def exercise_bond(): for i_trial in xrange(5): sites = random_sites(n_sites=2) b = geometry_restraints.bond(sites=sites, distance_ideal=0, weight=0) distance_ideal = b.distance_model sigma = distance_ideal * 0.01 weight = 1 / sigma**2 residual_obj = residual_functor( restraint_type=geometry_restraints.bond, distance_ideal=distance_ideal, weight=weight) for i_pert in xrange(5): if (i_pert == 0): sites_mod = sites else: sites_mod = [] for site in sites: shift = col([random.uniform(-3,3)*sigma for i in xrange(3)]) sites_mod.append(site+shift) b = geometry_restraints.bond( sites=sites_mod, distance_ideal=distance_ideal, weight=weight) ag = b.gradients() fg = finite_differences(sites_mod, residual_obj) for analytical,finite in zip(ag,fg): assert approx_equal(analytical, finite)
def exercise_bond(): for i_trial in range(5): sites = random_sites(n_sites=2) b = geometry_restraints.bond(sites=sites, distance_ideal=0, weight=0) distance_ideal = b.distance_model sigma = distance_ideal * 0.01 weight = 1 / sigma**2 residual_obj = residual_functor( restraint_type=geometry_restraints.bond, distance_ideal=distance_ideal, weight=weight) for i_pert in range(5): if (i_pert == 0): sites_mod = sites else: sites_mod = [] for site in sites: shift = col( [random.uniform(-3, 3) * sigma for i in range(3)]) sites_mod.append(site + shift) b = geometry_restraints.bond(sites=sites_mod, distance_ideal=distance_ideal, weight=weight) ag = b.gradients() fg = finite_differences(sites_mod, residual_obj) for analytical, finite in zip(ag, fg): assert approx_equal(analytical, finite)
def get_bond_outliers(bond_proxies, chain, sites_cart, hierarchy): i_seq_name_hash = build_name_hash(pdb_hierarchy=hierarchy) kin_text = "@subgroup {length devs} dominant\n" for bp in bond_proxies.simple: restraint = geometry_restraints.bond(sites_cart=sites_cart, proxy=bp) res = i_seq_name_hash[bp.i_seqs[0]][5:] altloc = i_seq_name_hash[bp.i_seqs[0]][4:5].lower() cur_chain = i_seq_name_hash[bp.i_seqs[0]][8:10] if chain.id.strip() is not cur_chain.strip(): continue atom1 = i_seq_name_hash[bp.i_seqs[0]][0:4].strip() atom2 = i_seq_name_hash[bp.i_seqs[1]][0:4].strip() if atom1[0] == "H" or atom2[0] == "H" or \ atom1[0] == "D" or atom2[0] == "D": continue sigma = ((1/restraint.weight)**(.5)) num_sigmas = -(restraint.delta / sigma) #negative to match MolProbity direction if abs(num_sigmas) >= 4.0: bond_key = altloc+res[0:3].lower()+res[3:]+\ ' '+atom1.lower()+'-'+atom2.lower() kin = add_spring(sites=restraint.sites, num_sigmas=num_sigmas, bond_key=bond_key) kin_text += kin return kin_text
def distances_as_cif_loop(xray_structure, proxies): space_group_info = sgtbx.space_group_info( group=xray_structure.space_group()) unit_cell = xray_structure.unit_cell() sites_cart = xray_structure.sites_cart() site_labels = xray_structure.scatterers().extract_labels() fmt = "%.4f" loop = model.loop(header=("_restr_distance_atom_site_label_1", "_restr_distance_atom_site_label_2", "_restr_distance_site_symmetry_2", "_restr_distance_target", "_restr_distance_target_weight_param", "_restr_distance_diff")) for proxy in proxies: restraint = geometry_restraints.bond(unit_cell=unit_cell, sites_cart=sites_cart, proxy=proxy) i_seqs = proxy.i_seqs sym_op = proxy.rt_mx_ji if sym_op is None: sym_op = sgtbx.rt_mx() loop.add_row( (site_labels[i_seqs[0]], site_labels[i_seqs[1]], space_group_info.cif_symmetry_code(sym_op), fmt % restraint.distance_ideal, fmt % math.sqrt(1 / restraint.weight), fmt % restraint.delta)) return loop
def distances_as_cif_loop(xray_structure, proxies): space_group_info = sgtbx.space_group_info(group=xray_structure.space_group()) unit_cell = xray_structure.unit_cell() sites_cart = xray_structure.sites_cart() site_labels = xray_structure.scatterers().extract_labels() fmt = "%.4f" loop = model.loop(header=( "_restr_distance_atom_site_label_1", "_restr_distance_atom_site_label_2", "_restr_distance_site_symmetry_2", "_restr_distance_target", "_restr_distance_target_weight_param", "_restr_distance_diff" )) for proxy in proxies: restraint = geometry_restraints.bond( unit_cell=unit_cell, sites_cart=sites_cart, proxy=proxy) i_seqs = proxy.i_seqs sym_op = proxy.rt_mx_ji if sym_op is None: sym_op = sgtbx.rt_mx() loop.add_row((site_labels[i_seqs[0]], site_labels[i_seqs[1]], space_group_info.cif_symmetry_code(sym_op), fmt % restraint.distance_ideal, fmt % math.sqrt(1/restraint.weight), fmt % restraint.delta)) return loop
