def set_rota_result(self): from mmtbx.rotamer.sidechain_angles import SidechainAngles sidechain_angles = SidechainAngles(show_errs=True) if self.resname == "MSE": curres = "MET" else: curres = self.resname all_dict = construct_complete_sidechain(self.three[self.index], self.altloc) #print all_dict kwargs = self.get_start_kwargs() try: chis = sidechain_angles.measureChiAngles(self.three[self.index], all_dict.get(self.altloc)) except AttributeError: kwargs['incomplete'] = True result = rotamer(**kwargs) print('%s is missing some sidechain atoms' % result.id_str(), file=sys.stderr) self.rota_result = rotalyze.rotamer(**kwargs) return #print all_dict.get(self.altloc).keys() if None in chis: result = rotamer(**kwargs) print('%s may be missing some sidechain atoms' %\ result.id_str(), file=sys.stderr) self.rota_result = rotalyze.rotamer(**kwargs) return cur_res = self.resname.lower().strip() if cur_res == 'mse': cur_res = 'met' value = self.rota_eval.evaluate(cur_res, chis) if value == None: self.rota_result = rotalyze.rotamer(**kwargs) return kwargs['score'] = value * 100 wrap_chis = self.rotamer_id.wrap_chis(self.resname.strip(), chis, symmetry=False) if value >= rotalyze.ALLOWED_THRESHOLD: evaluation = "Favored" elif value >= rotalyze.OUTLIER_THRESHOLD: evaluation = "Allowed" else: evaluation = "OUTLIER" kwargs['outlier'] = True kwargs['rotamer_name'] = evaluation kwargs['evaluation'] = evaluation if evaluation != "OUTLIER": kwargs['outlier'] = False kwargs['rotamer_name'] = self.rotamer_id.identify( self.resname, wrap_chis) # deal with unclassified rotamers if kwargs['rotamer_name'] == '': kwargs['rotamer_name'] = "UNCLASSIFIED" # fill out wrap_chis win None til len == 4 while (len(wrap_chis) < 4): wrap_chis.append(None) kwargs['chi_angles'] = wrap_chis self.rota_result = rotalyze.rotamer(**kwargs)
def set_rota_result(self) : from mmtbx.rotamer.sidechain_angles import SidechainAngles sidechain_angles = SidechainAngles(show_errs=True) if self.resname == "MSE" : curres = "MET" else : curres = self.resname all_dict = construct_complete_sidechain(self.three[self.index],self.altloc) #print all_dict kwargs = self.get_start_kwargs() try : chis = sidechain_angles.measureChiAngles( self.three[self.index], all_dict.get(self.altloc)) except AttributeError : kwargs['incomplete'] = True result = rotamer(**kwargs) print >> sys.stderr, '%s is missing some sidechain atoms'%result.id_str() self.rota_result = rotalyze.rotamer(**kwargs) return #print all_dict.get(self.altloc).keys() if None in chis : result = rotamer(**kwargs) print >> sys.stderr, '%s may be missing some sidechain atoms' %\ result.id_str() self.rota_result = rotalyze.rotamer(**kwargs) return cur_res = self.resname.lower().strip() if cur_res == 'mse': cur_res = 'met' value = self.rota_eval.evaluate(cur_res, chis) if value == None : self.rota_result = rotalyze.rotamer(**kwargs) return kwargs['score'] = value * 100 wrap_chis = self.rotamer_id.wrap_chis(self.resname.strip(), chis,symmetry=False) if value >= rotalyze.ALLOWED_THRESHOLD : evaluation = "Favored" elif value >= rotalyze.OUTLIER_THRESHOLD : evaluation = "Allowed" else : evaluation = "OUTLIER" kwargs['outlier'] = True kwargs['rotamer_name'] = evaluation kwargs['evaluation'] = evaluation if evaluation != "OUTLIER" : kwargs['outlier'] = False kwargs['rotamer_name'] = self.rotamer_id.identify(self.resname, wrap_chis) # deal with unclassified rotamers if kwargs['rotamer_name'] == '' : kwargs['rotamer_name'] = "UNCLASSIFIED" # fill out wrap_chis win None til len == 4 while (len(wrap_chis) < 4) : wrap_chis.append(None) kwargs['chi_angles'] = wrap_chis self.rota_result = rotalyze.rotamer(**kwargs)
def set_rotamer_to_reference(self, xray_structure, mon_lib_srv=None, log=None, quiet=False): if self.mon_lib_srv is None: self.mon_lib_srv = mon_lib_srv assert isinstance(self.mon_lib_srv, mmtbx.monomer_library.server.server) if (log is None): log = sys.stdout make_sub_header("Correcting rotamer outliers to match reference model", out=log) sa = SidechainAngles(False) r = rotalyze.rotalyze(pdb_hierarchy=self.pdb_hierarchy) rot_list_reference = {} coot_reference = {} for key in self.pdb_hierarchy_ref.keys(): hierarchy = self.pdb_hierarchy_ref[key] rot_list_reference[key] = \ rotalyze.rotalyze(pdb_hierarchy=hierarchy) model_hash = {} model_chis = {} reference_hash = {} reference_chis = {} model_outliers = 0 for rot in r.results: model_hash[rot.id_str()] = rot.rotamer_name if rot.rotamer_name == "OUTLIER": model_outliers += 1 for key in rot_list_reference.keys(): reference_hash[key] = {} for rot in rot_list_reference[key].results: reference_hash[key][rot.id_str()] = rot.rotamer_name print >> log, "** evaluating rotamers for working model **" for model in self.pdb_hierarchy.models(): for chain in model.chains(): for residue_group in chain.residue_groups(): all_dict = rotalyze.construct_complete_sidechain( residue_group) for atom_group in residue_group.atom_groups(): try: atom_dict = all_dict.get(atom_group.altloc) chis = sa.measureChiAngles(atom_group, atom_dict) if chis is not None: key = utils.id_str(chain_id=chain.id, resseq=residue_group.resseq, resname=atom_group.resname, icode=residue_group.icode, altloc=atom_group.altloc) model_chis[key] = chis except Exception: print >> log, \ ' %s%5s %s is missing some sidechain atoms, **skipping**' % ( chain.id, residue_group.resid(), atom_group.altloc+atom_group.resname) if model_outliers == 0: print >> log, "No rotamer outliers detected in working model" return else: print >> log, "Number of rotamer outliers: %d" % model_outliers print >> log, "\n** evaluating rotamers for reference model **" for file in self.pdb_hierarchy_ref.keys(): hierarchy = self.pdb_hierarchy_ref[file] reference_chis[file] = {} for model in hierarchy.models(): for chain in model.chains(): for residue_group in chain.residue_groups(): all_dict = rotalyze.construct_complete_sidechain( residue_group) for atom_group in residue_group.atom_groups(): try: atom_dict = all_dict.get(atom_group.altloc) chis = sa.measureChiAngles( atom_group, atom_dict) if chis is not None: key = utils.id_str( chain_id=chain.id, resseq=residue_group.resseq, resname=atom_group.resname, icode=residue_group.icode, altloc=atom_group.altloc) reference_chis[file][key] = chis except Exception: print >> log, \ ' %s%5s %s is missing some sidechain atoms, **skipping**' % ( chain.id, residue_group.resid(), atom_group.altloc+atom_group.resname) print >> log, "\n** fixing outliers **" sites_cart_start = xray_structure.sites_cart() for model in self.pdb_hierarchy.models(): for chain in model.chains(): for residue_group in chain.residue_groups(): if len(residue_group.conformers()) > 1: print >> log, " %s%5s %s has multiple conformations, **skipping**" % ( chain.id, residue_group.resid(), " " + residue_group.atom_groups()[0].resname) continue for conformer in residue_group.conformers(): for residue in conformer.residues(): if residue.resname == "PRO": continue key = utils.id_str( chain_id=chain.id, resseq=residue_group.resseq, resname=residue_group.atom_groups()[0].resname, icode=residue_group.icode, altloc=conformer.altloc) if len(chain.id) == 1: chain_id = " " + chain.id else: chain_id = chain.id file_key = '%s%s%s' % (residue.resname, chain_id, residue_group.resid()) file_key = file_key.strip() file_match = self.residue_match_hash.get(file_key) if file_match is not None: file = file_match[0] else: continue model_rot = model_hash.get(key) reference_rot = reference_hash[file].get( self.one_key_to_another(file_match[1])) m_chis = model_chis.get(key) r_chis = reference_chis[file].get( self.one_key_to_another(file_match[1])) if model_rot is not None and reference_rot is not None and \ m_chis is not None and r_chis is not None: if (model_rot == 'OUTLIER' and \ reference_rot != 'OUTLIER'): # or \ #atom_group.resname in ["LEU", "VAL", "THR"]: self.change_residue_rotamer_in_place( sites_cart_start, residue, m_chis, r_chis, self.mon_lib_srv) xray_structure.set_sites_cart( sites_cart_start) elif self.params.strict_rotamer_matching and \ (model_rot != 'OUTLIER' and reference_rot != 'OUTLIER'): if model_rot != reference_rot: self.change_residue_rotamer_in_place( sites_cart_start, residue, m_chis, r_chis, self.mon_lib_srv) xray_structure.set_sites_cart( sites_cart_start)
