def test_remove_nodes_from(atoms, bonds, interactions, removed, expected):
"""
Test whether molecule.remove_nodes_from also removes the corresponding
interactions
"""
molecule = vermouth.molecule.Molecule()
molecule.add_nodes_from(atoms)
molecule.add_edges_from(bonds)
for type_, atoms, params in interactions:
molecule.add_interaction(type_, atoms, params)
molecule.remove_nodes_from(removed)
assert molecule.interactions == expected
def molecule():
molecule = vermouth.molecule.Molecule()
molecule.meta['test'] = True
molecule.meta['test_mutable'] = [0, 1, 2]
# The node keys should not be in a sorted order as it would mask any issue
# due to the keys being accidentally sorted.
molecule.add_node(2, atomname='CC')
molecule.add_node(0, atomname='AA', mutable=[7, 8, 9])
molecule.add_node(1, atomname='BB')
molecule.add_edge(0, 1)
molecule.add_edge(0, 2)
molecule.add_interaction(
type_='bonds',
atoms=(0, 1),
parameters=['1', '2'],
meta={'unmutable': 0, 'mutable': [4, 5, 6]},
)
molecule.add_interaction(
type_='bonds',
atoms=(0, 2),
parameters=['a', 'b'],
)
return molecule