 +ATOM 17 NE ARG 2 5.587 7.569 0.258 -0.5295 1.8240 +ATOM 18 CZ ARG 2 5.351 8.857 0.036 0.8076 1.9080 +ATOM 19 NH1 ARG 2 4.254 9.233 -0.607 -0.8627 1.8240 +ATOM 20 NH2 ARG 2 6.213 9.774 0.458 -0.8627 1.8240 +ATOM 21 H ARG 2 2.520 2.279 -0.241 0.2747 0.6000 +ATOM 22 HA ARG 2 5.008 2.885 -1.368 0.1560 1.3870 +ATOM 23 HB2 ARG 2 3.320 4.419 -0.152 0.0327 1.4870 +ATOM 24 HB3 ARG 2 4.144 3.919 1.318 0.0327 1.4870 +ATOM 25 HG2 ARG 2 5.973 5.156 0.876 0.0285 1.4870 +ATOM 26 HG3 ARG 2 5.880 4.868 -0.863 0.0285 1.4870 +ATOM 27 HD2 ARG 2 4.462 6.632 -1.218 0.0687 1.3870 +ATOM 28 HD3 ARG 2 3.781 6.549 0.406 0.0687 1.3870 +ATOM 29 HE ARG 2 6.403 7.314 0.736 0.3456 0.6000 +ATOM 30 HH11 ARG 2 3.602 8.545 -0.926 0.4478 0.6000 +ATOM 31 HH12 ARG 2 4.078 10.203 -0.772 0.4478 0.6000 +ATOM 32 HH21 ARG 2 7.041 9.494 0.944 0.4478 0.6000 +ATOM 33 HH22 ARG 2 6.035 10.743 0.290 0.4478 0.6000 +ATOM 34 N CYX 3 6.882 2.303 0.277 -0.4157 1.8240 +ATOM 35 CA CYX 3 7.958 1.666 1.028 0.0429 1.9080 +ATOM 36 C CYX 3 9.226 2.514 0.985 0.5973 1.9080 +ATOM 37 O CYX 3 9.385 3.371 0.115 -0.5679 1.6612 +ATOM 38 CB CYX 3 8.243 0.272 0.467 -0.0790 1.9080 +ATOM 39 SG CYX 3 8.882 -0.908 1.699 -0.1081 2.0000 +ATOM 40 H CYX 3 7.104 2.995 -0.381 0.2719 0.6000 +ATOM 41 HA CYX 3 7.637 1.573 2.054 0.0766 1.3870 +ATOM 42 HB2 CYX 3 7.330 -0.139 0.063 0.0910 1.3870 +ATOM 43 HB3 CYX 3 8.976 0.353 -0.322 0.0910 1.3870 +ATOM 44 N THR 4 10.128 2.267 1.930 -0.4157 1.8240 +ATOM 45 CA THR 4 11.382 3.007 2.001 -0.0389 1.9080 +ATOM 46 C THR 4 12.480 2.306 1.209 0.5973 1.9080 +ATOM 47 O THR 4 12.651 1.091 1.310 -0.5679 1.6612 +ATOM 48 CB THR 4 11.849 3.182 3.458 0.3654 1.9080 +ATOM 49 OG1 THR 4 11.642 1.968 4.188 -0.6761 1.7210 +ATOM 50 CG2 THR 4 11.098 4.320 4.134 -0.2438 1.9080 +ATOM 51 H THR 4 9.944 1.571 2.595 0.2719 0.6000 +ATOM 52 HA THR 4 11.216 3.987 1.578 0.1007 1.3870 +ATOM 53 HB THR 4 12.904 3.417 3.457 0.0043 1.3870 +ATOM 54 HG21 THR 4 10.802 4.016 5.127 0.0642 1.4870 +ATOM 55 HG22 THR 4 10.220 4.565 3.555 0.0642 1.4870 +ATOM 56 HG23 THR 4 11.740 5.185 4.199 0.0642 1.4870 +ATOM 57 HG1 THR 4 10.659 1.800 4.316 0.4102 0.0000 +ATOM 58 N GLN 5 13.221 3.079 0.421 -0.4157 1.8240 +ATOM 59 CA GLN 5 14.302 2.531 -0.388 -0.0031 1.9080 +ATOM 60 C GLN 5 15.496 2.152 0.482 0.5973 1.9080 +ATOM 61 O GLN 5 16.171 1.155 0.227 -0.5679 1.6612 +ATOM 62 CB GLN 5 14.733 3.540 -1.453 -0.0036 1.9080 +ATOM 63 CG GLN 5 13.592 4.012 -2.341 -0.0645 1.9080 +ATOM 64 CD GLN 5 13.196 2.982 -3.379 0.6951 1.9080 +ATOM 65 H GLN 5 13.035 4.040 0.384 0.2719 0.6000 +ATOM 66 HA GLN 5 13.933 1.642 -0.877 0.0850 1.3870 +ATOM 67 HB2 GLN 5 15.160 4.402 -0.963 0.0171 1.4870 +ATOM 68 HB3 GLN 5 15.484 3.084 -2.082 0.0171 1.4870 +ATOM 69 HG2 GLN 5 12.734 4.224 -1.720 0.0352 1.4870 +ATOM 70 HG3 GLN 5 13.899 4.915 -2.849 0.0352 1.4870 +ATOM 71 OE1 GLN 5 12.086 2.450 -3.351 -0.6086 1.6612 +ATOM 72 NE2 GLN 5 14.104 2.694 -4.305 -0.9407 1.8240 +ATOM 73 HE21 GLN 5 14.967 3.157 -4.265 0.4251 0.6000 +ATOM 74 HE22 GLN 5 13.874 2.031 -4.988 0.4251 0.6000 +ATOM 75 N ALA 6 15.750 2.954 1.511 -0.4157 1.8240 +ATOM 76 CA ALA 6 16.861 2.702 2.420 0.0337 1.9080 +ATOM 77 C ALA 6 16.362 2.199 3.771 0.5973 1.9080 +ATOM 78 O ALA 6 15.167 1.966 3.954 -0.5679 1.6612 +ATOM 79 CB ALA 6 17.693 3.963 2.600 -0.1825 1.9080 +ATOM 80 H ALA 6 15.175 3.733 1.663 0.2719 0.6000 +ATOM 81 HA ALA 6 17.490 1.945 1.976 0.0823 1.3870 +ATOM 82 HB1 ALA 6 17.553 4.610 1.745 0.0603 1.4870 +ATOM 83 HB2 ALA 6 17.379 4.477 3.496 0.0603 1.4870 +ATOM 84 HB3 ALA 6 18.736 3.697 2.683 0.0603 1.4870 +ATOM 85 N TRP 7 17.283 2.033 4.712 -0.4157 1.8240 +ATOM 86 CA TRP 7 16.936 1.556 6.046 -0.0275 1.9080 +ATOM 87 C TRP 7 16.604 2.721 6.971 0.5973 1.9080 +ATOM 88 O TRP 7 16.957 3.872 6.711 -0.5679 1.6612 +ATOM 89 CB TRP 7 18.086 0.735 6.632 -0.0050 1.9080 +ATOM 90 CG TRP 7 17.949 -0.737 6.388 -0.1415 1.9080 +ATOM 91 CD1 TRP 7 17.280 -1.339 5.361 -0.1638 1.9080 +ATOM 92 CD2 TRP 7 18.494 -1.793 7.188 0.1243 1.9080 +ATOM 93 NE1 TRP 7 17.376 -2.705 5.474 -0.3418 1.8240 +ATOM 94 CE2 TRP 7 18.116 -3.009 6.586 0.1380 1.9080 +ATOM 95 CE3 TRP 7 19.265 -1.829 8.352 -0.2387 1.9080 +ATOM 96 CZ2 TRP 7 18.483 -4.245 7.111 -0.2601 1.9080 +ATOM 97 CZ3 TRP 7 19.629 -3.056 8.873 -0.1972 1.9080 +ATOM 98 CH2 TRP 7 19.239 -4.251 8.252 -0.1134 1.9080 +ATOM 99 H TRP 7 18.220 2.235 4.506 0.2719 0.6000 +ATOM 100 HA TRP 7 16.065 0.924 5.955 0.1123 1.3870 +ATOM 101 HB2 TRP 7 19.015 1.061 6.190 0.0339 1.4870 +ATOM 102 HB3 TRP 7 18.124 0.895 7.700 0.0339 1.4870 +ATOM 103 HD1 TRP 7 16.755 -0.807 4.583 0.2062 1.4090 +ATOM 104 HE1 TRP 7 16.979 -3.356 4.857 0.3412 0.6000 +ATOM 105 HE3 TRP 7 19.576 -0.919 