msmbuilder.msm_analysis.check_for_bad_eigenvalues

msmbuilder.msm_analysis.check_for_bad_eigenvalues(eigenvalues, decimal=5, cutoff_value=0.999999)

Ensure that all eigenvalues are less than or equal to one

Having multiple eigenvalues of lambda>=1 suggests either non-ergodicity or numerical error.

Parameters:

Eigenvalues : ndarray

1D array of eigenvalues to check

decimal : deprecated (marked 6/27)

this doesn’t do anything

CutoffValue: float, optional :

Tolerance used

Notes

Checks that the first eigenvalue is within CutoffValue of 1, and that the second eigenvalue is not greater than CutoffValue