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 23.341 28.568 19.164 90.00 90.00 90.00 P 1 ATOM 1 N PHE A 58 8.659 20.073 11.185 1.00 7.73 N ATOM 2 CA PHE A 58 9.250 19.144 10.233 1.00 8.65 C ATOM 3 C PHE A 58 9.039 17.721 10.706 1.00 9.84 C ATOM 4 O PHE A 58 9.023 17.464 11.919 1.00 8.58 O ATOM 5 CB PHE A 58 10.754 19.416 10.061 1.00 8.60 C ATOM 6 CG PHE A 58 11.066 20.536 9.101 1.00 10.13 C ATOM 7 CD1 PHE A 58 11.673 21.701 9.544 1.00 8.55 C ATOM 9 CE1 PHE A 58 11.950 22.730 8.669 1.00 9.55 C ATOM 10 CE2 PHE A 58 11.009 21.455 6.871 1.00 10.11 C ATOM 11 CZ PHE A 58 11.621 22.610 7.327 1.00 10.71 C ATOM 12 N HIS A 59 8.887 16.797 9.756 1.00 9.65 N ATOM 13 CA HIS A 59 8.720 15.382 10.080 1.00 5.80 C ATOM 14 C HIS A 59 9.606 14.539 9.169 1.00 10.35 C ATOM 15 O HIS A 59 9.972 14.972 8.075 1.00 10.56 O ATOM 16 CB HIS A 59 7.250 14.977 9.971 1.00 7.59 C ATOM 17 CG HIS A 59 6.333 15.874 10.738 1.00 9.83 C ATOM 19 CD2 HIS A 59 5.689 17.009 10.376 1.00 8.78 C ATOM 20 CE1 HIS A 59 5.211 16.616 12.481 1.00 9.20 C ATOM 21 NE2 HIS A 59 5.000 17.452 11.479 1.00 9.98 N ATOM 22 N TRP A 60 9.964 13.344 9.625 1.00 9.39 N ATOM 23 CA TRP A 60 11.067 12.594 9.017 1.00 11.89 C ATOM 24 C TRP A 60 10.635 11.189 8.608 1.00 9.81 C ATOM 25 O TRP A 60 10.120 10.434 9.430 1.00 8.97 O ATOM 26 CB TRP A 60 12.197 12.509 10.046 1.00 11.46 C ATOM 27 CG TRP A 60 12.933 13.782 10.392 1.00 14.68 C ATOM 28 CD1 TRP A 60 12.677 14.629 11.446 1.00 12.97 C ATOM 29 CD2 TRP A 60 13.987 14.394 9.638 1.00 14.91 C ATOM 30 NE1 TRP A 60 13.524 15.715 11.398 1.00 9.65 N ATOM 32 CE3 TRP A 60 14.673 14.043 8.472 1.00 8.58 C ATOM 33 CZ2 TRP A 60 15.350 16.433 9.839 1.00 12.03 C ATOM 34 CZ3 TRP A 60 15.670 14.879 8.017 1.00 14.50 C ATOM 35 CH2 TRP A 60 16.002 16.057 8.697 1.00 11.88 C ATOM 36 N ARG A 61 10.858 10.832 7.348 1.00 7.72 N ATOM 37 CA ARG A 61 10.510 9.497 6.870 1.00 9.11 C ATOM 38 C ARG A 61 11.692 8.812 6.178 1.00 10.61 C ATOM 39 O ARG A 61 11.963 9.081 5.006 1.00 11.05 O ATOM 40 CB ARG A 61 9.318 9.570 5.914 1.00 20.00 C ATOM 41 CG ARG A 61 9.425 8.639 4.717 1.00 20.00 C ATOM 42 CD ARG A 61 8.264 8.745 3.741 1.00 20.00 C ATOM 43 NE ARG A 61 7.574 10.028 3.848 1.00 20.00 N ATOM 44 CZ ARG A 61 6.414 10.300 3.269 1.00 20.00 C ATOM 47 N PRO A 62 12.408 7.927 6.895 1.00 10.62 N ATOM 48 CA