PyMOL is an OpenGL based molecular visualization system
PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!
(Historical) PyAcad makes Python available as a scripting language to AutoCAD/IntelliCAD. A builtin module "ads" allows to access and control most aspects of AutoCAD/IntelliCAD from Python programs.