from __future__ import division from cctbx.array_family import flex from libtbx import adopt_init_args import iotbx.pdb import iotbx.ccp4_map import mmtbx.refinement.real_space import mmtbx.refinement.real_space.fit_residue from mmtbx.rotamer.rotamer_eval import RotamerEval import time, sys class manager(object): def __init__(self, structure_monitor, mon_lib_srv, map_cc_all_threshold = 0.8, map_cc_sidechain_threshold=0.8, use_slope = True, use_torsion_search = True, use_rotamer_iterator = True, torsion_search_all_start = 0, torsion_search_all_stop = 360, torsion_search_all_step = 1, torsion_search_local_start = -50, torsion_search_local_stop = 50, torsion_search_local_step = 5, log = None): adopt_init_args(self, locals()) if(self.log is None): self.log = sys.stdout self.special_position_indices = \ self.structure_monitor.xray_structure.special_position_indices() self.rotamer_manager = RotamerEval() self.atom_radius_to_negate_map_within = None if(self.structure_monitor.target_map_object.miller_array.d_min()>3.5): self.atom_radius_to_negate_map_within = 2.0 else: self.atom_radius_to_negate_map_within = 1.5 # self.selection_good = self.structure_monitor.map_cc_per_atom > 0.8 self.iselection_backbone=flex.size_t() for r in self.structure_monitor.residue_monitors: if(r.selection_backbone is not None): self.iselection_backbone.extend(r.selection_backbone) self.loop_over_residues() clash_list = self.structure_monitor.find_sidechain_clashes() if(clash_list.size()>0): self.loop_over_residues(iselection = clash_list, use_clash_filter=True) clash_list = self.structure_monitor.find_sidechain_clashes() if(clash_list.size()>0): self.loop_over_residues(iselection = clash_list, use_clash_filter=True, use_torsion_search=True, use_rotamer_iterator=False) #### # TODO: attemp to search valid rotamer outliers #for r in self.structure_monitor.residue_monitors: # print r.id_str, r.map_cc_all, r.map_cc_backbone, r.map_cc_sidechain # if(r.map_cc_backbone>0.9 and r.map_cc_sidechain<0.5): # print r.id_str #### def on_special_position(self, sm_residue): if(self.special_position_indices.size()==0): return False for i_seq in sm_residue.selection_all: if(i_seq in self.special_position_indices): return True return False def loop_over_residues(self, iselection = None, use_clash_filter = False, debug = False, use_slope = None, use_torsion_search = None, use_rotamer_iterator = None): if(use_slope is None): use_slope = self.use_slope if(use_torsion_search is None): use_torsion_search = self.use_torsion_search if(use_rotamer_iterator is None): use_rotamer_iterator = self.use_rotamer_iterator sm = self.structure_monitor xrs = sm.xray_structure.deep_copy_scatterers() sites_cart = sm.xray_structure.sites_cart() get_class = iotbx.pdb.common_residue_names_get_class for i_res, r in enumerate(sm.residue_monitors): if(iselection is not None and not i_res in iselection): continue if(get_class(r.residue.resname) != "common_amino_acid"): continue go = r.rotamer_status=="OUTLIER" or \ r.map_cc_all < self.map_cc_all_threshold or \ r.map_cc_sidechain < self.map_cc_sidechain_threshold or \ use_clash_filter if(go): if(self.on_special_position(sm_residue=r)): continue iselection_n_external=None iselection_c_external=None if(i_res!=0 and i_res!=len(sm.residue_monitors)-1): iselection_c_external = sm.residue_monitors[i_res-1].selection_c iselection_n_external = sm.residue_monitors[i_res+1].selection_n elif(i_res==0 and len(sm.residue_monitors)>1): iselection_n_external = sm.residue_monitors[i_res+1].selection_n elif(i_res==len(sm.residue_monitors)-1 and len(sm.residue_monitors)>1): iselection_c_external = sm.residue_monitors[i_res-1].selection_c #print r.residue.resname, r.residue.resseq #t0=time.time() negate_selection = mmtbx.refinement.real_space.selection_around_to_negate( xray_structure = xrs, selection_within_radius = 5, # XXX make residue dependent !!!! iselection = r.residue.atoms().extract_i_seq(), selection_good = self.selection_good, iselection_backbone = self.iselection_backbone, iselection_n_external = iselection_n_external, iselection_c_external = iselection_c_external) #print "sel: %6.4f"%(time.time()-t0) target_map_ = mmtbx.refinement.real_space.\ negate_map_around_selected_atoms_except_selected_atoms( xray_structure = xrs, map_data = sm.target_map_object.data.deep_copy(), negate_selection = negate_selection, atom_radius = self.atom_radius_to_negate_map_within) #print "neg: %6.4f"%(time.time()-t0) if(debug): # DEBUG iotbx.ccp4_map.write_ccp4_map( file_name = "AMap.map", unit_cell = sm.xray_structure.unit_cell(), space_group = sm.xray_structure.space_group(), gridding_first = (0,0,0), gridding_last = tuple(sm.target_map_object.crystal_gridding.n_real()), map_data = target_map_, labels = flex.std_string(["DEBUG"])) mmtbx.refinement.real_space.fit_residue.manager( target_map = target_map_, mon_lib_srv = self.mon_lib_srv, special_position_settings = xrs.special_position_settings(), residue = r.residue, sites_cart_all = sites_cart, rotamer_manager = self.rotamer_manager, use_clash_filter = use_clash_filter, debug = debug, use_slope = use_slope, use_torsion_search = use_torsion_search, use_rotamer_iterator = use_rotamer_iterator, torsion_search_all_start = self.torsion_search_all_start, torsion_search_all_stop = self.torsion_search_all_stop , torsion_search_all_step = self.torsion_search_all_step , torsion_search_local_start = self.torsion_search_local_start, torsion_search_local_stop = self.torsion_search_local_stop, torsion_search_local_step = self.torsion_search_local_step, log = self.log) sites_cart = sites_cart.set_selected(r.residue.atoms().extract_i_seq(), r.residue.atoms().extract_xyz()) xrs.set_sites_cart(sites_cart) #print "ref: %6.4f"%(time.time()-t0) sm.update(xray_structure = xrs, accept_as_is=False)