def setUp(self):
self.compound1 = compounds.Compound({
"a1": "H",
"a2": "O"
}, {"b1": ("a1", "a2", {
'order': 1,
'chirality': None
})}, {"id": "Hydroxide"})
self.compound2 = compounds.Compound(
{
"a1": "H",
"a2": "H",
"a3": "O",
"a4": "H"
}, {
"b1": ("a1", "a3", {
'order': 1,
'chirality': None
}),
"b2": ("a2", "a3", {
'order': 1,
'chirality': None
}),
"b3": ("a3", "a4", {
'order': 1,
'chirality': None
})
}, {"id": "Hydronium"})
self.acid1 = Acid(self.compound2, 'a1', -1.74)
self.base1 = Base(self.compound1, 'a2', 15.7)
self.conditions1 = Conditions({})
self.acidbase1 = AcidBase(self.acid1, self.base1, self.conditions1)
def test_negative_charge(self):
compound = compounds.Compound({
"a1": "H",
"a2": "O"
}, {"b1": ("a1", "a2", {
"order": 1
})}, {})
self.assertEqual(compound.charge, -1)
def setUp(self):
self.compound1 = compounds.Compound({
"a1": "H",
"a2": "O"
}, {"b1": ("a1", "a2", {
'order': 1,
'chirality': None
})}, {"id": "Hydroxide"})
self.compound2 = compounds.Compound(
{
"a1": "H",
"a2": "H",
"a3": "O",
"a4": "H"
}, {
"b1": ("a1", "a3", {
'order': 1,
'chirality': None
}),
"b2": ("a2", "a3", {
'order': 1,
'chirality': None
}),
"b3": ("a3", "a4", {
'order': 1,
'chirality': None
})
}, {"id": "Hydronium"})
self.compound3 = compounds.Compound({
'a1': 'H',
'a2': 'O',
'a3': 'H'
}, {
'b1': ('a1', 'a2', {
'order': 1,
'chirality': None
}),
'b2': ('a2', 'a3', {
'order': 1,
'chirality': None
})
}, {'id': "Water"})
self.acid = Acid(self.compound2, 'a1', -1.74)
self.base = Base(self.compound1, 'a2', 16)
self.conj_acid = Acid(self.compound3, 'a3', 16)
self.conditions = Conditions({})
def test_hydroxide_hydronium(self):
self.maxDiff = None
parts = self.acidbase1.react()
majors, minors = parts.major, parts.minor
major = (Product(
compounds.Compound({
"a1": "H",
"a2": "O",
"a3": "H"
}, {
"b1": ("a1", "a2", {
'order': 1,
'chirality': None
}),
"b2": ("a2", "a3", {
'order': 1,
'chirality': None
})
}, {"id": "Conjugate acid of Hydroxide"}), 50),
Product(
compounds.Compound({
"a1": "H",
"a2": "O",
"a3": "H"
}, {
"b1": ("a1", "a2", {
'order': 1,
'chirality': None
}),
"b2": ("a2", "a3", {
'order': 1,
'chirality': None
})
}, {"id": "Conjugate base of Hydronium"}), 50))
minor = ()
expected = Products(major, minor)
exp_majors, exp_minors = expected.major, expected.minor
self.assertEqual(exp_minors, minors)
self.assertEqual(exp_majors, majors)
def setUp(self):
self.compound1 = compounds.Compound({
"a1": "H",
"a2": "H",
"a3": "O"
}, {
"b1": ("a1", "a3", {
'order': 1,
'chirality': None
}),
"b2": ("a2", "a3", {
'order': 1,
'chirality': None
})
}, {"id": "Water"})
def test_isomorphism2(self):
self.compound4 = compounds.Compound({
'a1': 'H',
'a3': 'O',
'a2': 'H'
}, {
'b1': ('a1', 'a3', {
'order': 1,
'chirality': None
}),
'b2': ('a2', 'a3', {
'order': 1,
'chirality': None
})
})
self.assertEquals(self.compound3, self.compound4)
def test_positive_charge(self):
compound = compounds.Compound(
{
"a1": "H",
"a2": "H",
"a3": "H",
"a4": "O"
}, {
"b1": ("a1", "a4", {
"order": 1
}),
"b2": ("a2", "a4", {
"order": 1
}),
"b3": ("a3", "a4", {
"order": 1
})
}, {})
self.assertEqual(compound.charge, 1)
def _calculate_products(self):
"""Determines the expected products of the reaction.
