def test_adjacency_matrix_from_mol(mol) -> None:
natoms = io.numatoms(mol)
nbonds = io.numbonds(mol)
A = io.adjacency_matrix(mol)
assert A.shape == (natoms, natoms)
assert np.alltrue(A == A.T)
assert np.sum(A) == nbonds * 2
for i, j in io.bonds(mol):
assert A[i, j] == 1
def test_graph_from_adjacency_matrix(mol) -> None:
natoms = io.numatoms(mol)
nbonds = io.numbonds(mol)
A = io.adjacency_matrix(mol)
assert A.shape == (natoms, natoms)
assert np.alltrue(A == A.T)
assert np.sum(A) == nbonds * 2
G = graph.graph_from_adjacency_matrix(A)
assert graph.num_vertices(G) == natoms
assert graph.num_edges(G) == nbonds
def test_graph_from_adjacency_matrix_atomicnums(rawmol, mol) -> None:
natoms = io.numatoms(rawmol)
nbonds = io.numbonds(rawmol)
A = io.adjacency_matrix(rawmol)
assert len(mol) == natoms
assert mol.adjacency_matrix.shape == (natoms, natoms)
assert np.alltrue(mol.adjacency_matrix == A)
assert np.sum(mol.adjacency_matrix) == nbonds * 2
G = mol.to_graph()
assert graph.num_vertices(G) == natoms
assert graph.num_edges(G) == nbonds
for idx, atomicnum in enumerate(mol.atomicnums):
assert graph.vertex_property(G, "atomicnum", idx) == atomicnum