def rotate_atoms(atomlist, axis, angle):
"""
rotate all atoms around an axis
"""
R = MolCo.rotation_matrix(axis, angle)
atomlist_rot = []
for (Z, pos) in atomlist:
atomlist_rot.append((Z, np.dot(R, pos)))
return atomlist_rot
def __init__(self, axis, angle):
self.axis = axis
self.angle = angle
self.R = MolCo.rotation_matrix(axis, angle)
self.S = MolCo.reflection_matrix(axis)