def psi_from_sites(resN, resCA, resC, nextN): from cctbx import geometry_restraints b = geometry_restraints.bond(sites=[resC, nextN], distance_ideal=1, weight=1) if (b.distance_model > 4): return None d = geometry_restraints.dihedral(sites=[resN, resCA, resC, nextN], angle_ideal=-40, weight=1) return d.angle_model
def phi_from_sites(prevC, resN, resCA, resC): from cctbx import geometry_restraints b = geometry_restraints.bond(sites=[prevC, resN], distance_ideal=1, weight=1) # check to see if residues are actually bonded. if (b.distance_model > 4): return None d = geometry_restraints.dihedral(sites=[prevC, resN, resCA, resC], angle_ideal=-40, weight=1) return d.angle_model
def psi_from_sites (resN, resCA, resC, nextN) : from cctbx import geometry_restraints b = geometry_restraints.bond( sites=[resC,nextN], distance_ideal=1, weight=1) if (b.distance_model > 4): return None d = geometry_restraints.dihedral( sites=[resN,resCA,resC,nextN], angle_ideal=-40, weight=1) return d.angle_model
def phi_from_sites (prevC, resN, resCA, resC) : from cctbx import geometry_restraints b = geometry_restraints.bond( sites=[prevC,resN], distance_ideal=1, weight=1) # check to see if residues are actually bonded. if (b.distance_model > 4): return None d = geometry_restraints.dihedral( sites=[prevC,resN,resCA,resC], angle_ideal=-40, weight=1) return d.angle_model
def __init__(self, pdb_hierarchy, pdb_atoms, geometry_restraints_manager, outliers_only=True): rna_geometry.__init__(self) cutoff = 4 sites_cart = pdb_atoms.extract_xyz() flags = geometry_restraints.flags.flags(default=True) pair_proxies = geometry_restraints_manager.pair_proxies( flags=flags, sites_cart=sites_cart) bond_proxies = pair_proxies.bond_proxies for proxy in bond_proxies.simple: restraint = geometry_restraints.bond(sites_cart=sites_cart, proxy=proxy) atom1 = pdb_atoms[proxy.i_seqs[0]].name atom2 = pdb_atoms[proxy.i_seqs[1]].name labels = pdb_atoms[proxy.i_seqs[0]].fetch_labels() if (atom1.strip() not in rna_backbone_atoms or atom2.strip() not in rna_backbone_atoms): continue self.n_total += 1 sigma = sqrt(1 / restraint.weight) num_sigmas = restraint.delta / sigma is_outlier = (abs(num_sigmas) >= cutoff) if (is_outlier or not outliers_only): self.n_outliers += 1 self.results.append( rna_bond(chain_id=labels.chain_id, resseq=labels.resseq, icode=labels.icode, altloc=labels.altloc, resname=labels.resname, atoms_info=validation.get_atoms_info( pdb_atoms, proxy.i_seqs), sigma=sigma, score=num_sigmas, delta=restraint.delta, outlier=is_outlier))
def __init__ (self, pdb_hierarchy, pdb_atoms, geometry_restraints_manager, outliers_only=True) : rna_geometry.__init__(self) cutoff = 4 sites_cart = pdb_atoms.extract_xyz() flags = geometry_restraints.flags.flags(default=True) pair_proxies = geometry_restraints_manager.pair_proxies( flags=flags, sites_cart=sites_cart) bond_proxies = pair_proxies.bond_proxies for proxy in bond_proxies.simple: restraint = geometry_restraints.bond( sites_cart=sites_cart, proxy=proxy) atom1 = pdb_atoms[proxy.i_seqs[0]].name atom2 = pdb_atoms[proxy.i_seqs[1]].name labels = pdb_atoms[proxy.i_seqs[0]].fetch_labels() if (atom1.strip() not in rna_backbone_atoms or atom2.strip() not in rna_backbone_atoms) : continue self.n_total += 1 sigma = sqrt(1 / restraint.weight) num_sigmas = restraint.delta / sigma is_outlier = (abs(num_sigmas) >= cutoff) if (is_outlier or not outliers_only): self.n_outliers += 1 self.results.append(rna_bond( chain_id=labels.chain_id, resseq=labels.resseq, icode=labels.icode, altloc=labels.altloc, resname=labels.resname, atoms_info=validation.get_atoms_info(pdb_atoms, proxy.i_seqs), sigma=sigma, score=num_sigmas, delta=restraint.delta, outlier=is_outlier))
