These guys have great ideas. I was thinking it would be easy to use the Atom Array to create your molecule look, but realized it only works with geometry and not points. I was thinking you could just make a medium-density mesh of your helix model, select points on it where you wanted your atoms, and then delete the rest and put it under an Atom Array. No luck. Your best bet is probably to model it in a straight line and then use the Spline Wrap deformer to twist it into the helix. To create your connector cylinders, you could try the Tracer. One Tracer won't do what you want, but if you have multiple connecting just the objects you want in the right places, it could be a good dynamic option. Throw it under a Sweep and you've got your connections.