Controlling a rigged models muscle groups via script (C#)

I'm currently working on mapping real time movement that is input to unity as Quaternions or Euler angles to a rigged model. I've been able to get this input to control the transform.eulerAngles of the rigged models body parts, but that movement does look fluid or lifelike, and doesn't respect the models rotation limits.

         (ex:       `bodypart.eulerAngles = Input.transform.eulerAngles;`)

When Importing the model and configuring the rigging I see I can manipulate the models muscles in all appendages. When manipulating the muscle groups in that manner, all appendages move in respect to that muscle group the way they would in the real world (forearm moves, and shoulder moves slightly with it). Is there a way I can manipulate the muscle groups via script? Or what what would be a better way to map this realtime movement to the model that would give it more realistic motion?