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 14.074 16.834 17.360 90.00 90.00 90.00 P 1 ATOM 1 N ARG A 21 8.318 11.834 9.960 1.00 10.00 N ATOM 2 CA ARG A 21 7.146 11.154 9.422 1.00 10.00 C ATOM 3 C ARG A 21 6.012 11.120 10.440 1.00 10.00 C ATOM 4 O ARG A 21 5.000 10.449 10.235 1.00 10.00 O ATOM 5 CB ARG A 21 7.505 9.732 8.987 1.00 10.00 C ATOM 6 CG ARG A 21 7.923 8.820 10.129 0.70 20.00 C ATOM 7 CD ARG A 21 8.312 7.441 9.621 0.70 20.00 C ATOM 8 NE ARG A 21 8.694 6.545 10.708 0.70 20.00 N ATOM 9 CZ ARG A 21 7.839 5.785 11.385 0.70 20.00 C ATOM 10 NH1 ARG A 21 6.546 5.811 11.088 0.70 20.00 N ATOM 11 NH2 ARG A 21 8.275 5.000 12.360 0.70 20.00 N ATOM 0 HA ARG A 21 6.805 11.715 8.552 1.00 10.00 H new ATOM 0 HB2 ARG A 21 6.647 9.291 8.480 1.00 10.00 H new ATOM 0 HB3 ARG A 21 8.315 9.780 8.259 1.00 10.00 H new ATOM 0 HG2 ARG A 21 8.764 9.264 10.662 0.70 20.00 H new ATOM 0 HG3 ARG A 21 7.104 8.729 10.843 0.70 20.00 H new ATOM 0 HD2 ARG A 21 7.476 7.008 9.071 0.70 20.00 H new ATOM 0 HD3 ARG A 21 9.141 7.534 8.919 0.70 20.00 H new ATOM 0 HE ARG A 21 9.680 6.499 10.965 0.70 20.00 H new ATOM 0 HH11 ARG A 21 6.207 6.415 10.339 0.70 20.00 H new ATOM 0 HH12 ARG A 21 5.891 5.227 11.609 0.70 20.00 H new ATOM 0 HH21 ARG A 21 9.268 4.978 12.592 0.70 20.00 H new ATOM 0 HH22 ARG A 21 7.617 4.418 12.878 0.70 20.00 H new TER HETATM 1 U U B 1 9.074 7.848 5.000 1.00 10.00 U TER """ pdb_poor0 = """\ CRYST1 14.074 16.834 17.360 90.00 90.00 90.00 P 1 ATOM 1 N ARG A 21 8.318 11.834 9.960 1.00 10.00 N ATOM 2 CA ARG A 21 7.146 11.154 9.422 1.00 10.00 C ATOM 3 C ARG A 21 6.012 11.120 10.440 1.00 10.00 C ATOM 4 O ARG A 21 5.000 10.449 10.235 1.00 10.00 O ATOM 5 CB ARG A 21 7.505 9.732 8.987 1.00 10.00 C ATOM 6 CG ARG A 21 6.612 8.656 9.584 0.70 20.00 C ATOM 7 CD ARG A 21 6.020 7.767 8.502 0.70 20.00 C ATOM 8 NE ARG A 21 4.569 7.657 8.617 0.70 20.00 N ATOM 9 CZ ARG A 21 3.771 7.248 7.637 0.70 20.00 C ATOM 10 NH1 ARG A 21 4.282 6.909 6.460 0.70 20.00 N ATOM 11 NH2 ARG A 21 2.461 7.180 7.830 0.70 20.00 N ATOM 0 HA ARG A 21 6.805 11.715 8.552 1.00 10.00 H new ATOM 0 HB2 ARG A 21 7.451 9.672 7.900 1.00 10.00 H new ATOM 0 HB3 ARG A 21 8.538 9.528 9.267 1.00 10.00 H new ATOM 0 HG2 ARG A 21 7.188 8.048 10.282 0.70 20.00 H new ATOM 0 HG3 ARG A 21 5.809 9.122 10.155 0.70 20.00 H new ATOM 0 HD2 ARG A 21 6.276 8.169 7.522 0.70 20.00 H new ATOM 0 HD3 ARG A 21 6.465 6.774 8.565 0.70 20.00 H new ATOM 0 HE ARG A 21 4.140 7.911 9.507 0.70 20.00 H new ATOM 0 HH11 ARG A 21 5.289 6.962 6.307 0.70 20.00 H new ATOM 0 HH12 ARG A 21 3.668 6.595 5.709 0.70 20.00 H new ATOM 0 HH21 