def test_topology_atom_element(self):
"""Test getters of TopologyAtom element and atomic number"""
topology = Topology()
topology.add_molecule(self.toluene_from_sdf)
first_element = topology.atom(0).element
eighth_element = topology.atom(7).element
# Check if types/instances are correct
assert isinstance(first_element, element.Element)
assert isinstance(eighth_element, element.Element)
# Make sure first is a carbon element and eighth is a hydrogen element
assert first_element == element.carbon
assert eighth_element == element.hydrogen
def test_get_atom(self):
"""Test Topology.atom function (atom lookup from index)"""
topology = Topology()
topology.add_molecule(self.ethane_from_smiles)
with self.assertRaises(Exception) as context:
topology_atom = topology.atom(-1)
# Make sure we get 2 carbons and 8 hydrogens
n_carbons = 0
n_hydrogens = 0
for index in range(8):
if topology.atom(index).atomic_number == 6:
n_carbons += 1
if topology.atom(index).atomic_number == 1:
n_hydrogens += 1
assert n_carbons == 2
assert n_hydrogens == 6
with self.assertRaises(Exception) as context:
topology_atom = topology.atom(8)