def ensemble_mean_geometry_stats(self, restraints_manager, xray_structure, ensemble_xray_structures, ignore_hd = True, verbose = False, out = None, return_pdb_string = False): if (out is None): out = sys.stdout if verbose: utils.print_header("Ensemble mean geometry statistics", out = out) ensemble_size = len(ensemble_xray_structures) print("Ensemble size : ", ensemble_size, file=out) # Dictionaries to store deltas ensemble_bond_deltas = {} ensemble_angle_deltas = {} ensemble_chirality_deltas = {} ensemble_planarity_deltas = {} ensemble_dihedral_deltas = {} # List to store rmsd of each model structures_bond_rmsd = flex.double() structures_angle_rmsd = flex.double() structures_chirality_rmsd = flex.double() structures_planarity_rmsd = flex.double() structures_dihedral_rmsd = flex.double() # Remove water and hd atoms from global restraints manager selection = flex.bool() for sc in xray_structure.scatterers(): if sc.label.find('HOH') > -1: selection.append(True) else: selection.append(False) if ignore_hd: hd_selection = xray_structure.hd_selection() assert hd_selection.size() == selection.size() for n in range(hd_selection.size()): if hd_selection[n] or selection[n]: selection[n] = True restraints_manager = restraints_manager.select(selection = ~selection) # Get all deltas for n, structure in enumerate(ensemble_xray_structures): if verbose: print("\nModel : ", n+1, file=out) sites_cart = structure.sites_cart() # Remove water and hd atoms from individual structures sites cart selection = flex.bool() for sc in structure.scatterers(): if sc.label.find('HOH') > -1: selection.append(True) else: selection.append(False) if ignore_hd: hd_selection = structure.hd_selection() assert hd_selection.size() == selection.size() for n in range(hd_selection.size()): if hd_selection[n] or selection[n]: selection[n] = True sites_cart = sites_cart.select(~selection) assert sites_cart is not None site_labels = None energies_sites = restraints_manager.energies_sites( sites_cart = sites_cart, compute_gradients = False) # Rmsd of individual model bond_rmsd = energies_sites.geometry.bond_deviations()[2] angle_rmsd = energies_sites.geometry.angle_deviations()[2] chirality_rmsd = energies_sites.geometry.chirality_deviations()[2] planarity_rmsd = energies_sites.geometry.planarity_deviations()[2] dihedral_rmsd = energies_sites.geometry.dihedral_deviations()[2] structures_bond_rmsd.append(bond_rmsd) structures_angle_rmsd.append(angle_rmsd) structures_chirality_rmsd.append(chirality_rmsd) structures_planarity_rmsd.append(planarity_rmsd) structures_dihedral_rmsd.append(dihedral_rmsd) if verbose: print(" Model RMSD", file=out) print(" bond : %.6g" % bond_rmsd, file=out) print(" angle : %.6g" % angle_rmsd, file=out) print(" chirality : %.6g" % chirality_rmsd, file=out) print(" planarity : %.6g" % planarity_rmsd, file=out) print(" dihedral : %.6g" % dihedral_rmsd, file=out) # Bond pair_proxies = restraints_manager.geometry.pair_proxies(flags=None, sites_cart=sites_cart) assert pair_proxies is not None if verbose: pair_proxies.bond_proxies.show_histogram_of_deltas( sites_cart = sites_cart, n_slots = 10, f = out) for proxy in pair_proxies.bond_proxies.simple: bond_simple_proxy = geometry_restraints.bond( sites_cart = sites_cart, proxy = proxy) if proxy.i_seqs in ensemble_bond_deltas: ensemble_bond_deltas[proxy.i_seqs][0]+=bond_simple_proxy.delta ensemble_bond_deltas[proxy.i_seqs][1]+=1 else: ensemble_bond_deltas[proxy.i_seqs] = [bond_simple_proxy.delta, 1] if verbose: print("bond simple :", proxy.i_seqs, file=out) print(" distance_ideal : %.6g" % proxy.distance_ideal, file=out) print(" distance_model : %.6g" % bond_simple_proxy.distance_model, file=out) print(" detla : %.6g" % bond_simple_proxy.delta, file=out) if (pair_proxies.bond_proxies.asu.size() > 0): asu_mappings = pair_proxies.bond_proxies.asu_mappings() for proxy in pair_proxies.bond_proxies.asu: rt_mx = asu_mappings.get_rt_mx_ji(pair=proxy) bond_asu_proxy = geometry_restraints.bond( sites_cart = sites_cart, asu_mappings = asu_mappings, proxy = proxy) proxy_i_seqs = (proxy.i_seq, proxy.j_seq) if proxy_i_seqs in ensemble_bond_deltas: ensemble_bond_deltas[proxy_i_seqs][0]+=bond_asu_proxy.delta ensemble_bond_deltas[proxy_i_seqs][1]+=1 else: ensemble_bond_deltas[proxy_i_seqs] = [bond_asu_proxy.delta, 1] if verbose: print("bond asu :", (proxy.i_seq, proxy.j_seq), rt_mx, file=out) print(" distance_ideal : %.6g" % proxy.distance_ideal, file=out) print(" distance_model : %.6g" % bond_asu_proxy.distance_model, file=out) print(" delta : %.6g" % bond_asu_proxy.delta, file=out) # Angle if verbose: restraints_manager.geometry.angle_proxies.show_histogram_of_deltas( sites_cart = sites_cart, n_slots = 10, f = out) for proxy in restraints_manager.geometry.angle_proxies: angle_proxy = geometry_restraints.angle( sites_cart = sites_cart, proxy = proxy) if proxy.i_seqs in ensemble_angle_deltas: ensemble_angle_deltas[proxy.i_seqs][0]+=angle_proxy.delta ensemble_angle_deltas[proxy.i_seqs][1]+=1 else: ensemble_angle_deltas[proxy.i_seqs] = [angle_proxy.delta, 1] if verbose: print("angle : ", proxy.i_seqs, file=out) print(" angle_ideal : %.6g" % proxy.angle_ideal, file=out) print(" angle_model : %.6g" % angle_proxy.angle_model, file=out) print(" delta : %.6g" % angle_proxy.delta, file=out) # Chirality if verbose: restraints_manager.geometry.chirality_proxies.show_histogram_of_deltas( sites_cart = sites_cart, n_slots = 10, f = out) for proxy in restraints_manager.geometry.chirality_proxies: chirality_proxy = geometry_restraints.chirality( sites_cart = sites_cart, proxy = proxy) if proxy.i_seqs in ensemble_chirality_deltas: ensemble_chirality_deltas[proxy.i_seqs][0]+=chirality_proxy.delta ensemble_chirality_deltas[proxy.i_seqs][1]+=1 else: ensemble_chirality_deltas[proxy.i_seqs] = [chirality_proxy.delta, 1] if verbose: print("chirality : ", proxy.i_seqs, file=out) print(" chirality_ideal : %.6g" % proxy.volume_ideal, file=out) print(" chirality_model : %.6g" % chirality_proxy.volume_model, file=out) print(" chirality : %.6g" % chirality_proxy.delta, file=out) # Planarity for proxy in restraints_manager.geometry.planarity_proxies: planarity_proxy = geometry_restraints.planarity( sites_cart = sites_cart, proxy = proxy) proxy_i_seqs = [] for i_seq in proxy.i_seqs: proxy_i_seqs.append(i_seq) proxy_i_seqs = tuple(proxy_i_seqs) if proxy_i_seqs in ensemble_planarity_deltas: ensemble_planarity_deltas[proxy_i_seqs][0]+=planarity_proxy.rms_deltas() ensemble_planarity_deltas[proxy_i_seqs][1]+=1 else: ensemble_planarity_deltas[proxy_i_seqs] = [planarity_proxy.rms_deltas(), 1] if verbose: print("planarity : ", proxy_i_seqs, file=out) print(" planarity rms_deltas : %.6g" % planarity_proxy.rms_deltas(), file=out) # Dihedral if verbose: restraints_manager.geometry.dihedral_proxies.show_histogram_of_deltas( sites_cart = sites_cart, n_slots = 10, f = out) for proxy in restraints_manager.geometry.dihedral_proxies: dihedral_proxy = geometry_restraints.dihedral( sites_cart = sites_cart, proxy = proxy) if proxy.i_seqs in ensemble_dihedral_deltas: ensemble_dihedral_deltas[proxy.i_seqs][0]+=dihedral_proxy.delta ensemble_dihedral_deltas[proxy.i_seqs][1]+=1 else: ensemble_dihedral_deltas[proxy.i_seqs] = [dihedral_proxy.delta, 1] if verbose: print("dihedral : ", proxy.i_seqs, file=out) print(" dihedral_ideal : %.6g" % proxy.angle_ideal, file=out) print(" periodicity : %.6g" % proxy.periodicity, file=out) print(" dihedral_model : %.6g" % dihedral_proxy.angle_model, file=out) print(" delta : %.6g" % dihedral_proxy.delta, file=out) # Calculate RMSDs for ensemble model # Bond mean_bond_delta = flex.double() for proxy, info in six.iteritems(ensemble_bond_deltas): # assert info[1] == ensemble_size if info[1]!