def test_rotate():
atom = Atom(H, 0, 2, 0)
r = atom.rotation_matrix_to(x=4, y=0, z=0)
rotated = atom.rotated(r)
expected = Atom(H, 2, 0, 0)
assert rotated == expected
m = Molecule([atom])
assert m.with_atom_aligned_to(atom, x=1.0, y=0.0, z=0.0) == Molecule([expected])
assert m.rotated_about_z(np.pi / 2) == Molecule(atoms=[Atom(H, -2.0, 0.0, 0.0)])
def with_atom_aligned_to(self, atom: Atom, x: float, y: float,
z: float) -> "Molecule":
r = atom.rotation_matrix_to(x=x, y=y, z=z)
return self.rotated(r)
def test_atom_rotated():
a = Atom(H, 0.0, 2.0, 0.0)
r = a.rotation_matrix_to(1, 0, 0)
assert a.rotated(r) == Atom(H, 2.0, 0.0, 0.0)
