def __init__(self, seq=None):
super(TestDnaForm, self).__init__(
seq=seq,
alphabet=alphabet,
backbone=core.Backbone(
structure='OC1CCOC1COP([O-])([O-])=O',
monomer_bond_atoms=[
core.Atom(core.Backbone, element='C', position=4)
],
monomer_displaced_atoms=[
core.Atom(core.Backbone, element='H', position=4)
]),
bond=core.Bond(l_bond_atoms=[
core.Atom(core.Backbone, element='O', position=1)
],
r_bond_atoms=[
core.Atom(core.Backbone,
element='P',
position=9)
],
l_displaced_atoms=[
core.Atom(core.Backbone,
element='H',
position=1)
],
r_displaced_atoms=[
core.Atom(core.Backbone,
element='O',
position=11,
charge=-1)
]))
def __init__(self, seq=None):
super(TestDnaForm, self).__init__(
seq=seq,
alphabet=dna.canonical_dna_alphabet,
backbone=None,
bond=core.Bond(r_bond_atoms=[
core.Atom(core.Monomer, element='O', position=None)
],
l_bond_atoms=[
core.Atom(core.Monomer,
element='P',
position=None)
],
r_displaced_atoms=[
core.Atom(core.Monomer,
element='H',
position=None)
],
l_displaced_atoms=[
core.Atom(core.Monomer,
element='O',
position=None,
charge=-1)
]))