[TODO] Split `analysis.py`

[slochower]

It's getting unwieldy and not everything needs to be in the same class.

[jeff231li]

Maybe to improve the speed we could Cythonize some of the code and/or parallelize. Analyzing large trajectory files and convergence analysis with fractions takes a very long time to complete.

[slochower]

That's a good idea. I think some of the for loops can probably be avoided, and if not, can be coded in C since they're generally just looping through frames or coordinates.