msmbuilder.cfep.CutCoordinate.set_coordinate_as_eigvector2

CutCoordinate.set_coordinate_as_eigvector2(lag_time=1, symmetrize='transpose')

Set the reaction coordinate to be the second eigenvector of the MSM generated by counts, the provided lag_time, and the provided symmetrization method.

Parameters:

lag_time : int

The MSM lag time to use (in units of frames) in the estimation of the MSM transition probability matrix from the counts matrix.

symmetrize : str {‘mle’, ‘transpose’, ‘none’}

Which symmetrization method to employ in the estimation of the MSM transition probability matrix from the counts matrix.