Translated everything to python. Also added functionality: now searches through
entire "molecules" directory, finds each .json.bak
1) Translated everything to Python
2) Added file generateBaks.py: this finds every .json file and copies it to a .json.bak
3) Added functionality: now calling filter.py searches all json files and filters them based on a
simple atom-counting distance function. The threshold distance is determined by a command line parameter.