I would like to represent the movement of some parts of a molecule and divide it by criteria, I lready have the data and think I should use a driver to represent closely the distance I measured, while linking each sphere to each other with some sort of elastic ribbon.

As I am still new with blender, I do not know all options I have, I already tried armatures but have failed terribly, as it has way too parameters for me.

My problematic represented in images :