test_featurereader_and_tica_projection.py 文件源码

def test_covariances_and_eigenvalues(self):
        reader = FeatureReader(self.trajnames, self.temppdb)
        for tau in [1, 10, 100, 1000, 2000]:
            trans = tica(lag=tau, dim=self.dim, kinetic_map=False)
            trans.data_producer = reader

            log.info('number of trajectories reported by tica %d' % trans.number_of_trajectories())
            trans.parametrize()
            data = trans.get_output()

            log.info('max. eigenvalue: %f' % np.max(trans.eigenvalues))
            self.assertTrue(np.all(trans.eigenvalues <= 1.0))
            # check ICs
            check = tica(data=data, lag=tau, dim=self.dim)

            np.testing.assert_allclose(np.eye(self.dim), check.cov, atol=1e-8)
            np.testing.assert_allclose(check.mean, 0.0, atol=1e-8)
            ic_cov_tau = np.zeros((self.dim, self.dim))
            ic_cov_tau[np.diag_indices(self.dim)] = trans.eigenvalues
            np.testing.assert_allclose(ic_cov_tau, check.cov_tau, atol=1e-8)