def unify_residue_names_and_order(r1, r2):
r1n = get_one_letter_rna_dna_name(r1.resname)
r2n = get_one_letter_rna_dna_name(r2.resname)
message_template = "Residue with name '%s' cannot be processed "
message_template += "automatically \nfor nucleic acid basepair restraints "
message_template += "because of non-standard residue name."
if r1n is None:
raise Sorry(message_template % r1.resname)
if r2n is None:
raise Sorry(message_template % r2.resname)
# Translate DNA resname to RNA for unification
# RNA
if r1n > r2n:
t = r1
r1 = r2
r2 = t
t = r1n
r1n = r2n
r2n = t
r1n = 'U' if r1n == "T" else r1n
r2n = 'U' if r2n == "T" else r2n
return r1, r2, r1n, r2n
def get_angle_proxies_for_bond(atoms):
angle_values = {'O6 N4': [(122.8, 3.00), (117.3, 2.86)],
'N4 O6': [(117.3, 2.86), (122.8, 3.00)],
'N2 O2': [(122.2, 2.88), (120.7, 2.20)],
'O2 N2': [(120.7, 2.20), (122.2, 2.88)],
'N6 O4': [(115.6, 8.34), (121.2, 4.22)],
'O4 N6': [(121.2, 4.22), (115.6, 8.34)]}
proxies = []
anames = [atoms[0].name.strip(),
atoms[1].name.strip()]
rnames = [atoms[0].id_str().split()[1],
atoms[1].id_str().split()[1]]
if sorted(anames) == ['N1', 'N3']:
if get_one_letter_rna_dna_name(rnames[0]) in ['G', 'C']:
if anames[0] == 'N1':
vals = [(119.1, 2.59), (116.3, 2.66)]
else:
vals = [(116.3, 2.66), (119.1, 2.59)]
else:
if anames[0] == 'N1':
vals = [(116.2, 3.46), (115.8, 2.88)]
else:
vals = [(115.8, 2.88), (116.2, 3.46)]
else:
key = "%s %s" % (anames[0], anames[1])
vals = angle_values.get(key, None)
if vals is not None:
for i in range(2):
atoms_for_angle = [None, None, None]
aname = anames[i]
if (aname == 'N1' or aname == 'N2' or aname == 'N3' or aname == 'O2'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C2')
elif (aname == 'N4' or aname == 'O4'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C4')
elif (aname == 'N6' or aname == 'O6'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C6')
if atoms_for_angle[0] is not None:
atoms_for_angle[1] = atoms[i]
atoms_for_angle[2] = atoms[1-i]
if atoms_for_angle.count(None) == 0:
i_seqs_for_angle = [x.i_seq for x in atoms_for_angle]
p = geometry_restraints.angle_proxy(
i_seqs=i_seqs_for_angle,
angle_ideal=vals[i][0],
weight=1./vals[i][1]**2,
origin_id=1)
proxies.append(p)
return proxies
def get_angle_proxies_for_bond(atoms):
angle_values = {'O6 N4': [(122.8, 3.00), (117.3, 2.86)],
'N4 O6': [(117.3, 2.86), (122.8, 3.00)],
'N2 O2': [(122.2, 2.88), (120.7, 2.20)],
'O2 N2': [(120.7, 2.20), (122.2, 2.88)],
'N6 O4': [(115.6, 8.34), (121.2, 4.22)],
'O4 N6': [(121.2, 4.22), (115.6, 8.34)]}
proxies = []
anames = [atoms[0].name.strip(),
atoms[1].name.strip()]
rnames = [atoms[0].id_str().split()[1],
atoms[1].id_str().split()[1]]
if sorted(anames) == ['N1', 'N3']:
if get_one_letter_rna_dna_name(rnames[0]) in ['G', 'C']:
if anames[0] == 'N1':
vals = [(119.1, 2.59), (116.3, 2.66)]
else:
vals = [(116.3, 2.66), (119.1, 2.59)]
else:
if anames[0] == 'N1':
vals = [(116.2, 3.46), (115.8, 2.88)]
else:
vals = [(115.8, 2.88), (116.2, 3.46)]
else:
key = "%s %s" % (anames[0], anames[1])
vals = angle_values.get(key, None)
if vals is not None:
for i in range(2):
atoms_for_angle = [None, None, None]
aname = anames[i]
if (aname == 'N1' or aname == 'N2' or aname == 'N3' or aname == 'O2'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C2')
elif (aname == 'N4' or aname == 'O4'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C4')
elif (aname == 'N6' or aname == 'O6'):
atoms_for_angle[0] = atoms[i].parent().get_atom('C6')
if atoms_for_angle[0] is not None:
atoms_for_angle[1] = atoms[i]
atoms_for_angle[2] = atoms[1-i]
if atoms_for_angle.count(None) == 0:
i_seqs_for_angle = [x.i_seq for x in atoms_for_angle]
p = geometry_restraints.angle_proxy(
i_seqs=i_seqs_for_angle,
angle_ideal=vals[i][0],
weight=1./vals[i][1]**2,
origin_id=1)
proxies.append(p)
return proxies
def get_hb_lenght_targets(atoms):
restraint_values = {
'N6 O4': (3.00, 0.11),
'O6 N4': (2.93, 0.10),
'N2 O2': (2.78, 0.10)
}
anames = [atoms[0].name.strip(), atoms[1].name.strip()]
rnames = [atoms[0].parent().resname, atoms[1].parent().resname]
if sorted(anames) == ['N1', 'N3']:
if get_one_letter_rna_dna_name(rnames[0]) in ['G', 'C']:
return (2.88, 0.07) # G-C
else:
return (2.82, 0.08) # A-T
else:
key1 = "%s %s" % (anames[0], anames[1])
key2 = "%s %s" % (anames[1], anames[0])
vals = restraint_values.get(key1, None)
if vals is not None:
return vals
vals = restraint_values.get(key2, None)
if vals is not None:
return vals
return (2.91, 0.15) # values for all other bonds
def get_hb_lenght_targets(atoms):
restraint_values = { 'N6 O4' : (3.00, 0.11),
'O6 N4' : (2.93, 0.10),
'N2 O2' : (2.78, 0.10)
}
anames = [atoms[0].name.strip(),
atoms[1].name.strip()]
rnames = [atoms[0].parent().resname,
atoms[1].parent().resname]
if sorted(anames) == ['N1', 'N3']:
if get_one_letter_rna_dna_name(rnames[0]) in ['G', 'C']:
return (2.88, 0.07) # G-C
else:
return (2.82, 0.08) # A-T
else:
key1 = "%s %s" % (anames[0], anames[1])
key2 = "%s %s" % (anames[1], anames[0])
vals = restraint_values.get(key1, None)
if vals is not None:
return vals
vals = restraint_values.get(key2, None)
if vals is not None:
return vals
return (2.91, 0.15) # values for all other bonds
