Fix docs [WIP]

I'm working on creating a draft of the documentation based on MDTraj's documentation framework.
no problem. I should figure out how to just `pip install sphinx_rtd_theme`, and be done with it. the problem is that I made a couple custom modifications to the CSS, and added the version dropdown menu. Perhaps I should just make a separate package for the customized theme on github/pypi/binstar, so that it doesn't have to be duplicated.