def conditions(self, cond):
if isinstance(cond, dict):
self.conditions = Conditions(cond)
elif isinstance(cond, Conditions):
self._conditions = cond
else:
raise TypeError("Conditions must be a Conditions object")
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 setUp(self):
self.compound1 = Compound({
"a1": "H",
"a2": "O"
}, {"b1": ("a1", "a2", {
'order': 1,
'chirality': None
})}, {"id": "Hydroxide"})
self.compound2 = 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 = 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 build_reaction_conditions(molecules, solvent, **kwargs):
"""Generates a Conditions object based on various factors.
Parameters
----------
molecules : list
A list of molecules present in the reaction. Each of these should
already have pertinent information, if possible.
solvent : Solvent
The solvent in the reaction. Should have information such as type of
solvent, pka, concentration, etc.
Returns
-------
cond : Conditions
The reaction conditions.
"""
cond_dict = {'molecules': molecules, 'solvent': solvent}
cond_dict.update(kwargs)
cond = Conditions(cond_dict)
return cond
def generate_conditions(self):
"""Generates the reaction conditions"""
self.conditions = Conditions({})
print self.conditions
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)