PRO A 62 13.520 7.240 6.220 1.00 7.26 C ATOM 49 C PRO A 62 13.019 6.486 5.000 1.00 10.75 C ATOM 50 O PRO A 62 11.946 5.890 5.048 1.00 11.44 O ATOM 51 CB PRO A 62 14.025 6.257 7.281 1.00 6.15 C ATOM 52 CG PRO A 62 13.701 6.929 8.583 1.00 9.40 C ATOM 53 CD PRO A 62 12.359 7.621 8.338 1.00 8.83 C TER 54 PRO A 62 HETATM 55 O HOH S 30 9.529 12.770 12.418 1.00 9.26 O HETATM 56 O HOH S 63 17.561 6.671 6.582 1.00 8.34 O HETATM 57 O HOH S 102 16.677 8.520 10.394 1.00 6.42 O HETATM 58 O HOH S 116 7.555 10.547 10.276 1.00 11.56 O HETATM 59 O HOH S 167 8.683 23.568 14.164 1.00 17.13 O HETATM 60 O HOH S 171 15.615 21.403 10.635 1.00 9.12 O HETATM 61 O HOH S 176 10.243 21.293 13.219 1.00 18.50 O HETATM 62 O HOH S 192 9.980 5.000 7.291 1.00 24.87 O HETATM 63 O HOH S 277 18.341 19.685 8.800 1.00 14.61 O TER 64 HOH S 277 END """ pdb_poor = """\ CRYST1 23.341 28.568 19.164 90.00 90.00 90.00 P 1 ATOM 1 N PHE A 58 8.659 20.073 11.185 1.00 7.73 N ATOM 2 CA PHE A 58 9.250 19.144 10.233 1.00 8.65 C ATOM 3 C PHE A 58 9.039 17.721 10.706 1.00 9.84 C ATOM 4 O PHE A 58 9.023 17.464 11.919 1.00 8.58 O ATOM 5 CB PHE A 58 10.754 19.416 10.061 1.00 8.60 C ATOM 6 CG PHE A 58 11.545 19.305 11.340 1.00 10.13 C ATOM 7 CD1 PHE A 58 12.066 18.088 11.748 1.00 8.55 C ATOM 9 CE1 PHE A 58 12.781 17.983 12.923 1.00 9.55 C ATOM 10 CE2 PHE A 58 12.466 20.325 13.323 1.00 10.11 C ATOM 11 CZ PHE A 58 12.986 19.103 13.714 1.00 10.71 C ATOM 12 N HIS A 59 8.887 16.797 9.756 1.00 9.65 N ATOM 13 CA HIS A 59 8.720 15.382 10.080 1.00 5.80 C ATOM 14 C HIS A 59 9.606 14.539 9.169 1.00 10.35 C ATOM 15 O HIS A 59 9.972 14.972 8.075 1.00 10.56 O ATOM 16 CB HIS A 59 7.250 14.977 9.971 1.00 7.59 C ATOM 17 CG HIS A 59 6.357 15.744 10.892 1.00 9.83 C ATOM 19 CD2 HIS A 59 6.246 15.728 12.242 1.00 8.78 C ATOM 20 CE1 HIS A 59 4.758 17.143 11.468 1.00 9.20 C ATOM 21 NE2 HIS A 59 5.242 16.606 12.575 1.00 9.98 N ATOM 22 N TRP A 60 9.964 13.344 9.625 1.00 9.39 N ATOM 23 CA TRP A 60 11.067 12.594 9.017 1.00 11.89 C ATOM 24 C TRP A 60 10.635 11.189 8.608 1.00 9.81 C ATOM 25 O TRP A 60 10.120 10.434 9.430 1.00 8.97 O ATOM 26 CB TRP A 60 12.197 12.509 10.046 1.00 11.46 C ATOM 27 CG TRP A 60 13.439 11.737 9.668 1.00 14.68 C ATOM 28 CD1 TRP A 60 13.807 10.487 10.111 1.00 12.97 C ATOM 29 CD2 TRP A 60 14.513 12.195 8.837 1.00 14.91 