def validate_residues(self): from mmtbx.conformation_dependent_library import generate_protein_threes from mmtbx.rotamer import ramachandran_eval, rotamer_eval # this is so we generate rama_eval only once rama_eval = ramachandran_eval.RamachandranEval() rota_eval = rotamer_eval.RotamerEval() rotamer_id = rotamer_eval.RotamerID() # loads in the rotamer names threes = generate_protein_threes(hierarchy=self.pdb_hierarchy, include_non_linked=True, backbone_only=False, geometry=None) for i, three in enumerate(threes): if i == 0: self.residues.append( ValidationResidue(three, rama_eval, rota_eval, rotamer_id, index=0)) self.residues.append( ValidationResidue(three, rama_eval, rota_eval, rotamer_id)) if three.end: self.residues.append( ValidationResidue(three, rama_eval, rota_eval, rotamer_id, index=2))
def __init__(self, pdb_hierarchy, xray_structure, range_start=-10.0, range_stop=10.0, step=1.0, min_angle_between_solutions=0.5, name_hash=None, selection=None, log=None): if (log is None): log = sys.stdout self.log = log self.mon_lib_srv = mmtbx.monomer_library.server.server() self.unit_cell = xray_structure.unit_cell() self.exclude_free_r_reflections = False self.torsion_params = \ fit_rotamers.torsion_search_params().extract().torsion_search self.torsion_params.range_start = range_start self.torsion_params.range_stop = range_stop self.torsion_params.step = step self.torsion_params.min_angle_between_solutions = \ min_angle_between_solutions self.selection = selection if self.selection is None: sites_cart = pdb_hierarchy.atoms().extract_xyz() self.selection = flex.bool(len(sites_cart), True) self.c_alpha_hinges = torsion_utils.get_c_alpha_hinges( pdb_hierarchy=pdb_hierarchy, xray_structure=xray_structure, selection=self.selection) self.name_hash = name_hash if self.name_hash is None: self.name_hash = build_name_hash(pdb_hierarchy) from mmtbx.rotamer.sidechain_angles import SidechainAngles from mmtbx.rotamer import rotamer_eval self.sa = SidechainAngles(False) self.rotamer_id = rotamer_eval.RotamerID() self.rotamer_evaluator = rotamer_eval.RotamerEval( mon_lib_srv=self.mon_lib_srv) self.target_map_data = None self.residual_map_data = None
def update_restraints(hierarchy, geometry, # restraints_manager, current_geometry=None, # xray_structure!! sites_cart=None, rdl_proxies=None, esd_factor=1., exclude_backbone=False, assert_rotamer_found=False, rdl_selection=None, log=None, verbose=False, data_version="8000", ): assert data_version == "8000","data_version not recognized." assert not exclude_backbone loud=True and False if loud: verbose=1 from mmtbx.rotamer.sidechain_angles import SidechainAngles from mmtbx.rotamer import rotamer_eval from mmtbx.validation import rotalyze # def _set_or_reset_angle_restraints(geometry, lookup, use_rdl_weights=False, verbose=False, ): count = 0 for angle_proxy in geometry.angle_proxies: if angle_proxy.i_seqs in lookup: if verbose: print(" i_seqs %-15s initial %12.3f %12.3f" % ( angle_proxy.i_seqs, angle_proxy.angle_ideal, angle_proxy.weight, )) assert angle_proxy.angle_ideal<181 angle_proxy.angle_ideal = lookup[angle_proxy.i_seqs][0] if use_rdl_weights: angle_proxy.weight = esd_factor/lookup[angle_proxy.i_seqs][1]**2 if verbose: print(" i_seqs %-15s final %12.3f %12.3f" % ( angle_proxy.i_seqs, angle_proxy.angle_ideal, angle_proxy.weight, )) count += 1 return count # def _set_or_reset_dihedral_restraints(geometry, lookup, use_rdl_weights=False, verbose=False, ): count = 0 for angle_proxy in geometry.dihedral_proxies: if angle_proxy.i_seqs in lookup: if verbose: print(" i_seqs %-15s initial %12.3f %12.3f %s %d" % ( angle_proxy.i_seqs, angle_proxy.angle_ideal, angle_proxy.weight, angle_proxy.alt_angle_ideals, angle_proxy.periodicity, )) angle_proxy.angle_ideal = lookup[angle_proxy.i_seqs][0] if use_rdl_weights: angle_proxy.weight = esd_factor/lookup[angle_proxy.i_seqs][1]**2 angle_proxy.alt_angle_ideals=None angle_proxy.periodicity = lookup[angle_proxy.i_seqs][2] if verbose: print(" i_seqs %-15s final %12.3f %12.3f %s %d" % ( angle_proxy.i_seqs, angle_proxy.angle_ideal, angle_proxy.weight, angle_proxy.alt_angle_ideals, angle_proxy.periodicity, )) count += 1 return count # t0=time.time() sa = SidechainAngles(False) rotamer_id = rotamer_eval.RotamerID() rotamer_evaluator = rotamer_eval.RotamerEval(data_version=data_version) sites_cart = None if current_geometry: sites_cart = current_geometry.sites_cart() # if rdl_proxies is None: rdl_proxies = [] i_seqs_restraints = {} i_seqs_restraints_reverse = {} # def _alt_loc_atom_generator(residue_group, atom_group): atoms = [] for ag in residue_group.atom_groups(): if ag.altloc.strip()=="" or ag.altloc.strip()==atom_group.altloc.strip(): for atom in ag.atoms(): yield atom # for model in hierarchy.models(): #if verbose: print 'model: "%s"' % model.id for chain in model.chains(): #if verbose: print 'chain: "%s"' % chain.id for residue_group in chain.residue_groups(): all_dict = rotalyze.construct_complete_sidechain(residue_group) for atom_group in residue_group.atom_groups(): if rdl_selection is None: pass elif 'all' in rdl_selection: pass elif atom_group.resname in rdl_selection: pass else: continue rc = get_rotamer_data(atom_group, sa, rotamer_evaluator, rotamer_id, all_dict=all_dict, sites_cart=sites_cart, ) if rc is None: continue rotamer_name, chis, value = rc if verbose: chis_str = "[" if chis: for chi in chis: chis_str += " %6.1f," % chi chis_str = chis_str[:-1]+']' try: print(" %s %s %s %-5s %-60s %0.1f" % ( chain.id, atom_group.resname, residue_group.resseq, rotamer_name, chis_str, value, ), file=log) except TypeError as e: print(" %s %s %s %-5s %-60s %s" % ( chain.id, atom_group.resname, residue_group.resseq, rotamer_name, chis_str, value, ), file=log) if loud: print('exclude_backbone',exclude_backbone) if rotamer_name in ["OUTLIER"]: continue resname_lookup = substitute_residue_lookup.get(atom_group.resname, atom_group.resname, ) if rotamer_name not in rdl_database[resname_lookup]: if assert_rotamer_found: raise Sorry("rotamer %s not found in db" % rotamer_name) else: continue if loud: print('not outlier') if rotamer_name not in rdl_database[resname_lookup]: if loud: print("rotamer_name %s not in RDL db" % rotamer_name) continue if loud: print('rotamer_name %s found' % rotamer_name) restraints = rdl_database[resname_lookup][rotamer_name] defaults = rdl_database[resname_lookup]["default"] rdl_proxies.append(atom_group.id_str()) for names, values in restraints.items(): i_seqs = [] if exclude_backbone and names[1] in ["N", "CA", "C"]: continue for name in names: for atom in _alt_loc_atom_generator(residue_group, atom_group): if name.strip()==atom.name.strip(): i_seqs.append(atom.i_seq) break if len(i_seqs)!=len(names): continue i_seqs_restraints[tuple(i_seqs)] = values i_seqs.reverse() i_seqs_restraints[tuple(i_seqs)] = values if names in defaults: i_seqs_restraints_reverse[tuple(i_seqs)] = defaults[names] i_seqs.reverse() i_seqs_restraints_reverse[tuple(i_seqs)] = defaults[names] # if loud: for i, atom in enumerate(hierarchy.atoms()): print(i, atom.quote()) count = _set_or_reset_dihedral_restraints(geometry, i_seqs_restraints_reverse, #verbose=loud, ) count_d = _set_or_reset_dihedral_restraints(geometry, i_seqs_restraints, verbose=loud, ) count = _set_or_reset_angle_restraints(geometry, i_seqs_restraints_reverse, #verbose=loud, ) count_a = _set_or_reset_angle_restraints(geometry, i_seqs_restraints, verbose=loud, ) # print(" Number of angles, dihedrals RDL adjusted : %d, %d" % ( count_a, count_d, ), file=log) print(" Time to adjust : %0.1fs" % ( time.time()-t0), file=log) return rdl_proxies
