Index

_

__init__() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.CustomFeature method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.estimation.covariance.LaggedCovariance method) (pyemma.coordinates.pipelines.Pipeline method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator method) (pyemma.coordinates.transform.VAMPModel method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.ChapmanKolmogorovValidator method) (pyemma.msm.HMSM method) (pyemma.msm.ImpliedTimescales method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.PCCA method) (pyemma.msm.ReactiveFlux method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.plots.NetworkPlot method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.MEMM method) (pyemma.thermo.MultiThermModel method) (pyemma.thermo.StationaryModel method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method)

A

A (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) active_count_fraction (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) active_set (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.MultiThermModel attribute) (pyemma.thermo.StationaryModel attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] active_state_fraction (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) active_state_indexes (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) add_all() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_angles() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_backbone_torsions() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_chi1_torsions() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method)

add_contacts() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_custom_feature() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_custom_func() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_dihedrals() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_distances() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_distances_ca() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_element() (pyemma.coordinates.pipelines.Discretizer method) (pyemma.coordinates.pipelines.Pipeline method), [1], [2], [3] add_group_COM() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_group_mindist() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_inverse_distances() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_minrmsd_to_ref() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_residue_COM() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_residue_mindist() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_selection() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) add_sidechain_torsions() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) assign() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) assign_to_centers() (in module pyemma.coordinates) AssignCenters (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.assign)

B

B (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) backward_committor (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) bayesian_hidden_markov_model() (in module pyemma.msm)

bayesian_markov_model() (in module pyemma.msm) BayesianHMSM (class in pyemma.msm) (class in pyemma.msm.estimators.bayesian_hmsm) BayesianMSM (class in pyemma.msm) (class in pyemma.msm.estimators.bayesian_msm)

C

C00_ (pyemma.coordinates.estimation.covariance.LaggedCovariance attribute) C0t_ (pyemma.coordinates.estimation.covariance.LaggedCovariance attribute) cfg_dir (pyemma.util._config.Config attribute) ChapmanKolmogorovValidator (class in pyemma.msm) check_version (pyemma.util._config.Config attribute) chunksize (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.pipelines.Pipeline attribute), [1] (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) cktest() (pyemma.coordinates.transform.VAMP method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) cluster_centers_ (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) cluster_kmeans() (in module pyemma.coordinates) cluster_mini_batch_kmeans() (in module pyemma.coordinates) cluster_regspace() (in module pyemma.coordinates) cluster_uniform_time() (in module pyemma.coordinates) clustercenters (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) coarse_grain() (pyemma.msm.BayesianMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.ReactiveFlux method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.ReactiveFlux method) combine_sources() (in module pyemma.coordinates) committor (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) committor_backward() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method)

committor_forward() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) Config (class in pyemma.util._config) connected_sets (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) connectivity (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) converged (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) coordinates_check_output (pyemma.util._config.Config attribute) correlation() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) count_matrix_active (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) count_matrix_full (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) cov (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.tica.TICA attribute) cov_tau (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.tica.TICA attribute) covariance_lagged() (in module pyemma.coordinates) Ctt_ (pyemma.coordinates.estimation.covariance.LaggedCovariance attribute) cumvar (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.VAMPModel attribute) (pyemma.coordinates.transform.tica.TICA attribute) CustomFeature (class in pyemma.coordinates.data)

D

data (pyemma.coordinates.data.DataInMemory attribute) data_producer (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) DataInMemory (class in pyemma.coordinates.data) default_chunksize (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) (pyemma.util._config.Config attribute) DEFAULT_CONFIG_DIR (pyemma.util._config.Config attribute) default_config_file (pyemma.util._config.Config attribute) DEFAULT_CONFIG_FILE_NAME (pyemma.util._config.Config attribute) default_logging_file (pyemma.util._config.Config attribute) DEFAULT_LOGGING_FILE_NAME (pyemma.util._config.Config attribute) describe() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) dim (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.tica.TICA attribute) dimension() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPModel method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method)