8.845 0.1700 1.4590 +ATOM 106 HZ2 TRP 7 18.191 -5.174 6.645 0.1572 1.4590 +ATOM 107 HZ3 TRP 7 20.225 -3.104 9.772 0.1447 1.4590 +ATOM 108 HH2 TRP 7 19.545 -5.186 8.694 0.1417 1.4590 +ATOM 109 N PRO 8 15.909 2.420 8.078 -0.2548 1.8240 +ATOM 110 CA PRO 8 15.483 1.055 8.399 -0.0266 1.9080 +ATOM 111 C PRO 8 14.392 0.553 7.459 0.5896 1.9080 +ATOM 112 O PRO 8 13.795 1.315 6.699 -0.5748 1.6612 +ATOM 113 CB PRO 8 14.945 1.177 9.826 -0.0070 1.9080 +ATOM 114 CG PRO 8 14.529 2.602 9.954 0.0189 1.9080 +ATOM 115 CD PRO 8 15.485 3.390 9.102 0.0192 1.9080 +ATOM 116 HA PRO 8 16.315 0.366 8.383 0.0641 1.3870 +ATOM 117 HB2 PRO 8 14.107 0.507 9.956 0.0253 1.4870 +ATOM 118 HB3 PRO 8 15.724 0.928 10.531 0.0253 1.4870 +ATOM 119 HG2 PRO 8 13.519 2.723 9.594 0.0213 1.4870 +ATOM 120 HG3 PRO 8 14.602 2.914 10.985 0.0213 1.4870 +ATOM 121 HD2 PRO 8 14.983 4.232 8.651 0.0391 1.3870 +ATOM 122 HD3 PRO 8 16.329 3.722 9.690 0.0391 1.3870 +ATOM 123 N PRO 9 14.124 -0.761 7.511 -0.2548 1.8240 +ATOM 124 CA PRO 9 13.102 -1.394 6.671 -0.0266 1.9080 +ATOM 125 C PRO 9 11.688 -0.989 7.075 0.5896 1.9080 +ATOM 126 O PRO 9 11.022 -1.696 7.831 -0.5748 1.6612 +ATOM 127 CB PRO 9 13.320 -2.889 6.914 -0.0070 1.9080 +ATOM 128 CG PRO 9 13.952 -2.966 8.261 0.0189 1.9080 +ATOM 129 CD PRO 9 14.796 -1.729 8.393 0.0192 1.9080 +ATOM 130 HA PRO 9 13.254 -1.171 5.625 0.0641 1.3870 +ATOM 131 HB2 PRO 9 12.369 -3.402 6.893 0.0253 1.4870 +ATOM 132 HB3 PRO 9 13.969 -3.291 6.150 0.0253 1.4870 +ATOM 133 HG2 PRO 9 13.190 -2.983 9.024 0.0213 1.4870 +ATOM 134 HG3 PRO 9 14.570 -3.849 8.326 0.0213 1.4870 +ATOM 135 HD2 PRO 9 14.799 -1.381 9.416 0.0391 1.3870 +ATOM 136 HD3 PRO 9 15.804 -1.921 8.056 0.0391 1.3870 +ATOM 137 N ILE 10 11.236 0.152 6.565 -0.4157 1.8240 +ATOM 138 CA ILE 10 9.900 0.648 6.871 -0.0597 1.9080 +ATOM 139 C ILE 10 8.992 0.571 5.649 0.5973 1.9080 +ATOM 140 O ILE 10 9.158 1.325 4.689 -0.5679 1.6612 +ATOM 141 CB ILE 10 9.943 2.103 7.374 0.1303 1.9080 +ATOM 142 CG1 ILE 10 10.997 2.255 8.473 -0.0430 1.9080 +ATOM 143 CG2 ILE 10 8.574 2.527 7.885 -0.3204 1.9080 +ATOM 144 CD1 ILE 10 10.755 1.364 9.671 -0.0660 1.9080 +ATOM 145 H ILE 10 11.814 0.671 5.968 0.2719 0.6000 +ATOM 146 HA ILE 10 9.486 0.029 7.654 0.0869 1.3870 +ATOM 147 HB ILE 10 10.204 2.741 6.544 0.0187 1.4870 +ATOM 148 HG12 ILE 10 11.967 2.010 8.069 0.0236 1.4870 +ATOM 149 HG13 ILE 10 11.003 3.280 8.816 0.0236 1.4870 +ATOM 150 HG21 ILE 10 8.671 3.432 8.466 0.0882 1.4870 +ATOM 151 HG22 ILE 10 7.918 2.708 7.047 0.0882 1.4870 +ATOM 152 HG23 ILE 10 8.161 1.744 8.503 0.0882 1.4870 +ATOM 153 HD11 ILE 10 9.708 1.391 9.934 0.0186 1.4870 +ATOM 154 HD12 ILE 10 11.041 0.352 9.431 0.0186 1.4870 +ATOM 155 HD13 ILE 10 11.344 1.716 10.506 0.0186 1.4870 +ATOM 156 N CYX 11 8.028 -0.343 5.691 -0.4157 1.8240 +ATOM 157 CA CYX 11 7.091 -0.519 4.589 0.0429 1.9080 +ATOM 158 C CYX 11 5.666 -0.195 5.030 0.5973 1.9080 +ATOM 159 O CYX 11 5.208 -0.657 6.075 -0.5679 1.6612 +ATOM 160 CB CYX 11 7.159 -1.952 4.058 -0.0790 1.9080 +ATOM 161 SG CYX 11 7.305 -2.067 2.245 -0.1081 2.0000 +ATOM 162 H CYX 11 7.946 -0.915 6.484 0.2719 0.6000 +ATOM 163 HA CYX 11 7.374 0.162 3.801 0.0766 1.3870 +ATOM 164 HB2 CYX 11 8.018 -2.447 4.488 0.0910 1.3870 +ATOM 165 HB3 CYX 11 6.263 -2.479 4.350 0.0910 1.3870 +ATOM 166 N PHE 12 4.971 0.602 4.225 -0.4157 1.8240 +ATOM 167 CA PHE 12 3.598 0.988 4.532 -0.0024 1.9080 +ATOM 168 C PHE 12 2.613 -0.070 4.043 0.5973 1.9080 +ATOM 169 O PHE 12 2.926 -0.897 3.186 -0.5679 1.6612 +ATOM 170 CB PHE 12 3.272 2.339 3.892 -0.0343 1.9080 +ATOM 171 CG PHE 12 3.477 3.505 4.817 0.0118 1.9080 +ATOM 172 CD1 PHE 12 2.415 4.323 5.168 -0.1256 1.9080 +ATOM 173 CD2 PHE 12 4.732 3.783 5.334 -0.1256 1.9080 +ATOM 174 CE1 PHE 12 2.600 5.396 6.019 -0.1704 1.9080 +ATOM 175 CE2 PHE 12 4.923 4.855 6.186 -0.1704 1.9080 +ATOM 176 CZ PHE 12 3.856 5.663 6.528 -0.1072 1.9080 +ATOM 177 H PHE 12 5.391 0.938 3.406 0.2719 0.6000 +ATOM 178 HA PHE 12 3.511 1.076 5.603 0.0978 1.3870 +ATOM 179 HB2 PHE 12 3.906 2.485 3.031 0.0295 1.4870 +ATOM 180 HB3 PHE 12 2.239 2.341 3.579 0.0295 1.4870 +ATOM 181 HD1 PHE 12 1.432 4.115 4.770 0.1330 1.4590 +ATOM 182 HD2 PHE 12 5.567 3.153 5.067 0.1330 1.4590 +ATOM 183 HE1 PHE 12 1.764 6.026 6.284 0.1430 1.4590 +ATOM 184 HE2 PHE 12 5.906 5.062 6.582 0.1430 1.4590 +ATOM 185 HZ PHE 12 4.003 6.501 7.193 0.1297 1.4590 +ATOM 186 N PRO 13 1.394 -0.045 4.601 -0.2548 1.8240 +ATOM 187 CA PRO 13 0.338 -0.994 4.238 -0.0266 1.9080 +ATOM 188 C PRO 13 -0.195 -0.758 2.829 0.5896 1.9080 +ATOM 189 O PRO 13 -0.596 -1.697 2.141 -0.5748 1.6612 +ATOM 190 CB PRO 13 -0.755 -0.723 5.275 -0.0070 1.9080 +ATOM 191 CG PRO 13 -0.533 0.688 5.699 0.0189 1.9080 +ATOM 192 CD PRO 13 0.952 0.913 5.629 0.0192 1.9080 +ATOM 193 HA PRO 13 0.675 -2.016 4.327 0.0641 1.3870 +ATOM 194 HB2 PRO 13 -1.727 -0.851 4.820 0.0253 1.4870 +ATOM 195 HB3 PRO 13 -0.647 -1.405 6.104 0.0253 1.4870 +ATOM 196 HG2 PRO 13 -1.046 1.359 5.026 0.0213 1.4870 +ATOM 197 HG3 PRO 13 -0.886 0.827 6.710 0.0213 1.4870 +ATOM 198 HD2 PRO 13 1.166 1.928 5.328 0.0391 1.3870 +ATOM 199 HD3 PRO 13 1.412 0.695 6.581 0.0391 1.3870 +ATOM 200 N ASP 14 -0.196 0.501 2.405 -0.5192 1.8240 +ATOM 201 CA ASP 14 -0.678 0.860 1.076 -0.1817 1.9080 +ATOM 202 C ASP 14 -0.004 0.008 0.005 0.7256 1.9080 +ATOM 203 O ASP 14 -0.659 -0.782 -0.677 -0.7887 1.6612 +ATOM 204 CB ASP 14 -0.422 2.343 0.801 -0.0677 1.9080 +ATOM 205 CG ASP 14 -1.701 3.156 0.776 0.8851 1.9080 +ATOM 206 OD1 ASP 14 -2.280 3.319 -0.319 -0.8162 1.6612 +ATOM 207 OD2 ASP 14 -2.124 3.629 1.851 -0.8162 1.6612 +ATOM 208 H ASP 14 0.137 1.206 3.000 0.3055 0.6000 +ATOM 209 HA ASP 14 -1.741 0.676 1.048 0.1046 1.3870 +ATOM 210 HB2 ASP 14 0.220 2.740 1.574 -0.0212 1.4870 +ATOM 211 HB3 ASP 14 0.068 2.446 -0.156 -0.0212 1.4870 +ATOM 212 OXT ASP 14 -2.261 0.462 -0.819 -0.7887 1.6612 +TER +END \ No newline at end of file From 08f6c68b633a4be2e13990641367878a008631ec Mon Sep 17 00:00:00 2001 From: Stefan Doerr Date: Fri, 25 Feb 2022 14:55:52 +0200 Subject: [PATCH 2/4] fix cyclic peptide protonation --- pdb2pqr/biomolecule.py | 17 +- tests/data/5vav_cyclic_peptide_out.pqr | 421 ++++++++++++------------- 2 files changed, 223 insertions(+), 215 deletions(-) diff --git a/pdb2pqr/biomolecule.py b/pdb2pqr/biomolecule.py index 7f3ac613..a039407a 100644 --- a/pdb2pqr/biomolecule.py +++ b/pdb2pqr/biomolecule.py @@ -501,11 +501,20 @@ def assign_termini(self, chain, neutraln=False, neutralc=False): if len(chain.residues) == 0: text = f'Error: chain "{chain.chain_id}" has 0 residues!' raise IndexError(text) - # Set the N-Terminus/ 5' Terminus + res0 = chain.residues[0] + reslast = chain.residues[-1] + # Check if chain is cyclic. Amide distance ranges between 1.325 - 1.346 + if util.distance(res0.map["N"].coords, reslast.map["C"].coords) < 1.35: + # If the chain is cyclic, don't apply termini. + return + + # Set the N-Terminus/ 5' Terminus if isinstance(res0, aa.Amino): res0.is_n_term = True - if isinstance(res0, aa.PRO) or neutraln: + # If N is bonded to more than one heavy atom switch to neutral-nterm + heavy_bonds = [a for a in res0.map["N"].bonds if a.name[0] != "H"] + if neutraln or len(heavy_bonds) > 1: self.apply_patch("NEUTRAL-NTERM", res0) else: self.apply_patch("NTERM", res0) @@ -513,7 +522,6 @@ def assign_termini(self, chain, neutraln=False, neutralc=False): res0.is5term = True self.apply_patch("5TERM", res0) # Set the C-Terminus/ 3' Terminus - reslast = chain.residues[-1] if isinstance(reslast, aa.Amino): reslast.is_c_term = True if neutralc: @@ -752,6 +760,9 @@ def apply_name_scheme(self, forcefield_): # Remove the C/N prefix to keep the protonation state of the residue # in the terminal residues rname = rname[1:] + elif rname.startswith("NEUTRAL-"): + # Remove the NEUTRAL-C and NEUTRAL-N prefixes to keep protonation state + rname = rname[9:] else: # This is the old code which will overwrite the protonation state # of the residue but have wrong hydrogens. Not sure if needed but diff --git a/tests/data/5vav_cyclic_peptide_out.pqr b/tests/data/5vav_cyclic_peptide_out.pqr index 14420854..ede3a851 100644 --- a/tests/data/5vav_cyclic_peptide_out.pqr +++ b/tests/data/5vav_cyclic_peptide_out.pqr @@ -1,214 +1,211 @@ -ATOM 1 N GLY 1 1.330 0.000 0.000 0.2943 1.8240 -ATOM 2 CA GLY 1 2.071 0.001 -1.247 -0.0100 1.9080 -ATOM 3 C GLY 1 3.401 0.721 -1.131 0.6163 1.9080 -ATOM 4 O GLY 1 4.434 0.202 -1.554 -0.5722 1.6612 -ATOM 5 H1 GLY 1 1.811 -0.001 0.854 0.1642 0.6000 -ATOM 6 HA2 GLY 1 2.252 -1.021 -1.547 0.0895 1.1000 -ATOM 7 HA3 GLY 1 1.477 0.488 -2.006 0.0895 1.1000 -ATOM 8 H2 GLY 1 0.715 0.736 0.204 0.1642 0.6000 -ATOM 9 H3 GLY 1 0.715 -0.736 0.202 0.1642 0.6000 -ATOM 10 N ARG 2 3.374 1.919 -0.558 -0.3479 1.8240 -ATOM 11 CA ARG 2 4.586 2.712 -0.390 -0.2637 1.9080 -ATOM 12 C ARG 2 5.609 1.968 0.463 0.7341 1.9080 -ATOM 13 O ARG 2 5.254 1.109 1.271 -0.5894 1.6612 -ATOM 14 CB ARG 2 4.254 4.060 0.254 -0.0007 1.9080 -ATOM 15 CG ARG 2 5.314 5.124 0.021 0.0390 1.9080 -ATOM 16 CD ARG 2 4.692 6.498 -0.171 0.0486 1.9080 -ATOM 17 NE ARG 2 5.587 7.569 0.258 -0.5295 1.8240 -ATOM 18 CZ ARG 2 5.351 8.857 0.036 0.8076 1.9080 -ATOM 19 NH1 ARG 2 4.254 9.233 -0.607 -0.8627 1.8240 -ATOM 20 NH2 ARG 2 6.213 9.774 0.458 -0.8627 1.8240 -ATOM 21 H ARG 2 2.520 2.279 -0.241 0.2747 0.6000 -ATOM 22 HA ARG 2 5.008 2.885 -1.368 0.1560 