from __future__ import absolute_import, division, print_function from libtbx.test_utils import show_diff from libtbx import easy_run import libtbx.load_env import os def exercise_basic(): # extracted from 1ywf pdb_in = """\ ATOM 1 N ASP A 181 27.197 36.852 5.496 1.00 33.48 N ATOM 2 CA ASP A 181 27.251 36.418 4.117 1.00 34.90 C ATOM 3 C ASP A 181 26.472 37.390 3.236 1.00 34.37 C ATOM 4 O ASP A 181 25.509 38.039 3.694 1.00 33.69 O ATOM 5 CB ASP A 181 26.657 34.998 3.964 1.00 36.77 C ATOM 6 N ARG A 182 26.880 37.461 1.974 1.00 33.47 N ATOM 7 CA ARG A 182 26.256 38.318 1.002 1.00 33.32 C ATOM 8 C ARG A 182 24.744 38.107 0.932 1.00 31.55 C ATOM 9 O ARG A 182 23.984 39.056 0.794 1.00 29.58 O ATOM 10 CB ARG A 182 26.877 38.089 -0.369 1.00 34.00 C ATOM 11 N ASP A 183 24.289 36.868 1.010 1.00 31.07 N ATOM 12 CA ASP A 183 22.878 36.632 0.774 1.00 31.07 C ATOM 13 C ASP A 183 22.032 37.273 1.878 1.00 29.65 C ATOM 14 O ASP A 183 20.955 37.773 1.618 1.00 27.98 O ATOM 15 CB ASP A 183 22.592 35.148 0.636 1.00 32.71 C ATOM 16 N VAL A 184 22.537 37.250 3.102 1.00 28.40 N ATOM 17 CA VAL A 184 21.844 37.855 4.221 1.00 28.15 C ATOM 18 C VAL A 184 21.822 39.403 4.109 1.00 26.40 C ATOM 19 O VAL A 184 20.785 40.046 4.308 1.00 25.30 O ATOM 20 CB VAL A 184 22.533 37.460 5.501 1.00 28.88 C ATOM 21 N ILE A 185 22.961 39.970 3.749 1.00 25.19 N ATOM 22 CA ILE A 185 23.099 41.414 3.509 1.00 23.33 C ATOM 23 C ILE A 185 22.123 41.852 2.412 1.00 23.71 C ATOM 24 O ILE A 185 21.376 42.811 2.561 1.00 22.57 O ATOM 25 CB ILE A 185 24.556 41.728 3.091 1.00 23.73 C ATOM 26 N VAL A 186 22.112 41.120 1.311 1.00 23.54 N ATOM 27 CA VAL A 186 21.221 41.455 0.194 1.00 24.20 C ATOM 28 C VAL A 186 19.738 41.300 0.563 1.00 23.20 C ATOM 29 O VAL A 186 18.906 42.075 0.105 1.00 24.19 O ATOM 30 CB VAL A 186 21.584 40.632 -1.092 1.00 24.98 C ATOM 31 N ALA A 187 19.403 40.316 1.385 1.00 23.05 N ATOM 32 CA ALA A 187 18.035 40.114 1.854 1.00 23.26 C ATOM 33 C ALA A 187 17.523 41.382 2.547 1.00 22.44 C ATOM 34 O ALA A 187 16.427 41.902 2.256 1.00 21.80 O ATOM 35 CB ALA A 187 17.988 38.991 2.765 1.00 23.85 C ATOM 36 N ASP A 188 18.365 41.932 3.397 1.00 21.03 N ATOM 37 CA ASP A 188 17.956 43.118 4.149 1.00 21.44 C ATOM 38 C ASP A 188 17.939 44.349 3.264 1.00 20.78 C ATOM 39 O ASP A 188 17.042 45.182 3.399 1.00 22.01 O ATOM 40 CB ASP A 188 18.867 43.342 5.384 1.00 21.37 C ATOM 41 N TYR A 189 18.896 44.462 2.354 1.00 20.83 N ATOM 42 CA TYR A 189 18.982 45.542 1.424 1.00 20.65 C ATOM 43 C TYR A 189 17.722 45.582 0.535 1.00 21.46 C ATOM 44 O