from __future__ import absolute_import, division, print_function from mmtbx import monomer_library import mmtbx.monomer_library.pdb_interpretation import mmtbx.monomer_library.server import sys from six.moves import range test_pdb_file = """\ CRYST1 201.710 68.060 86.350 90.00 90.00 90.00 P 21 21 2 8 ATOM 1 N SER A 1 79.022 -1.487 39.367 1.00 97.85 N ATOM 2 CA SER A 1 78.722 -1.348 37.919 1.00 98.11 C ATOM 3 C SER A 1 77.318 -0.760 37.705 1.00 97.34 C ATOM 4 O SER A 1 76.305 -1.440 37.908 1.00 98.14 O ATOM 5 CB SER A 1 78.826 -2.717 37.217 1.00 98.90 C ATOM 6 OG SER A 1 80.160 -3.231 37.252 1.00 99.99 O ATOM 7 N GLU A 2 77.245 0.508 37.315 1.00 95.57 N ATOM 8 CA GLU A 2 75.961 1.137 37.056 1.00 91.95 C ATOM 9 C GLU A 2 76.189 1.866 35.740 1.00 88.32 C ATOM 10 O GLU A 2 77.119 2.688 35.625 1.00 86.70 O ATOM 11 CB GLU A 2 75.615 2.131 38.169 1.00 92.62 C ATOM 12 CG GLU A 2 76.373 3.428 38.057 1.00 96.62 C ATOM 13 CD GLU A 2 76.044 4.392 39.120 1.00 99.90 C ATOM 14 OE1 GLU A 2 74.977 4.253 39.777 1.00 99.99 O ATOM 15 OE2 GLU A 2 76.841 5.347 39.313 1.00 99.99 O ATOM 16 N SER A 3 75.396 1.547 34.723 1.00 83.22 N ATOM 17 CA SER A 3 75.583 2.238 33.461 1.00 78.14 C ATOM 18 C SER A 3 75.232 3.680 33.734 1.00 73.03 C ATOM 19 O SER A 3 74.305 3.974 34.499 1.00 72.80 O ATOM 20 CB SER A 3 74.678 1.646 32.370 1.00 80.23 C ATOM 21 OG SER A 3 75.170 0.385 31.930 1.00 80.78 O ATOM 2377 N LEU A 313 82.669 33.333 -17.857 1.00 53.08 N ATOM 2378 CA LEU A 313 81.629 32.854 -16.955 1.00 53.14 C ATOM 2379 C LEU A 313 81.630 33.876 -15.842 1.00 54.15 C ATOM 2380 O LEU A 313 82.643 34.503 -15.597 1.00 55.52 O ATOM 2381 CB LEU A 313 82.006 31.491 -16.387 1.00 54.25 C ATOM 2382 CG LEU A 313 82.274 30.386 -17.411 1.00 56.18 C ATOM 2383 CD1 LEU A 313 82.747 29.098 -16.751 1.00 52.25 C ATOM 2384 CD2 LEU A 313 81.002 30.149 -18.180 1.00 59.92 C ATOM 2385 N VAL A 314 80.512 34.069 -15.166 1.00 56.43 N ATOM 2386 CA VAL A 314 80.488 35.043 -14.074 1.00 56.85 C ATOM 2387 C VAL A 314 80.903 34.401 -12.731 1.00 60.38 C ATOM 2388 O VAL A 314 81.023 33.150 -12.658 1.00 61.26 O ATOM 2389 CB VAL A 314 79.087 35.666 -13.946 1.00 52.88 C ATOM 2390 CG1 VAL A 314 79.074 36.727 -12.868 1.00 47.39 C ATOM 2391 CG2 VAL A 314 78.677 36.241 -15.293 1.00 52.66 C ATOM 2392 OXT VAL A 314 81.110 35.156 -11.751 1.00 62.47 O TER 2393 VAL A 314 ATOM 2394 N SER B 1 85.404 -33.823 39.687 1.00 91.56 N ATOM 2395 CA SER B 1 84.670 -32.782 38.908 1.00 91.48 C ATOM 2396 C SER B 1 83.295 -33.255 38.414 1.00 92.36 C ATOM 2397 O SER B 1 83.109 -34.423 38.036 1.00 92.95 O ATOM 2398 CB SER B 1 85.529 -32.298 37.718 1.00 89.71 C ATOM 2399 OG SER B 1 85.912 -33.355 36.850 1.00 80.92 O ATOM 2400 N GLU B 2 82.331 -32.338 38.418 1.00 91.53 N ATOM 2401 CA GLU B 2 80.983 -32.666 37.980 1.00 89.92 C ATOM 2402 C GLU B 2 80.567 -31.880 36.725 1.00 86.18 C ATOM 2403 O GLU B 2 81.233 -30.933 36.292 1.00 84.19 O ATOM 2404 CB GLU B 2 79.993 -32.434 39.136 1.00 92.51 C ATOM 2405 CG GLU B 2 78.594 -33.015 38.906 1.00 97.08 C ATOM 2406 CD GLU B 2 77.710 -32.959 40.153 1.00 99.61 