from __future__ import absolute_import, division, print_function import time import mmtbx.refinement.real_space.fit_residues import mmtbx.refinement.real_space from mmtbx.rotamer.rotamer_eval import RotamerEval rotamer_eval = RotamerEval() pdb_poor = """\ CRYST1 36.039 33.133 33.907 90.00 90.00 90.00 P 1 ATOM 369 N GLN A 23 12.323 18.703 12.553 1.00 0.00 N ATOM 370 CA GLN A 23 12.181 19.413 11.273 1.00 0.00 C ATOM 371 C GLN A 23 12.652 18.596 10.060 1.00 0.00 C ATOM 372 O GLN A 23 12.591 19.108 8.942 1.00 0.00 O ATOM 373 CB GLN A 23 12.912 20.768 11.283 1.00 0.00 C ATOM 374 CG GLN A 23 12.633 21.683 12.491 1.00 0.00 C ATOM 375 CD GLN A 23 11.920 22.989 12.156 1.00 0.00 C ATOM 376 OE1 GLN A 23 10.721 23.090 12.304 1.00 0.00 O ATOM 377 NE2 GLN A 23 12.465 23.786 11.261 1.00 0.00 N ATOM 378 H GLN A 23 13.024 19.067 13.190 1.00 0.00 H ATOM 379 HA GLN A 23 11.130 19.627 11.113 1.00 0.00 H ATOM 380 HB2 GLN A 23 13.985 20.581 11.232 1.00 0.00 H ATOM 381 HB3 GLN A 23 12.646 21.297 10.366 1.00 0.00 H ATOM 382 HG2 GLN A 23 12.047 21.165 13.248 1.00 0.00 H ATOM 383 HG3 GLN A 23 13.584 21.937 12.941 1.00 0.00 H ATOM 384 HE21 GLN A 23 13.373 23.615 10.881 1.00 0.00 H ATOM 385 HE22 GLN A 23 11.850 24.502 10.909 1.00 0.00 H ATOM 386 N LYS A 24 13.104 17.339 10.235 1.00 0.00 N ATOM 387 CA LYS A 24 13.177 16.380 9.120 1.00 0.00 C ATOM 388 C LYS A 24 12.362 15.085 9.207 1.00 0.00 C ATOM 389 O LYS A 24 12.509 14.250 8.322 1.00 0.00 O ATOM 390 CB LYS A 24 14.585 16.121 8.540 1.00 0.00 C ATOM 391 CG LYS A 24 15.222 17.335 7.850 1.00 0.00 C ATOM 392 CD LYS A 24 16.336 16.882 6.887 1.00 0.00 C ATOM 393 CE LYS A 24 16.513 17.834 5.699 1.00 0.00 C ATOM 394 NZ LYS A 24 16.975 19.185 6.105 1.00 0.00 N ATOM 395 H LYS A 24 13.162 16.988 11.180 1.00 0.00 H ATOM 396 HA LYS A 24 12.652 16.912 8.352 1.00 0.00 H ATOM 397 HB2 LYS A 24 15.242 15.676 9.281 1.00 0.00 H ATOM 398 HB3 LYS A 24 14.484 15.365 7.765 1.00 0.00 H ATOM 399 HG2 LYS A 24 14.449 17.841 7.271 1.00 0.00 H ATOM 400 HG3 LYS A 24 15.616 18.028 8.593 1.00 0.00 H ATOM 401 HD2 LYS A 24 17.272 16.766 7.432 1.00 0.00 H ATOM 402 HD3 LYS A 24 16.079 15.911 6.457 1.00 0.00 H ATOM 403 HE2 LYS A 24 17.224 17.384 5.000 1.00 0.00 H ATOM 404 HE3 LYS A 24 15.550 17.907 5.179 1.00 0.00 H ATOM 405 HZ1 LYS A 24 17.842 19.131 6.619 1.00 0.00 H ATOM 406 HZ2 LYS A 24 17.127 19.760 5.284 1.00 0.00 H ATOM 407 HZ3 LYS A 24 16.271 19.638 6.677 1.00 0.00 H ATOM 408 N ILE A 25 11.585 14.851 10.259 1.00 0.00 N ATOM 409 CA ILE A 25 10.847 13.577 10.386 1.00 0.00 C ATOM 410 C ILE A 25 9.429 13.760 10.915 1.00 0.00 C ATOM 411 O ILE A 25 8.548 12.967 10.595 1.00 0.00 O ATOM 412 CB ILE A 25 11.688 12.555 11.204 1.00 0.00 C ATOM 413 CG1 ILE A 25 12.819 11.934 10.342 1.00 0.00 C ATOM 414 CG2 ILE A 25 10.821 11.423 11.770 1.00 0.00 C ATOM 415 CD1 ILE A 25 14.186 12.604 10.544 1.00 0.00 C ATOM 416 