TYR A 189 17.134 46.647 0.250 1.00 20.62 O ATOM 45 CB TYR A 189 20.232 45.356 0.573 1.00 21.85 C ATOM 46 N LEU A 190 17.306 44.409 0.093 1.00 22.68 N ATOM 47 CA LEU A 190 16.176 44.366 -0.846 1.00 22.91 C ATOM 48 C LEU A 190 14.848 44.614 -0.155 1.00 22.51 C ATOM 49 O LEU A 190 13.859 44.905 -0.830 1.00 22.82 O ATOM 50 CB LEU A 190 16.116 43.032 -1.594 1.00 22.51 C ATOM 51 N ARG A 191 14.793 44.581 1.175 1.00 22.46 N ATOM 52 CA ARG A 191 13.551 44.901 1.906 1.00 23.66 C ATOM 53 C ARG A 191 13.025 46.291 1.588 1.00 22.52 C ATOM 54 O ARG A 191 11.824 46.554 1.794 1.00 21.76 O ATOM 55 CB ARG A 191 13.735 44.792 3.436 1.00 24.11 C ATOM 56 N SER A 192 13.878 47.175 1.057 1.00 22.09 N ATOM 57 CA SER A 192 13.454 48.520 0.682 1.00 21.85 C ATOM 58 C SER A 192 12.449 48.512 -0.485 1.00 22.55 C ATOM 59 O SER A 192 11.624 49.409 -0.607 1.00 22.52 O ATOM 60 CB SER A 192 14.639 49.422 0.322 1.00 22.37 C ATOM 61 N ASN A 193 12.467 47.441 -1.269 1.00 22.93 N ATOM 62 CA ASN A 193 11.435 47.276 -2.282 1.00 23.18 C ATOM 63 C ASN A 193 10.046 47.185 -1.736 1.00 22.19 C ATOM 64 O ASN A 193 9.094 47.629 -2.388 1.00 23.39 O ATOM 65 CB ASN A 193 11.770 46.077 -3.193 1.00 24.30 C ATOM 66 N ASP A 194 9.878 46.683 -0.515 1.00 23.18 N ATOM 67 CA ASP A 194 8.554 46.586 0.069 1.00 23.55 C ATOM 68 C ASP A 194 7.939 47.961 0.370 1.00 24.28 C ATOM 69 O ASP A 194 6.720 48.105 0.555 1.00 23.59 O ATOM 70 CB ASP A 194 8.605 45.788 1.353 1.00 22.75 C ATOM 71 N SER A 195 8.809 48.958 0.499 1.00 23.92 N ATOM 72 CA SER A 195 8.409 50.341 0.846 1.00 24.19 C ATOM 73 C SER A 195 8.150 51.237 -0.368 1.00 23.29 C ATOM 74 O SER A 195 7.884 52.429 -0.240 1.00 23.19 O ATOM 75 CB SER A 195 9.521 50.937 1.693 1.00 24.32 C ATOM 76 N VAL A 196 8.253 50.699 -1.568 1.00 23.63 N ATOM 77 CA VAL A 196 8.152 51.513 -2.768 1.00 23.74 C ATOM 78 C VAL A 196 6.773 52.193 -2.856 1.00 23.84 C ATOM 79 O VAL A 196 6.718 53.397 -3.105 1.00 23.11 O ATOM 80 CB VAL A 196 8.465 50.710 -4.027 1.00 24.47 C ATOM 81 N PRO A 197 5.665 51.486 -2.598 1.00 24.39 N ATOM 82 CA PRO A 197 4.365 52.177 -2.602 1.00 26.12 C ATOM 83 C PRO A 197 4.278 53.337 -1.596 1.00 26.03 C ATOM 84 O PRO A 197 3.742 54.399 -1.930 1.00 25.76 O ATOM 85 CB PRO A 197 3.363 51.049 -2.246 1.00 26.62 C ATOM 86 N GLN A 198 4.859 53.168 -0.408 1.00 25.67 N ATOM 87 CA GLN A 198 4.860 54.206 0.603 1.00 26.81 C ATOM 88 C GLN A 198 5.732 55.384 0.158 1.00 25.59 C ATOM 89 O GLN A 198 5.341 56.545 0.339 1.00 25.72 O ATOM 90 CB GLN A 198 5.290 53.638 1.967 1.00 27.38 C ATOM 91 N LEU A 199 6.903 