=ensemble_size: print('skipping bond RMSD calns of ensemble %s' % info, file=out) continue mean_delta = info[0] / info[1] mean_bond_delta.append(mean_delta) bond_delta_sq = mean_bond_delta * mean_bond_delta ensemble_bond_rmsd = math.sqrt(flex.mean_default(bond_delta_sq, 0)) # Angle mean_angle_delta = flex.double() for proxy, info in six.iteritems(ensemble_angle_deltas): assert info[1] == ensemble_size mean_delta = info[0] / info[1] mean_angle_delta.append(mean_delta) angle_delta_sq = mean_angle_delta * mean_angle_delta ensemble_angle_rmsd = math.sqrt(flex.mean_default(angle_delta_sq, 0)) # Chirality mean_chirality_delta = flex.double() for proxy, info in six.iteritems(ensemble_chirality_deltas): assert info[1] == ensemble_size mean_delta = info[0] / info[1] mean_chirality_delta.append(mean_delta) chirality_delta_sq = mean_chirality_delta * mean_chirality_delta ensemble_chirality_rmsd = math.sqrt(flex.mean_default(chirality_delta_sq, 0)) # Planarity mean_planarity_delta = flex.double() for proxy, info in six.iteritems(ensemble_planarity_deltas): assert info[1] == ensemble_size mean_delta = info[0] / info[1] mean_planarity_delta.append(mean_delta) planarity_delta_sq = mean_planarity_delta * mean_planarity_delta ensemble_planarity_rmsd = math.sqrt(flex.mean_default(planarity_delta_sq, 0)) # Dihedral mean_dihedral_delta = flex.double() for proxy, info in six.iteritems(ensemble_dihedral_deltas): assert info[1] == ensemble_size mean_delta = info[0] / info[1] mean_dihedral_delta.append(mean_delta) dihedral_delta_sq = mean_dihedral_delta * mean_dihedral_delta ensemble_dihedral_rmsd = math.sqrt(flex.mean_default(dihedral_delta_sq, 0)) # Calculate <structure rmsd> assert ensemble_size == structures_bond_rmsd assert ensemble_size == structures_angle_rmsd assert ensemble_size == structures_chirality_rmsd assert ensemble_size == structures_planarity_rmsd assert ensemble_size == structures_dihedral_rmsd structure_bond_rmsd_mean = structures_bond_rmsd.min_max_mean().mean structure_angle_rmsd_mean = structures_angle_rmsd.min_max_mean().mean structure_chirality_rmsd_mean = structures_chirality_rmsd.min_max_mean().mean structure_planarity_rmsd_mean = structures_planarity_rmsd.min_max_mean().mean structure_dihedral_rmsd_mean = structures_dihedral_rmsd.min_max_mean().mean # Show summary utils.print_header("Ensemble RMSD summary", out = out) print(" RMSD (mean delta per restraint)", file=out) print(" bond : %.6g" % ensemble_bond_rmsd, file=out) print(" angle : %.6g" % ensemble_angle_rmsd, file=out) print(" chirality : %.6g" % ensemble_chirality_rmsd, file=out) print(" planarity : %.6g" % ensemble_planarity_rmsd, file=out) print(" dihedral : %.6g" % ensemble_dihedral_rmsd, file=out) print(" RMSD (mean RMSD per structure)", file=out) print(" bond : %.6g" % structure_bond_rmsd_mean, file=out) print(" angle : %.6g" % structure_angle_rmsd_mean, file=out) print(" chirality : %.6g" % structure_chirality_rmsd_mean, file=out) print(" planarity : %.6g" % structure_planarity_rmsd_mean, file=out) print(" dihedral : %.6g" % structure_dihedral_rmsd_mean, file=out) if ignore_hd: print("\n Calculated excluding H/D", file=out) else: print("\n Calculated including H/D", file=out) if return_pdb_string: ens_geo_pdb_string = "REMARK 3" ens_geo_pdb_string += "\nREMARK 3 NUMBER STRUCTURES IN ENSEMBLE : {0:5d}".format(ensemble_size) if ignore_hd: ens_geo_pdb_string += "\nREMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (EXCLUDING H/D)" else: ens_geo_pdb_string += "\nREMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (INCLUDING H/D)" ens_geo_pdb_string += "\nREMARK 3 RMSD (MEAN DELTA PER RESTRAINT)" ens_geo_pdb_string += "\nREMARK 3 BOND : {0:5.3f}".format(ensemble_bond_rmsd) ens_geo_pdb_string += "\nREMARK 3 ANGLE : {0:5.3f}".format(ensemble_angle_rmsd) ens_geo_pdb_string += "\nREMARK 3 CHIRALITY : {0:5.3f}".format(ensemble_chirality_rmsd) ens_geo_pdb_string += "\nREMARK 3 PLANARITY : {0:5.3f}".format(ensemble_planarity_rmsd) ens_geo_pdb_string += "\nREMARK 3 DIHEDRAL : {0:5.2f}".format(ensemble_dihedral_rmsd) ens_geo_pdb_string += "\nREMARK 3 RMSD (MEAN RMSD PER STRUCTURE)" ens_geo_pdb_string += "\nREMARK 3 BOND : {0:5.3f}".format(structure_bond_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3 ANGLE : {0:5.3f}".format(structure_angle_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3 CHIRALITY : {0:5.3f}".format(structure_chirality_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3 PLANARITY : {0:5.3f}".format(structure_planarity_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3 DIHEDRAL : {0:5.2f}".format(structure_dihedral_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3" return ens_geo_pdb_string
