def _add_edge(self, key, first, second, rest=None):
"""Adds a single edge.
Parameters
----------
key : string
The key associated with the given atom.
first : string
The key of one of the atoms in the bond
second : string
The key of the other atom in the bond
rest : dict, optional
Other information relevant to the bond.
"""
if rest is None:
rest = {}
if key in self.bonds:
raise KeyError("There is already a bond {}".format(key))
else:
bond = Bond(self.atoms[first], self.atoms[second], **rest)
self.add_edge(first, second, key=key, bond_obj=bond)
self.bonds[key] = bond
def test_add_lone_pair_raises_VE_if_bonded(self):
oxygen = Atom('O')
Bond(oxygen, self.atom, order=1)
with self.assertRaises(ValenceError):
self.atom.add_lone_pair()
def test_remove_bond(self):
oxygen = Atom('O')
bond = Bond(oxygen, self.atom, order=1)
self.atom.remove_bond(bond, other=oxygen)
self.assertNotIn(bond, self.atom.bonds)
self.assertNotIn(bond, oxygen.bonds)
def test_bonded_hydrogen_steric_num(self):
oxygen = Atom('O')
Bond(oxygen, self.atom, order=1)
self.assertEqual(self.atom.steric_num, 1)
def test_add_bond(self):
oxygen = Atom('O')
bond = Bond(oxygen, self.atom, order=1)
self.assertIs(bond, oxygen.bonds[0])
self.assertIs(bond, self.atom.bonds[0])
def test_hydrogen_bonded_charge(self):
oxygen = Atom('O')
oxygen.add_lone_pair(3)
Bond(oxygen, self.atom, order=1)
self.assertEqual(self.atom.charge, 0)
self.assertEqual(oxygen.charge, -1)
def test_serialize_bond(self):
self.assertEqual(
json.dumps(Bond(Atom('H'), Atom('H')),
cls=compounds._ChemicalSerializer),
'{"members": [{"symbol": "H"}, {"symbol": "H"}]}')