1.3870 -ATOM 23 HB2 ARG 2 3.320 4.419 -0.152 0.0327 1.4870 -ATOM 24 HB3 ARG 2 4.144 3.919 1.318 0.0327 1.4870 -ATOM 25 HG2 ARG 2 5.973 5.156 0.876 0.0285 1.4870 -ATOM 26 HG3 ARG 2 5.880 4.868 -0.863 0.0285 1.4870 -ATOM 27 HD2 ARG 2 4.462 6.632 -1.218 0.0687 1.3870 -ATOM 28 HD3 ARG 2 3.781 6.549 0.406 0.0687 1.3870 -ATOM 29 HE ARG 2 6.403 7.314 0.736 0.3456 0.6000 -ATOM 30 HH11 ARG 2 3.602 8.545 -0.926 0.4478 0.6000 -ATOM 31 HH12 ARG 2 4.078 10.203 -0.772 0.4478 0.6000 -ATOM 32 HH21 ARG 2 7.041 9.494 0.944 0.4478 0.6000 -ATOM 33 HH22 ARG 2 6.035 10.743 0.290 0.4478 0.6000 -ATOM 34 N CYX 3 6.882 2.303 0.277 -0.4157 1.8240 -ATOM 35 CA CYX 3 7.958 1.666 1.028 0.0429 1.9080 -ATOM 36 C CYX 3 9.226 2.514 0.985 0.5973 1.9080 -ATOM 37 O CYX 3 9.385 3.371 0.115 -0.5679 1.6612 -ATOM 38 CB CYX 3 8.243 0.272 0.467 -0.0790 1.9080 -ATOM 39 SG CYX 3 8.882 -0.908 1.699 -0.1081 2.0000 -ATOM 40 H CYX 3 7.104 2.995 -0.381 0.2719 0.6000 -ATOM 41 HA CYX 3 7.637 1.573 2.054 0.0766 1.3870 -ATOM 42 HB2 CYX 3 7.330 -0.139 0.063 0.0910 1.3870 -ATOM 43 HB3 CYX 3 8.976 0.353 -0.322 0.0910 1.3870 -ATOM 44 N THR 4 10.128 2.267 1.930 -0.4157 1.8240 -ATOM 45 CA THR 4 11.382 3.007 2.001 -0.0389 1.9080 -ATOM 46 C THR 4 12.480 2.306 1.209 0.5973 1.9080 -ATOM 47 O THR 4 12.651 1.091 1.310 -0.5679 1.6612 -ATOM 48 CB THR 4 11.849 3.182 3.458 0.3654 1.9080 -ATOM 49 OG1 THR 4 11.642 1.968 4.188 -0.6761 1.7210 -ATOM 50 CG2 THR 4 11.098 4.320 4.134 -0.2438 1.9080 -ATOM 51 H THR 4 9.944 1.571 2.595 0.2719 0.6000 -ATOM 52 HA THR 4 11.216 3.987 1.578 0.1007 1.3870 -ATOM 53 HB THR 4 12.904 3.417 3.457 0.0043 1.3870 -ATOM 54 HG21 THR 4 10.802 4.016 5.127 0.0642 1.4870 -ATOM 55 HG22 THR 4 10.220 4.565 3.555 0.0642 1.4870 -ATOM 56 HG23 THR 4 11.740 5.185 4.199 0.0642 1.4870 -ATOM 57 HG1 THR 4 10.659 1.800 4.316 0.4102 0.0000 -ATOM 58 N GLN 5 13.221 3.079 0.421 -0.4157 1.8240 -ATOM 59 CA GLN 5 14.302 2.531 -0.388 -0.0031 1.9080 -ATOM 60 C GLN 5 15.496 2.152 0.482 0.5973 1.9080 -ATOM 61 O GLN 5 16.171 1.155 0.227 -0.5679 1.6612 -ATOM 62 CB GLN 5 14.733 3.540 -1.453 -0.0036 1.9080 -ATOM 63 CG GLN 5 13.592 4.012 -2.341 -0.0645 1.9080 -ATOM 64 CD GLN 5 13.196 2.982 -3.379 0.6951 1.9080 -ATOM 65 H GLN 5 13.035 4.040 0.384 0.2719 0.6000 -ATOM 66 HA GLN 5 13.933 1.642 -0.877 0.0850 1.3870 -ATOM 67 HB2 GLN 5 15.160 4.402 -0.963 0.0171 1.4870 -ATOM 68 HB3 GLN 5 15.484 3.084 -2.082 0.0171 1.4870 -ATOM 69 HG2 GLN 5 12.734 4.224 -1.720 0.0352 1.4870 -ATOM 70 HG3 GLN 5 13.899 4.915 -2.849 0.0352 1.4870 -ATOM 71 OE1 GLN 5 12.086 2.450 -3.351 -0.6086 1.6612 -ATOM 72 NE2 GLN 5 14.104 2.694 -4.305 -0.9407 1.8240 -ATOM 73 HE21 GLN 5 14.967 3.157 -4.265 0.4251 0.6000 -ATOM 74 HE22 GLN 5 13.874 2.031 -4.988 0.4251 0.6000 -ATOM 75 N ALA 6 15.750 2.954 1.511 -0.4157 1.8240 -ATOM 76 CA ALA 6 16.861 2.702 2.420 0.0337 1.9080 -ATOM 77 C ALA 6 16.362 2.199 3.771 0.5973 1.9080 -ATOM 78 O ALA 6 15.167 1.966 3.954 -0.5679 1.6612 -ATOM 79 CB ALA 6 17.693 3.963 2.600 -0.1825 1.9080 -ATOM 80 H ALA 6 15.175 3.733 1.663 0.2719 0.6000 -ATOM 81 HA ALA 6 17.490 1.945 1.976 0.0823 1.3870 -ATOM 82 HB1 ALA 6 17.553 4.610 1.745 0.0603 1.4870 -ATOM 83 HB2 ALA 6 17.379 4.477 3.496 0.0603 1.4870 -ATOM 84 HB3 ALA 6 18.736 3.697 2.683 0.0603 1.4870 -ATOM 85 N TRP 7 17.283 2.033 4.712 -0.4157 1.8240 -ATOM 86 CA TRP 7 16.936 1.556 6.046 -0.0275 1.9080 -ATOM 87 C TRP 7 16.604 2.721 6.971 0.5973 1.9080 -ATOM 88 O TRP 7 16.957 3.872 6.711 -0.5679 1.6612 -ATOM 89 CB TRP 7 18.086 0.735 6.632 -0.0050 1.9080 -ATOM 90 CG TRP 7 17.949 -0.737 6.388 -0.1415 1.9080 -ATOM 91 CD1 TRP 7 17.280 -1.339 5.361 -0.1638 1.9080 -ATOM 92 CD2 TRP 7 18.494 -1.793 7.188 0.1243 1.9080 -ATOM 93 NE1 TRP 7 17.376 -2.705 5.474 -0.3418 1.8240 -ATOM 94 CE2 TRP 7 18.116 -3.009 6.586 0.1380 1.9080 -ATOM 95 CE3 TRP 7 19.265 -1.829 8.352 -0.2387 1.9080 -ATOM 96 CZ2 TRP 7 18.483 -4.245 7.111 -0.2601 1.9080 -ATOM 97 CZ3 TRP 7 19.629 -3.056 8.873 -0.1972 1.9080 -ATOM 98 CH2 TRP 7 19.239 -4.251 8.252 -0.1134 1.9080 -ATOM 99 H TRP 7 18.220 2.235 4.506 0.2719 0.6000 -ATOM 100 HA TRP 7 16.065 0.924 5.955 0.1123 1.3870 -ATOM 101 HB2 TRP 7 19.015 1.061 6.190 0.0339 1.4870 -ATOM 102 HB3 TRP 7 18.124 0.895 7.700 0.0339 1.4870 -ATOM 103 HD1 TRP 7 16.755 -0.807 4.583 0.2062 1.4090 -ATOM 104 HE1 TRP 7 16.979 -3.356 4.857 0.3412 0.6000 -ATOM 105 HE3 TRP 7 19.576 -0.919 8.845 0.1700 1.4590 -ATOM 106 HZ2 TRP 7 18.191 -5.174 6.645 0.1572 1.4590 -ATOM 107 HZ3 TRP 7 20.225 -3.104 9.772 0.1447 1.4590 -ATOM 108 HH2 TRP 7 19.545 -5.186 8.694 0.1417 1.4590 -ATOM 109 N PRO 8 15.909 2.420 8.078 -0.2548 1.8240 -ATOM 110 CA PRO 8 15.483 1.055 8.399 -0.0266 1.9080 -ATOM 111 C