55.119 -0.416 1.00 25.48 N ATOM 92 CA LEU A 199 7.726 56.192 -0.941 1.00 25.93 C ATOM 93 C LEU A 199 6.996 56.972 -2.047 1.00 26.39 C ATOM 94 O LEU A 199 7.020 58.180 -2.064 1.00 25.38 O ATOM 95 CB LEU A 199 9.033 55.633 -1.490 1.00 25.66 C ATOM 96 N ARG A 200 6.361 56.258 -2.980 1.00 27.31 N ATOM 97 CA ARG A 200 5.576 56.913 -3.993 1.00 28.53 C ATOM 98 C ARG A 200 4.520 57.823 -3.397 1.00 27.54 C ATOM 99 O ARG A 200 4.397 58.949 -3.851 1.00 27.50 O ATOM 100 CB ARG A 200 4.933 55.879 -4.899 1.00 30.38 C ATOM 101 N ALA A 201 3.790 57.365 -2.357 1.00 26.90 N ATOM 102 CA ALA A 201 2.764 58.200 -1.713 1.00 26.49 C ATOM 103 C ALA A 201 3.406 59.407 -1.045 1.00 26.59 C ATOM 104 O ALA A 201 2.866 60.516 -1.082 1.00 26.58 O ATOM 105 CB ALA A 201 1.959 57.412 -0.715 1.00 25.11 C ATOM 106 N ARG A 202 4.566 59.205 -0.419 1.00 25.66 N ATOM 107 CA ARG A 202 5.245 60.296 0.240 1.00 26.93 C ATOM 108 C ARG A 202 5.676 61.346 -0.767 1.00 26.93 C ATOM 109 O ARG A 202 5.555 62.541 -0.489 1.00 25.79 O ATOM 110 CB ARG A 202 6.493 59.779 0.996 1.00 28.25 C ATOM 111 N ILE A 203 6.154 60.912 -1.931 1.00 26.99 N ATOM 112 CA ILE A 203 6.611 61.848 -2.965 1.00 27.49 C ATOM 113 C ILE A 203 5.430 62.674 -3.480 1.00 28.29 C ATOM 114 O ILE A 203 5.548 63.905 -3.624 1.00 27.82 O ATOM 115 CB ILE A 203 7.322 61.125 -4.075 1.00 28.09 C ATOM 116 N SER A 204 4.288 62.025 -3.678 1.00 27.96 N ATOM 117 CA SER A 204 3.119 62.736 -4.184 1.00 28.04 C ATOM 118 C SER A 204 2.683 63.793 -3.199 1.00 28.16 C ATOM 119 O SER A 204 2.311 64.910 -3.605 1.00 28.25 O ATOM 120 CB SER A 204 1.962 61.780 -4.504 1.00 27.64 C ATOM 121 N GLU A 205 2.756 63.477 -1.904 1.00 27.27 N ATOM 122 CA GLU A 205 2.419 64.414 -0.849 1.00 28.81 C ATOM 123 C GLU A 205 3.430 65.594 -0.782 1.00 28.51 C ATOM 124 O GLU A 205 3.035 66.755 -0.615 1.00 29.81 O ATOM 125 CB GLU A 205 2.370 63.667 0.461 1.00 29.74 C ATOM 126 N MET A 206 4.709 65.295 -0.984 1.00 28.00 N ATOM 127 CA MET A 206 5.726 66.347 -1.029 1.00 27.28 C ATOM 128 C MET A 206 5.494 67.315 -2.173 1.00 27.94 C ATOM 129 O MET A 206 5.672 68.524 -2.010 1.00 27.36 O ATOM 130 CB MET A 206 7.152 65.714 -1.123 1.00 27.25 C ATOM 131 N ILE A 207 5.092 66.772 -3.319 1.00 29.22 N ATOM 132 CA ILE A 207 4.824 67.562 -4.510 1.00 29.58 C ATOM 133 C ILE A 207 3.606 68.471 -4.277 1.00 30.18 C ATOM 134 O ILE A 207 3.601 69.645 -4.680 1.00 28.59 O ATOM 135 CB ILE A 207 4.648 66.646 -5.716 1.00 30.41 C ATOM 136 N GLN A 208 2.586 67.940 -3.614 1.00 29.64 N ATOM 137 CA GLN A 208 1.415 68.721 -3.231 1.00 30.71 C ATOM 