from __future__ import absolute_import, division, print_function import time import iotbx.pdb import mmtbx.utils from scitbx.array_family import flex from cctbx import maptbx from libtbx import adopt_init_args from mmtbx import monomer_library import mmtbx.refinement.real_space.explode_and_refine pdb_str_answer = """\ CRYST1 29.475 46.191 27.490 90.00 90.00 90.00 P 21 21 21 HELIX 1 1 ALA E 1 ALA E 16 1 16 ATOM 1 N ALA E 1 14.622 35.477 13.274 1.00 40.00 N ATOM 2 CA ALA E 1 14.323 35.055 14.635 1.00 40.00 C ATOM 3 C ALA E 1 13.442 33.808 14.656 1.00 40.00 C ATOM 4 O ALA E 1 13.848 32.796 15.227 1.00 40.00 O ATOM 5 CB ALA E 1 13.675 36.191 15.414 1.00 40.00 C ATOM 6 N ALA E 2 12.256 33.870 14.012 1.00 40.00 N ATOM 7 CA ALA E 2 11.288 32.768 13.916 1.00 40.00 C ATOM 8 C ALA E 2 11.847 31.573 13.125 1.00 40.00 C ATOM 9 O ALA E 2 11.553 30.422 13.462 1.00 40.00 O ATOM 10 CB ALA E 2 10.000 33.267 13.276 1.00 40.00 C ATOM 11 N ALA E 3 12.664 31.856 12.084 1.00 40.00 N ATOM 12 CA ALA E 3 13.313 30.854 11.231 1.00 40.00 C ATOM 13 C ALA E 3 14.391 30.082 11.994 1.00 40.00 C ATOM 14 O ALA E 3 14.616 28.906 11.687 1.00 40.00 O ATOM 15 CB ALA E 3 13.915 31.517 10.000 1.00 40.00 C ATOM 16 N ALA E 4 15.063 30.744 12.976 1.00 40.00 N ATOM 17 CA ALA E 4 16.089 30.116 13.822 1.00 40.00 C ATOM 18 C ALA E 4 15.441 29.043 14.703 1.00 40.00 C ATOM 19 O ALA E 4 15.888 27.897 14.671 1.00 40.00 O ATOM 20 CB ALA E 4 16.785 31.160 14.683 1.00 40.00 C ATOM 21 N ALA E 5 14.338 29.398 15.423 1.00 40.00 N ATOM 22 CA ALA E 5 13.573 28.488 16.298 1.00 40.00 C ATOM 23 C ALA E 5 13.042 27.288 15.513 1.00 40.00 C ATOM 24 O ALA E 5 12.981 26.179 16.048 1.00 40.00 O ATOM 25 CB ALA E 5 12.433 29.233 16.975 1.00 40.00 C ATOM 26 N ALA E 6 12.715 27.518 14.221 1.00 40.00 N ATOM 27 CA ALA E 6 12.258 26.514 13.260 1.00 40.00 C ATOM 28 C ALA E 6 13.440 25.620 12.865 1.00 40.00 C ATOM 29 O ALA E 6 13.361 24.405 13.060 1.00 40.00 O ATOM 30 CB ALA E 6 11.664 27.193 12.032 1.00 40.00 C ATOM 31 N ALA E 7 14.556 26.234 12.374 1.00 40.00 N ATOM 32 CA ALA E 7 15.788 25.543 11.962 1.00 40.00 C ATOM 33 C ALA E 7 16.411 24.694 13.075 1.00 40.00 C ATOM 34 O ALA E 7 16.954 23.625 12.782 1.00 40.00 O ATOM 35 CB ALA E 7 16.806 26.540 11.433 1.00 40.00 C ATOM 36 N ALA E 8 16.327 25.168 14.343 1.00 40.00 N ATOM 37 CA ALA E 8 16.846 24.459 15.515 1.00 40.00 C ATOM 38 C ALA E 8 16.009 23.197 15.768 1.00 40.00 C ATOM 39 O ALA E 8 16.568 22.097 15.858 1.00 40.00 O ATOM 40 CB ALA E 8 16.833 25.368 16.742 1.00 40.00 C ATOM 41 N ALA E 9 14.664 23.357 15.803 1.00 40.00 N ATOM 42 CA ALA E 9 13.716 22.261 15.994 1.00 40.00 C ATOM 43 C ALA E 9 13.754 21.279 14.822 1.00 40.00 C ATOM 44 O ALA E 9 13.654 20.075 15.051 1.00 40.00 O ATOM 45 CB ALA E 9 12.314 22.805 16.193 1.00 40.00 C ATOM 46 N ALA E 10 13.942 21.791 13.578 1.00 40.00 N ATOM 47 CA ALA E 10 14.063 20.985 12.357 1.00 40.00 C ATOM 48 C ALA E 10 15.322 20.116 12.421 1.00 40.00 C ATOM 49 O ALA E 10 15.235 18.910 12.169 1.00 40.00 O ATOM 50 CB ALA E 10 14.105 21.881 11.130 1.00 40.00 C ATOM 51 N ALA E 11 16.480 20.722 12.803 1.00 