def test_add_node():
a = Molecule(
{'a1': 'H', 'a2': 'O'},
{'b1': {'nodes': ('a1', 'a2')}}
)
a._add_node('a3', 'H')
assert 'a3' in a.atoms
assert a.atoms['a3'] == 'H'
def test_to_default():
a = Molecule(
{'a1': 'H', 'a2': 'O'},
{'b1': {'nodes': ('a1', 'a2')}}
)
b = a.to_default()
assert a == b
assert a is b
def test_add_edge():
a = Molecule(
{'a1': 'H', 'a2': 'O'},
{'b1': {'nodes': ('a1', 'a2')}}
)
a._add_edge('b2', {'nodes': ('a1', 'a2')})
assert 'b2' in a.bonds
assert a.bonds['b2'] == {'nodes': ('a1', 'a2'), 'id': 'b2'}
def test_add_existing_edge():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
args = ['b1', {'nodes': ('a1', 'a2')}]
function = a._add_edge
exception_type = KeyError
assert raises(exception_type, function, args)
def test_from_default():
a = Molecule(
{'a1': 'H', 'a2': 'O'},
{'b1': {'nodes': ('a1', 'a2')}}
)
b = Molecule.from_default(a)
assert a == b
assert a is b
def test_simple_acid_base_reaction():
acid = Molecule(
{'a1': 'H', 'a2': 'H', 'a3': 'H', 'a4': 'O'},
{'b1': {'nodes': ('a1', 'a4'), 'order': 1},
'b2': {'nodes': ('a2', 'a4'), 'order': 1},
'b3': {'nodes': ('a3', 'a4'), 'order': 1}
},
**{'id': 'Hydronium'}
)
base = Molecule(
{'a1': 'H', 'a2': 'O'},
{'b1': {'nodes': ('a1', 'a2'), 'order': 1}},
**{'id': 'Hydroxide'}
)
conditions = {
'pkas': {'Hydronium': -1.74, 'Hydroxide': 15.7},
'pka_points': {'Hydronium': 'a1', 'Hydroxide': 'a2'}
}
products = react([acid, base], conditions)
conjugate_acid = Molecule(
{'a1': 'H', 'a2': 'H', 'a3': 'O'},
{'b1': {'nodes': ('a1', 'a3'), 'order': 1},
'b2': {'nodes': ('a2', 'a3'), 'order': 1}
}
)
conjugate_base = Molecule(
{'a1': 'H', 'a2': 'H', 'a3': 'O'},
{'b1': {'nodes': ('a1', 'a3'), 'order': 1},
'b2': {'nodes': ('a2', 'a3'), 'order': 1}
}
)
assert products[0] == conjugate_acid
assert products[1] == conjugate_base
# Determining the salt isn't implemented
assert products[2] is None
def test_add_node():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
a._add_node('a3', 'H')
assert 'a3' in a.atoms
assert a.atoms['a3'] == 'H'
def test_from_default():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
b = Molecule.from_default(a)
assert a == b
assert a is b
def test_simple_equality():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
b = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
assert a == b
def test_add_edge():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
a._add_edge('b2', {'nodes': ('a1', 'a2')})
assert 'b2' in a.bonds
assert a.bonds['b2'] == {'nodes': ('a1', 'a2'), 'id': 'b2'}
def test_next_id_bond():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
assert a._next_free_bond_id == 'b0'
def test_next_id_invalid():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
assert raises(ValueError, a._next_id, ('c', ))
def test_next_id_atom():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
assert a._next_free_atom_id == 'a0'
def test_stupid_repr_test():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
assert repr(a)
def test_to_default():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
b = a.to_default()
assert a == b
assert a is b
def test_inequality():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
b = Molecule({'a1': 'N', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
assert a != b
def test_isomorphic_equality():
a = Molecule({'a1': 'H', 'a2': 'O'}, {'b1': {'nodes': ('a1', 'a2')}})
b = Molecule({'a2': 'H', 'a1': 'O'}, {'b2': {'nodes': ('a1', 'a2')}})
assert a == b