C ATOM 2407 OE1 GLU B 2 77.422 -31.843 40.638 1.00 99.99 O ATOM 2408 OE2 GLU B 2 77.305 -34.037 40.650 1.00 99.99 O TER 4786 VAL B 314 ATOM 4788 P C C 1 47.241 23.887 -1.304 1.00 99.99 P ATOM 4789 O1P C C 1 47.437 24.960 -0.241 1.00 99.99 O ATOM 4790 O2P C C 1 46.407 22.725 -0.791 1.00 99.99 O ATOM 4791 O5' C C 1 48.722 23.275 -1.633 1.00 99.99 O ATOM 4792 C5' C C 1 49.588 22.811 -0.567 1.00 99.99 C ATOM 4793 C4' C C 1 49.474 21.311 -0.424 1.00 99.98 C ATOM 4794 O4' C C 1 48.276 20.855 -1.121 1.00 99.99 O ATOM 4795 C3' C C 1 50.570 20.506 -1.099 1.00 99.99 C ATOM 4796 O3' C C 1 51.727 20.252 -0.373 1.00 99.99 O ATOM 4797 C2' C C 1 49.934 19.165 -1.338 1.00 99.99 C ATOM 4798 O2' C C 1 50.017 18.352 -0.186 1.00 99.99 O ATOM 4799 C1' C C 1 48.505 19.564 -1.689 1.00 99.99 C ATOM 4800 N1 C C 1 48.330 19.637 -3.157 1.00 99.99 N ATOM 4801 C2 C C 1 48.881 18.604 -3.984 1.00 99.99 C ATOM 4802 O2 C C 1 49.493 17.647 -3.456 1.00 99.99 O ATOM 4803 N3 C C 1 48.728 18.684 -5.330 1.00 99.99 N ATOM 4804 C4 C C 1 48.065 19.714 -5.869 1.00 99.99 C ATOM 4805 N4 C C 1 47.945 19.750 -7.196 1.00 99.99 N ATOM 4806 C5 C C 1 47.497 20.758 -5.068 1.00 99.99 C ATOM 4807 C6 C C 1 47.655 20.682 -3.732 1.00 99.99 C ATOM 4808 P G C 2 52.970 19.524 -1.111 1.00 99.99 P ATOM 4809 O1P G C 2 52.775 18.136 -1.648 1.00 99.99 O ATOM 4810 O2P G C 2 53.883 19.724 -0.024 1.00 99.99 O ATOM 4811 O5* G C 2 53.329 20.523 -2.299 1.00 97.90 O ATOM 4812 C5* G C 2 52.379 21.525 -2.667 1.00 92.61 C ATOM 4813 C4* G C 2 53.032 22.857 -2.853 1.00 88.12 C ATOM 4814 O4* G C 2 54.015 23.115 -1.816 1.00 87.30 O ATOM 4815 C3* G C 2 53.805 22.945 -4.141 1.00 86.97 C ATOM 4816 O3* G C 2 52.918 23.175 -5.222 1.00 86.86 O ATOM 4817 C2* G C 2 54.790 24.065 -3.839 1.00 87.48 C ATOM 4818 O2* G C 2 54.217 25.351 -3.939 1.00 86.43 O ATOM 4819 C1* G C 2 55.146 23.758 -2.382 1.00 86.25 C ATOM 4820 N9 G C 2 56.247 22.803 -2.383 1.00 86.73 N ATOM 4821 C8 G C 2 56.229 21.497 -1.947 1.00 87.03 C ATOM 4822 N7 G C 2 57.342 20.861 -2.190 1.00 85.88 N ATOM 4823 C5 G C 2 58.151 21.807 -2.801 1.00 85.19 C ATOM 4824 C6 G C 2 59.462 21.698 -3.313 1.00 84.09 C ATOM 4825 O6 G C 2 60.198 20.699 -3.353 1.00 82.37 O ATOM 4826 N1 G C 2 59.905 22.912 -3.834 1.00 84.56 N ATOM 4827 C2 G C 2 59.174 24.077 -3.864 1.00 84.51 C ATOM 4828 N2 G C 2 59.774 25.156 -4.399 1.00 84.63 N ATOM 4829 N3 G C 2 57.946 24.181 -3.406 1.00 85.45 N ATOM 4830 C4 G C 2 57.499 23.018 -2.894 1.00 85.82 C ATOM 4831 P C C 3 53.092 22.329 -6.579 1.00 86.68 P ATOM 4832 O1P C C 3 51.825 22.390 -7.355 1.00 86.55 O ATOM 4833 O2P C C 3 53.667 21.001 -6.222 1.00 84.84 O ATOM 4834 O5* C C 3 54.167 23.202 -7.360 1.00 84.63 O ATOM 4835 C5* C C 3 53.965 24.621 -7.484 1.00 81.25 C ATOM 4836 C4* C C 3 55.164 25.277 -8.115 1.00 79.23 C ATOM 4837 O4* C C 3 56.262 25.305 -7.172 1.00 76.28 O ATOM 4838 C3* C C 3 55.737 24.591 -9.341 1.00 77.29 C ATOM 4839 O3* C C 3 55.051 24.887 -10.537 1.00 78.19 O ATOM 4840 C2* C C 3 57.158 25.115 -9.363 1.00 76.40 C ATOM 4842 C1* C C 3 57.483 25.148 -7.872 1.00 76.01 C ATOM 4843 N1 C C 3 