40.00 N ATOM 52 CA ALA E 11 17.754 20.018 12.967 1.00 40.00 C ATOM 53 C ALA E 11 17.631 18.976 14.089 1.00 40.00 C ATOM 54 O ALA E 11 18.074 17.837 13.908 1.00 40.00 O ATOM 55 CB ALA E 11 18.870 21.004 13.279 1.00 40.00 C ATOM 56 N ALA E 12 16.972 19.356 15.217 1.00 40.00 N ATOM 57 CA ALA E 12 16.721 18.483 16.371 1.00 40.00 C ATOM 58 C ALA E 12 15.851 17.277 15.972 1.00 40.00 C ATOM 59 O ALA E 12 16.201 16.140 16.310 1.00 40.00 O ATOM 60 CB ALA E 12 16.052 19.269 17.490 1.00 40.00 C ATOM 61 N ALA E 13 14.748 17.535 15.215 1.00 40.00 N ATOM 62 CA ALA E 13 13.821 16.516 14.708 1.00 40.00 C ATOM 63 C ALA E 13 14.530 15.563 13.752 1.00 40.00 C ATOM 64 O ALA E 13 14.266 14.360 13.793 1.00 40.00 O ATOM 65 CB ALA E 13 12.636 17.173 14.008 1.00 40.00 C ATOM 66 N ALA E 14 15.437 16.112 12.903 1.00 40.00 N ATOM 67 CA ALA E 14 16.246 15.367 11.939 1.00 40.00 C ATOM 68 C ALA E 14 17.277 14.511 12.676 1.00 40.00 C ATOM 69 O ALA E 14 17.512 13.363 12.286 1.00 40.00 O ATOM 70 CB ALA E 14 16.942 16.329 10.986 1.00 40.00 C ATOM 71 N ALA E 15 17.863 15.069 13.767 1.00 40.00 N ATOM 72 CA ALA E 15 18.847 14.407 14.629 1.00 40.00 C ATOM 73 C ALA E 15 18.213 13.257 15.427 1.00 40.00 C ATOM 74 O ALA E 15 18.922 12.322 15.816 1.00 40.00 O ATOM 75 CB ALA E 15 19.475 15.418 15.573 1.00 40.00 C ATOM 76 N ALA E 16 16.879 13.325 15.652 1.00 40.00 N ATOM 77 CA ALA E 16 16.099 12.317 16.370 1.00 40.00 C ATOM 78 C ALA E 16 15.822 11.106 15.488 1.00 40.00 C ATOM 79 O ALA E 16 15.658 10.000 15.999 1.00 40.00 O ATOM 80 CB ALA E 16 14.790 12.918 16.852 1.00 40.00 C TER END """ pdb_str_poor = """\ CRYST1 29.475 46.191 27.490 90.00 90.00 90.00 P 21 21 21 ATOM 1 N ALA E 1 17.517 34.071 6.538 1.00 40.00 N ATOM 2 CA ALA E 1 17.992 35.348 7.004 1.00 40.00 C ATOM 3 C ALA E 1 16.863 35.986 7.792 1.00 40.00 C ATOM 4 O ALA E 1 16.713 37.242 7.909 1.00 40.00 O ATOM 5 CB ALA E 1 18.477 36.116 5.812 1.00 40.00 C ATOM 6 N ALA E 2 16.080 35.113 8.348 1.00 40.00 N ATOM 7 CA ALA E 2 15.254 35.581 9.495 1.00 40.00 C ATOM 8 C ALA E 2 15.628 35.262 10.863 1.00 40.00 C ATOM 9 O ALA E 2 16.066 36.143 11.629 1.00 40.00 O ATOM 10 CB ALA E 2 13.821 35.144 9.297 1.00 40.00 C ATOM 11 N ALA E 3 15.670 34.035 11.221 1.00 40.00 N ATOM 12 CA ALA E 3 15.746 33.569 12.729 1.00 40.00 C ATOM 13 C ALA E 3 16.380 32.197 13.043 1.00 40.00 C ATOM 14 O ALA E 3 17.557 32.017 13.009 1.00 40.00 O ATOM 15 CB ALA E 3 14.390 33.574 13.297 1.00 40.00 C ATOM 16 N ALA E 4 15.437 31.334 13.516 1.00 40.00 N ATOM 17 CA ALA E 4 15.810 29.953 13.900 1.00 40.00 C ATOM 18 C ALA E 4 14.876 28.948 13.219 1.00 40.00 C ATOM 19 O ALA E 4 15.088 28.561 12.135 1.00 40.00 O ATOM 20 CB ALA E 4 15.807 29.747 15.562 1.00 40.00 C ATOM 21 N ALA E 5 13.827 28.582 13.930 1.00 40.00 N ATOM 22 CA ALA E 5 12.803 27.643 13.582 1.00 40.00 C ATOM 23 C ALA E 5 11.925 27.972 12.295 1.00 40.00 C ATOM 24 O ALA E 5 11.311 29.016 12.217 1.00 40.00 O ATOM 25 CB ALA E 5 11.884 27.496 14.800 1.00 40.00 C ATOM 26 N ALA E 6 11.824 27.002 11.326 1.00 40.00 N ATOM 27 CA ALA E 6 11.579 27.271 9.948 1.00 40.00 C ATOM 28 C ALA E 6 10.688 