Molecules have forever been modeled geometrically, either as stick-diagrams, emphasizing the covalent bonds between atoms, or as space-filling diagrams, representing the space they occupy. This talk aims at further developing the geometric view of the molecular world. It introduces the alpha complex, which is a combinatorial object that leads to fast and robust algorithms for visualization and analysis. As an example, we will see that the alpha complex can be used to compute the volume and surface area without constructing the space-filling diagram. Similarly, it can be used to compute the weighted area derivative of the surface, which is believed to have a significant contribution to the force that drives the folding process simulated by molecular dynamics.