H ILE A 25 11.460 15.580 10.945 1.00 0.00 H ATOM 417 HA ILE A 25 10.686 13.155 9.391 1.00 0.00 H ATOM 418 HB ILE A 25 12.120 13.047 12.071 1.00 0.00 H ATOM 419 HG12 ILE A 25 12.951 10.880 10.585 1.00 0.00 H ATOM 420 HG13 ILE A 25 12.546 11.962 9.288 1.00 0.00 H ATOM 421 HG21 ILE A 25 10.166 11.080 10.978 1.00 0.00 H ATOM 422 HG22 ILE A 25 11.417 10.590 12.132 1.00 0.00 H ATOM 423 HG23 ILE A 25 10.183 11.789 12.572 1.00 0.00 H ATOM 424 HD11 ILE A 25 14.120 13.685 10.454 1.00 0.00 H ATOM 425 HD12 ILE A 25 14.564 12.366 11.533 1.00 0.00 H ATOM 426 HD13 ILE A 25 14.886 12.233 9.796 1.00 0.00 H ATOM 427 N HIS A 26 9.285 14.608 11.927 1.00 0.00 N ATOM 428 CA HIS A 26 8.067 14.661 12.719 1.00 0.00 C ATOM 429 C HIS A 26 7.127 15.775 12.283 1.00 0.00 C ATOM 430 O HIS A 26 6.188 15.506 11.549 1.00 0.00 O ATOM 431 CB HIS A 26 8.452 14.761 14.176 1.00 0.00 C ATOM 432 CG HIS A 26 9.098 13.493 14.680 1.00 0.00 C ATOM 433 ND1 HIS A 26 8.446 12.311 14.909 1.00 0.00 N ATOM 434 CD2 HIS A 26 10.403 13.310 15.045 1.00 0.00 C ATOM 435 CE1 HIS A 26 9.327 11.419 15.377 1.00 0.00 C ATOM 436 NE2 HIS A 26 10.547 11.994 15.547 1.00 0.00 N ATOM 437 H HIS A 26 10.027 15.264 12.126 1.00 0.00 H ATOM 438 HA HIS A 26 7.503 13.734 12.601 1.00 0.00 H ATOM 439 HB2 HIS A 26 9.108 15.619 14.347 1.00 0.00 H ATOM 440 HB3 HIS A 26 7.511 14.924 14.690 1.00 0.00 H ATOM 441 HD1 HIS A 26 7.449 12.149 14.789 1.00 0.00 H ATOM 442 HD2 HIS A 26 11.175 14.064 14.986 1.00 0.00 H ATOM 443 HE1 HIS A 26 9.055 10.402 15.640 1.00 0.00 H ATOM 444 N SER A 27 7.594 17.013 12.432 1.00 0.00 N ATOM 445 CA SER A 27 7.087 18.141 11.666 1.00 0.00 C ATOM 446 C SER A 27 8.277 18.930 11.142 1.00 0.00 C ATOM 447 O SER A 27 8.951 19.586 11.932 1.00 0.00 O ATOM 448 CB SER A 27 6.114 18.989 12.498 1.00 0.00 C ATOM 449 OG SER A 27 5.000 19.320 11.696 1.00 0.00 O ATOM 450 H SER A 27 8.440 17.164 12.960 1.00 0.00 H ATOM 451 HA SER A 27 6.539 17.768 10.798 1.00 0.00 H ATOM 452 HB2 SER A 27 5.756 18.405 13.348 1.00 0.00 H ATOM 453 HB3 SER A 27 6.592 19.896 12.873 1.00 0.00 H ATOM 454 HG SER A 27 5.170 20.114 11.183 1.00 0.00 H """ pdb_answer = """ CRYST1 36.039 33.133 33.907 90.00 90.00 90.00 P 1 SCALE1 0.027748 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029492 0.00000 ATOM 1 N GLN A 23 12.323 18.703 12.553 1.00 0.00 N ATOM 2 CA GLN A 23 12.181 19.413 11.273 1.00 0.00 C ATOM 3 C GLN A 23 12.652 18.596 10.060 1.00 0.00 C ATOM 4 O GLN A 23 12.591 19.108 8.942 1.00 0.00 O ATOM 5 CB GLN A 23 12.912 20.768 11.283 1.00 0.00 C ATOM 6 CG GLN A 23 12.601 21.700 12.470 1.00 0.00 C ATOM 7 CD GLN A 23 11.817 22.958 12.110 1.00 0.00 C ATOM 8 OE1 GLN A 23 10.614 22.913 11.968 1.00 0.00 O ATOM 9 NE2 GLN A 23 12.443 23.921 11.465 1.00 0.00 N ATOM 10 H GLN A 23 13.024 19.067 13.190 1.00 0.00 H ATOM 11 HA GLN A 23 11.130 19.627 11.113 1.00 0.00 H ATOM 12 HB2 GLN A 23 13.986 