58.067 23.861 -7.480 1.00 73.97 N ATOM 4844 C2 C C 3 59.445 23.727 -7.509 1.00 71.90 C ATOM 4845 O2 C C 3 60.135 24.715 -7.840 1.00 66.31 O ATOM 4846 N3 C C 3 59.996 22.533 -7.175 1.00 70.72 N ATOM 4847 C4 C C 3 59.212 21.513 -6.810 1.00 69.96 C ATOM 4848 N4 C C 3 59.793 20.365 -6.470 1.00 71.43 N ATOM 4849 C5 C C 3 57.800 21.629 -6.772 1.00 69.13 C ATOM 4850 C6 C C 3 57.272 22.810 -7.109 1.00 72.22 C HETATM 1 N PCA C 4 61.815 -9.826 47.209 1.00 22.41 N HETATM 2 CA PCA C 4 63.251 -9.543 47.447 1.00 21.95 C HETATM 3 CB PCA C 4 64.110 -10.479 46.604 1.00 22.40 C HETATM 4 CG PCA C 4 63.238 -10.886 45.438 1.00 22.83 C HETATM 5 CD PCA C 4 61.855 -10.549 45.934 1.00 22.46 C HETATM 6 OE PCA C 4 60.846 -10.859 45.286 1.00 24.62 O HETATM 7 C PCA C 4 63.573 -8.105 47.060 1.00 21.16 C HETATM 8 O PCA C 4 62.762 -7.428 46.430 1.00 21.46 O HETATM 8099 MG MG 584 69.634 3.963 -22.036 1.00 45.86 MG HETATM 8100 MG MG 585 72.985 -30.470 -21.424 1.00 39.36 MG HETATM 8101 O HOH 501 50.104 -12.783 -34.164 1.00 76.32 O HETATM 8102 O HOH 502 50.327 -5.724 -17.983 1.00 53.54 O END """ def exercise_atom_selections(): verbose = "--verbose" in sys.argv[1:] log = None if (verbose): log = sys.stdout with open("tmp_selection.pdb", "w") as f: f.write(test_pdb_file) try: mon_lib_srv = monomer_library.server.server() except monomer_library.server.MonomerLibraryServerError: print("Skipping exercise_atom_selections(): monomer library not available.") return ener_lib = monomer_library.server.ener_lib() processed_pdb = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name="tmp_selection.pdb", log=log) isel = processed_pdb.all_chain_proxies.iselection assert list(isel("peptide")) == list(range(52)) + list(range(114,122)) assert list(isel("rna")) == list(range(52,95)) assert list(isel("dna")) == list(range(95,114)) assert list(isel("nucleotide")) == list(range(52,114)) assert list(isel("water")) == [124,125] assert list(isel("peptide backbone")) \ == list(isel("peptide and (name ca or name c or name o or name n)")) assert list(isel("nucleotide backbone")) \ == [52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105] assert list(isel("backbone and (rna or dna)")) \ == list(isel("nucleotide backbone")) assert list(isel("phosphate")) \ == [52, 53, 54, 55, 60, 72, 73, 74, 75, 80, 95, 96, 97, 98, 103] assert list(isel("ribose")) \ == [56, 57, 58, 59, 61, 62, 63, 76, 77, 78, 79, 81, 82, 83, 99, 100, 101, 102, 104, 105] assert list(isel("phosphate or ribose")) == list(isel("nuc backbone")) assert list(isel("backbone resname glu")) \ == [6, 7, 8, 9, 43, 44, 45, 46] assert list(isel("within(0.5, backbone resname glu)")) \ == [6, 7, 8, 9, 43, 44, 45, 46] assert list(isel("within(1.5, backbone resname glu)")) \ == [2, 6, 7, 8, 9, 15, 39, 43, 44, 45, 46] assert list(isel("within(2.5, backbone resname glu)")) \ == [1, 2, 3, 6, 7, 8, 9, 10, 15, 16, 38, 39, 40, 43, 44, 45, 46, 47] assert list(isel("resname ser sidechain")) == [4, 5, 19, 20, 41, 42] def exercise(): exercise_atom_selections() print("OK") if (__name__ == "__main__"): exercise()