from __future__ import absolute_import, division, print_function import mmtbx.monomer_library from scitbx.array_family import flex import iotbx.pdb from mmtbx.rotamer.rotamer_eval import RotamerEval from libtbx.test_utils import approx_equal pdb_str1 = """\ CRYST1 16.960 19.455 19.841 90.00 90.00 90.00 P 1 SCALE1 0.058962 0.000000 0.000000 0.00000 SCALE2 0.000000 0.051401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.050401 0.00000 ATOM 1 N TYR A 20 10.418 10.903 8.137 1.00 23.81 N ATOM 2 CA TYR A 20 10.810 9.981 7.034 1.00 35.69 C ATOM 3 C TYR A 20 9.703 8.988 6.760 1.00 28.94 C ATOM 4 O TYR A 20 9.364 8.158 7.667 1.00 25.26 O ATOM 5 CB TYR A 20 12.115 9.280 7.395 1.00 33.37 C ATOM 6 CG TYR A 20 13.316 10.201 7.509 1.00 31.48 C ATOM 7 CD1 TYR A 20 14.071 10.517 6.393 1.00 36.91 C ATOM 8 CD2 TYR A 20 13.704 10.721 8.703 1.00 21.36 C ATOM 9 CE1 TYR A 20 15.188 11.317 6.471 1.00 36.56 C ATOM 10 CE2 TYR A 20 14.835 11.519 8.817 1.00 29.56 C ATOM 11 CZ TYR A 20 15.540 11.837 7.694 1.00 35.08 C ATOM 12 OH TYR A 20 16.672 12.664 7.781 1.00 38.73 O ATOM 13 N AARG A 21 9.160 8.989 5.577 0.50 38.95 N ATOM 14 CA AARG A 21 8.073 8.140 5.126 0.50 38.77 C ATOM 15 C AARG A 21 6.863 8.252 6.048 0.50 27.69 C ATOM 16 O AARG A 21 6.208 7.218 6.352 0.50 22.82 O ATOM 17 CB AARG A 21 8.542 6.674 5.053 0.50 20.00 C ATOM 18 CG AARG A 21 7.471 5.695 4.562 0.50 20.00 C ATOM 19 CD AARG A 21 8.021 4.282 4.444 0.50 20.00 C ATOM 20 NE AARG A 21 6.983 3.348 3.946 0.50 20.00 N ATOM 21 CZ AARG A 21 5.878 3.748 3.337 0.50 20.00 C ATOM 22 NH1AARG A 21 5.643 5.047 3.127 0.50 20.00 N ATOM 23 NH2AARG A 21 4.997 2.854 2.938 0.50 20.00 N ATOM 13 N BTRP A 21 9.160 8.989 5.577 0.50 38.95 N ATOM 14 CA BTRP A 21 8.073 8.140 5.126 0.50 38.77 C ATOM 15 C BTRP A 21 6.863 8.252 6.048 0.50 27.69 C ATOM 16 O BTRP A 21 6.208 7.218 6.352 0.50 22.82 O ATOM 17 CB BTRP A 21 8.532 6.683 5.040 0.50 20.00 C ATOM 18 CG BTRP A 21 9.522 6.431 3.944 0.50 20.00 C ATOM 19 CD1BTRP A 21 10.883 6.417 4.051 0.50 20.00 C ATOM 20 CD2BTRP A 21 9.228 6.154 2.569 0.50 20.00 C ATOM 21 NE1BTRP A 21 11.453 6.152 2.830 0.50 20.00 N ATOM 22 CE2BTRP A 21 10.459 5.985 1.902 0.50 20.00 C ATOM 23 CE3BTRP A 21 8.047 6.033 1.829 0.50 20.00 C ATOM 24 CZ2BTRP A 21 10.541 5.702 0.540 0.50 20.00 C ATOM 25 CZ3BTRP A 21 8.131 5.752 0.478 0.50 20.00 C ATOM 26 CH2BTRP A 21 9.368 5.590 -0.152 0.50 20.00 C ATOM 29 N CHIS A 21 9.160 8.989 5.577 1.00 38.95 N ATOM 30 CA CHIS A 21 8.073 8.140 5.126 1.00 38.77 C ATOM 31 C CHIS A 21 6.863 8.252 6.048 1.00 27.69 C ATOM 32 O CHIS A 21 6.208 7.218 6.352 1.00 22.82 O ATOM 33 CB CHIS A 21 8.533 6.684 5.037 1.00 20.00 C ATOM 34 CG CHIS A 21 9.008 6.118 6.338 1.00 20.00 C ATOM 35 ND1CHIS A 21 8.412 6.420 7.544 1.00 20.00 N ATOM 36 CD2CHIS A 21 10.019 5.265 6.623 1.00 20.00 C ATOM 37 CE1CHIS A 21 9.038 5.781 8.515 1.00 20.00 C ATOM 38 NE2CHIS A 21 10.017 5.071 7.985 1.00 20.00 N ATOM 32 N GLY A 22 6.554 9.436 6.463 1.00 24.85 N ATOM 33 CA GLY A 22 5.410 9.707 7.327 1.00 29.53 C ATOM 34 C GLY A 22 5.748 9.622 8.821 1.00 33.22 C ATOM 35 O GLY A 22 5.479 10.518 9.577 1.00 30.06 O ATOM 36 N TYR A 23 6.330 8.487 9.201 1.00 27.25 N ATOM 37 CA TYR A 23 6.695 8.251 10.596 1.00 34.16 C ATOM 38 C TYR A 23 7.852 9.136 11.044 1.00 23.48 C ATOM 39 O TYR A 23 8.641 9.570 10.203 1.00 39.30 O ATOM 40 CB TYR A 23 7.052 6.786 10.831 1.00 29.65 C ATOM 41 CG TYR A 23 5.903 5.834 10.636 1.00 34.88 C ATOM 42 CD1 TYR A 23 5.022 5.540 11.687 1.00 30.77 C ATOM 43 CD2 TYR A 23 5.649 5.271 9.396 1.00 32.29 C ATOM 44 CE1 TYR A 23 3.990 4.674 11.505 1.00 39.91 C ATOM 45 CE2 