def _get_sorted(O,
unit_cell,
sites_cart,
pdb_atoms,
by_value="residual",
use_segids_in_place_of_chainids=False):
assert by_value in ["residual", "delta"]
if (O.size() == 0): return []
import cctbx.geometry_restraints
from scitbx.array_family import flex
deltas = flex.abs(O.deltas(sites_cart=sites_cart))
residuals = O.residuals(sites_cart=sites_cart)
if (by_value == "residual"):
data_to_sort = residuals
elif (by_value == "delta"):
data_to_sort = deltas
i_proxies_sorted = flex.sort_permutation(data=data_to_sort, reverse=True)
sorted_table = []
for i_proxy in i_proxies_sorted:
proxy = O[i_proxy]
sigma = cctbx.geometry_restraints.weight_as_sigma(proxy.weight)
score = sqrt(residuals[i_proxy]) / sigma
proxy_atoms = get_atoms_info(
pdb_atoms,
iselection=proxy.i_seqs,
use_segids_in_place_of_chainids=use_segids_in_place_of_chainids)
sorted_table.append((proxy, proxy_atoms))
return sorted_table
def _get_sorted (O,
unit_cell,
sites_cart,
pdb_atoms,
by_value="residual",
use_segids_in_place_of_chainids=False) :
assert by_value in ["residual", "delta"]
if (O.size() == 0): return []
import cctbx.geometry_restraints
from scitbx.array_family import flex
deltas = flex.abs(O.deltas(sites_cart=sites_cart))
residuals = O.residuals(sites_cart=sites_cart)
if (by_value == "residual"):
data_to_sort = residuals
elif (by_value == "delta"):
data_to_sort = deltas
i_proxies_sorted = flex.sort_permutation(data=data_to_sort, reverse=True)
sorted_table = []
for i_proxy in i_proxies_sorted:
proxy = O[i_proxy]
sigma = cctbx.geometry_restraints.weight_as_sigma(proxy.weight)
score = sqrt(residuals[i_proxy]) / sigma
proxy_atoms = get_atoms_info(pdb_atoms, iselection=proxy.i_seqs,
use_segids_in_place_of_chainids=use_segids_in_place_of_chainids)
sorted_table.append((proxy, proxy_atoms))
return sorted_table
def get_outliers(self,
proxies,
unit_cell,
sites_cart,
pdb_atoms,
sigma_cutoff,
outliers_only=True,
use_segids_in_place_of_chainids=False):
import cctbx.geometry_restraints
from scitbx.array_family import flex
site_labels = flex.bool(sites_cart.size(), True).iselection()
sorted_table, n_not_shown = proxies.get_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
unit_cell=unit_cell)
if (sorted_table is None): return []
outliers = []
for restraint_info in sorted_table:
(plane_atoms, rms_delta, residual) = restraint_info
i_seqs = [a[0] for a in plane_atoms]
deviation = max([a[1] / a[2] for a in plane_atoms])
plane_atoms_ = get_atoms_info(pdb_atoms, iselection=i_seqs)
outlier = planarity(atoms_info=plane_atoms_,
rms_deltas=rms_delta,
residual=residual,
delta_max=max([a[1] for a in plane_atoms]),
score=deviation,
outlier=True,
xyz=get_mean_xyz(plane_atoms_))
if (outlier.score > sigma_cutoff):
outliers.append(outlier)
elif (not outliers_only):
outlier.outlier = False
outliers.append(outlier)
return outliers
def get_outliers (self, proxies, unit_cell, sites_cart, pdb_atoms,
sigma_cutoff, outliers_only=True,
use_segids_in_place_of_chainids=False) :
import cctbx.geometry_restraints
from scitbx.array_family import flex
site_labels = flex.bool(sites_cart.size(), True).iselection()
sorted_table, n_not_shown = proxies.get_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
unit_cell=unit_cell)
if (sorted_table is None) : return []
outliers = []
for restraint_info in sorted_table :
(plane_atoms, rms_delta, residual) = restraint_info
i_seqs = [ a[0] for a in plane_atoms ]
deviation = max([ a[1] / a[2] for a in plane_atoms ])
plane_atoms_ = get_atoms_info(pdb_atoms, iselection=i_seqs)
outlier = planarity(
atoms_info=plane_atoms_,
rms_deltas=rms_delta,
residual=residual,
delta_max=max([ a[1] for a in plane_atoms ]),
score=deviation,
outlier=True,
xyz=get_mean_xyz(plane_atoms_))
if (outlier.score > sigma_cutoff) :
outliers.append(outlier)
elif (not outliers_only) :
outlier.outlier=False
outliers.append(outlier)
return outliers
def get_outliers (self, proxies, unit_cell, sites_cart, pdb_atoms,
sigma_cutoff, outliers_only=True,
use_segids_in_place_of_chainids=False) :
from scitbx.array_family import flex
site_labels = flex.bool(sites_cart.size(), True).iselection()
sorted_table, not_shown = proxies.get_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels)
