def test_loadall_sdf(molfile, natoms: int, nbonds: int) -> None:
ms = io.loadall(os.path.join(molpath, molfile))
assert len(ms) == 10
for m in ms:
assert io.numatoms(m) == natoms
assert io.numbonds(m) == nbonds
def test_loadall_mol2(molfile, natoms: int, nbonds: int) -> None:
try:
ms = io.loadall(os.path.join(molpath, molfile))
assert len(ms) == 10
for m in ms:
assert io.numatoms(m) == natoms
assert io.numbonds(m) == nbonds
except NotImplementedError: # Mol2MolSupplier in RDkit is not supported
pass # TODO: Warning
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_loadall_pdb_single_model() -> None:
"""
Test load_all function for PDB files when only a single model is present.
"""
try:
ms = io.loadall(os.path.join(molpath, "1a99_ligand.pdb"))
assert len(ms) == 1
assert io.numatoms(ms[0]) == 20
assert io.numbonds(ms[0]) == 19
except NotImplementedError: # PDBMolSupplier in RDkit is not supported
pass # TODO: Warning
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
def test_load_pdb(molfile, natoms: int, nbonds: int) -> None:
m = io.load(os.path.join(molpath, molfile))
assert io.numatoms(m) == natoms
assert io.numbonds(m) == nbonds