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