def test_rotate_z(z: np.ndarray) -> None:
for deg, rad in [(0, 0), (45, np.pi / 4), (90, np.pi / 2)]:
v_deg = utils.rotate(np.array([1, 0, 0]), deg, z, units="deg")
v_rad = utils.rotate(np.array([1, 0, 0]), rad, z, units="rad")
assert np.allclose(v_deg, v_rad)
assert np.allclose(v_deg, np.array([np.cos(rad), np.sin(rad), 0]))
def test_molecule_rotate_z(mol: molecule.Molecule) -> None:
z_axis = np.array([0, 0, 1])
for angle in [0, 45, 90]:
rotated = np.zeros((len(mol), 3))
for i, coord in enumerate(mol.coordinates):
rotated[i] = utils.rotate(coord, angle, z_axis, units="deg")
mol.rotate(angle, z_axis, units="deg")
assert np.allclose(mol.coordinates, rotated)
# Reset
mol.rotate(-angle, z_axis, units="deg")
def test_molecule_rotate(mol: molecule.Molecule) -> None:
axis = np.random.rand(3)
for angle in np.random.rand(10) * 180:
rotated = np.zeros((len(mol), 3))
for i, coord in enumerate(mol.coordinates):
rotated[i] = utils.rotate(coord, angle, axis, units="deg")
mol.rotate(angle, axis, units="deg")
assert np.allclose(mol.coordinates, rotated)
# Reset
mol.rotate(-angle, axis, units="deg")
def rotate(self,
angle: float,
axis: np.ndarray,
units: str = "rad") -> None:
"""
Rotate molecule.
Parameters
----------
angle: float
Rotation angle
axis: np.ndarray
Axis of rotation (in 3D)
units: {"rad", "deg"}
Units of the angle (radians `rad` or degrees `deg`)
"""
self.coordinates = utils.rotate(self.coordinates, angle, axis, units)
def test_rotate_invalid():
with pytest.raises(ValueError):
utils.rotate(np.array([1, 0, 0]), 0, np.array([0, 0, 1]), units="none")