C ATOM 30 NE1 TRP A 60 15.033 10.140 9.587 1.00 9.65 N ATOM 32 CE3 TRP A 60 14.745 13.369 8.116 1.00 8.58 C ATOM 33 CZ2 TRP A 60 16.663 11.282 8.064 1.00 12.03 C ATOM 34 CZ3 TRP A 60 15.913 13.478 7.392 1.00 14.50 C ATOM 35 CH2 TRP A 60 16.856 12.443 7.368 1.00 11.88 C ATOM 36 N ARG A 61 10.858 10.832 7.348 1.00 7.72 N ATOM 37 CA ARG A 61 10.510 9.497 6.870 1.00 9.11 C ATOM 38 C ARG A 61 11.692 8.812 6.178 1.00 10.61 C ATOM 39 O ARG A 61 11.963 9.081 5.006 1.00 11.05 O ATOM 40 CB ARG A 61 9.318 9.570 5.914 1.00 20.00 C ATOM 41 CG ARG A 61 8.017 9.993 6.576 1.00 20.00 C ATOM 42 CD ARG A 61 6.821 10.020 5.637 1.00 20.00 C ATOM 43 NE ARG A 61 5.613 10.499 6.303 1.00 20.00 N ATOM 44 CZ ARG A 61 4.463 10.727 5.686 1.00 20.00 C ATOM 47 N PRO A 62 12.408 7.927 6.895 1.00 10.62 N ATOM 48 CA PRO A 62 13.520 7.240 6.220 1.00 7.26 C ATOM 49 C PRO A 62 13.019 6.486 5.000 1.00 10.75 C ATOM 50 O PRO A 62 11.946 5.890 5.048 1.00 11.44 O ATOM 51 CB PRO A 62 14.025 6.257 7.281 1.00 6.15 C ATOM 52 CG PRO A 62 12.802 5.932 8.087 1.00 9.40 C ATOM 53 CD PRO A 62 12.029 7.250 8.167 1.00 8.83 C TER 54 PRO A 62 HETATM 55 O HOH S 30 9.529 12.770 12.418 1.00 9.26 O HETATM 56 O HOH S 63 17.561 6.671 6.582 1.00 8.34 O HETATM 57 O HOH S 102 16.677 8.520 10.394 1.00 6.42 O HETATM 58 O HOH S 116 7.555 10.547 10.276 1.00 11.56 O HETATM 59 O HOH S 167 8.683 23.568 14.164 1.00 17.13 O HETATM 60 O HOH S 171 15.615 21.403 10.635 1.00 9.12 O HETATM 61 O HOH S 176 10.243 21.293 13.219 1.00 18.50 O HETATM 62 O HOH S 192 9.980 5.000 7.291 1.00 24.87 O HETATM 63 O HOH S 277 18.341 19.685 8.800 1.00 14.61 O TER 64 HOH S 277 END """ pdb_for_map = pdb_answer def exercise(i_pdb=0, d_min=1.5, resolution_factor=0.1): """ Partial (incomplete) residues. Just run to make sure it does not crash. It will not fix incomplete residues. """ # t = mmtbx.refinement.real_space.setup_test( pdb_answer = pdb_answer, pdb_poor = pdb_poor, i_pdb = i_pdb, d_min = d_min, residues = ["ARG","PHE","TRP","PRO","HIS"], resolution_factor = resolution_factor, pdb_for_map = pdb_for_map) # ph = t.ph_poor for i in [1,]: 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 = True, 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) if(__name__ == "__main__"): t0 = time.time() exercise() print("Time: %6.4f"%(time.time()-t0))