def test_symmrmsd_rotated_benzene_stripped(angle: float) -> None:
mol1 = copy.deepcopy(molecules.benzene)
mol2 = copy.deepcopy(molecules.benzene)
mol2.rotate(angle, np.array([0, 0, 1]), units="deg")
mol1.strip()
mol2.strip()
assert (rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) > 0)
assert rmsd.rmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
minimize=True,
) == pytest.approx(0)
assert rmsd.hrmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(0, abs=1e-4)
assert rmsd.symmrmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
mol1.adjacency_matrix,
mol2.adjacency_matrix,
) == pytest.approx(0, abs=1e-4)
def test_rmsd_hungarian_centred(mol: molecule.Molecule) -> None:
mol1 = copy.deepcopy(mol)
mol2 = copy.deepcopy(mol)
mol2.translate(np.random.rand(3))
assert (rmsd.hrmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) > 0)
assert rmsd.hrmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
center=True,
) == pytest.approx(0)
def test_rmsd_hungarian_benzene_rotated(angle: float, tol: float) -> None:
mol1 = copy.deepcopy(molecules.benzene)
mol2 = copy.deepcopy(molecules.benzene)
assert rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(0)
assert rmsd.hrmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(0)
# Rotations different than 180 degrees introduce numerical errors (~1e-6)
mol2.rotate(angle, [0, 0, 1], units="deg")
assert (rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) > 0)
assert rmsd.hrmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(0, abs=tol)