138 C GLN A 208 1.799 69.877 -2.302 1.00 29.77 C ATOM 139 O GLN A 208 1.213 70.964 -2.365 1.00 30.52 O ATOM 140 CB GLN A 208 0.345 67.845 -2.558 1.00 30.05 C ATOM 141 N GLN A 209 2.776 69.641 -1.418 1.00 29.19 N ATOM 142 CA GLN A 209 3.254 70.616 -0.496 1.00 28.05 C ATOM 143 C GLN A 209 4.454 71.438 -1.005 1.00 26.36 C ATOM 144 O GLN A 209 5.077 72.111 -0.213 1.00 26.13 O ATOM 145 CB GLN A 209 3.663 69.913 0.841 1.00 28.70 C ATOM 146 N ARG A 210 4.719 71.435 -2.303 1.00 26.63 N ATOM 147 CA ARG A 210 5.975 72.001 -2.823 1.00 27.68 C ATOM 148 C ARG A 210 6.081 73.522 -2.641 1.00 28.32 C ATOM 149 O ARG A 210 7.167 74.068 -2.709 1.00 28.23 O ATOM 150 CB ARG A 210 6.178 71.657 -4.275 1.00 27.92 C END""" with open("tst_dssp_1ywf_helix.pdb", "w") as f: f.write(pdb_in) result = easy_run.fully_buffered("mmtbx.dssp tst_dssp_1ywf_helix.pdb" ).raise_if_errors() assert ("\n".join(result.stdout_lines) == """\ HELIX 1 1 ASP A 181 ARG A 191 1 11 HELIX 3 3 SER A 195 GLN A 209 1 15""") # these exercised depend on files in other SVN trees def exercise_advanced(): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/1ywf.pdb", test=os.path.isfile) if (pdb_file is None): print("phenix_regression not available, skipping test") return result = easy_run.fully_buffered("mmtbx.dssp \"%s\"" % pdb_file ).raise_if_errors() assert not show_diff("\n".join(result.stdout_lines), """\ HELIX 2 2 ASP A 14 THR A 18 5 5 HELIX 6 6 ASP A 37 GLY A 48 1 12 HELIX 8 8 SER A 57 GLY A 65 1 9 HELIX 10 10 ASN A 119 GLN A 132 1 14 HELIX 16 16 GLY A 138 ALA A 152 1 15 HELIX 19 19 ASP A 165 VAL A 178 1 14 HELIX 22 22 ASP A 181 ARG A 191 1 11 HELIX 24 24 SER A 195 GLN A 209 1 15 HELIX 29 29 ALA A 216 ALA A 225 1 10 HELIX 33 33 SER A 228 GLY A 233 1 6 HELIX 35 35 ARG A 235 TYR A 250 1 16 HELIX 38 38 SER A 252 ALA A 260 1 9 HELIX 41 41 SER A 263 LEU A 275 1 13 SHEET 1 1 5 ARG A 13 ASP A 14 0 SHEET 2 1 5 LEU A 27 SER A 30 -1 O ARG A 29 N ARG A 13 SHEET 3 1 5 VAL A 156 HIS A 159 1 O VAL A 156 N PHE A 28 SHEET 4 1 5 ASP A 51 ASP A 54 1 O ASP A 51 N LEU A 157 SHEET 5 1 5 ASP A 74 LEU A 77 1 O ASP A 74 N VAL A 52""") cctbx_p_dir = libtbx.env.find_in_repositories( relative_path="cctbx_project", test=os.path.isdir) if (cctbx_p_dir is not None): # mostly beta pdb_file_1 = os.path.join(cctbx_p_dir, "mmtbx", "regression", "pdbs", "p9.pdb") result = easy_run.fully_buffered("mmtbx.dssp \"%s\"" % pdb_file_1 ).raise_if_errors() # XXX interestingly, this appears to be more accurate than the output of # ksdssp, which finds an alpha helix from 111 