def ensemble_mean_geometry_stats(self, restraints_manager, xray_structure, ensemble_xray_structures, ignore_hd = True, verbose = False, out = None, return_pdb_string = False): if (out is None): out = sys.stdout if verbose: utils.print_header("Ensemble mean geometry statistics", out = out) ensemble_size = len(ensemble_xray_structures) print >> out, "Ensemble size : ", ensemble_size # Dictionaries to store deltas ensemble_bond_deltas = {} ensemble_angle_deltas = {} ensemble_chirality_deltas = {} ensemble_planarity_deltas = {} ensemble_dihedral_deltas = {} # List to store rmsd of each model structures_bond_rmsd = flex.double() structures_angle_rmsd = flex.double() structures_chirality_rmsd = flex.double() structures_planarity_rmsd = flex.double() structures_dihedral_rmsd = flex.double() # Remove water and hd atoms from global restraints manager selection = flex.bool() for sc in xray_structure.scatterers(): if sc.label.find('HOH') > -1: selection.append(True) else: selection.append(False) if ignore_hd: hd_selection = xray_structure.hd_selection() assert hd_selection.size() == selection.size() for n in xrange(hd_selection.size()): if hd_selection[n] or selection[n]: selection[n] = True restraints_manager = restraints_manager.select(selection = ~selection) # Get all deltas for n, structure in enumerate(ensemble_xray_structures): if verbose: print >> out, "\nModel : ", n+1 sites_cart = structure.sites_cart() # Remove water and hd atoms from individual structures sites cart selection = flex.bool() for sc in structure.scatterers(): if sc.label.find('HOH') > -1: selection.append(True) else: selection.append(False) if ignore_hd: hd_selection = structure.hd_selection() assert hd_selection.size() == selection.size() for n in xrange(hd_selection.size()): if hd_selection[n] or selection[n]: selection[n] = True sites_cart = sites_cart.select(~selection) assert sites_cart is not None site_labels = None energies_sites = restraints_manager.energies_sites( sites_cart = sites_cart, compute_gradients = False) # Rmsd of individual model bond_rmsd = energies_sites.geometry.bond_deviations()[2] angle_rmsd = energies_sites.geometry.angle_deviations()[2] chirality_rmsd = energies_sites.geometry.chirality_deviations()[2] planarity_rmsd = energies_sites.geometry.planarity_deviations()[2] dihedral_rmsd = energies_sites.geometry.dihedral_deviations()[2] structures_bond_rmsd.append(bond_rmsd) structures_angle_rmsd.append(angle_rmsd) structures_chirality_rmsd.append(chirality_rmsd) structures_planarity_rmsd.append(planarity_rmsd) structures_dihedral_rmsd.append(dihedral_rmsd) if verbose: print >> out, " Model RMSD" print >> out, " bond : %.6g" % bond_rmsd print >> out, " angle : %.6g" % angle_rmsd print >> out, " chirality : %.6g" % chirality_rmsd print >> out, " planarity : %.6g" % planarity_rmsd print >> out, " dihedral : %.6g" % dihedral_rmsd # Bond pair_proxies = restraints_manager.geometry.pair_proxies(flags=None, sites_cart=sites_cart) assert pair_proxies is not None if verbose: pair_proxies.bond_proxies.show_histogram_of_deltas( sites_cart = sites_cart, n_slots = 10, f = out) for proxy in pair_proxies.bond_proxies.simple: bond_simple_proxy = geometry_restraints.bond( sites_cart = sites_cart, proxy = proxy) if proxy.i_seqs in ensemble_bond_deltas: ensemble_bond_deltas[proxy.i_seqs][0]+=bond_simple_proxy.delta ensemble_bond_deltas[proxy.i_seqs][1]+=1 else: ensemble_bond_deltas[proxy.i_seqs] = [bond_simple_proxy.delta, 1] if verbose: print >> out, "bond simple :", proxy.i_seqs print >> out, " distance_ideal : %.6g" % proxy.distance_ideal print >> out, " distance_model : %.6g" % bond_simple_proxy.distance_model print >> out, " detla : %.6g" % bond_simple_proxy.delta if (pair_proxies.bond_proxies.asu.size() > 0): asu_mappings = pair_proxies.bond_proxies.asu_mappings() for proxy in pair_proxies.bond_proxies.asu: rt_mx = asu_mappings.get_rt_mx_ji(pair=proxy) bond_asu_proxy = geometry_restraints.bond( sites_cart = sites_cart, asu_mappings = asu_mappings, proxy = proxy) proxy_i_seqs = (proxy.i_seq, proxy.j_seq) if proxy_i_seqs in ensemble_bond_deltas: ensemble_bond_deltas[proxy_i_seqs][0]+=bond_asu_proxy.delta ensemble_bond_deltas[proxy_i_seqs][1]+=1 else: ensemble_bond_deltas[proxy_i_seqs] = [bond_asu_proxy.delta, 1] if verbose: print >> out, "bond asu :", (proxy.i_seq, proxy.j_seq), rt_mx print >> out, " distance_ideal : %.6g" % proxy.distance_ideal print >> out, " distance_model : %.6g" % bond_asu_proxy.distance_model print >> out, " delta : %.6g" % bond_asu_proxy.delta # Angle if verbose: restraints_manager.geometry.angle_proxies.show_histogram_of_deltas( sites_cart = sites_cart, n_slots = 10, f = out) for proxy in restraints_manager.geometry.angle_proxies: angle_proxy = geometry_restraints.angle( sites_cart = sites_cart, proxy = proxy) if proxy.i_seqs in ensemble_angle_deltas: ensemble_angle_deltas[proxy.i_seqs][0]+=angle_proxy.delta ensemble_angle_deltas[proxy.i_seqs][1]+=1 else: ensemble_angle_deltas[proxy.i_seqs] = [angle_proxy.delta, 1] if verbose: print >> out, "angle : ", proxy.i_seqs print >> out, " angle_ideal : %.6g" % proxy.angle_ideal print >> out, " angle_model : %.6g" % angle_proxy.angle_model print >> out, " delta : %.6g" % angle_proxy.delta # Chirality if verbose: restraints_manager.geometry.chirality_proxies.show_histogram_of_deltas( sites_cart = sites_cart, n_slots = 10, f = out) for proxy in restraints_manager.geometry.chirality_proxies: chirality_proxy = geometry_restraints.chirality( sites_cart = sites_cart, proxy = proxy) if proxy.i_seqs in ensemble_chirality_deltas: ensemble_chirality_deltas[proxy.i_seqs][0]+=chirality_proxy.delta ensemble_chirality_deltas[proxy.i_seqs][1]+=1 else: ensemble_chirality_deltas[proxy.i_seqs] = [chirality_proxy.delta, 1] if verbose: print >> out, "chirality : ", proxy.i_seqs print >> out, " chirality_ideal : %.6g" % proxy.volume_ideal print >> out, " chirality_model : %.6g" % chirality_proxy.volume_model print >> out, " chirality : %.6g" % chirality_proxy.delta # Planarity for proxy in restraints_manager.geometry.planarity_proxies: planarity_proxy = geometry_restraints.planarity( sites_cart = sites_cart, proxy = proxy) proxy_i_seqs = [] for i_seq in proxy.i_seqs: proxy_i_seqs.append(i_seq) proxy_i_seqs = tuple(proxy_i_seqs) if proxy_i_seqs in ensemble_planarity_deltas: ensemble_planarity_deltas[proxy_i_seqs][0]+=planarity_proxy.rms_deltas() ensemble_planarity_deltas[proxy_i_seqs][1]+=1 else: ensemble_planarity_deltas[proxy_i_seqs] = [planarity_proxy.rms_deltas(), 1] if verbose: print >> out, "planarity : ", proxy_i_seqs print >> out, " planarity rms_deltas : %.6g" % planarity_proxy.rms_deltas() # Dihedral if verbose: restraints_manager.geometry.dihedral_proxies.show_histogram_of_deltas( sites_cart = sites_cart, n_slots = 10, f = out) for proxy in restraints_manager.geometry.dihedral_proxies: dihedral_proxy = geometry_restraints.dihedral( sites_cart = sites_cart, proxy = proxy) if proxy.i_seqs in ensemble_dihedral_deltas: ensemble_dihedral_deltas[proxy.i_seqs][0]+=dihedral_proxy.delta ensemble_dihedral_deltas[proxy.i_seqs][1]+=1 else: ensemble_dihedral_deltas[proxy.i_seqs] = [dihedral_proxy.delta, 1] if verbose: print >> out, "dihedral : ", proxy.i_seqs print >> out, " dihedral_ideal : %.6g" % proxy.angle_ideal print >> out, " periodicity : %.6g" % proxy.periodicity print >> out, " dihedral_model : %.6g" % dihedral_proxy.angle_model print >> out, " delta : %.6g" % dihedral_proxy.delta # Calculate RMSDs for ensemble model # Bond mean_bond_delta = flex.double() for proxy, info in ensemble_bond_deltas.iteritems(): assert info[1] == ensemble_size mean_delta = info[0] / info[1] mean_bond_delta.append(mean_delta) bond_delta_sq = mean_bond_delta * mean_bond_delta ensemble_bond_rmsd = math.sqrt(flex.mean_default(bond_delta_sq, 0)) # Angle mean_angle_delta = flex.double() for proxy, info in ensemble_angle_deltas.iteritems(): assert info[1] == ensemble_size mean_delta = info[0] / info[1] mean_angle_delta.append(mean_delta) angle_delta_sq = mean_angle_delta * mean_angle_delta ensemble_angle_rmsd = math.sqrt(flex.mean_default(angle_delta_sq, 0)) # Chirality mean_chirality_delta = flex.double() for proxy, info in ensemble_chirality_deltas.iteritems(): assert info[1] == ensemble_size mean_delta = info[0] / info[1] mean_chirality_delta.append(mean_delta) chirality_delta_sq = mean_chirality_delta * mean_chirality_delta ensemble_chirality_rmsd = math.sqrt(flex.mean_default(chirality_delta_sq, 0)) # Planarity mean_planarity_delta = flex.double() for proxy, info in ensemble_planarity_deltas.iteritems(): assert info[1] == ensemble_size mean_delta = info[0] / info[1] mean_planarity_delta.append(mean_delta) planarity_delta_sq = mean_planarity_delta * mean_planarity_delta ensemble_planarity_rmsd = math.sqrt(flex.mean_default(planarity_delta_sq, 0)) # Dihedral mean_dihedral_delta = flex.double() for proxy, info in ensemble_dihedral_deltas.iteritems(): assert info[1] == ensemble_size mean_delta = info[0] / info[1] mean_dihedral_delta.append(mean_delta) dihedral_delta_sq = mean_dihedral_delta * mean_dihedral_delta ensemble_dihedral_rmsd = math.sqrt(flex.mean_default(dihedral_delta_sq, 0)) # Calculate <structure rmsd> assert ensemble_size == structures_bond_rmsd assert ensemble_size == structures_angle_rmsd assert ensemble_size == structures_chirality_rmsd assert ensemble_size == structures_planarity_rmsd assert ensemble_size == structures_dihedral_rmsd structure_bond_rmsd_mean = structures_bond_rmsd.min_max_mean().mean structure_angle_rmsd_mean = structures_angle_rmsd.min_max_mean().mean structure_chirality_rmsd_mean = structures_chirality_rmsd.min_max_mean().mean structure_planarity_rmsd_mean = structures_planarity_rmsd.min_max_mean().mean structure_dihedral_rmsd_mean = structures_dihedral_rmsd.min_max_mean().mean # Show summary utils.print_header("Ensemble RMSD summary", out = out) print >> out, " RMSD (mean delta per restraint)" print >> out, " bond : %.6g" % ensemble_bond_rmsd print >> out, " angle : %.6g" % ensemble_angle_rmsd print >> out, " chirality : %.6g" % ensemble_chirality_rmsd print >> out, " planarity : %.6g" % ensemble_planarity_rmsd print >> out, " dihedral : %.6g" % ensemble_dihedral_rmsd print >> out, " RMSD (mean RMSD per structure)" print >> out, " bond : %.6g" % structure_bond_rmsd_mean print >> out, " angle : %.6g" % structure_angle_rmsd_mean print >> out, " chirality : %.6g" % structure_chirality_rmsd_mean print >> out, " planarity : %.6g" % structure_planarity_rmsd_mean print >> out, " dihedral : %.6g" % structure_dihedral_rmsd_mean if ignore_hd: print >> out, "\n Calculated excluding H/D" else: print >> out, "\n Calculated including H/D" if return_pdb_string: ens_geo_pdb_string = "REMARK 3" ens_geo_pdb_string += "\nREMARK 3 NUMBER STRUCTURES IN ENSEMBLE : {0:5d}".format(ensemble_size) if ignore_hd: ens_geo_pdb_string += "\nREMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (EXCLUDING H/D)" else: ens_geo_pdb_string += "\nREMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (INCLUDING H/D)" ens_geo_pdb_string += "\nREMARK 3 RMSD (MEAN DELTA PER RESTRAINT)" ens_geo_pdb_string += "\nREMARK 3 BOND : {0:5.3f}".format(ensemble_bond_rmsd) ens_geo_pdb_string += "\nREMARK 3 ANGLE : {0:5.3f}".format(ensemble_angle_rmsd) ens_geo_pdb_string += "\nREMARK 3 CHIRALITY : {0:5.3f}".format(ensemble_chirality_rmsd) ens_geo_pdb_string += "\nREMARK 3 PLANARITY : {0:5.3f}".format(ensemble_planarity_rmsd) ens_geo_pdb_string += "\nREMARK 3 DIHEDRAL : {0:5.2f}".format(ensemble_dihedral_rmsd) ens_geo_pdb_string += "\nREMARK 3 RMSD (MEAN RMSD PER STRUCTURE)" ens_geo_pdb_string += "\nREMARK 3 BOND : {0:5.3f}".format(structure_bond_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3 ANGLE : {0:5.3f}".format(structure_angle_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3 CHIRALITY : {0:5.3f}".format(structure_chirality_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3 PLANARITY : {0:5.3f}".format(structure_planarity_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3 DIHEDRAL : {0:5.2f}".format(structure_dihedral_rmsd_mean) ens_geo_pdb_string += "\nREMARK 3" return ens_geo_pdb_string