discrete_trajectories_active (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) discrete_trajectories_full (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) discrete_trajectories_lagged (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) discrete_trajectories_obs (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) Discretizer (class in pyemma.coordinates.pipelines) discretizer() (in module pyemma.coordinates) dmin (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) dt_model (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.models.msm.MSM attribute) dt_traj (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) dtrajs (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.pipelines.Discretizer attribute) dtrajs_active (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) dtrajs_full (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) dtrajs_lagged (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) dtrajs_obs (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) DTRAM (class in pyemma.thermo) dtram() (in module pyemma.thermo)

E

effective_count_matrix (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) eigenvalues (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.tica.TICA attribute) eigenvalues() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) eigenvalues_OOM (pyemma.msm.OOMReweightedMSM attribute) eigenvectors (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.tica.TICA attribute) eigenvectors_left() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) eigenvectors_left_obs (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) eigenvectors_right() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) eigenvectors_right_obs (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) epsilon (pyemma.coordinates.transform.VAMP attribute) estimate() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.estimation.covariance.LaggedCovariance method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.ChapmanKolmogorovValidator method) (pyemma.msm.ImpliedTimescales method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2] (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method)

estimate_hidden_markov_model() (in module pyemma.msm) estimate_markov_model() (in module pyemma.msm) estimate_multi_temperature() (in module pyemma.thermo) estimate_umbrella_sampling() (in module pyemma.thermo) estimates (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator attribute) (pyemma.msm.ChapmanKolmogorovValidator attribute) estimates_conf (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator attribute) (pyemma.msm.ChapmanKolmogorovValidator attribute) estimators (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) expectation() (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPModel method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.MEMM method) (pyemma.thermo.MultiThermModel method) (pyemma.thermo.StationaryModel method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method) (pyemma.thermo.models.memm.MEMM method), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel method), [1], [2], [3]

F

f (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.MultiThermModel attribute) (pyemma.thermo.StationaryModel attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] f_full_state (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] feature_PC_correlation (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.pca.PCA attribute) feature_TIC_correlation (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.tica.TICA attribute) FeatureReader (class in pyemma.coordinates.data) featurizer() (in module pyemma.coordinates) filenames (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) fingerprint_correlation() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) fingerprint_relaxation() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) fit() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.estimation.covariance.LaggedCovariance method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.ChapmanKolmogorovValidator method) (pyemma.msm.ImpliedTimescales method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2] (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method)

fit_predict() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) fit_transform() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) fixed_seed (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) flux (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) force_constants (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) forward_committor (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) fraction_of_frames (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) FragmentedTrajectoryReader (class in pyemma.coordinates.data) free_energies (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.MultiThermModel attribute) (pyemma.thermo.StationaryModel attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] free_energies_full_state (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3]

G

generate_traj() (pyemma.msm.BayesianMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) get_model_params() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.transform.VAMPModel method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.ReactiveFlux method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.ReactiveFlux method) (pyemma.msm.models.msm.MSM method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.MEMM method) (pyemma.thermo.MultiThermModel method) (pyemma.thermo.StationaryModel method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method) (pyemma.thermo.models.memm.MEMM method), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel method), [1], [2], [3] get_output() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method)

get_params() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.estimation.covariance.LaggedCovariance method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.ChapmanKolmogorovValidator method) (pyemma.msm.ImpliedTimescales method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2] (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method) get_sample_conf() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2] (pyemma.msm.ImpliedTimescales method) get_sample_mean() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2] (pyemma.msm.ImpliedTimescales method) get_sample_std() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2] (pyemma.msm.ImpliedTimescales method) get_timescales() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2] (pyemma.msm.ImpliedTimescales method) gross_flux (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute)

H

hmm() (pyemma.msm.BayesianMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method)

HMSM (class in pyemma.msm)

