relative entropy between two MSM matrices

[euhruska]

feature request: calculation of the relative entropy between two MSM matrices of the same protein, like in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637129/

[marscher]

Do you need to have the same discretization for both matrices or does the method recover for slightly different state spaces?

[euhruska]

It will show a much higher relative entropy, but yes it will work. Just needs the same number of microstates. The easiest is to let the user specify which two MSM count matrices to compare. The reason to specify the count matrix instead of the transition matrix is the 1/N addition step.