Now that we are adding more files we should be good about project
organization early while it is manageable and clean. 

We should try to keep data files in relevant folders (I'm uploading
the files I was testing with in a pdb_files directory - I didn't move
all the files into it yet and delete redundant files because I didn't
want to break anyone else's code ... try to do this though). We might
also consider making a "docs" folder for documentation (storing
proposal, writeup, relevant papers, etc...).