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
