mask.py module

Reads an Assignments.h5 file and 'masks' all unwanted (cis or trans) states by replacing the states with -1's. Then writes a modified assignments file which can be used to build cis/trans MSMs, etc.

At the moment this script is extremely specific and only usable for segregating CheY into cis/trans states, but I think it can easily be modified to be more general if need be (i.e. by adding new functions to calculate other masks which can be used by 'save_new_assignments')