def set_rotamer_to_reference(self, xray_structure, mon_lib_srv=None, log=None, quiet=False): if self.mon_lib_srv is None: self.mon_lib_srv = mon_lib_srv assert isinstance(self.mon_lib_srv, mmtbx.monomer_library.server.server) if(log is None): log = sys.stdout make_sub_header( "Correcting rotamer outliers to match reference model", out=log) sa = SidechainAngles(False) r = rotalyze.rotalyze(pdb_hierarchy=self.pdb_hierarchy) rot_list_reference = {} coot_reference = {} for key in self.pdb_hierarchy_ref.keys(): hierarchy = self.pdb_hierarchy_ref[key] rot_list_reference[key] = \ rotalyze.rotalyze(pdb_hierarchy=hierarchy) model_hash = {} model_chis = {} reference_hash = {} reference_chis = {} model_outliers = 0 for rot in r.results: model_hash[rot.id_str()] = rot.rotamer_name if rot.rotamer_name == "OUTLIER": model_outliers += 1 for key in rot_list_reference.keys(): reference_hash[key] = {} for rot in rot_list_reference[key].results: reference_hash[key][rot.id_str()] = rot.rotamer_name print >> log, "** evaluating rotamers for working model **" for model in self.pdb_hierarchy.models(): for chain in model.chains(): for residue_group in chain.residue_groups(): all_dict = rotalyze.construct_complete_sidechain(residue_group) for atom_group in residue_group.atom_groups(): try: atom_dict = all_dict.get(atom_group.altloc) chis = sa.measureChiAngles(atom_group, atom_dict) if chis is not None: key = utils.id_str( chain_id=chain.id, resseq=residue_group.resseq, resname=atom_group.resname, icode=residue_group.icode, altloc=atom_group.altloc) model_chis[key] = chis except Exception: print >> log, \ ' %s%5s %s is missing some sidechain atoms, **skipping**' % ( chain.id, residue_group.resid(), atom_group.altloc+atom_group.resname) if model_outliers == 0: print >> log, "No rotamer outliers detected in working model" return else: print >> log, "Number of rotamer outliers: %d" % model_outliers print >> log, "\n** evaluating rotamers for reference model **" for file in self.pdb_hierarchy_ref.keys(): hierarchy = self.pdb_hierarchy_ref[file] reference_chis[file] = {} for model in hierarchy.models(): for chain in model.chains(): for residue_group in chain.residue_groups(): all_dict = rotalyze.construct_complete_sidechain(residue_group) for atom_group in residue_group.atom_groups(): try: atom_dict = all_dict.get(atom_group.altloc) chis = sa.measureChiAngles(atom_group, atom_dict) if chis is not None: key = utils.id_str( chain_id=chain.id, resseq=residue_group.resseq, resname=atom_group.resname, icode=residue_group.icode, altloc=atom_group.altloc) reference_chis[file][key] = chis except Exception: print >> log, \ ' %s%5s %s is missing some sidechain atoms, **skipping**' % ( chain.id, residue_group.resid(), atom_group.altloc+atom_group.resname) print >> log, "\n** fixing outliers **" sites_cart_start = xray_structure.sites_cart() for model in self.pdb_hierarchy.models(): for chain in model.chains(): for residue_group in chain.residue_groups(): if len(residue_group.conformers()) > 1: print >> log, " %s%5s %s has multiple conformations, **skipping**" % ( chain.id, residue_group.resid(), " "+residue_group.atom_groups()[0].resname) continue for conformer in residue_group.conformers(): for residue in conformer.residues(): if residue.resname == "PRO": continue key = utils.id_str( chain_id=chain.id, resseq=residue_group.resseq, resname=residue_group.atom_groups()[0].resname, icode=residue_group.icode, altloc=conformer.altloc) if len(chain.id) == 1: chain_id = " "+chain.id else: chain_id = chain.id file_key = '%s%s%s' %(residue.resname, chain_id, residue_group.resid()) file_key = file_key.strip() file_match = self.residue_match_hash.get(file_key) if file_match is not None: file = file_match[0] else: continue model_rot = model_hash.get(key) reference_rot = reference_hash[file].get(self.one_key_to_another(file_match[1])) m_chis = model_chis.get(key) r_chis = reference_chis[file].get(self.one_key_to_another(file_match[1])) if model_rot is not None and reference_rot is not None and \ m_chis is not None and r_chis is not None: if (model_rot == 'OUTLIER' and \ reference_rot != 'OUTLIER'): # or \ #atom_group.resname in ["LEU", "VAL", "THR"]: self.change_residue_rotamer_in_place( sites_cart_start,residue, m_chis,r_chis,self.mon_lib_srv) xray_structure.set_sites_cart(sites_cart_start) elif self.params.strict_rotamer_matching and \ (model_rot != 'OUTLIER' and reference_rot != 'OUTLIER'): if model_rot != reference_rot: self.change_residue_rotamer_in_place( sites_cart_start,residue, m_chis,r_chis,self.mon_lib_srv) xray_structure.set_sites_cart(sites_cart_start)
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
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 = 0.003 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