PRO 8 14.392 0.553 7.459 0.5896 1.9080 -ATOM 112 O PRO 8 13.795 1.315 6.699 -0.5748 1.6612 -ATOM 113 CB PRO 8 14.945 1.177 9.826 -0.0070 1.9080 -ATOM 114 CG PRO 8 14.529 2.602 9.954 0.0189 1.9080 -ATOM 115 CD PRO 8 15.485 3.390 9.102 0.0192 1.9080 -ATOM 116 HA PRO 8 16.315 0.366 8.383 0.0641 1.3870 -ATOM 117 HB2 PRO 8 14.107 0.507 9.956 0.0253 1.4870 -ATOM 118 HB3 PRO 8 15.724 0.928 10.531 0.0253 1.4870 -ATOM 119 HG2 PRO 8 13.519 2.723 9.594 0.0213 1.4870 -ATOM 120 HG3 PRO 8 14.602 2.914 10.985 0.0213 1.4870 -ATOM 121 HD2 PRO 8 14.983 4.232 8.651 0.0391 1.3870 -ATOM 122 HD3 PRO 8 16.329 3.722 9.690 0.0391 1.3870 -ATOM 123 N PRO 9 14.124 -0.761 7.511 -0.2548 1.8240 -ATOM 124 CA PRO 9 13.102 -1.394 6.671 -0.0266 1.9080 -ATOM 125 C PRO 9 11.688 -0.989 7.075 0.5896 1.9080 -ATOM 126 O PRO 9 11.022 -1.696 7.831 -0.5748 1.6612 -ATOM 127 CB PRO 9 13.320 -2.889 6.914 -0.0070 1.9080 -ATOM 128 CG PRO 9 13.952 -2.966 8.261 0.0189 1.9080 -ATOM 129 CD PRO 9 14.796 -1.729 8.393 0.0192 1.9080 -ATOM 130 HA PRO 9 13.254 -1.171 5.625 0.0641 1.3870 -ATOM 131 HB2 PRO 9 12.369 -3.402 6.893 0.0253 1.4870 -ATOM 132 HB3 PRO 9 13.969 -3.291 6.150 0.0253 1.4870 -ATOM 133 HG2 PRO 9 13.190 -2.983 9.024 0.0213 1.4870 -ATOM 134 HG3 PRO 9 14.570 -3.849 8.326 0.0213 1.4870 -ATOM 135 HD2 PRO 9 14.799 -1.381 9.416 0.0391 1.3870 -ATOM 136 HD3 PRO 9 15.804 -1.921 8.056 0.0391 1.3870 -ATOM 137 N ILE 10 11.236 0.152 6.565 -0.4157 1.8240 -ATOM 138 CA ILE 10 9.900 0.648 6.871 -0.0597 1.9080 -ATOM 139 C ILE 10 8.992 0.571 5.649 0.5973 1.9080 -ATOM 140 O ILE 10 9.158 1.325 4.689 -0.5679 1.6612 -ATOM 141 CB ILE 10 9.943 2.103 7.374 0.1303 1.9080 -ATOM 142 CG1 ILE 10 10.997 2.255 8.473 -0.0430 1.9080 -ATOM 143 CG2 ILE 10 8.574 2.527 7.885 -0.3204 1.9080 -ATOM 144 CD1 ILE 10 10.755 1.364 9.671 -0.0660 1.9080 -ATOM 145 H ILE 10 11.814 0.671 5.968 0.2719 0.6000 -ATOM 146 HA ILE 10 9.486 0.029 7.654 0.0869 1.3870 -ATOM 147 HB ILE 10 10.204 2.741 6.544 0.0187 1.4870 -ATOM 148 HG12 ILE 10 11.967 2.010 8.069 0.0236 1.4870 -ATOM 149 HG13 ILE 10 11.003 3.280 8.816 0.0236 1.4870 -ATOM 150 HG21 ILE 10 8.671 3.432 8.466 0.0882 1.4870 -ATOM 151 HG22 ILE 10 7.918 2.708 7.047 0.0882 1.4870 -ATOM 152 HG23 ILE 10 8.161 1.744 8.503 0.0882 1.4870 -ATOM 153 HD11 ILE 10 9.708 1.391 9.934 0.0186 1.4870 -ATOM 154 HD12 ILE 10 11.041 0.352 9.431 0.0186 1.4870 -ATOM 155 HD13 ILE 10 11.344 1.716 10.506 0.0186 1.4870 -ATOM 156 N CYX 11 8.028 -0.343 5.691 -0.4157 1.8240 -ATOM 157 CA CYX 11 7.091 -0.519 4.589 0.0429 1.9080 -ATOM 158 C CYX 11 5.666 -0.195 5.030 0.5973 1.9080 -ATOM 159 O CYX 11 5.208 -0.657 6.075 -0.5679 1.6612 -ATOM 160 CB CYX 11 7.159 -1.952 4.058 -0.0790 1.9080 -ATOM 161 SG CYX 11 7.305 -2.067 2.245 -0.1081 2.0000 -ATOM 162 H CYX 11 7.946 -0.915 6.484 0.2719 0.6000 -ATOM 163 HA CYX 11 7.374 0.162 3.801 0.0766 1.3870 -ATOM 164 HB2 CYX 11 8.018 -2.447 4.488 0.0910 1.3870 -ATOM 165 HB3 CYX 11 6.263 -2.479 4.350 0.0910 1.3870 -ATOM 166 N PHE 12 4.971 0.602 4.225 -0.4157 1.8240 -ATOM 167 CA PHE 12 3.598 0.988 4.532 -0.0024 1.9080 -ATOM 168 C PHE 12 2.613 -0.070 4.043 0.5973 1.9080 -ATOM 169 O PHE 12 2.926 -0.897 3.186 -0.5679 1.6612 -ATOM 170 CB PHE 12 3.272 2.339 3.892 -0.0343 1.9080 -ATOM 171 CG PHE 12 3.477 3.505 4.817 0.0118 1.9080 -ATOM 172 CD1 PHE 12 2.415 4.323 5.168 -0.1256 1.9080 -ATOM 173 CD2 PHE 12 4.732 3.783 5.334 -0.1256 1.9080 -ATOM 174 CE1 PHE 12 2.600 5.396 6.019 -0.1704 1.9080 -ATOM 175 CE2 PHE 12 4.923 4.855 6.186 -0.1704 1.9080 -ATOM 176 CZ PHE 12 3.856 5.663 6.528 -0.1072 1.9080 -ATOM 177 H PHE 12 5.391 0.938 3.406 0.2719 0.6000 -ATOM 178 HA PHE 12 3.511 1.076 5.603 0.0978 1.3870 -ATOM 179 HB2 PHE 12 3.906 2.485 3.031 0.0295 1.4870 -ATOM 180 HB3 PHE 12 2.239 2.341 3.579 0.0295 1.4870 -ATOM 181 HD1 PHE 12 1.432 4.115 4.770 0.1330 1.4590 -ATOM 182 HD2 PHE 12 5.567 3.153 5.067 0.1330 1.4590 -ATOM 183 HE1 PHE 12 1.764 6.026 6.284 0.1430 1.4590 -ATOM 184 HE2 PHE 12 5.906 5.062 6.582 0.1430 1.4590 -ATOM 185 HZ PHE 12 4.003 6.501 7.193 0.1297 1.4590 -ATOM 186 N PRO 13 1.394 -0.045 4.601 -0.2548 1.8240 -ATOM 187 CA PRO 13 0.338 -0.994 4.238 -0.0266 1.9080 -ATOM 188 C PRO 13 -0.195 -0.758 2.829 0.5896 1.9080 -ATOM 189 O PRO 13 -0.596 -1.697 2.141 -0.5748 1.6612 -ATOM 190 CB PRO 13 -0.755 -0.723 5.275 -0.0070 1.9080 -ATOM 191 CG PRO 13 -0.533 0.688 5.699 0.0189 1.9080 -ATOM 192 CD PRO 13 0.952 0.913 5.629 0.0192 1.9080 -ATOM 193 HA PRO 13 0.675 -2.016 4.327 0.0641 1.3870 -ATOM 194 HB2 PRO 13 -1.727 -0.851 4.820 0.0253 1.4870 -ATOM 195 HB3 PRO 13 -0.647 -1.405 6.104 0.0253 1.4870 -ATOM 196 HG2 PRO 13 -1.046 1.359 5.026 0.0213 1.4870 -ATOM 197 HG3 PRO 13 -0.886 0.827 