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)
]))
def test_validate_bpform_bonds(self):
class TestDnaForm(core.BpForm):
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)
]))
util.validate_bpform_bonds(TestDnaForm)
alphabet = core.Alphabet()
alphabet.monomers.A = core.Monomer(
id='adenine',
structure='NC1=C2N=CNC2=NC=N1',
backbone_bond_atoms=[
core.Atom(molecule=core.Monomer, element='N', position=6)
],
backbone_displaced_atoms=[
core.Atom(molecule=core.Monomer, element='H', position=6)
],
)
class TestDnaForm(core.BpForm):
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=1000)
],
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)
]))
with self.assertRaises(ValueError):
util.validate_bpform_bonds(TestDnaForm)
alphabet = core.Alphabet()
alphabet.monomers.A = core.Monomer(
id='adenine',
structure='NC1=C2N=CNC2=NC=N1',
backbone_bond_atoms=[
core.Atom(molecule=core.Monomer, element='N', position=6)
],
backbone_displaced_atoms=[
core.Atom(molecule=core.Monomer, element='H', position=6)
],
)
class TestDnaForm(core.BpForm):
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='E', 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)
]))
with self.assertRaises(ValueError):
util.validate_bpform_bonds(TestDnaForm)
alphabet = core.Alphabet()
alphabet.monomers.A = core.Monomer(
id='adenine',
structure='NC1=C2N=CNC2=NC=N1',
backbone_bond_atoms=[
core.Atom(molecule=core.Monomer, element='N', position=6)
],
backbone_displaced_atoms=[
core.Atom(molecule=core.Monomer, element='H', position=6)
],
)
class TestDnaForm(core.BpForm):
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)
]))
util.validate_bpform_bonds(TestDnaForm)
alphabet = core.Alphabet()
alphabet.monomers.A = core.Monomer(
id='adenine',
structure='NC1=C2N=CNC2=NC=N1',
backbone_bond_atoms=[
core.Atom(molecule=core.Monomer, element='N', position=1000)
],
backbone_displaced_atoms=[
core.Atom(molecule=core.Monomer, element='H', position=6)
],
)
class TestDnaForm(core.BpForm):
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)
]))
with self.assertRaises(ValueError):
util.validate_bpform_bonds(TestDnaForm)
alphabet = core.Alphabet()
alphabet.monomers.A = core.Monomer(
id='adenine',
structure='NC1=C2N=CNC2=NC=N1',
backbone_bond_atoms=[
core.Atom(molecule=core.Monomer, element='E', position=6)
],
backbone_displaced_atoms=[
core.Atom(molecule=core.Monomer, element='H', position=6)
],
)
class TestDnaForm(core.BpForm):
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)
]))
with self.assertRaises(ValueError):
util.validate_bpform_bonds(TestDnaForm)
alphabet = core.Alphabet()
alphabet.monomers.A = core.Monomer(
id='adenine',
structure='NC1=C2N=CNC2=NC=N1',
backbone_bond_atoms=[
core.Atom(molecule=core.Monomer, element='N', position=6)
],
backbone_displaced_atoms=[
core.Atom(molecule=core.Monomer, element='H', position=6)
],
)
class TestDnaForm(core.BpForm):
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)
]))
with self.assertRaises(ValueError):
with mock.patch('wc_utils.util.chem.OpenBabelUtils.export',
side_effect=['smiles1', 'inchi1', 'inchi2']):
util.validate_bpform_bonds(TestDnaForm)
with self.assertRaises(ValueError):
with mock.patch.object(core.BpForm,
'get_formula',
return_value=EmpiricalFormula()):
util.validate_bpform_bonds(TestDnaForm)
with self.assertRaises(ValueError):
with mock.patch.object(core.BpForm,
'get_formula',
side_effect=[
EmpiricalFormula('C10H12N5O6P'),
EmpiricalFormula()
]):
util.validate_bpform_bonds(TestDnaForm)
with self.assertRaises(ValueError):
with mock.patch.object(core.BpForm,
'get_charge',
return_value=-100):
util.validate_bpform_bonds(TestDnaForm)
with self.assertRaises(ValueError):
with mock.patch.object(core.BpForm,
'get_charge',
side_effect=[-2, -100]):
util.validate_bpform_bonds(TestDnaForm)