ARG A 21 2.064 7.442 8.732 0.70 20.00 H new ATOM 0 HH22 ARG A 21 1.850 6.866 7.076 0.70 20.00 H new TER HETATM 12 U U B 1 9.074 7.848 5.000 1.00 10.00 U TER """ pdb_poor1 = """\ CRYST1 14.074 16.834 17.360 90.00 90.00 90.00 P 1 ATOM 1 N ARG A 21 8.318 11.834 9.960 1.00 10.00 N ATOM 2 CA ARG A 21 7.248 10.924 9.570 1.00 10.00 C ATOM 3 C ARG A 21 6.012 11.120 10.440 1.00 10.00 C ATOM 4 O ARG A 21 5.064 10.337 10.375 1.00 10.00 O ATOM 5 CB ARG A 21 7.724 9.472 9.652 1.00 10.00 C ATOM 6 CG ARG A 21 8.797 9.112 8.637 1.00 10.00 C ATOM 7 CD ARG A 21 9.187 7.647 8.741 1.00 10.00 C ATOM 8 NE ARG A 21 10.266 7.301 7.820 1.00 10.00 N ATOM 9 CZ ARG A 21 10.871 6.118 7.790 1.00 10.00 C ATOM 10 NH1 ARG A 21 10.505 5.162 8.634 1.00 10.00 N ATOM 11 NH2 ARG A 21 11.844 5.891 6.920 1.00 10.00 N ATOM 0 HA ARG A 21 6.977 11.151 8.539 1.00 10.00 H new ATOM 0 HB2 ARG A 21 8.109 9.283 10.654 1.00 10.00 H new ATOM 0 HB3 ARG A 21 6.868 8.812 9.510 1.00 10.00 H new ATOM 0 HG2 ARG A 21 8.434 9.323 7.631 1.00 10.00 H new ATOM 0 HG3 ARG A 21 9.676 9.737 8.797 1.00 10.00 H new ATOM 0 HD2 ARG A 21 9.497 7.426 9.762 1.00 10.00 H new ATOM 0 HD3 ARG A 21 8.317 7.025 8.531 1.00 10.00 H new ATOM 0 HE ARG A 21 10.575 8.012 7.158 1.00 10.00 H new ATOM 0 HH11 ARG A 21 9.758 5.334 9.307 1.00 10.00 H new ATOM 0 HH12 ARG A 21 10.970 4.255 8.610 1.00 10.00 H new ATOM 0 HH21 ARG A 21 12.130 6.625 6.272 1.00 10.00 H new ATOM 0 HH22 ARG A 21 12.307 4.982 6.898 1.00 10.00 H new TER HETATM 12 U U B 1 9.074 7.848 5.000 1.00 10.00 U TER """ pdb_poor2 = """\ CRYST1 14.074 16.834 17.360 90.00 90.00 90.00 P 1 ATOM 1 N ARG A 21 8.318 11.834 9.960 1.00 10.00 N ATOM 2 CA ARG A 21 7.146 11.154 9.422 1.00 10.00 C ATOM 3 C ARG A 21 6.012 11.120 10.440 1.00 10.00 C ATOM 4 O ARG A 21 5.000 10.449 10.235 1.00 10.00 O ATOM 5 CB ARG A 21 7.505 9.732 8.987 1.00 10.00 C ATOM 6 CG ARG A 21 7.923 8.820 10.129 0.70 20.00 C ATOM 7 CD ARG A 21 8.312 7.441 9.621 0.70 20.00 C ATOM 8 NE ARG A 21 8.694 6.545 10.708 0.70 20.00 N ATOM 9 CZ ARG A 21 7.839 5.785 11.385 0.70 20.00 C ATOM 10 NH1 ARG A 21 6.546 5.811 11.088 0.70 20.00 N ATOM 11 NH2 ARG A 21 8.275 5.000 12.360 0.70 20.00 N ATOM 0 HA ARG A 21 6.805 11.715 8.552 1.00 10.00 H new ATOM 0 HB2 ARG A 21 6.647 9.291 8.480 1.00 10.00 H new ATOM 0 HB3 ARG A 21 8.315 9.780 8.259 1.00 10.00 H new ATOM 0 HG2 ARG A 21 8.764 9.264 10.662 0.70 20.00 H new ATOM 0 HG3 ARG A 21 7.104 8.729 10.843 0.70 20.00 H new ATOM 0 HD2 ARG A 21 7.476 7.008 9.071 0.70 20.00 H new ATOM 0 HD3 ARG A 21 9.141 7.534 8.919 0.70 20.00 H new ATOM 0 HE ARG A 21 9.680 6.499 10.965 0.70 