you'd need a tracer with a distance parameter - there have been a couple in the past but none that I have now (don't know if that's because they stopped working due to version changes or if I just haven't needed one and haven't kept up) and given the construction I don't know if the distance method would work either. I played with it for a bit and I think this is it, maybe fewer cloners are possible... 11596_moleculegridtrial.c4d.zip
You could also just make a spline the shape you want one layer to be with points on the spline where each sphere goes. Put that spline (or splines) in a cloner and have it generate all the layers - then collapse that cloner with make polygonal. Then use the atom array on the resutling objects and just make the spheres bigger than the tubes.