How to combine three non-orthogonal cylinders with sphere Description

I am trying to use blender to visualize a molecular systems. One of the issues I am running into is creating a box that shows the domain of the molecules. In order to do this I need to combine three non-orthogonal cylinders with a sphere in 8 places to form the box. I would prefer a solution that ends up with one fully connected mesh that is rounded (not necessarily perfectly spherical) and could be implemented using blender scripting.



What I have attempted


Adding a uv sphere to the end of the same radius 





Adding a uv sphere of slightly larger radius leads to jagged edges at sphere cylinder interface. If worst come to worst this is the solution I will use.
It might be an idea to use the skin modifier in combination with particles? It's pretty easy to set up and manipulate.


Create a mesh and then in Edit Mode delete 'Only Faces' - essentially leaving
you with a wire-frame.
Add the skin modifier and then a sub-surf modifier to smooth.
Create a Sphere object.
Add a particle system set to hair and choose Verts from Advanced
settings.
Under Display choose the Sphere object.


The particle system will have to be moved up to the top of the modifier stack.