6.710 0.0213 1.4870 -ATOM 198 HD2 PRO 13 1.166 1.928 5.328 0.0391 1.3870 -ATOM 199 HD3 PRO 13 1.412 0.695 6.581 0.0391 1.3870 -ATOM 200 N ASP 14 -0.196 0.501 2.405 -0.5192 1.8240 -ATOM 201 CA ASP 14 -0.678 0.860 1.076 -0.1817 1.9080 -ATOM 202 C ASP 14 -0.004 0.008 0.005 0.7256 1.9080 -ATOM 203 O ASP 14 -0.659 -0.782 -0.677 -0.7887 1.6612 -ATOM 204 CB ASP 14 -0.422 2.343 0.801 -0.0677 1.9080 -ATOM 205 CG ASP 14 -1.701 3.156 0.776 0.8851 1.9080 -ATOM 206 OD1 ASP 14 -2.280 3.319 -0.319 -0.8162 1.6612 -ATOM 207 OD2 ASP 14 -2.124 3.629 1.851 -0.8162 1.6612 -ATOM 208 H ASP 14 0.137 1.206 3.000 0.3055 0.6000 -ATOM 209 HA ASP 14 -1.741 0.676 1.048 0.1046 1.3870 -ATOM 210 HB2 ASP 14 0.220 2.740 1.574 -0.0212 1.4870 -ATOM 211 HB3 ASP 14 0.068 2.446 -0.156 -0.0212 1.4870 -ATOM 212 OXT ASP 14 -2.261 0.462 -0.819 -0.7887 1.6612 +ATOM 1 N GLY 1 1.330 0.000 0.000 -0.4157 1.8240 +ATOM 2 CA GLY 1 2.071 0.001 -1.247 -0.0252 1.9080 +ATOM 3 C GLY 1 3.401 0.721 -1.131 0.5973 1.9080 +ATOM 4 O GLY 1 4.434 0.202 -1.554 -0.5679 1.6612 +ATOM 5 H GLY 1 1.811 -0.001 0.854 0.2719 0.6000 +ATOM 6 HA2 GLY 1 2.252 -1.021 -1.547 0.0698 1.3870 +ATOM 7 HA3 GLY 1 1.477 0.488 -2.006 0.0698 1.3870 +ATOM 8 N ARG 2 3.374 1.919 -0.558 -0.3479 1.8240 +ATOM 9 CA ARG 2 4.586 2.712 -0.390 -0.2637 1.9080 +ATOM 10 C ARG 2 5.609 1.968 0.463 0.7341 1.9080 +ATOM 11 O ARG 2 5.254 1.109 1.271 -0.5894 1.6612 +ATOM 12 CB ARG 2 4.254 4.060 0.254 -0.0007 1.9080 +ATOM 13 CG ARG 2 5.314 5.124 0.021 0.0390 1.9080 +ATOM 14 CD ARG 2 4.692 6.498 -0.171 0.0486 1.9080 +ATOM 15 NE ARG 2 5.587 7.569 0.258 -0.5295 1.8240 +ATOM 16 CZ ARG 2 5.351 8.857 0.036 0.8076 1.9080 +ATOM 17 NH1 ARG 2 4.254 9.233 -0.607 -0.8627 1.8240 +ATOM 18 NH2 ARG 2 6.213 9.774 0.458 -0.8627 1.8240 +ATOM 19 H ARG 2 2.520 2.279 -0.241 0.2747 0.6000 +ATOM 20 HA ARG 2 5.008 2.885 -1.368 0.1560 1.3870 +ATOM 21 HB2 ARG 2 3.320 4.419 -0.152 0.0327 1.4870 +ATOM 22 HB3 ARG 2 4.144 3.919 1.318 0.0327 1.4870 +ATOM 23 HG2 ARG 2 5.973 5.156 0.876 0.0285 1.4870 +ATOM 24 HG3 ARG 2 5.880 4.868 -0.863 0.0285 1.4870 +ATOM 25 HD2 ARG 2 4.462 6.632 -1.218 0.0687 1.3870 +ATOM 26 HD3 ARG 2 3.781 6.549 0.406 0.0687 1.3870 +ATOM 27 HE ARG 2 6.403 7.314 0.736 0.3456 0.6000 +ATOM 28 HH11 ARG 2 3.602 8.545 -0.926 0.4478 0.6000 +ATOM 29 HH12 ARG 2 4.078 10.203 -0.772 0.4478 0.6000 +ATOM 30 HH21 ARG 2 7.041 9.494 0.944 0.4478 0.6000 +ATOM 31 HH22 ARG 2 6.035 10.743 0.290 0.4478 0.6000 +ATOM 32 N CYX 3 6.882 2.303 0.277 -0.4157 1.8240 +ATOM 33 CA CYX 3 7.958 1.666 1.028 0.0429 1.9080 +ATOM 34 C CYX 3 9.226 2.514 0.985 0.5973 1.9080 +ATOM 35 O CYX 3 9.385 3.371 0.115 -0.5679 1.6612 +ATOM 36 CB CYX 3 8.243 0.272 0.467 -0.0790 1.9080 +ATOM 37 SG CYX 3 8.882 -0.908 1.699 -0.1081 2.0000 +ATOM 38 H CYX 3 7.104 2.995 -0.381 0.2719 0.6000 +ATOM 39 HA CYX 3 7.637 1.573 2.054 0.0766 1.3870 +ATOM 40 HB2 CYX 3 7.330 -0.139 0.063 0.0910 1.3870 +ATOM 41 HB3 CYX 3 8.976 0.353 -0.322 0.0910 1.3870 +ATOM 42 N THR 4 10.128 2.267 1.930 -0.4157 1.8240 +ATOM 43 CA THR 4 11.382 3.007 2.001 -0.0389 1.9080 +ATOM 44 C THR 4 12.480 2.306 1.209 0.5973 1.9080 +ATOM 45 O THR 4 12.651 1.091 1.310 -0.5679 1.6612 +ATOM 46 CB THR 4 11.849 3.182 3.458 0.3654 1.9080 +ATOM 47 OG1 THR 4 11.642 1.968 4.188 -0.6761 1.7210 +ATOM 48 CG2 THR 4 11.098 4.320 4.134 -0.2438 1.9080 +ATOM 49 H THR 4 9.944 1.571 2.595 0.2719 0.6000 +ATOM 50 HA THR 4 11.216 3.987 1.578 0.1007 1.3870 +ATOM 51 HB THR 4 12.904 3.417 3.457 0.0043 1.3870 +ATOM 52 HG21 THR 4 10.802 4.016 5.127 0.0642 1.4870 +ATOM 53 HG22 THR 4 10.220 4.565 3.555 0.0642 1.4870 +ATOM 54 HG23 THR 4 11.740 5.185 4.199 0.0642 1.4870 +ATOM 55 HG1 THR 4 10.659 1.800 4.316 0.4102 0.0000 +ATOM 56 N GLN 5 13.221 3.079 0.421 -0.4157 1.8240 +ATOM 57 CA GLN 5 14.302 2.531 -0.388 -0.0031 1.9080 +ATOM 58 C GLN 5 15.496 2.152 0.482 0.5973 1.9080 +ATOM 59 O GLN 5 16.171 1.155 0.227 -0.5679 1.6612 +ATOM 60 CB GLN 5 14.733 3.540 -1.453 -0.0036 1.9080 +ATOM 61 CG GLN 5 13.592 4.012 -2.341 -0.0645 1.9080 +ATOM 62 CD GLN 5 13.196 2.982 -3.379 0.6951 1.9080 +ATOM 63 H GLN 5 13.035 4.040 0.384 0.2719 0.6000 +ATOM 64 HA GLN 5 13.933 1.642 -0.877 0.0850 1.3870 +ATOM 65 HB2 GLN 5 15.160 4.402 -0.963 0.0171 1.4870 +ATOM 66 HB3 GLN 5 15.484 3.084 -2.082 0.0171 1.4870 +ATOM 67 HG2 GLN 5 12.734 4.224 -1.720 0.0352 1.4870 +ATOM 68 HG3 GLN 5 13.899 4.915 -2.849 0.0352 1.4870 +ATOM 69 OE1 GLN 5 12.086 2.450 -3.351 -0.6086 1.6612 +ATOM 70 NE2 GLN 5 14.104 2.694 -4.305 -0.9407 1.8240 +ATOM 71 HE21 GLN 5 14.967 3.157 -4.265 0.4251 0.6000 +ATOM 72 HE22 GLN 5 13.874 2.031 -4.988 0.4251 0.6000 +ATOM 73 N ALA 6 15.750 2.954 1.511 -0.4157 1.8240 +ATOM 74 CA ALA 6 