def test_graph_from_adjacency_matrix(mol: molecule.Molecule, n_bonds: int) -> None:
G = mol.to_graph()
assert graph.num_vertices(G) == len(mol)
assert graph.num_edges(G) == n_bonds
for idx, atomicnum in enumerate(mol.atomicnums):
assert graph.vertex_property(G, "atomicnum", idx) == atomicnum
def test_adjacency_matrix_from_atomic_coordinates(mol: molecule.Molecule,
n_bonds: int) -> None:
A = graph.adjacency_matrix_from_atomic_coordinates(mol.atomicnums,
mol.coordinates)
G = graph.graph_from_adjacency_matrix(A)
assert graph.num_vertices(G) == len(mol)
assert graph.num_edges(G) == n_bonds
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_adjacency_matrix_from_atomic_coordinates_distance() -> None:
# Lithium hydride (LiH)
# H and Li have very different covalent radii
atomicnums = np.array([1, 3])
# Distance is the sum of covalent radii
d = sum([constants.anum_to_covalentradius[anum] for anum in atomicnums])
# Distance between two atoms is barely enough to create a bond
# If the covalent radii are not correct, no bond will be created
coordinates = np.array(
[[0, 0, 0], [0, 0, d + constants.connectivity_tolerance - 0.01]])
A = graph.adjacency_matrix_from_atomic_coordinates(atomicnums, coordinates)
G = graph.graph_from_adjacency_matrix(A)
assert graph.num_edges(G) == 1
def test_graph_from_atomic_coordinates_perception(mol: molecule.Molecule,
n_bonds: int) -> None:
m = copy.deepcopy(mol)
delattr(m, "adjacency_matrix")
m.G = None
with pytest.warns(UserWarning):
# Uses automatic bond perception
G = m.to_graph()
assert graph.num_vertices(G) == len(m)
assert graph.num_edges(G) == n_bonds
for idx, atomicnum in enumerate(mol.atomicnums):
assert graph.vertex_property(G, "aprops", idx) == atomicnum
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
def test_build_graph_node_features(property) -> None:
A = np.array([[0, 1, 1], [1, 0, 0], [1, 0, 1]])
G = graph.graph_from_adjacency_matrix(A, property)
assert graph.num_edges(G) == 3