from __future__ import absolute_import, division, print_function import time import mmtbx.refinement.real_space.fit_residues import mmtbx.refinement.real_space pdb_answer = """\ CRYST1 16.402 13.234 20.833 90.00 90.00 90.00 P 1 ATOM 1 N PHE A 364 3.630 3.286 4.228 1.00 9.46 N ATOM 2 CA PHE A 364 4.866 4.027 4.477 1.00 10.15 C ATOM 3 C PHE A 364 6.107 3.219 4.071 1.00 11.38 C ATOM 4 O PHE A 364 6.958 3.695 3.331 1.00 11.71 O ATOM 5 CB PHE A 364 4.987 4.446 5.947 1.00 9.57 C ATOM 6 CG PHE A 364 6.322 5.060 6.261 1.00 10.71 C ATOM 7 CD1 PHE A 364 6.708 6.251 5.660 1.00 11.42 C ATOM 8 CD2 PHE A 364 7.223 4.410 7.089 1.00 9.88 C ATOM 9 CE1 PHE A 364 7.965 6.803 5.906 1.00 12.47 C ATOM 10 CE2 PHE A 364 8.485 4.967 7.348 1.00 12.45 C ATOM 11 CZ PHE A 364 8.844 6.165 6.756 1.00 12.01 C ATOM 12 CA THR A 401 5.525 3.293 16.950 1.00 7.97 C ATOM 13 C THR A 401 6.000 3.929 15.643 1.00 9.81 C ATOM 14 O THR A 401 6.802 3.348 14.900 1.00 9.23 O ATOM 15 N ALA A 402 5.502 5.133 15.362 1.00 8.84 N ATOM 16 CA ALA A 402 5.936 5.844 14.166 1.00 8.49 C ATOM 17 C ALA A 402 7.443 6.099 14.165 1.00 8.21 C ATOM 18 O ALA A 402 8.116 5.862 13.150 1.00 8.01 O ATOM 19 CB ALA A 402 5.174 7.167 14.035 1.00 7.75 C ATOM 20 N PHE A 403 7.977 6.586 15.283 1.00 9.12 N ATOM 21 CA PHE A 403 9.405 6.873 15.345 1.00 8.30 C ATOM 22 C PHE A 403 10.246 5.627 15.062 1.00 9.33 C ATOM 23 O PHE A 403 11.192 5.667 14.279 1.00 11.43 O ATOM 24 CB PHE A 403 9.775 7.458 16.711 1.00 9.28 C ATOM 25 CG PHE A 403 11.202 7.901 16.805 1.00 12.22 C ATOM 26 CD1 PHE A 403 11.566 9.176 16.412 1.00 12.95 C ATOM 27 CD2 PHE A 403 12.176 7.050 17.291 1.00 14.12 C ATOM 28 CE1 PHE A 403 12.887 9.593 16.493 1.00 14.50 C ATOM 29 N PHE A 407 9.045 6.777 10.558 1.00 10.36 N ATOM 30 CA PHE A 407 7.962 7.610 10.037 1.00 10.78 C ATOM 31 C PHE A 407 7.986 8.907 10.843 1.00 8.79 C ATOM 32 O PHE A 407 7.084 9.187 11.629 1.00 10.53 O ATOM 33 CB PHE A 407 6.620 6.885 10.202 1.00 7.96 C ATOM 34 CG PHE A 407 5.960 6.454 8.919 1.00 9.05 C ATOM 35 CD1 PHE A 407 6.506 5.396 8.202 1.00 8.53 C ATOM 36 CD2 PHE A 407 4.826 7.076 8.421 1.00 9.48 C ATOM 37 CE1 PHE A 407 5.954 4.976 7.010 1.00 10.10 C ATOM 38 CE2 PHE A 407 4.261 6.653 7.220 1.00 9.34 C ATOM 39 CZ PHE A 407 4.841 5.602 6.515 1.00 9.45 C TER """ pdb_poor = pdb_answer pdb_for_map_1 = pdb_answer pdb_for_map_2 = """\ CRYST1 16.402 13.234 20.833 90.00 90.00 90.00 P 1 ATOM 1 N PHE A 364 3.630 3.286 4.228 1.00 9.46 N ATOM 2 CA PHE A 364 4.866 4.027 4.477 1.00 10.15 C ATOM 3 C PHE A 364 6.107 3.219 4.071 1.00 11.38 C ATOM 4 O PHE A 364 6.958 3.695 3.331 1.00 11.71 O ATOM 5 CB PHE A 364 4.987 4.446 5.947 1.00 9.57 C ATOM 6 CG PHE A 364 6.322 5.060 6.261 1.00 10.71 C ATOM 7 CD1 PHE A 364 6.708 6.251 5.660 1.00 11.42 C ATOM 8 CD2 PHE A 364 7.223 4.410 7.089 1.00 9.88 C ATOM 9 CE1 PHE A 364 7.965 6.803 5.906 1.00 12.47 C ATOM 10 CE2 PHE A 364 