def are_linked(
self,
return_value=False,
use_distance_always=False,
bond_cut_off=3., # Same as link_distance_cutoff of pdb_interpretation
allow_poly_ca=False,
poly_ca_cut_off=4.,
verbose=True):
'''
Need to add poly-Calpha chains
CA-CA 4.5 is use in CaBLAM, maybe shorter
'''
if allow_poly_ca:
assert 0
d2 = None
bond_cut_off *= bond_cut_off
for i, residue in enumerate(self):
if i == 0: continue
ccn1, outl1 = get_c_ca_n(residue, return_subset=True)
if self[i - 1] is None: # place holder for omega CDL
return False
ccn2, outl2 = get_c_ca_n(self[i - 1], return_subset=True)
if ccn1 is None:
for line in outl1:
if line not in self.errors:
self.errors.append(line)
break
if ccn2 is None:
for line in outl2:
if line not in self.errors:
self.errors.append(line)
break
n = ccn1[2]
c = ccn2[0]
if n is None or c is None: return False
if self.bond_params_table is None:
d2 = distance2(n, c)
if d2 < bond_cut_off: bond = True
else: bond = False
else:
bond = self.bond_params_table.lookup(c.i_seq, n.i_seq)
if not bond and use_distance_always:
# needed for situations where atoms are added and the i_seq is updated
if distance2(n, c) < bond_cut_off: bond = True
if not bond:
break
else:
return True
if return_value: return d2
return False
def are_linked(self,
return_value=False,
verbose=True):
d2 = None
for i, residue in enumerate(self):
if i==0: continue
ccn1, outl1 = get_c_ca_n(residue, return_subset=True)
if self[i-1] is None: # place holder for omega CDL
return False
ccn2, outl2 = get_c_ca_n(self[i-1], return_subset=True)
if ccn1 is None:
for line in outl1:
if line not in self.errors:
self.errors.append(line)
break
if ccn2 is None:
for line in outl2:
if line not in self.errors:
self.errors.append(line)
break
n = ccn1[2]
c = ccn2[0]
if n is None or c is None: return False
if self.bond_params_table is None:
d2 = distance2(n,c)
if d2<4: bond=True
else: bond=False
else:
bond=self.bond_params_table.lookup(c.i_seq, n.i_seq)
if not bond:
break
else:
return True
if return_value: return d2
return False
def are_linked(self, return_value=False, verbose=True):
d2 = None
for i, residue in enumerate(self):
if i==0: continue
ccn1, outl1 = get_c_ca_n(residue)
if self[i-1] is None: # place holder for omega CDL
return False
ccn2, outl2 = get_c_ca_n(self[i-1])
if ccn1 is None:
for line in outl1:
if line not in self.errors:
self.errors.append(line)
break
if ccn2 is None:
for line in outl2:
if line not in self.errors:
self.errors.append(line)
break
n = ccn1[2]
c = ccn2[0]
if self.bond_params_table is None:
d2 = distance2(n,c)
if d2<4: bond=True
else: bond=False
else:
bond=self.bond_params_table.lookup(c.i_seq, n.i_seq)
if not bond:
#assert c.i_seq
#assert n.i_seq
break
else:
return True
#assert d2
if return_value: return d2
return False
def are_linked(
self,
return_value=False,
use_distance_always=False,
bond_cut_off=3.5, # Same as link_distance_cutoff of pdb_interpretation
verbose=True,
):
bond_cut_off *= bond_cut_off
for i, residue in enumerate(self):
if i == 0: continue
op1, outl1 = self.get_o3prime_p(residue, return_subset=True)
# if self[i-1] is None: # place holder for omega CDL
# return False
op2, outl2 = self.get_o3prime_p(self[i - 1], return_subset=True)
# if ccn1 is None:
# for line in outl1:
# if line not in self.errors:
# self.errors.append(line)
# break
# if ccn2 is None:
# for line in outl2:
# if line not in self.errors:
# self.errors.append(line)
# break
p = op1[1]
o3prime = op2[0]
if p is None or o3prime is None: return False
if self.bond_params_table is None:
d2 = distance2(p, o3prime)
if d2 < bond_cut_off: bond = True
else: bond = False
else:
bond = self.bond_params_table.lookup(p.i_seq, o3prime.i_seq)
if not bond and use_distance_always:
# needed for situations where atoms are added and the i_seq is updated
if distance2(p, o3prime) < bond_cut_off: bond = True
if not bond:
break
else:
return True
if return_value: return d2
return False
def are_linked(self,
return_value=False,
use_distance_always=False,
bond_cut_off=2.,
verbose=True):
d2 = None
bond_cut_off *= bond_cut_off
for i, residue in enumerate(self):
if i == 0: continue
ccn1, outl1 = get_c_ca_n(residue, return_subset=True)
if self[i - 1] is None: # place holder for omega CDL
return False
ccn2, outl2 = get_c_ca_n(self[i - 1], return_subset=True)
if ccn1 is None:
for line in outl1:
if line not in self.errors:
self.errors.append(line)
break
if ccn2 is None:
for line in outl2:
if line not in self.errors:
self.errors.append(line)
break
n = ccn1[2]
c = ccn2[0]
if n is None or c is None: return False
if self.bond_params_table is None:
d2 = distance2(n, c)
if d2 < bond_cut_off: bond = True
else: bond = False
else:
bond = self.bond_params_table.lookup(c.i_seq, n.i_seq)
if not bond and use_distance_always:
# needed for situations where atoms are added and the i_seq is updated
if distance2(n, c) < bond_cut_off: bond = True
if not bond:
break
else:
return True
if return_value: return d2
return False