16.861 2.702 2.420 0.0337 1.9080 +ATOM 75 C ALA 6 16.362 2.199 3.771 0.5973 1.9080 +ATOM 76 O ALA 6 15.167 1.966 3.954 -0.5679 1.6612 +ATOM 77 CB ALA 6 17.693 3.963 2.600 -0.1825 1.9080 +ATOM 78 H ALA 6 15.175 3.733 1.663 0.2719 0.6000 +ATOM 79 HA ALA 6 17.490 1.945 1.976 0.0823 1.3870 +ATOM 80 HB1 ALA 6 17.553 4.610 1.745 0.0603 1.4870 +ATOM 81 HB2 ALA 6 17.379 4.477 3.496 0.0603 1.4870 +ATOM 82 HB3 ALA 6 18.736 3.697 2.683 0.0603 1.4870 +ATOM 83 N TRP 7 17.283 2.033 4.712 -0.4157 1.8240 +ATOM 84 CA TRP 7 16.936 1.556 6.046 -0.0275 1.9080 +ATOM 85 C TRP 7 16.604 2.721 6.971 0.5973 1.9080 +ATOM 86 O TRP 7 16.957 3.872 6.711 -0.5679 1.6612 +ATOM 87 CB TRP 7 18.086 0.735 6.632 -0.0050 1.9080 +ATOM 88 CG TRP 7 17.949 -0.737 6.388 -0.1415 1.9080 +ATOM 89 CD1 TRP 7 17.280 -1.339 5.361 -0.1638 1.9080 +ATOM 90 CD2 TRP 7 18.494 -1.793 7.188 0.1243 1.9080 +ATOM 91 NE1 TRP 7 17.376 -2.705 5.474 -0.3418 1.8240 +ATOM 92 CE2 TRP 7 18.116 -3.009 6.586 0.1380 1.9080 +ATOM 93 CE3 TRP 7 19.265 -1.829 8.352 -0.2387 1.9080 +ATOM 94 CZ2 TRP 7 18.483 -4.245 7.111 -0.2601 1.9080 +ATOM 95 CZ3 TRP 7 19.629 -3.056 8.873 -0.1972 1.9080 +ATOM 96 CH2 TRP 7 19.239 -4.251 8.252 -0.1134 1.9080 +ATOM 97 H TRP 7 18.220 2.235 4.506 0.2719 0.6000 +ATOM 98 HA TRP 7 16.065 0.924 5.955 0.1123 1.3870 +ATOM 99 HB2 TRP 7 19.015 1.061 6.190 0.0339 1.4870 +ATOM 100 HB3 TRP 7 18.124 0.895 7.700 0.0339 1.4870 +ATOM 101 HD1 TRP 7 16.755 -0.807 4.583 0.2062 1.4090 +ATOM 102 HE1 TRP 7 16.979 -3.356 4.857 0.3412 0.6000 +ATOM 103 HE3 TRP 7 19.576 -0.919 8.845 0.1700 1.4590 +ATOM 104 HZ2 TRP 7 18.191 -5.174 6.645 0.1572 1.4590 +ATOM 105 HZ3 TRP 7 20.225 -3.104 9.772 0.1447 1.4590 +ATOM 106 HH2 TRP 7 19.545 -5.186 8.694 0.1417 1.4590 +ATOM 107 N PRO 8 15.909 2.420 8.078 -0.2548 1.8240 +ATOM 108 CA PRO 8 15.483 1.055 8.399 -0.0266 1.9080 +ATOM 109 C PRO 8 14.392 0.553 7.459 0.5896 1.9080 +ATOM 110 O PRO 8 13.795 1.315 6.699 -0.5748 1.6612 +ATOM 111 CB PRO 8 14.945 1.177 9.826 -0.0070 1.9080 +ATOM 112 CG PRO 8 14.529 2.602 9.954 0.0189 1.9080 +ATOM 113 CD PRO 8 15.485 3.390 9.102 0.0192 1.9080 +ATOM 114 HA PRO 8 16.315 0.366 8.383 0.0641 1.3870 +ATOM 115 HB2 PRO 8 14.107 0.507 9.956 0.0253 1.4870 +ATOM 116 HB3 PRO 8 15.724 0.928 10.531 0.0253 1.4870 +ATOM 117 HG2 PRO 8 13.519 2.723 9.594 0.0213 1.4870 +ATOM 118 HG3 PRO 8 14.602 2.914 10.985 0.0213 1.4870 +ATOM 119 HD2 PRO 8 14.983 4.232 8.651 0.0391 1.3870 +ATOM 120 HD3 PRO 8 16.329 3.722 9.690 0.0391 1.3870 +ATOM 121 N PRO 9 14.124 -0.761 7.511 -0.2548 1.8240 +ATOM 122 CA PRO 9 13.102 -1.394 6.671 -0.0266 1.9080 +ATOM 123 C PRO 9 11.688 -0.989 7.075 0.5896 1.9080 +ATOM 124 O PRO 9 11.022 -1.696 7.831 -0.5748 1.6612 +ATOM 125 CB PRO 9 13.320 -2.889 6.914 -0.0070 1.9080 +ATOM 126 CG PRO 9 13.952 -2.966 8.261 0.0189 1.9080 +ATOM 127 CD PRO 9 14.796 -1.729 8.393 0.0192 1.9080 +ATOM 128 HA PRO 9 13.254 -1.171 5.625 0.0641 1.3870 +ATOM 129 HB2 PRO 9 12.369 -3.402 6.893 0.0253 1.4870 +ATOM 130 HB3 PRO 9 13.969 -3.291 6.150 0.0253 1.4870 +ATOM 131 HG2 PRO 9 13.190 -2.983 9.024 0.0213 1.4870 +ATOM 132 HG3 PRO 9 14.570 -3.849 8.326 0.0213 1.4870 +ATOM 133 HD2 PRO 9 14.799 -1.381 9.416 0.0391 1.3870 +ATOM 134 HD3 PRO 9 15.804 -1.921 8.056 0.0391 1.3870 +ATOM 135 N ILE 10 11.236 0.152 6.565 -0.4157 1.8240 +ATOM 136 CA ILE 10 9.900 0.648 6.871 -0.0597 1.9080 +ATOM 137 C ILE 10 8.992 0.571 5.649 0.5973 1.9080 +ATOM 138 O ILE 10 9.158 1.325 4.689 -0.5679 1.6612 +ATOM 139 CB ILE 10 9.943 2.103 7.374 0.1303 1.9080 +ATOM 140 CG1 ILE 10 10.997 2.255 8.473 -0.0430 1.9080 +ATOM 141 CG2 ILE 10 8.574 2.527 7.885 -0.3204 1.9080 +ATOM 142 CD1 ILE 10 10.755 1.364 9.671 -0.0660 1.9080 +ATOM 143 H ILE 10 11.814 0.671 5.968 0.2719 0.6000 +ATOM 144 HA ILE 10 9.486 0.029 7.654 0.0869 1.3870 +ATOM 145 HB ILE 10 10.204 2.741 6.544 0.0187 1.4870 +ATOM 146 HG12 ILE 10 11.967 2.010 8.069 0.0236 1.4870 +ATOM 147 HG13 ILE 10 11.003 3.280 8.816 0.0236 1.4870 +ATOM 148 HG21 ILE 10 8.671 3.432 8.466 0.0882 1.4870 +ATOM 149 HG22 ILE 10 7.918 2.708 7.047 0.0882 1.4870 +ATOM 150 HG23 ILE 10 8.161 1.744 8.503 0.0882 1.4870 +ATOM 151 HD11 ILE 10 9.708 1.391 9.934 0.0186 1.4870 +ATOM 152 HD12 ILE 10 11.041 0.352 9.431 0.0186 1.4870 +ATOM 153 HD13 ILE 10 11.344 1.716 10.506 0.0186 1.4870 +ATOM 154 N CYX 11 8.028 -0.343 5.691 -0.4157 1.8240 +ATOM 155 CA CYX 11 7.091 -0.519 4.589 0.0429 1.9080 +ATOM 156 C CYX 11 5.666 -0.195 5.030 0.5973 1.9080 +ATOM 157 O CYX 11 5.208 -0.657 6.075 -0.5679 1.6612 +ATOM 158 CB CYX 11 7.159 -1.952 4.058 -0.0790 1.9080 +ATOM 159 SG CYX 11 7.305 -2.067 2.245 -0.1081 2.0000 +ATOM 160 H CYX 11 7.946 -0.915 6.484 0.2719 0.6000 +ATOM 161 HA CYX 