molecule in 3d

Hello,

I want to represent chemical molecules in 3D. it comes to no complex molecules, rather simple like alcohol or methane. ok, the player gets a choice of atoms and this can attach to a given atom, he moves the atom to another atom,the connection blends in. I have no experience with Stage3D, I'm only using starling,

is there a simple Stage3D framework with which I can implement this?

I would like to build the molecule in cinema and export as colada. if the individual groups inside the model, like atoms or connections, are named, I could fade them in.

would be very nice if someone shows the right way.

regards