I

I (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) ImpliedTimescales (class in pyemma.msm) (class in pyemma.msm.estimators.implied_timescales), [1], [2] in_memory (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) index_clusters (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) init_hmsm (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) init_strategy (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) is_random_accessible (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) is_reader (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute)

is_reversible (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) is_sparse (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) iterator() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) its() (in module pyemma.msm)

K

keys() (pyemma.util._config.Config method)

KmeansClustering (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.kmeans)

L

label (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.MultiThermModel attribute) (pyemma.thermo.StationaryModel attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] lag (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.tica.TICA attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) LaggedCovariance (class in pyemma.coordinates.estimation.covariance) lags (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) lagtime (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) lagtimes (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) largest_connected_set (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) lifetimes (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) list_models() (in module pyemma) load() (in module pyemma) (in module pyemma.coordinates) (pyemma.coordinates.clustering.AssignCenters class method) (pyemma.coordinates.clustering.KmeansClustering class method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering class method) (pyemma.coordinates.clustering.RegularSpaceClustering class method) (pyemma.coordinates.clustering.UniformTimeClustering class method) (pyemma.coordinates.clustering.assign.AssignCenters class method) (pyemma.coordinates.clustering.kmeans.KmeansClustering class method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering class method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering class method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering class method) (pyemma.coordinates.data.CustomFeature class method) (pyemma.coordinates.data.DataInMemory class method) (pyemma.coordinates.data.FeatureReader class method) (pyemma.coordinates.data.FragmentedTrajectoryReader class method) (pyemma.coordinates.data.MDFeaturizer class method) (pyemma.coordinates.data.NumPyFileReader class method) (pyemma.coordinates.data.PyCSVReader class method) (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer class method) (pyemma.coordinates.estimation.covariance.LaggedCovariance class method) (pyemma.coordinates.transform.PCA class method) (pyemma.coordinates.transform.TICA class method) (pyemma.coordinates.transform.VAMP class method) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator class method) (pyemma.coordinates.transform.VAMPModel class method) (pyemma.coordinates.transform.pca.PCA class method) (pyemma.coordinates.transform.tica.TICA class method) (pyemma.msm.BayesianHMSM class method) (pyemma.msm.BayesianMSM class method) (pyemma.msm.ChapmanKolmogorovValidator class method) (pyemma.msm.HMSM class method) (pyemma.msm.ImpliedTimescales class method) (pyemma.msm.MSM class method) (pyemma.msm.MaximumLikelihoodHMSM class method) (pyemma.msm.MaximumLikelihoodMSM class method) (pyemma.msm.OOMReweightedMSM class method) (pyemma.msm.ReactiveFlux class method) (pyemma.msm.SampledHMSM class method) (pyemma.msm.SampledMSM class method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM class method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM class method) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales class method), [1], [2] (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM class method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM class method) (pyemma.msm.models.ReactiveFlux class method) (pyemma.msm.models.msm.MSM class method) (pyemma.thermo.DTRAM class method) (pyemma.thermo.MBAR class method) (pyemma.thermo.MEMM class method) (pyemma.thermo.MultiThermModel class method) (pyemma.thermo.StationaryModel class method) (pyemma.thermo.TRAM class method) (pyemma.thermo.WHAM class method) (pyemma.thermo.models.memm.MEMM class method), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel class method), [1], [2], [3] (pyemma.util._config.Config method)

load_from_files() (pyemma.coordinates.data.DataInMemory class method) log_likelihood() (pyemma.thermo.TRAM method) logger (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.MDFeaturizer attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer attribute) (pyemma.coordinates.estimation.covariance.LaggedCovariance attribute) (pyemma.coordinates.pipelines.Discretizer attribute) (pyemma.coordinates.pipelines.Pipeline attribute), [1], [2], [3] (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.ChapmanKolmogorovValidator attribute) (pyemma.msm.ImpliedTimescales attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) logging_config (pyemma.util._config.Config attribute)