def __init__(self, pdb_hierarchy, data_version="8000", outliers_only=False, show_errors=False, out=sys.stdout, quiet=False): validation.__init__(self) self.n_allowed = 0 self.n_favored = 0 from mmtbx.rotamer.sidechain_angles import SidechainAngles from mmtbx.rotamer import rotamer_eval from mmtbx.rotamer.rotamer_eval import RotamerID from mmtbx.validation import utils self.data_version = data_version # if self.data_version == "500": self.outlier_threshold = 0.01 if self.data_version == "8000": self.outlier_threshold = OUTLIER_THRESHOLD else: raise ValueError( "data_version given to RotamerEval not recognized (%s)." % data_version) sidechain_angles = SidechainAngles(show_errors) rotamer_evaluator = rotamer_eval.RotamerEval( data_version=data_version) rotamer_id = rotamer_eval.RotamerID() # loads in the rotamer names use_segids = utils.use_segids_in_place_of_chainids( hierarchy=pdb_hierarchy) current_rotamers = {} for model in pdb_hierarchy.models(): for chain in model.chains(): if use_segids: chain_id = utils.get_segid_as_chainid(chain=chain) else: chain_id = chain.id for rg in chain.residue_groups(): all_dict = construct_complete_sidechain(rg) for atom_group in rg.atom_groups(): coords = get_center(atom_group) resname = atom_group.resname occupancy = get_occupancy(atom_group) kwargs = { "chain_id" : chain_id, "resseq" : rg.resseq, "icode" : rg.icode, "altloc" : atom_group.altloc, "resname" : resname, "xyz" : coords, "occupancy" : occupancy, } atom_dict = all_dict.get(atom_group.altloc) res_key = get_residue_key(atom_group=atom_group) try: chis = sidechain_angles.measureChiAngles( atom_group, atom_dict)#.get(conformer.altloc)) except AttributeError: if show_errors: kwargs['incomplete'] = True result = rotamer(**kwargs) print >> out, '%s is missing some sidechain atoms' % \ result.id_str() self.results.append(result) continue if (chis is not None): if None in chis: continue cur_res = resname.lower().strip() if cur_res == 'mse': cur_res = 'met' value = rotamer_evaluator.evaluate(cur_res, chis) if value is not None: self.n_total += 1 kwargs['score'] = value * 100 wrap_chis = rotamer_id.wrap_chis(resname.strip(), chis, symmetry=False) sym_chis = wrap_chis[:] sym_chis = rotamer_id.wrap_sym(resname.strip(), sym_chis) evaluation = self.evaluateScore(value) kwargs['evaluation'] = evaluation if evaluation == "OUTLIER": kwargs['outlier'] = True kwargs['rotamer_name'] = evaluation else: kwargs['outlier'] = False kwargs['rotamer_name'] = rotamer_id.identify(resname, wrap_chis) #deal with unclassified rotamers if kwargs['rotamer_name'] == '': kwargs['rotamer_name'] = "UNCLASSIFIED" while (len(wrap_chis) < 4): wrap_chis.append(None) kwargs['chi_angles'] = wrap_chis result = rotamer(**kwargs) if (result.is_outlier()) or (not outliers_only): self.results.append(result) out_count, out_percent = self.get_outliers_count_and_fraction() self.out_percent = out_percent * 100.0
}, 'PHE': { 'm-10': { lookup['PHE'][2]: [-14.7, 19.8, 2] }, }, 'TYR': { 'm-10': { lookup['PHE'][2]: [-14.7, 20.2, 2] }, }, 'VAL': 1, } rotamer_evaluator = rotamer_eval.RotamerEval(data_version='8000') rotamer_id = rotamer_eval.RotamerID() # loads in the rotamer names def generate_chis( chis=None, n=2, step=10, depth=0, starting_chis=None, ): if chis is None: if starting_chis: chis = [] for c in starting_chis: chis.append(c) depth += 1