Making an assignments file optional in PCCA.py

[jadeshi]

Hey, I was wondering if it might be worthwhile to give the PCCA.py script an option to only output MacroMappings.dat, and thus only require a transition matrix as an input. Right now, I'm working with a microstate transition matrix with some experimental transition probabilities that I added myself to describe a cis/trans isomerization that would otherwise be impractical to simulate, since it's on the order of several seconds. When I try to make a macrostate model using PCCA.py, it asks me for Assignments.Fixed.h5 as a required argument in order to write MacroAssignments.h5. However, since this is a custom-made transition matrix, I have no corresponding Assignments file for it, and I think all I need anyway is the MacroMappings.dat file to convert my microstate transition matrix into a macrostate one.

Thanks, Jade

EDIT: Actually, never mind. I didn't realize that there was a function in msmbuilder.lumping that does just this.