animatable soft transition between sphere and cylinder

Question

I'm searching for a good way to animate a molecule-like structure with nice transitions between the spheres and the cylinders. So far, I'm using a skin modifier for the structure and a particle system to generate the spheres, but I'm afraid in this setup it would be hard to built in the tapering effect. I also tried to model the transition, but that resulted in a lot of z-fighting between the different links.

Here is a simplified setup to start with. On another layer, you can also find a modeled link, with the desired transition softness for reference, or to use in a different setup.

Answer 1

We can make use of Metaballs and Animation Nodes to achieve the desired effect.

The vertices of the mesh can be represented by a Ball Metaball, using such node tree:

We instance a Metaball Ball object, position it in place of the vertices and change its radius as we wish using an Object Attribute Output node and possibly its stiffness if you like.

Next, we can represent edges using Capsule Metaball, using such node tree:

We instance a Capsule Metaball, position it in the center of each edge, scale it using the size_x property based on the length of the edges using the Object Attribute Output node (We multiply it by 0.5 because capsule goes both ways), orient it along the edges using the Direction To Rotation node and control its stiffness and radius using Object Attribute Output node.

Which results:

Blend file for study:

Animating it and using non meshes structures is pretty easy in Animation Nodes. You may ask a question specific to exactly what you want to create. An example animation:

Answer 2

Okay, I found a way that works for me. It has some flaws, but will do the trick. I just modeled the transition, kept the origin of that part where the origin of the sphere is. Adding a copy location constraint and a track to constraint makes it follow nicely.

Here is the result:

there still is some z-fighting, but it's better than before.