M

major_flux() (pyemma.msm.models.ReactiveFlux method) (pyemma.msm.ReactiveFlux method) markov_model() (in module pyemma.msm) max_centers (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) MaximumLikelihoodHMSM (class in pyemma.msm) (class in pyemma.msm.estimators.maximum_likelihood_hmsm) MaximumLikelihoodMSM (class in pyemma.msm) (class in pyemma.msm.estimators.maximum_likelihood_msm) MBAR (class in pyemma.thermo) mbar() (in module pyemma.thermo) MDFeaturizer (class in pyemma.coordinates.data) (class in pyemma.coordinates.data.featurization.featurizer) mean (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.tica.TICA attribute) MEMM (class in pyemma.thermo) (class in pyemma.thermo.models.memm), [1], [2], [3] metastable_assignment (pyemma.msm.PCCA attribute) metastable_assignments (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) metastable_distributions (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) metastable_memberships (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) metastable_sets (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.PCCA attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute)

meval() (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.MEMM method) (pyemma.thermo.MultiThermModel method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method) (pyemma.thermo.models.memm.MEMM method), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel method), [1], [2], [3] mfpt (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) mfpt() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) MiniBatchKmeansClustering (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.kmeans) model (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.estimation.covariance.LaggedCovariance attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.ChapmanKolmogorovValidator attribute) (pyemma.msm.ImpliedTimescales attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) models (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) MSM (class in pyemma.msm) (class in pyemma.msm.models.msm) msm (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] msm_init (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) mu (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) MultiThermModel (class in pyemma.thermo) (class in pyemma.thermo.models.multi_therm), [1], [2], [3] mute (pyemma.util._config.Config attribute)

N

n_chunks() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) n_clusters (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) n_frames_total() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) n_jobs (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.ChapmanKolmogorovValidator attribute) (pyemma.msm.ImpliedTimescales attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] n_metastable (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) name (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.MDFeaturizer attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer attribute) (pyemma.coordinates.estimation.covariance.LaggedCovariance attribute) (pyemma.coordinates.pipelines.Discretizer attribute) (pyemma.coordinates.pipelines.Pipeline attribute), [1], [2], [3] (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.ChapmanKolmogorovValidator attribute) (pyemma.msm.ImpliedTimescales attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute)

ndim (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) neig (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) net_flux (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) NetworkPlot (class in pyemma.plots) nits (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) nstates (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.ReactiveFlux attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.models.msm.MSM attribute) (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.MultiThermModel attribute) (pyemma.thermo.StationaryModel attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] nstates_full (pyemma.msm.BayesianMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.MultiThermModel attribute) (pyemma.thermo.StationaryModel attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] nstates_obs (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) ntraj (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) number_of_timescales (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) number_of_trajectories() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) NumPyFileReader (class in pyemma.coordinates.data)

O

observable_set (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) observable_state_indexes (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) observation_probabilities (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) OOM_components (pyemma.msm.OOMReweightedMSM attribute) OOM_omega (pyemma.msm.OOMReweightedMSM attribute) OOM_rank (pyemma.msm.OOMReweightedMSM attribute) OOM_sigma (pyemma.msm.OOMReweightedMSM attribute) OOMReweightedMSM (class in pyemma.msm) output_type() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method)

overwrite_dtrajs (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute)

P

P (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) pairs() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer static method) (pyemma.coordinates.data.MDFeaturizer static method) parametrize() (pyemma.coordinates.pipelines.Discretizer method) (pyemma.coordinates.pipelines.Pipeline method), [1], [2], [3] partial_fit() (pyemma.coordinates.estimation.covariance.LaggedCovariance method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) pathways() (pyemma.msm.models.ReactiveFlux method) (pyemma.msm.ReactiveFlux method) PCA (class in pyemma.coordinates.transform) (class in pyemma.coordinates.transform.pca) pca() (in module pyemma.coordinates) PCCA (class in pyemma.msm) pcca() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) pi (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.MultiThermModel attribute) (pyemma.thermo.StationaryModel attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3]

