def get_rna_pucker_ref(self, test_pucker=False):
flags = geometry_restraints.flags.flags(default=True)
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
self.bond_dict = {}
self.angle_dict = {}
self.processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=self.sample_bases)
self.geometry = self.processed_pdb_file.geometry_restraints_manager()
#confirm puckers are correct
if test_pucker:
r = rna_validate()
r.pucker_evaluate(hierarchy=self.processed_pdb_file.
all_chain_proxies.pdb_hierarchy)
assert not r.pucker_states[0].is_2p
assert r.pucker_states[1].is_2p
i_seq_name_hash = utils.build_name_hash(
pdb_hierarchy=self.processed_pdb_file.all_chain_proxies.
pdb_hierarchy)
pair_proxies = self.geometry.pair_proxies(
flags=flags,
sites_cart=self.processed_pdb_file.all_chain_proxies.sites_cart)
bond_proxies = pair_proxies.bond_proxies
for bond in bond_proxies.simple:
atom1 = i_seq_name_hash[bond.i_seqs[0]][0:4]
atom2 = i_seq_name_hash[bond.i_seqs[1]][0:4]
if (atom1.strip() not in self.rna_backbone_atoms
and atom2.strip() not in self.rna_backbone_atoms):
continue
key = atom1 + atom2
sigma = (1 / bond.weight)**(.5)
try:
self.bond_dict[key].append((bond.distance_ideal, sigma))
except Exception:
self.bond_dict[key] = []
self.bond_dict[key].append((bond.distance_ideal, sigma))
for angle in self.geometry.angle_proxies:
atom1 = i_seq_name_hash[angle.i_seqs[0]][0:4]
atom2 = i_seq_name_hash[angle.i_seqs[1]][0:4]
atom3 = i_seq_name_hash[angle.i_seqs[2]][0:4]
if (atom1.strip() not in self.rna_backbone_atoms
and atom2.strip() not in self.rna_backbone_atoms
and atom3.strip() not in self.rna_backbone_atoms):
continue
key = atom1 + atom2 + atom3
sigma = (1 / angle.weight)**(.5)
try:
self.angle_dict[key].append((angle.angle_ideal, sigma))
except Exception:
self.angle_dict[key] = []
self.angle_dict[key].append((angle.angle_ideal, sigma))
def get_rna_pucker_ref(self, test_pucker=False):
flags = geometry_restraints.flags.flags(default=True)
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
self.bond_dict = {}
self.angle_dict = {}
self.processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=self.sample_bases)
self.geometry = self.processed_pdb_file.geometry_restraints_manager()
#confirm puckers are correct
if test_pucker:
r = rna_validate()
r.pucker_evaluate(
hierarchy=self.processed_pdb_file.all_chain_proxies.pdb_hierarchy)
assert not r.pucker_states[0].is_2p
assert r.pucker_states[1].is_2p
i_seq_name_hash = utils.build_name_hash(
pdb_hierarchy=self.processed_pdb_file.all_chain_proxies.pdb_hierarchy)
pair_proxies = self.geometry.pair_proxies(
flags=flags,
sites_cart=self.processed_pdb_file.all_chain_proxies.sites_cart)
bond_proxies = pair_proxies.bond_proxies
for bond in bond_proxies.simple:
atom1 = i_seq_name_hash[bond.i_seqs[0]][0:4]
atom2 = i_seq_name_hash[bond.i_seqs[1]][0:4]
if (atom1.strip() not in self.rna_backbone_atoms and
atom2.strip() not in self.rna_backbone_atoms):
continue
key = atom1+atom2
sigma = (1/bond.weight)**(.5)
try:
self.bond_dict[key].append((bond.distance_ideal, sigma))
except Exception:
self.bond_dict[key] = []
self.bond_dict[key].append((bond.distance_ideal, sigma))
for angle in self.geometry.angle_proxies:
atom1 = i_seq_name_hash[angle.i_seqs[0]][0:4]
atom2 = i_seq_name_hash[angle.i_seqs[1]][0:4]
atom3 = i_seq_name_hash[angle.i_seqs[2]][0:4]
if (atom1.strip() not in self.rna_backbone_atoms and
atom2.strip() not in self.rna_backbone_atoms and
atom3.strip() not in self.rna_backbone_atoms):
continue
key = atom1+atom2+atom3
sigma = (1/angle.weight)**(.5)
try:
self.angle_dict[key].append((angle.angle_ideal, sigma))
except Exception:
self.angle_dict[key] = []
self.angle_dict[key].append((angle.angle_ideal, sigma))
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)
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))