TYR A 23 4.589 4.378 9.190 1.00 30.45 C ATOM 46 CZ TYR A 23 3.770 4.107 10.257 1.00 37.13 C ATOM 47 OH TYR A 23 2.693 3.226 10.097 1.00 38.59 O ATOM 48 N SER A 24 7.948 9.408 12.310 1.00 36.25 N ATOM 49 CA SER A 24 9.013 10.264 12.855 1.00 26.44 C ATOM 50 C SER A 24 9.607 9.636 14.109 1.00 20.40 C ATOM 51 O SER A 24 8.916 9.382 15.096 1.00 39.27 O ATOM 52 CB SER A 24 8.482 11.655 13.176 1.00 21.07 C ATOM 53 OG SER A 24 7.498 11.601 14.206 1.00 34.95 O TER 54 SER A 24 END """ pdb_str2 = """\ ATOM 28 N PRO C 29 61.293 16.365 38.366 1.00 45.42 N ATOM 29 CA PRO C 29 61.610 17.144 39.554 1.00 51.27 C ATOM 30 C PRO C 29 60.399 17.813 40.109 1.00 50.43 C ATOM 31 O PRO C 29 59.324 17.664 39.560 1.00 47.67 O ATOM 32 CB PRO C 29 62.495 18.235 38.993 1.00 49.45 C ATOM 33 CG PRO C 29 61.908 18.507 37.705 1.00 55.39 C ATOM 34 CD PRO C 29 61.575 17.152 37.157 1.00 56.41 C """ pdb_str3 = """\ ATOM 127 N PRO L 18 18.596 -78.410 66.845 1.00 33.30 N ATOM 128 CA PRO L 18 19.467 -77.234 66.790 1.00 32.71 C ATOM 129 C PRO L 18 20.924 -77.585 66.494 1.00 30.96 C ATOM 130 O PRO L 18 21.369 -78.705 66.735 1.00 30.74 O ATOM 131 CB PRO L 18 19.289 -76.622 68.173 1.00 31.82 C ATOM 132 CG PRO L 18 19.175 -77.838 69.037 1.00 33.36 C ATOM 133 CD PRO L 18 18.236 -78.728 68.240 1.00 34.01 C ATOM 134 N ALA L 19 21.657 -76.614 65.963 1.00 28.50 N ATOM 135 CA ALA L 19 23.064 -76.802 65.641 1.00 27.23 C ATOM 136 C ALA L 19 23.816 -75.537 66.027 1.00 27.07 C ATOM 137 O ALA L 19 23.265 -74.434 65.976 1.00 24.32 O ATOM 138 CB ALA L 19 23.231 -77.079 64.157 1.00 30.04 C ATOM 139 N SER L 20 25.075 -75.694 66.411 1.00 24.81 N ATOM 140 CA SER L 20 25.874 -74.549 66.816 1.00 27.97 C ATOM 141 C SER L 20 27.304 -74.675 66.310 1.00 26.96 C ATOM 142 O SER L 20 27.912 -75.739 66.408 1.00 27.07 O ATOM 143 CB SER L 20 25.863 -74.436 68.344 1.00 29.31 C ATOM 144 OG SER L 20 26.505 -73.254 68.779 1.00 39.96 O """ def run(pdb_str, expected_ids): get_class = iotbx.pdb.common_residue_names_get_class mon_lib_srv = mmtbx.monomer_library.server.server() rotamer_manager = RotamerEval() pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str) pdb_hierarchy = pdb_inp.construct_hierarchy() result_ids = [] for residue_group in pdb_hierarchy.residue_groups(): for conformer in residue_group.conformers(): for residue in conformer.residues(): sites_cart = residue.atoms().extract_xyz() rotamer_name = rotamer_manager.evaluate_residue(residue=residue) print(residue.resname, residue.resseq, rotamer_name) result_ids.append(rotamer_name) if(get_class(residue.resname) == "common_amino_acid"): rotamer_iterator = mon_lib_srv.rotamer_iterator( fine_sampling = True, comp_id = residue.resname, atom_names = residue.atoms().extract_name(), sites_cart = sites_cart) if(rotamer_iterator is None or rotamer_iterator.problem_message is not None or rotamer_iterator.rotamer_info is None): rotamer_iterator = None if(rotamer_iterator is not None): d1_min, d2_min = 1.e+9, 1.e+9 for r, rotamer_sites_cart in rotamer_iterator: sites_cart_rot = rotamer_manager.nearest_rotamer_sites_cart( residue=residue) d1= flex.mean(flex.sqrt((sites_cart - sites_cart_rot).dot())) d2= flex.mean(flex.sqrt((sites_cart - rotamer_sites_cart).dot())) if(d1 < d1_min): d1_min = d1 if(d2 < d2_min): d2_min = d2 assert approx_equal(d1_min, d2_min) assert result_ids == expected_ids if(__name__ == "__main__"): run(pdb_str = pdb_str1, expected_ids=['m-80', 'OUTLIER', 'm100', 'OUTLIER', None, 'm-80', 'p']) run(pdb_str = pdb_str2, expected_ids=['Cg_endo']) run(pdb_str = pdb_str3, expected_ids=['Cg_endo', 'EXCEPTION', 't'])