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.acid1 = Acid(self.compound2, 'a1', -1.74)
self.base1 = Base(self.compound1, 'a2', 16)
def to_compound(self):
"""Transforms the molecule dictionary into a Compound object"""
self.compound = [
Compound(self.molecule['atoms'], self.molecule['bonds'],
self.molecule['other_info']),
Compound({}, {}, {})
]
def compound_from_dict(atoms, bonds, other):
"""Builds a compound from dictionaries representing the atoms, bonds, and
other necessary information.
Parameters
----------
atoms : dict
Dictionary storing all of the atomic information. Should be in form
`{'a1': 'H', 'a2': 'O', 'a3': 'H'}`.
bonds : dict
Dictionary storing all of the bond information. Should be in form
`{'b1': ('a1', 'a2', {'order': 1}), 'b2': ('a2', 'a3', {'order': 1})}`.
other : dict
Dictionary storing any other available information about the molecule.
Returns
-------
Compound
The compound object that stores all of this information.
Notes
-----
- The `other` dictionary can have a lot of information. For example, data
necessary to write the data to a specific filetype. This should be stored
as something like `cml`: {information necessary}. Certain assumptions
are/will be made by the API and will be documented as necessary.
- This function is a thin wrapper for the Compound constructor.
"""
return Compound(atoms, bonds, other)
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 setUp(self):
self.water = Compound({
'a1': 'H',
'a2': 'H',
'a3': 'O'
}, {
'b1': ('a1', 'a3', {
'order': 1
}),
'b2': ('a2', 'a3', {
'order': 1
})
}, {})
def _parser_to_compound(parsed_file):
"""Takes the result of parsing a file and turns it into a compound object.
Parameters
----------
parsed_file : some parser object
The parser object that has already parsed a molecular file.
Returns
-------
Compound
The resulting compound.
"""
return Compound(parsed_file.atoms, parsed_file.bonds, parsed_file.other)
def test_water(self):
water = Compound({
'a1': 'H',
'a2': 'H',
'a3': 'O'
}, {
'b1': ('a1', 'a3', {
'order': 1
}),
'b2': ('a2', 'a3', {
'order': 1
})
}, {})
self.assertFalse(water.resonance_structures)
for atom in water.atoms.itervalues():
self.assertFalse(atom.could_resonate())
for bond in water.bonds.itervalues():
self.assertFalse(bond.could_resonate())
def test_eq_compound(self):
comp = Compound({}, {}, {})
prod = Product(comp, {})
self.assertEqual(prod, comp)
def test_getattr(self):
comp = Compound({}, {}, {})
prod = Product(comp, {})
self.assertFalse('node' in vars(prod))
self.assertTrue('node' in vars(comp))
self.assertIs(prod.node, comp.node)