Returns
-------
tuple
A tuple of tuples. The form is something like
(Major Product, Minor Product)
which can be further broken down into
((Conj. Acid, Conj. Base, Salt), (Empty Product))
Notes
-----
This will generally be the conjugate acid and base, as well as some salt
(or other byproduct). This method is still incomplete - it lacks
support for generating the salt from ionic compounds.
"""
conjugate_acid = None
conjugate_base = None
salt = None # NYI
acid, base = deepcopy(self.acid[0]), deepcopy(self.base[0])
conjugate_acid = base.to_conjugate_acid()
other = acid.other_info
try:
other['id'] = "Conjugate base of {}".format(acid.other_info['id'])
except KeyError:
other['id'] = "Unknown Base"
conjugate_base = compounds.Compound(
*self._remove_node(acid, self.acid[1]), other_info=other)
return ((Product(conjugate_acid, 50),
Product(conjugate_base, 50),
Product(salt, 0)),
(Product(None, 0),))
def setUp(self):
self.compound1 = compounds.Compound({
"a1": "H",
"a2": "H",
"a3": "O"
}, {
"b1": ("a1", "a3", {
'order': 1,
'chirality': None
}),
"b2": ("a2", "a3", {
'order': 1,
'chirality': None
})
}, {"id": "Water"})
self.compound2 = compounds.Compound(
{
"a1": "H",
"a2": "H",
"a3": "O",
"a4": "H"
}, {
"b1": ("a1", "a3", {
'order': 1,
'chirality': None
}),
"b2": ("a2", "a3", {
'order': 1,
'chirality': None
}),
"b3": ("a3", "a4", {
'order': 1,
'chirality': None
})
}, {"id": "Hydronium"})
self.acid1 = Acid(self.compound2, 'a1', -1.74)
self.base1 = Base(self.compound1, 'a2', -1.74)
self.conditions1 = Conditions({})
self.acidbase1 = AcidBase(self.acid1, self.base1, self.conditions1)
self.hydroiodic = Acid(
compounds.Compound({
"a1": "H",
"a2": "I"
}, {"b1": ("a1", "a2", {
'order': 1,
'chirality': None
})}, {"id": "Hydroiodic acid"}), 'a1', -10)
self.conditions2 = Conditions({
'pka': -10,
'acidic': True,
'pka_molecule': self.hydroiodic,
'pka_location': 'a1'
})
self.acidbase2 = AcidBase(self.acid1, self.base1, self.conditions2)
self.hydroxide = Base(
compounds.Compound({
"a1": "H",
"a2": "O",
"a3": "Na"
}, {
"b1": ("a1", "a2", {
'order': 1,
'chirality': None
}),
"b2": ("a2", "a3", {
'order': 1,
'chirality': None
})
}, {"id": "Sodium Hydroxide"}), 'a2', 15.7)
self.conditions3 = Conditions({
'pka': 15.7,
'basic': True,
'pka_molecule': self.hydroxide,
'pka_location': 'a2'
})
self.acidbase3 = AcidBase(self.acid1, self.base1, self.conditions3)
def test_repr(self):
assert repr(compounds._CompoundWrapper(compounds.Compound({}, {}, {})))
def test_string(self):
assert str(compounds._CompoundWrapper(compounds.Compound({}, {}, {})))
def setUp(self):
# Water
self.compound1 = compounds.Compound({
"a1": "H",
"a2": "H",
"a3": "O"
}, {
"b1": ("a1", "a3", {
'order': 1,
'chirality': None
}),
"b2": ("a2", "a3", {
'order': 1,
'chirality': None
})
}, {"id": "Water"})
# Ketone
self.compound2 = compounds.Compound(
{
"a1": "H",
"a2": "H",
"a3": "H",
"a4": "H",
"a5": "H",
"a6": "H",
"a7": "C",
"a8": "C",
"a9": "C",
"a10": "O"
}, {
"b0": ("a1", "a7", {
'order': 1,
'chirality': None
}),
"b1": ("a2", "a7", {
'order': 1,
'chirality': None
}),
"b2": ("a3", "a7", {
'order': 1,
'chirality': None
}),
"b3": ("a4", "a9", {
'order': 1,
'chirality': None
}),
"b4": ("a5", "a9", {
'order': 1,
'chirality': None
}),
"b5": ("a6", "a9", {
'order': 1,
'chirality': None
}),
"b6": ("a7", "a8", {
'order': 1,
'chirality': None
}),
"b7": ("a9", "a8", {
'order': 1,
'chirality': None
}),
"b8": ("a8", "a10", {
'order': 2,
'chirality': None
})
}, {})