# this can happen for C-alpha-only models, etc.
if (sorted_table is None) :
return []
outliers = []
for restraint_info in sorted_table :
(i_seqs, ideal, model, slack, delta, sigma, weight, residual, sym_op_j,
rt_mx) = restraint_info
bond_atoms = get_atoms_info(pdb_atoms, iselection=i_seqs,
use_segids_in_place_of_chainids=use_segids_in_place_of_chainids)
outlier = bond(
atoms_info=bond_atoms,
target=ideal,
model=model,
sigma=sigma,
slack=slack,
delta=delta,
residual=residual,
symop=sym_op_j,
outlier=True,
xyz=get_mean_xyz(bond_atoms))
if (outlier.score > sigma_cutoff) :
outliers.append(outlier)
elif (not outliers_only) :
outlier.outlier=False
outliers.append(outlier)
return outliers
def get_outliers(self,
proxies,
unit_cell,
sites_cart,
pdb_atoms,
sigma_cutoff,
outliers_only=True,
use_segids_in_place_of_chainids=False):
from scitbx.array_family import flex
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
site_labels = flex.bool(sites_cart.size(), True).iselection()
sorted_table, not_shown = proxies.get_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
origin_id=origin_ids.get_origin_id('covalent geometry'))
# this can happen for C-alpha-only models, etc.
if (sorted_table is None):
return []
outliers = []
for restraint_info in sorted_table:
(i_seq, j_seq, i_seqs, ideal, model, slack, delta, sigma, weight,
residual, sym_op_j, rt_mx) = restraint_info
bond_atoms = get_atoms_info(
pdb_atoms,
iselection=i_seqs,
use_segids_in_place_of_chainids=use_segids_in_place_of_chainids
)
if sym_op_j:
import scitbx
m3 = rt_mx.r().as_double()
m3 = scitbx.matrix.sqr(m3)
t = rt_mx.t().as_double()
t = scitbx.matrix.col((t[0], t[1], t[2]))
xyz = unit_cell.fractionalize(
flex.vec3_double([bond_atoms[1].xyz]))
new_xyz = unit_cell.orthogonalize(m3.elems * xyz + t)
bond_atoms[1].xyz = new_xyz[0]
outlier = bond(atoms_info=bond_atoms,
target=ideal,
model=model,
sigma=sigma,
slack=slack,
delta=delta,
residual=residual,
symop=sym_op_j,
outlier=True,
xyz=get_mean_xyz(bond_atoms))
if (outlier.score > sigma_cutoff):
outliers.append(outlier)
elif (not outliers_only):
outlier.outlier = False
outliers.append(outlier)
return outliers
def get_outliers (self, proxies, unit_cell, sites_cart, pdb_atoms,
sigma_cutoff, outliers_only=True,
use_segids_in_place_of_chainids=False) :
from scitbx.array_family import flex
site_labels = flex.bool(sites_cart.size(), True).iselection()
sorted_table, not_shown = proxies.get_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels)
# this can happen for C-alpha-only models, etc.
if (sorted_table is None) :
return []
outliers = []
for restraint_info in sorted_table :
(i_seqs, ideal, model, slack, delta, sigma, weight, residual, sym_op_j,
rt_mx) = restraint_info
bond_atoms = get_atoms_info(pdb_atoms, iselection=i_seqs,
use_segids_in_place_of_chainids=use_segids_in_place_of_chainids)
if sym_op_j:
import scitbx
m3 = rt_mx.r().as_double()
m3 = scitbx.matrix.sqr(m3)
t = rt_mx.t().as_double()
t = scitbx.matrix.col((t[0],t[1],t[2]))
xyz = unit_cell.fractionalize(flex.vec3_double([bond_atoms[1].xyz]))
new_xyz = unit_cell.orthogonalize(m3.elems*xyz+t)
bond_atoms[1].xyz = new_xyz[0]
outlier = bond(
atoms_info=bond_atoms,
target=ideal,
model=model,
sigma=sigma,
slack=slack,
delta=delta,
residual=residual,
symop=sym_op_j,
outlier=True,
xyz=get_mean_xyz(bond_atoms))
if (outlier.score > sigma_cutoff) :
outliers.append(outlier)
elif (not outliers_only) :
outlier.outlier=False
outliers.append(outlier)
return outliers
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)
i_seq_name_hash = utils.build_name_hash(pdb_hierarchy=pdb_hierarchy)
for proxy in geometry_restraints_manager.angle_proxies:
restraint = geometry_restraints.angle(sites_cart=sites_cart,
proxy=proxy)
atom1 = pdb_atoms[proxy.i_seqs[0]].name
atom2 = pdb_atoms[proxy.i_seqs[1]].name
atom3 = pdb_atoms[proxy.i_seqs[2]].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
or atom3.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_angle(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))