8.485 4.967 7.348 1.00 12.45 C ATOM 11 CZ PHE A 364 8.844 6.165 6.756 1.00 12.01 C ATOM 12 CA THR A 401 5.525 3.293 16.950 1.00 7.97 C ATOM 13 C THR A 401 6.000 3.929 15.643 1.00 9.81 C ATOM 14 O THR A 401 6.802 3.348 14.900 1.00 9.23 O ATOM 15 N ALA A 402 5.502 5.133 15.362 1.00 8.84 N ATOM 16 CA ALA A 402 5.936 5.844 14.166 1.00 8.49 C ATOM 17 C ALA A 402 7.443 6.099 14.165 1.00 8.21 C ATOM 18 O ALA A 402 8.116 5.862 13.150 1.00 8.01 O ATOM 19 CB ALA A 402 5.174 7.167 14.035 1.00 7.75 C ATOM 20 N PHE A 403 7.977 6.586 15.283 1.00 9.12 N ATOM 21 CA PHE A 403 9.405 6.873 15.345 1.00 8.30 C ATOM 22 C PHE A 403 10.246 5.627 15.062 1.00 9.33 C ATOM 23 O PHE A 403 11.192 5.667 14.279 1.00 11.43 O ATOM 24 CB PHE A 403 9.775 7.458 16.711 1.00 9.28 C ATOM 25 CG PHE A 403 11.202 7.901 16.805 1.00 12.22 C ATOM 26 CD1 PHE A 403 11.566 9.176 16.412 1.00 12.95 C ATOM 27 CD2 PHE A 403 12.176 7.050 17.291 1.00 14.12 C ATOM 28 CE1 PHE A 403 12.887 9.593 16.493 1.00 14.50 C ATOM 29 N PHE A 407 9.045 6.777 10.558 1.00 10.36 N ATOM 30 CA PHE A 407 7.962 7.610 10.037 1.00 10.78 C ATOM 31 C PHE A 407 7.986 8.907 10.843 1.00 8.79 C ATOM 32 O PHE A 407 7.084 9.187 11.629 1.00 10.53 O ATOM 33 CB PHE A 407 6.620 6.885 10.202 1.00 7.96 C ATOM 34 CG PHE A 407 5.960 6.454 8.919 1.00 9.05 C ATOM 35 CD1 PHE A 407 6.506 5.396 8.202 1.00 8.53 C ATOM 36 CD2 PHE A 407 4.826 7.076 8.421 1.00 9.48 C ATOM 37 CE1 PHE A 407 5.954 4.976 7.010 1.00 10.10 C ATOM 38 CE2 PHE A 407 4.261 6.653 7.220 1.00 9.34 C ATOM 39 CZ PHE A 407 4.841 5.602 6.515 1.00 9.45 C TER """ def exercise(i_pdb, pdb_for_map, d_min = 1.5, resolution_factor = 0.1): """ Best fitting residue is a rotamer outlier (PHE 407), two scenarious: - outlier fits density perfectly - outlier fits not so good. No better options to fit other than keep the outlier unchanged. """ t = mmtbx.refinement.real_space.setup_test( pdb_answer = pdb_answer, pdb_poor = pdb_poor, i_pdb = i_pdb, d_min = d_min, residues = ["PHE","THR","ALA"], resolution_factor = resolution_factor, pdb_for_map = pdb_for_map) # ph = t.ph_poor for i in [1,2,3]: result = mmtbx.refinement.real_space.fit_residues.run( pdb_hierarchy = ph, vdw_radii = t.vdw, crystal_symmetry = t.crystal_symmetry, map_data = t.target_map, backbone_sample = False, rotatable_hd = t.rotatable_hd, rotamer_manager = t.rotamer_manager, sin_cos_table = t.sin_cos_table, mon_lib_srv = t.mon_lib_srv) ph = result.pdb_hierarchy result.pdb_hierarchy.write_pdb_file(file_name = "refined_%s.pdb"%str(i_pdb), crystal_symmetry = t.crystal_symmetry) # mmtbx.refinement.real_space.check_sites_match( ph_answer = t.ph_answer, ph_refined = result.pdb_hierarchy, tol = 0.16) if(__name__ == "__main__"): t0 = time.time() for i_pdb, pdb_for_map in enumerate([pdb_for_map_1, pdb_for_map_2]): exercise( i_pdb = i_pdb, pdb_for_map = pdb_for_map) print("Time: %6.4f"%(time.time()-t0))