msmbuilder.SCRE.ConstructRateFromParams¶

msmbuilder.SCRE.ConstructRateFromParams(parameters, mapping, populations, K0)[source]¶

Construct a rate matrix from a flat array of parameters.

Parameters:	parameters : list Flat list of parameters mapping : list Mapping from flat indices to (2d) array indices. populations : ndarray stationary populations of model K0 : ndarray Initial rate matrix.
Returns:	K : ndarray rate matrix

Notes

The returned matrix K is such that

K[mapping.T[0],mapping.T[1]] = abs(parameters)