Added final project with parser working.
Added project for Homework 5
Implemented a trivial Monty Hall simulation in a non-naive way.
Using N from 1 to 2000 generate Mathematica graph
Added HW3-II to Repository
Added HW3-I to repository
Fixed bugs in ProteinCavityFinder#updateBounds() and added "fat" Atom
support.
Implemented a Void class and a basic search algorithm.
Implemented cavity output
Added .gitignore for bin folder
Removed thrown exception from ProteinCavityFinder#main()
Removed files from package
Added some status output
Extended search boundaries and tweaked output file formatting
Added more progress messages and comments.
Fixed progress output
Fix progress and output file writing properly
Fixed misplaced paren
Fixed major void identifying logic issue
Switched to a long-based 3d point class key for the void hashmap, seems
to possibly be working now.