pi_full_state (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] Pipeline (class in pyemma.coordinates.pipelines), [1], [2], [3] pipeline() (in module pyemma.coordinates) plot_cktest() (in module pyemma.plots) plot_contour() (in module pyemma.plots) plot_density() (in module pyemma.plots) plot_flux() (in module pyemma.plots) plot_free_energy() (in module pyemma.plots) plot_implied_timescales() (in module pyemma.plots) plot_markov_model() (in module pyemma.plots) plot_network() (in module pyemma.plots) (pyemma.plots.NetworkPlot method) plot_state_map() (in module pyemma.plots) pointwise_free_energies() (pyemma.thermo.TRAM method) predictions (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator attribute) (pyemma.msm.ChapmanKolmogorovValidator attribute) predictions_conf (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator attribute) (pyemma.msm.ChapmanKolmogorovValidator attribute) propagate() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) PyCSVReader (class in pyemma.coordinates.data) pyemma.coordinates (module) pyemma.coordinates.clustering (module) pyemma.coordinates.data (module) pyemma.coordinates.pipelines (module) pyemma.coordinates.transform (module) pyemma.msm (module) pyemma.plots (module) pyemma.thermo (module)

Q

qminus (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute)

qplus (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute)

R

ra_itraj_cuboid (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) ra_itraj_jagged (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) ra_itraj_linear (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute)

ra_linear (pyemma.coordinates.clustering.assign.AssignCenters attribute) (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.FragmentedTrajectoryReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.data._base.transformer.StreamingTransformer attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.pca.PCA attribute) (pyemma.coordinates.transform.tica.TICA attribute) rate (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) ReactiveFlux (class in pyemma.msm) (class in pyemma.msm.models) RegularSpaceClustering (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.regspace) relaxation() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) remove_all_custom_funcs() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) reversible (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute)

S

sample_by_distributions() (pyemma.msm.BayesianMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) sample_by_observation_probabilities() (pyemma.msm.BayesianHMSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) sample_by_state() (pyemma.msm.BayesianMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) sample_conf() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) sample_f() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) sample_indexes_by_cluster() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) sample_mean (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) sample_mean() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) sample_std (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) sample_std() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) SampledHMSM (class in pyemma.msm) SampledMSM (class in pyemma.msm) samples (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) samples_available (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] (pyemma.msm.ImpliedTimescales attribute) save() (pyemma._base.serialization.SerializableMixIn method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.CustomFeature method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.estimation.covariance.LaggedCovariance method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator method) (pyemma.coordinates.transform.VAMPModel method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.ChapmanKolmogorovValidator method) (pyemma.msm.HMSM method) (pyemma.msm.ImpliedTimescales method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.ReactiveFlux method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2] (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.ReactiveFlux method) (pyemma.msm.models.msm.MSM method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.MEMM method) (pyemma.thermo.MultiThermModel method) (pyemma.thermo.StationaryModel method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method) (pyemma.thermo.models.memm.MEMM method), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel method), [1], [2], [3] (pyemma.util._config.Config method) save_dtrajs() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.pipelines.Discretizer method) save_traj() (in module pyemma.coordinates) save_trajs() (in module pyemma.coordinates) scaling (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.VAMPModel attribute) scatter_contour() (in module pyemma.plots) score() (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPModel method) (pyemma.msm.BayesianMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) score_cv() (pyemma.msm.BayesianMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) select() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) select_Backbone() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) select_Ca() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) select_Heavy() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.data.MDFeaturizer method) set_element() (pyemma.coordinates.pipelines.Discretizer method) (pyemma.coordinates.pipelines.Pipeline method), [1], [2], [3] set_model_params() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.ReactiveFlux method) (pyemma.msm.models.msm.MSM method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.MEMM method) (pyemma.thermo.MultiThermModel method) (pyemma.thermo.StationaryModel method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method) (pyemma.thermo.models.memm.MEMM method), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel method), [1], [2], [3]