20.580 11.264 1.00 0.00 H ATOM 13 HB3 GLN A 23 12.671 21.284 10.352 1.00 0.00 H ATOM 14 HG2 GLN A 23 12.052 21.174 13.248 1.00 0.00 H ATOM 15 HG3 GLN A 23 13.543 22.015 12.900 1.00 0.00 H ATOM 16 HE21 GLN A 23 13.371 23.807 11.112 1.00 0.00 H ATOM 17 HE22 GLN A 23 11.873 24.724 11.256 1.00 0.00 H ATOM 18 N LYS A 24 13.104 17.339 10.235 1.00 0.00 N ATOM 19 CA LYS A 24 13.177 16.380 9.120 1.00 0.00 C ATOM 20 C LYS A 24 12.362 15.085 9.207 1.00 0.00 C ATOM 21 O LYS A 24 12.509 14.250 8.322 1.00 0.00 O ATOM 22 CB LYS A 24 14.585 16.121 8.540 1.00 0.00 C ATOM 23 CG LYS A 24 15.232 17.342 7.872 1.00 0.00 C ATOM 24 CD LYS A 24 16.382 16.900 6.946 1.00 0.00 C ATOM 25 CE LYS A 24 16.502 17.777 5.695 1.00 0.00 C ATOM 26 NZ LYS A 24 16.826 19.191 6.009 1.00 0.00 N ATOM 27 H LYS A 24 13.162 16.988 11.180 1.00 0.00 H ATOM 28 HA LYS A 24 12.652 16.912 8.352 1.00 0.00 H ATOM 29 HB2 LYS A 24 15.237 15.660 9.276 1.00 0.00 H ATOM 30 HB3 LYS A 24 14.481 15.378 7.753 1.00 0.00 H ATOM 31 HG2 LYS A 24 14.474 17.840 7.267 1.00 0.00 H ATOM 32 HG3 LYS A 24 15.594 18.038 8.627 1.00 0.00 H ATOM 33 HD2 LYS A 24 17.319 16.888 7.500 1.00 0.00 H ATOM 34 HD3 LYS A 24 16.195 15.886 6.584 1.00 0.00 H ATOM 35 HE2 LYS A 24 17.271 17.347 5.046 1.00 0.00 H ATOM 36 HE3 LYS A 24 15.551 17.722 5.151 1.00 0.00 H ATOM 37 HZ1 LYS A 24 16.876 19.746 5.167 1.00 0.00 H ATOM 38 HZ2 LYS A 24 16.110 19.586 6.608 1.00 0.00 H ATOM 39 HZ3 LYS A 24 17.710 19.246 6.503 1.00 0.00 H ATOM 40 N ILE A 25 11.585 14.851 10.259 1.00 0.00 N ATOM 41 CA ILE A 25 10.847 13.577 10.386 1.00 0.00 C ATOM 42 C ILE A 25 9.429 13.760 10.915 1.00 0.00 C ATOM 43 O ILE A 25 8.548 12.967 10.595 1.00 0.00 O ATOM 44 CB ILE A 25 11.688 12.555 11.204 1.00 0.00 C ATOM 45 CG1 ILE A 25 12.838 11.957 10.351 1.00 0.00 C ATOM 46 CG2 ILE A 25 10.826 11.407 11.744 1.00 0.00 C ATOM 47 CD1 ILE A 25 14.168 12.711 10.496 1.00 0.00 C ATOM 48 H ILE A 25 11.460 15.580 10.945 1.00 0.00 H ATOM 49 HA ILE A 25 10.686 13.155 9.391 1.00 0.00 H ATOM 50 HB ILE A 25 12.102 13.042 12.083 1.00 0.00 H ATOM 51 HG12 ILE A 25 13.033 10.925 10.641 1.00 0.00 H ATOM 52 HG13 ILE A 25 12.547 11.919 9.302 1.00 0.00 H ATOM 53 HG21 ILE A 25 11.483 10.708 12.248 1.00 0.00 H ATOM 54 HG22 ILE A 25 10.067 11.754 12.439 1.00 0.00 H ATOM 55 HG23 ILE A 25 10.352 10.863 10.930 1.00 0.00 H ATOM 56 HD11 ILE A 25 14.948 12.270 9.880 1.00 0.00 H ATOM 57 HD12 ILE A 25 14.035 13.744 10.191 1.00 0.00 H ATOM 58 HD13 ILE A 25 14.489 12.685 11.537 1.00 0.00 H ATOM 59 N HIS A 26 9.285 14.608 11.927 1.00 0.00 N ATOM 60 CA HIS A 26 8.067 14.661 12.719 1.00 0.00 C ATOM 61 C HIS A 26 7.127 15.775 12.283 1.00 0.00 C ATOM 62 O HIS A 26 6.188 15.506 11.549 1.00 0.00 O ATOM 63 CB HIS A 26 8.452 14.761 14.176 1.00 0.00 C ATOM 64 CG HIS A 26 9.094 13.491 14.681 1.00 0.00 C ATOM 65 ND1 HIS A 26 8.436 12.314 14.919 1.00 0.00 N ATOM 66 CD2 HIS