20.00 H new ATOM 0 HH11 ARG A 21 6.207 6.415 10.339 0.70 20.00 H new ATOM 0 HH12 ARG A 21 5.891 5.227 11.609 0.70 20.00 H new ATOM 0 HH21 ARG A 21 9.268 4.978 12.592 0.70 20.00 H new ATOM 0 HH22 ARG A 21 7.617 4.418 12.878 0.70 20.00 H new TER HETATM 12 U U B 1 9.074 7.848 5.000 1.00 10.00 U TER """ pdb_poor3 = """\ CRYST1 14.074 16.834 17.360 90.00 90.00 90.00 P 1 ATOM 1 N ARG A 21 8.318 11.834 9.960 1.00 10.00 N ATOM 2 CA ARG A 21 7.146 11.154 9.422 1.00 10.00 C ATOM 3 C ARG A 21 6.012 11.120 10.440 1.00 10.00 C ATOM 4 O ARG A 21 5.000 10.449 10.235 1.00 10.00 O ATOM 5 CB ARG A 21 7.505 9.732 8.987 1.00 10.00 C ATOM 6 CG ARG A 21 8.469 9.666 7.814 0.70 20.00 C ATOM 7 CD ARG A 21 8.724 8.229 7.388 0.70 20.00 C ATOM 8 NE ARG A 21 9.667 8.147 6.277 0.70 20.00 N ATOM 9 CZ ARG A 21 9.331 8.301 5.000 0.70 20.00 C ATOM 10 NH1 ARG A 21 8.070 8.545 4.668 0.70 20.00 N ATOM 11 NH2 ARG A 21 10.255 8.208 4.054 0.70 20.00 N ATOM 0 HA ARG A 21 6.805 11.715 8.552 1.00 10.00 H new ATOM 0 HB2 ARG A 21 7.944 9.204 9.834 1.00 10.00 H new ATOM 0 HB3 ARG A 21 6.590 9.203 8.721 1.00 10.00 H new ATOM 0 HG2 ARG A 21 8.062 10.230 6.974 0.70 20.00 H new ATOM 0 HG3 ARG A 21 9.412 10.139 8.089 0.70 20.00 H new ATOM 0 HD2 ARG A 21 9.112 7.663 8.235 0.70 20.00 H new ATOM 0 HD3 ARG A 21 7.782 7.764 7.099 0.70 20.00 H new ATOM 0 HE ARG A 21 10.646 7.960 6.494 0.70 20.00 H new ATOM 0 HH11 ARG A 21 7.356 8.615 5.393 0.70 20.00 H new ATOM 0 HH12 ARG A 21 7.814 8.663 3.688 0.70 20.00 H new ATOM 0 HH21 ARG A 21 11.225 8.018 4.306 0.70 20.00 H new ATOM 0 HH22 ARG A 21 9.996 8.326 3.075 0.70 20.00 H new TER HETATM 12 U U B 1 9.074 7.848 5.000 1.00 10.00 U TER """ def exercise(pdb_poor_str, i_pdb, d_min = 1.0, resolution_factor = 0.1): """ Fit one residue. There is a huge heavy atom nearby that overlaps with a plausible rotamer. With H. """ # t = mmtbx.refinement.real_space.setup_test( pdb_answer = pdb_answer, pdb_poor = pdb_poor_str, i_pdb = i_pdb, d_min = d_min, residues = ["ARG"], resolution_factor = resolution_factor) # result = mmtbx.refinement.real_space.fit_residues.run( pdb_hierarchy = t.ph_poor, 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) result.pdb_hierarchy.write_pdb_file(file_name = "refined_%s.pdb"%str(i_pdb)) # mmtbx.refinement.real_space.check_sites_match( ph_answer = t.ph_answer, ph_refined = result.pdb_hierarchy, tol = 0.15) if(__name__ == "__main__"): t0 = time.time() for i_pdb, pdb_poor_str in enumerate( [pdb_poor0, pdb_poor1, pdb_poor2, pdb_poor3]): exercise( pdb_poor_str = pdb_poor_str, i_pdb = i_pdb) print("Time: %6.4f"%(time.time()-t0))