to 116. both the PDB and # ksdssp have 131-137 as a continuous strand, but residue 135 actually # breaks the hydrogen bonding pattern, and the hydrogen bonds cannot be # accurately recovered from those annotations. assert not show_diff("\n".join(result.stdout_lines), """\ HELIX 10 10 PRO 105 VAL 109 5 5 HELIX 13 13 ALA 113 LEU 117 5 5 SHEET 1 1 2 TYR 11 GLU 13 0 SHEET 2 1 2 GLN 70 GLU 72 -1 O VAL 71 N VAL 12 SHEET 1 2 4 TYR 22 ILE 25 0 SHEET 2 2 4 GLU 28 VAL 32 -1 O CYS 30 N VAL 23 SHEET 3 2 4 LYS 47 GLY 54 -1 O VAL 53 N ARG 31 SHEET 4 2 4 LYS 60 PRO 66 -1 O LEU 65 N ALA 48 SHEET 1 3 2 GLU 34 SER 38 0 SHEET 2 3 2 LYS 47 VAL 51 -1 O VAL 51 N GLU 34 SHEET 1 4 5 SER 85 VAL 86 0 SHEET 2 4 5 ILE 91 ASP 95 -1 O GLN 92 N SER 85 SHEET 3 4 5 GLU 77 ILE 83 -1 O GLN 82 N MET 94 SHEET 4 4 5 GLU 122 ILE 128 -1 O GLN 127 N GLU 77 SHEET 5 4 5 ARG 131 ILE 134 -1 O LYS 133 N TRP 126 SHEET 1 5 2 VAL 90 MET 94 0 SHEET 2 5 2 THR 101 PRO 105 -1 O VAL 104 N ILE 91 SHEET 1 6 2 VAL 123 GLU 124 0 SHEET 2 6 2 ARG 136 VAL 137 -1 O ARG 136 N GLU 124""") # beta barrel examples_dir = libtbx.env.find_in_repositories( relative_path="phenix_examples", test=os.path.isdir) if examples_dir is not None: pdb_file_2 = os.path.join(examples_dir, "porin-twin", "porin.pdb") result = easy_run.fully_buffered("mmtbx.dssp \"%s\"" % pdb_file_2 ).raise_if_errors() assert not show_diff("\n".join(result.stdout_lines), """\ HELIX 5 5 ASP 59 GLY 63 5 5 HELIX 7 7 THR 87 VAL 92 1 6 HELIX 18 18 ASP 156 VAL 160 5 5 HELIX 19 19 ASP 184 ILE 188 5 5 SHEET 1 117 ILE 2 TYR 14 0 SHEET 2 117 THR 25 GLU 40 -1 O VAL 36 N SER 3 SHEET 3 117 THR 46 ASP 56 -1 O TRP 55 N LEU 31 SHEET 4 117 GLN 70 TYR 75 -1 O SER 74 N THR 46 SHEET 5 117 VAL 78 GLY 83 -1 O VAL 82 N PHE 71 SHEET 6 117 ASN 131 ILE 139 -1 O THR 136 N THR 79 SHEET 7 117 VAL 142 ASP 150 -1 O ASP 150 N ASN 131 SHEET 8 117 GLU 163 SER 171 -1 O ASP 169 N ASN 143 SHEET 9 117 ILE 175 THR 183 -1 O THR 183 N PHE 164 SHEET 10 117 ILE 193 LYS 201 -1 O ALA 199 N SER 176 SHEET 11 117 GLY 206 ASP 214 -1 O ASP 214 N ALA 194 SHEET 12 117 GLN 223 PHE 232 -1 O ASN 229 N THR 207 SHEET 13 117 THR 235 ILE 244 -1 O ASP 243 N VAL 224 SHEET 14 117 ALA 252 GLN 260 -1 O ASP 258 N THR 236 SHEET 15 117 VAL 265 SER 273 -1 O SER 273 N TYR 253 SHEET 16 117 THR 279 ASP 288 -1 O ARG 286 N LYS 266 SHEET 17 117 TYR 7 VAL 15 -1 O TYR 14 N ALA 281""") else : print("WARNING: phenix_examples not available, some tests skipped") # TODO add 1lfh test print("OK") if (__name__ == "__main__"): exercise_basic() exercise_advanced()