A 26 10.400 13.302 15.039 1.00 0.00 C ATOM 67 CE1 HIS A 26 9.314 11.419 15.385 1.00 0.00 C ATOM 68 NE2 HIS A 26 10.539 11.987 15.546 1.00 0.00 N ATOM 69 H HIS A 26 10.027 15.264 12.126 1.00 0.00 H ATOM 70 HA HIS A 26 7.503 13.734 12.601 1.00 0.00 H ATOM 71 HB2 HIS A 26 9.111 15.617 14.346 1.00 0.00 H ATOM 72 HB3 HIS A 26 7.511 14.928 14.690 1.00 0.00 H ATOM 73 HD1 HIS A 26 7.437 12.157 14.805 1.00 0.00 H ATOM 74 HD2 HIS A 26 11.176 14.051 14.973 1.00 0.00 H ATOM 75 HE1 HIS A 26 9.038 10.404 15.654 1.00 0.00 H ATOM 76 N SER A 27 7.594 17.013 12.432 1.00 0.00 N ATOM 77 CA SER A 27 7.087 18.141 11.666 1.00 0.00 C ATOM 78 C SER A 27 8.277 18.930 11.142 1.00 0.00 C ATOM 79 O SER A 27 8.951 19.586 11.932 1.00 0.00 O ATOM 80 CB SER A 27 6.114 18.989 12.498 1.00 0.00 C ATOM 81 OG SER A 27 5.157 19.563 11.632 1.00 0.00 O ATOM 82 H SER A 27 8.440 17.164 12.960 1.00 0.00 H ATOM 83 HA SER A 27 6.539 17.768 10.798 1.00 0.00 H ATOM 84 HB2 SER A 27 5.586 18.348 13.207 1.00 0.00 H ATOM 85 HB3 SER A 27 6.637 19.770 13.054 1.00 0.00 H ATOM 86 HG SER A 27 4.531 20.102 12.122 1.00 0.00 H TER """ pdb_for_map = pdb_answer def count_outliers(h): n_outliers = 0 for model in h.models(): for chain in model.chains(): for residue_group in chain.residue_groups(): conformers = residue_group.conformers() for conformer in residue_group.conformers(): residue = conformer.only_residue() fl = rotamer_eval.evaluate_residue(residue = residue) if fl.strip().upper()=="OUTLIER": n_outliers += 1 return n_outliers def exercise(i_pdb=0, d_min = 3, resolution_factor = 0.1): """ Testing selections """ t = mmtbx.refinement.real_space.setup_test( pdb_answer = pdb_answer, pdb_poor = pdb_poor, i_pdb = i_pdb, d_min = d_min, residues = ["SER","HIS","ILE","LYS","GLN"], resolution_factor = resolution_factor, pdb_for_map = pdb_for_map) # assert count_outliers(t.ph_poor) == 3 assert count_outliers(t.ph_answer) == 0 # 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 = 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) result.pdb_hierarchy.write_pdb_file(file_name = "refined_%s.pdb"%str(i_pdb), crystal_symmetry = t.crystal_symmetry) assert count_outliers(result.pdb_hierarchy) == 0 # Now with selection t = mmtbx.refinement.real_space.setup_test( pdb_answer = pdb_answer, pdb_poor = pdb_poor, i_pdb = i_pdb, d_min = d_min, resolution_factor = resolution_factor, pdb_for_map = pdb_for_map) bselection = t.ph_poor.atom_selection_cache().selection('resid 23:25') 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, bselection = bselection, 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) result.pdb_hierarchy.write_pdb_file(file_name = "refined_%s.pdb"%str(i_pdb), crystal_symmetry = t.crystal_symmetry) assert count_outliers(result.pdb_hierarchy) == 1 if(__name__ == "__main__"): t0 = time.time() exercise() print("Time: %6.4f"%(time.time()-t0))