def toebinding(seq, T=GLOBAL_TEMPERATURE, material='dna'):
n = len(seq)
(toe5len, toe3len) = toeholds(seq, T=T, material=material)
if toe5len < n:
toe5seq = seq[:toe5len] if toe5len > 0 else ''
toe3seq = seq[-toe3len:] if toe3len > 0 else ''
base = seq[toe5len]
fake_seq1 = toe5seq + base + 'GGGGTTTTCCCC' + WC(base) + toe3seq
fake_struct1 = '.' * toe5len + '(((((....)))))' + '.' * toe3len
fake_seq2 = WC(fake_seq1)
fake_struct2 = '.' * toe3len + '(((((....)))))' + '.' * toe5len
fake_struct_toe5 = '(' * toe5len + '(((((....)))))' + '.' * toe3len + '+' + '.' * toe3len + '(((((....)))))' + ')' * toe5len
fake_struct_toe3 = '.' * toe5len + '(((((....)))))' + '(' * toe3len + '+' + ')' * toe3len + '(((((....)))))' + '.' * toe5len
fake_struct_toes = '(' * toe5len + '(((((....)))))' + '(' * toe3len + '+' + ')' * toe3len + '(((((....)))))' + ')' * toe5len
# print "Sequence %s: %s %s and %s %s" % (seq,fake_seq1,fake_struct1,fake_seq2,fake_struct2)
dG1 = nupack.energy([fake_seq1], fake_struct1, T=T, material=material)
dG2 = nupack.energy([fake_seq2], fake_struct2, T=T, material=material)
if toe5len > 0:
dG_toe5 = nupack.energy([fake_seq1, fake_seq2], fake_struct_toe5, T=T, material=material) - dG1 - dG2
else:
dG_toe5 = 0
if toe3len > 0:
dG_toe3 = nupack.energy([fake_seq1, fake_seq2], fake_struct_toe3, T=T, material=material) - dG1 - dG2
else:
dG_toe3 = 0
if toe5len > 0 and toe3len > 0:
dG_toes = nupack.energy([fake_seq1, fake_seq2], fake_struct_toes, T=T, material=material) - dG1 - dG2
else:
dG_toes = 0
return max(-dG_toe5, -dG_toe3, -dG_toes)
else:
# print "Sequence %s: no structure!" % seq
return -duplex_dG(seq, T=T, material=material)
def _get_eos(self, sequence, structure, temperature, ligand=None):
#TODO nupack.energy can not handle unconnected cofold structures
return nupack.energy([self._change_cuts(sequence)],
self._change_cuts(structure),
material='rna',
pseudo=True,
T=temperature)