26.172 9.315 1.00 40.00 C ATOM 29 O ALA E 6 9.810 26.435 8.479 1.00 40.00 O ATOM 30 CB ALA E 6 12.892 27.434 9.163 1.00 40.00 C ATOM 31 N ALA E 7 10.985 24.936 9.568 1.00 40.00 N ATOM 32 CA ALA E 7 10.223 23.915 8.805 1.00 40.00 C ATOM 33 C ALA E 7 9.182 23.205 9.603 1.00 40.00 C ATOM 34 O ALA E 7 7.945 23.417 9.434 1.00 40.00 O ATOM 35 CB ALA E 7 11.183 22.804 8.200 1.00 40.00 C ATOM 36 N ALA E 8 9.745 22.435 10.542 1.00 40.00 N ATOM 37 CA ALA E 8 9.210 21.425 11.476 1.00 40.00 C ATOM 38 C ALA E 8 10.256 20.419 11.733 1.00 40.00 C ATOM 39 O ALA E 8 9.992 19.490 12.460 1.00 40.00 O ATOM 40 CB ALA E 8 7.965 20.817 10.947 1.00 40.00 C ATOM 41 N ALA E 9 11.466 20.737 11.268 1.00 40.00 N ATOM 42 CA ALA E 9 12.607 19.889 11.232 1.00 40.00 C ATOM 43 C ALA E 9 12.924 19.328 12.523 1.00 40.00 C ATOM 44 O ALA E 9 12.790 20.050 13.539 1.00 40.00 O ATOM 45 CB ALA E 9 13.739 20.662 10.656 1.00 40.00 C ATOM 46 N ALA E 10 13.495 18.150 12.482 1.00 40.00 N ATOM 47 CA ALA E 10 14.007 17.595 13.654 1.00 40.00 C ATOM 48 C ALA E 10 15.157 16.724 13.724 1.00 40.00 C ATOM 49 O ALA E 10 15.159 16.000 14.620 1.00 40.00 O ATOM 50 CB ALA E 10 12.870 16.878 14.366 1.00 40.00 C ATOM 51 N ALA E 11 16.092 16.782 12.766 1.00 40.00 N ATOM 52 CA ALA E 11 17.076 15.791 12.430 1.00 40.00 C ATOM 53 C ALA E 11 16.462 14.506 11.790 1.00 40.00 C ATOM 54 O ALA E 11 15.459 14.602 11.077 1.00 40.00 O ATOM 55 CB ALA E 11 17.943 15.352 13.622 1.00 40.00 C ATOM 56 N ALA E 12 17.191 13.458 11.773 1.00 40.00 N ATOM 57 CA ALA E 12 16.985 12.246 11.074 1.00 40.00 C ATOM 58 C ALA E 12 17.956 11.169 11.712 1.00 40.00 C ATOM 59 O ALA E 12 18.839 10.657 11.173 1.00 40.00 O ATOM 60 CB ALA E 12 17.278 12.440 9.655 1.00 40.00 C ATOM 61 N ALA E 13 17.693 10.781 12.936 1.00 40.00 N ATOM 62 CA ALA E 13 18.559 9.862 13.648 1.00 40.00 C ATOM 63 C ALA E 13 17.678 8.677 14.105 1.00 40.00 C ATOM 64 O ALA E 13 16.810 8.236 13.332 1.00 40.00 O ATOM 65 CB ALA E 13 19.221 10.551 14.826 1.00 40.00 C ATOM 66 N ALA E 14 17.647 8.453 15.439 1.00 40.00 N ATOM 67 CA ALA E 14 16.666 7.551 16.066 1.00 40.00 C ATOM 68 C ALA E 14 15.298 8.147 16.400 1.00 40.00 C ATOM 69 O ALA E 14 14.633 7.785 17.376 1.00 40.00 O ATOM 70 CB ALA E 14 17.224 7.034 17.308 1.00 40.00 C ATOM 71 N ALA E 15 14.855 9.000 15.485 1.00 40.00 N ATOM 72 CA ALA E 15 13.517 9.710 15.635 1.00 40.00 C ATOM 73 C ALA E 15 12.304 8.858 15.586 1.00 40.00 C ATOM 74 O ALA E 15 11.625 8.812 14.564 1.00 40.00 O ATOM 75 CB ALA E 15 13.302 10.842 14.526 1.00 40.00 C ATOM 76 N ALA E 16 12.014 8.140 16.649 1.00 40.00 N ATOM 77 CA ALA E 16 11.279 6.863 16.560 1.00 40.00 C ATOM 78 C ALA E 16 10.003 6.986 17.409 1.00 40.00 C ATOM 79 O ALA E 16 9.883 8.020 18.086 1.00 40.00 O ATOM 80 CB ALA E 16 12.188 5.653 16.999 1.00 40.00 C TER """ def ccp4_map(crystal_symmetry, file_name, map_data): from iotbx import mrcfile mrcfile.write_ccp4_map( file_name=file_name, unit_cell=crystal_symmetry.unit_cell(), space_group=crystal_symmetry.space_group(), #gridding_first=(0,0,0),# This causes a bug (map gets shifted) #gridding_last=n_real, # This causes a bug (map gets shifted) map_data=map_data, labels=flex.std_string([""])) class scorer(object): def __init__(self, pdb_hierarchy, unit_cell, map_data): adopt_init_args(self, locals()) self.sites_cart = self.pdb_hierarchy.atoms().extract_xyz() self.target = maptbx.real_space_target_simple( unit_cell = self.unit_cell, density_map = self.map_data, sites_cart = self.sites_cart) def update(self, sites_cart): target = maptbx.real_space_target_simple( unit_cell = self.unit_cell, density_map = self.map_data, sites_cart = sites_cart) if(target > self.target): self.target = target self.sites_cart = sites_cart print(self.target, target) # XXX for debugging def run(prefix="tst_00"): # Good answer model pdb_file_name_answer = "%s_answer.pdb"%prefix pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str_answer) pdb_inp.write_pdb_file(file_name="%s_answer.pdb"%prefix) ph_answer = pdb_inp.construct_hierarchy() ph_answer.atoms().reset_i_seq() xrs_answer = pdb_inp.xray_structure_simple() # Poor model that we want to refine so it matches the answer pdb_file_name_poor = "%s_poor.pdb"%prefix pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str_poor) pdb_inp.write_pdb_file(file_name="%s_poor.pdb"%prefix) ph_poor = pdb_inp.construct_hierarchy() ph_poor.atoms().reset_i_seq() xrs_poor = pdb_inp.xray_structure_simple() # Initialize states accumulator states = mmtbx.utils.states(pdb_hierarchy=ph_answer) states.add(sites_cart = xrs_poor.sites_cart()) # Compute target map fc = xrs_answer.structure_factors(d_min=3.5).f_calc() fft_map = fc.fft_map(resolution_factor = 0.25) fft_map.apply_sigma_scaling() target_map_data = fft_map.real_map_unpadded() ccp4_map(crystal_symmetry=fc.crystal_symmetry(), file_name="map.ccp4", map_data=target_map_data) # Output map coefficients mtz_dataset = fc.as_mtz_dataset(column_root_label="FC") mtz_object = mtz_dataset.mtz_object() mtz_object.write(file_name = "map.mtz") # Build geometry restraints params = monomer_library.pdb_interpretation.master_params.extract() #params.nonbonded_weight=200 #params.peptide_link.ramachandran_restraints=True #params.peptide_link.rama_potential="emsley" processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = monomer_library.server.server(), ener_lib = monomer_library.server.ener_lib(), raw_records = pdb_str_poor, params = params, strict_conflict_handling = True, force_symmetry = True, log = None) geometry = processed_pdb_file.geometry_restraints_manager( show_energies = False, plain_pairs_radius = 5, assume_hydrogens_all_missing = True) restraints_manager = mmtbx.restraints.manager( geometry = geometry, normalization = True) # Do real-space refinement t0=time.time() ear = mmtbx.refinement.real_space.explode_and_refine.run( xray_structure = xrs_poor, pdb_hierarchy = ph_poor, map_data = target_map_data, restraints_manager = restraints_manager, states = states, nproc=1) print("Time: %6.4f"%(time.time()-t0)) ear.pdb_hierarchy.write_pdb_file(file_name="%s_refined.pdb"%prefix) states.write(file_name="%s_refined_all_states.pdb"%prefix) if (__name__ == "__main__"): run() print("OK")