def exercise_planarity():
weights = flex.double([1, 2, 3, 4])
for points, norm in [
([(1, 1, 0), (-1, -1, 0), (-1, 1, 0), (1, -1, 0)], (0, 0, 1)),
([(0, 1, 1), (0, -1, -1), (0, -1, 1), (0, 1, -1)], (1, 0, 0)),
([(1, 0, 1), (-1, 0, -1), (-1, 0, 1), (1, 0, -1)], (0, 1, 0)),
([(1, 1, -1), (-1, -1, 1), (-1, 1, -1), (1, -1, 1)], (0, 1, 1))
]:
norm = col(norm)
norm /= abs(norm)
for i_trial in range(5):
for i_pert in range(5):
if (i_trial == 0 and i_pert == 0):
sites = [col(v) for v in points]
rot_norm = norm
else:
shift = col([random.uniform(-10, 10) for i in range(3)])
rot = sqr(
euler_angles_as_matrix(
[random.uniform(0, 360) for i in range(3)]))
rot_norm = rot * norm
if (i_pert == 0):
sites = [rot * col(v) + shift for v in points]
else:
sites = []
for v in points:
f = 0.1
pert = col([(random.random() - 0.5) * f
for i in range(3)])
sites.append(rot * col(v) + shift + pert)
pl = geometry_restraints.planarity(sites=sites,
weights=weights)
n = col(pl.normal())
gradients_analytical = pl.gradients()
if (i_pert == 0):
assert abs(abs(n.dot(rot_norm)) - 1) < 1.e-5
assert approx_equal(pl.residual(), 0)
for grad in gradients_analytical:
assert approx_equal(grad, [0, 0, 0])
assert approx_equal(pl.residual(), pl.lambda_min())
residual_obj = residual_functor(
restraint_type=geometry_restraints.planarity,
weights=weights)
gradients_finite = finite_differences(sites, residual_obj)
assert approx_equal(gradients_finite, gradients_analytical)
def exercise_planarity():
weights = flex.double([1,2,3,4])
for points,norm in [([(1,1,0), (-1,-1,0), (-1,1,0), (1,-1,0)], (0,0,1)),
([(0,1,1), (0,-1,-1), (0,-1,1), (0,1,-1)], (1,0,0)),
([(1,0,1), (-1,0,-1), (-1,0,1), (1,0,-1)], (0,1,0)),
([(1,1,-1), (-1,-1,1), (-1,1,-1), (1,-1,1)], (0,1,1))]:
norm = col(norm)
norm /= abs(norm)
for i_trial in xrange(5):
for i_pert in xrange(5):
if (i_trial == 0 and i_pert == 0):
sites = [col(v) for v in points]
rot_norm = norm
else:
shift = col([random.uniform(-10,10) for i in xrange(3)])
rot = sqr(euler_angles_as_matrix(
[random.uniform(0,360) for i in xrange(3)]))
rot_norm = rot * norm
if (i_pert == 0):
sites = [rot*col(v)+shift for v in points]
else:
sites = []
for v in points:
f = 0.1
pert = col([(random.random()-0.5)*f for i in xrange(3)])
sites.append(rot*col(v)+shift+pert)
pl = geometry_restraints.planarity(sites=sites, weights=weights)
n = col(pl.normal())
gradients_analytical = pl.gradients()
if (i_pert == 0):
assert abs(abs(n.dot(rot_norm))-1) < 1.e-5
assert approx_equal(pl.residual(), 0)
for grad in gradients_analytical:
assert approx_equal(grad, [0,0,0])
assert approx_equal(pl.residual(), pl.lambda_min())
residual_obj = residual_functor(
restraint_type=geometry_restraints.planarity,
weights=weights)
gradients_finite = finite_differences(sites, residual_obj)
assert approx_equal(gradients_finite, gradients_analytical)
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
