The molecule sample application from Oracle does much of what you are asking. Read the linked tutorial and study the source code provided for the sample application.
Regarding a couple of your questions.
if there is for example 2 cylinder between two sphere it must an arc or curved cylinder
This is possible. You would have to generate a custom TriangleMesh rather than using the pre-built Cylinder class. Essentially, you need to create an elliptical Torus and only display an arc portion of the Torus between your two nodes. I will not provide detailed instructions on how to do this in the context of a StackOverflow answer.
I want to know how the rotation can help in such situation and last question is it possible to make a scrollbar or just using event of Zoom ?
Study the Molecule sample code linked earlier as that has rotation and zoom capability.