0fba025c0d92308682c4fb2401781ce33e17d5dd,pyemma/coordinates/transform/tica.py,EquilibriumCorrectedTICA,_estimate,#EquilibriumCorrectedTICA#Any#,423

Before Change

        self._covar.estimate(iterable, **kwargs)
        C0 = self._covar.cov

        C_0_eq = np.hstack(( // in modified basis
                    np.vstack((R.T.dot(C0).dot(R), self._covar.mean.dot(R))),
                    np.vstack((self._covar.mean.dot(R), 1.0))
                 ))
        C_tau_eq = K
        // find R_eq s.t. R_eq.T.dot(C_0_eq).dot(R_eq) = np.eye(s)
        s, Q = scl.eigh(C_0_eq)
        evmin = np.min(s)

After Change

        self._covar.estimate(iterable, **kwargs)
        C0 = self._covar.cov

        C_0_eq = np.zeros(shape=(r+1, r+1)) // in modified basis
        C_0_eq[0:r,0:r] = R.T.dot(C0).dot(R)
        C_0_eq[0:r, r] = self._covar.mean.dot(R)
        C_0_eq[r, 0:r] = self._covar.mean.dot(R)
        C_0_eq[r,r] = 1.0
        C_tau_eq = K
        // find R_eq s.t. R_eq.T.dot(C_0_eq).dot(R_eq) = np.eye(s)
        s, Q = scl.eigh(C_0_eq)

Instances