Autophagy Python Prototyping

This repository is a place for me to work on a new module for my research project (https://github.com/StevenBackues/Autophagosome-Size-and-Number) in python (instead of R) where it will be easier for me to get help. The goal of this stuff is twofold. First, we want a better way to visualize how one of our simulated vacuoles might look if we could actually look at it with an electron microscope. standalone_vis.R does this and will ultimately be merged with some other visualization tools in the main project repository. Second, we want to take our model, which treats autophagic bodies in the vacuole as hard spheres, and squish those spheres together so they can pack more tightly and better mimic the actual biology. I am using a mass-spring-damper system with an attractive force to compress the spheres in a way that will hopefully look like a natural process. My two dimensional version works using a fake attractive force that simply pulls the centers of the bodies toward the center of mass. ThreeDimMSM is pretty broken at this point.