11 7.374 0.162 3.801 0.0766 1.3870 +ATOM 162 HB2 CYX 11 8.018 -2.447 4.488 0.0910 1.3870 +ATOM 163 HB3 CYX 11 6.263 -2.479 4.350 0.0910 1.3870 +ATOM 164 N PHE 12 4.971 0.602 4.225 -0.4157 1.8240 +ATOM 165 CA PHE 12 3.598 0.988 4.532 -0.0024 1.9080 +ATOM 166 C PHE 12 2.613 -0.070 4.043 0.5973 1.9080 +ATOM 167 O PHE 12 2.926 -0.897 3.186 -0.5679 1.6612 +ATOM 168 CB PHE 12 3.272 2.339 3.892 -0.0343 1.9080 +ATOM 169 CG PHE 12 3.477 3.505 4.817 0.0118 1.9080 +ATOM 170 CD1 PHE 12 2.415 4.323 5.168 -0.1256 1.9080 +ATOM 171 CD2 PHE 12 4.732 3.783 5.334 -0.1256 1.9080 +ATOM 172 CE1 PHE 12 2.600 5.396 6.019 -0.1704 1.9080 +ATOM 173 CE2 PHE 12 4.923 4.855 6.186 -0.1704 1.9080 +ATOM 174 CZ PHE 12 3.856 5.663 6.528 -0.1072 1.9080 +ATOM 175 H PHE 12 5.391 0.938 3.406 0.2719 0.6000 +ATOM 176 HA PHE 12 3.511 1.076 5.603 0.0978 1.3870 +ATOM 177 HB2 PHE 12 3.906 2.485 3.031 0.0295 1.4870 +ATOM 178 HB3 PHE 12 2.239 2.341 3.579 0.0295 1.4870 +ATOM 179 HD1 PHE 12 1.432 4.115 4.770 0.1330 1.4590 +ATOM 180 HD2 PHE 12 5.567 3.153 5.067 0.1330 1.4590 +ATOM 181 HE1 PHE 12 1.764 6.026 6.284 0.1430 1.4590 +ATOM 182 HE2 PHE 12 5.906 5.062 6.582 0.1430 1.4590 +ATOM 183 HZ PHE 12 4.003 6.501 7.193 0.1297 1.4590 +ATOM 184 N PRO 13 1.394 -0.045 4.601 -0.2548 1.8240 +ATOM 185 CA PRO 13 0.338 -0.994 4.238 -0.0266 1.9080 +ATOM 186 C PRO 13 -0.195 -0.758 2.829 0.5896 1.9080 +ATOM 187 O PRO 13 -0.596 -1.697 2.141 -0.5748 1.6612 +ATOM 188 CB PRO 13 -0.755 -0.723 5.275 -0.0070 1.9080 +ATOM 189 CG PRO 13 -0.533 0.688 5.699 0.0189 1.9080 +ATOM 190 CD PRO 13 0.952 0.913 5.629 0.0192 1.9080 +ATOM 191 HA PRO 13 0.675 -2.016 4.327 0.0641 1.3870 +ATOM 192 HB2 PRO 13 -1.727 -0.851 4.820 0.0253 1.4870 +ATOM 193 HB3 PRO 13 -0.647 -1.405 6.104 0.0253 1.4870 +ATOM 194 HG2 PRO 13 -1.046 1.359 5.026 0.0213 1.4870 +ATOM 195 HG3 PRO 13 -0.886 0.827 6.710 0.0213 1.4870 +ATOM 196 HD2 PRO 13 1.166 1.928 5.328 0.0391 1.3870 +ATOM 197 HD3 PRO 13 1.412 0.695 6.581 0.0391 1.3870 +ATOM 198 N ASP 14 -0.196 0.501 2.405 -0.5163 1.8240 +ATOM 199 CA ASP 14 -0.678 0.860 1.076 0.0381 1.9080 +ATOM 200 C ASP 14 -0.004 0.008 0.005 0.5366 1.9080 +ATOM 201 O ASP 14 -0.659 -0.782 -0.677 -0.5819 1.6612 +ATOM 202 CB ASP 14 -0.422 2.343 0.801 -0.0303 1.9080 +ATOM 203 CG ASP 14 -0.447 2.670 -0.679 0.7994 1.9080 +ATOM 204 OD1 ASP 14 0.628 2.632 -1.314 -0.8014 1.6612 +ATOM 205 OD2 ASP 14 -1.542 2.962 -1.203 -0.8014 1.6612 +ATOM 206 H ASP 14 0.137 1.206 3.000 0.2936 0.6000 +ATOM 207 HA ASP 14 -1.741 0.676 1.048 0.0880 1.3870 +ATOM 208 HB2 ASP 14 -1.184 2.930 1.293 -0.0122 1.4870 +ATOM 209 HB3 ASP 14 0.546 2.614 1.195 -0.0122 1.4870 TER END \ No newline at end of file From eeba1a1043ea391e2ead085c78d739c3a3e04684 Mon Sep 17 00:00:00 2001 From: Stefan Doerr Date: Fri, 25 Feb 2022 15:11:29 +0200 Subject: [PATCH 3/4] fix for residues without terminal C in regression_tests --- pdb2pqr/biomolecule.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/pdb2pqr/biomolecule.py b/pdb2pqr/biomolecule.py index a039407a..b2699cd5 100644 --- a/pdb2pqr/biomolecule.py +++ b/pdb2pqr/biomolecule.py @@ -505,9 +505,11 @@ def assign_termini(self, chain, neutraln=False, neutralc=False): res0 = chain.residues[0] reslast = chain.residues[-1] # Check if chain is cyclic. Amide distance ranges between 1.325 - 1.346 - if util.distance(res0.map["N"].coords, reslast.map["C"].coords) < 1.35: - # If the chain is cyclic, don't apply termini. - return + if "N" in res0.map and "C" in reslast.map: + dist = util.distance(res0.map["N"].coords, reslast.map["C"].coords) + if dist < 1.35: + # If the chain is cyclic, don't apply termini. + return # Set the N-Terminus/ 5' Terminus if isinstance(res0, aa.Amino): From 4fa2c1f09e97a2a5acf1e8635ea96fe86e0ae8f5 Mon Sep 17 00:00:00 2001 From: Stefan Doerr Date: Fri, 25 Feb 2022 15:41:57 +0200 Subject: [PATCH 4/4] handle case of no N atom --- pdb2pqr/biomolecule.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/pdb2pqr/biomolecule.py b/pdb2pqr/biomolecule.py index b2699cd5..d9e2a39d 100644 --- a/pdb2pqr/biomolecule.py +++ b/pdb2pqr/biomolecule.py @@ -515,8 +515,13 @@ def assign_termini(self, chain, neutraln=False, neutralc=False): if isinstance(res0, aa.Amino): res0.is_n_term = True # If N is bonded to more than one heavy atom switch to neutral-nterm - heavy_bonds = [a for a in res0.map["N"].bonds if a.name[0] != "H"] - if neutraln or len(heavy_bonds) > 1: + heavy_n_bonds = [] + if "N" in res0.map: + heavy_n_bonds = [ + a for a in res0.map["N"].bonds if a.name[0] != "H" + ] + + if neutraln or len(heavy_n_bonds) > 1: self.apply_patch("NEUTRAL-NTERM", res0) else: self.apply_patch("NTERM", res0)