set_params() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.estimation.covariance.LaggedCovariance method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.ChapmanKolmogorovValidator method) (pyemma.msm.ImpliedTimescales method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2] (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method) show_config_notification (pyemma.util._config.Config attribute) show_progress (pyemma.coordinates.clustering.kmeans.KmeansClustering attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.MiniBatchKmeansClustering attribute) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering attribute) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator attribute) (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.ChapmanKolmogorovValidator attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) show_progress_bars (pyemma.util._config.Config attribute) simulate() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) singular_values (pyemma.coordinates.transform.VAMP attribute) (pyemma.coordinates.transform.VAMPModel attribute) singular_vectors_left (pyemma.coordinates.transform.VAMP attribute) singular_vectors_right (pyemma.coordinates.transform.VAMP attribute) source() (in module pyemma.coordinates) sparse (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) stationary_distribution (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.ReactiveFlux attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.models.msm.MSM attribute) (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.MultiThermModel attribute) (pyemma.thermo.StationaryModel attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] stationary_distribution_full_state (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] stationary_distribution_obs (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) StationaryModel (class in pyemma.thermo) StreamingTransformer (class in pyemma.coordinates.data._base.transformer) submodel() (pyemma.msm.BayesianHMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) submodel_disconnect() (pyemma.msm.BayesianHMSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) submodel_largest() (pyemma.msm.BayesianHMSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) submodel_populous() (pyemma.msm.BayesianHMSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) supports_format() (pyemma.coordinates.data.FeatureReader static method)

T

temperatures (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) TICA (class in pyemma.coordinates.transform) (class in pyemma.coordinates.transform.tica) tica() (in module pyemma.coordinates) timescales (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.tica.TICA attribute) (pyemma.msm.ImpliedTimescales attribute) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2] timescales() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.msm.MSM method) timescales_hmsm() (in module pyemma.msm) timescales_msm() (in module pyemma.msm) timescales_OOM (pyemma.msm.OOMReweightedMSM attribute) timestep_model (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) topologyfile (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer attribute) total_flux (pyemma.msm.models.ReactiveFlux attribute) (pyemma.msm.ReactiveFlux attribute) tpt() (in module pyemma.msm) traj_info_max_entries (pyemma.util._config.Config attribute) traj_info_max_size (pyemma.util._config.Config attribute) trajectory_length() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method)

trajectory_lengths() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) trajectory_weights() (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) TRAM (class in pyemma.thermo) tram() (in module pyemma.thermo) transform() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) transition_matrix (pyemma.msm.BayesianHMSM attribute) (pyemma.msm.BayesianMSM attribute) (pyemma.msm.HMSM attribute) (pyemma.msm.MSM attribute) (pyemma.msm.MaximumLikelihoodHMSM attribute) (pyemma.msm.MaximumLikelihoodMSM attribute) (pyemma.msm.OOMReweightedMSM attribute) (pyemma.msm.SampledHMSM attribute) (pyemma.msm.SampledMSM attribute) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute) (pyemma.msm.estimators.bayesian_msm.BayesianMSM attribute) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM attribute) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM attribute) (pyemma.msm.models.msm.MSM attribute) transition_matrix_obs() (pyemma.msm.BayesianHMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.SampledHMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)

U

U (pyemma.coordinates.transform.VAMPModel attribute) umbrella_centers (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) unbiased_state (pyemma.thermo.DTRAM attribute) (pyemma.thermo.MBAR attribute) (pyemma.thermo.MEMM attribute) (pyemma.thermo.MultiThermModel attribute) (pyemma.thermo.TRAM attribute) (pyemma.thermo.WHAM attribute) (pyemma.thermo.models.memm.MEMM attribute), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel attribute), [1], [2], [3] UniformTimeClustering (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.uniform_time) update_model_params() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.transform.VAMPModel method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.HMSM method) (pyemma.msm.MSM method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.ReactiveFlux method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM method) (pyemma.msm.models.ReactiveFlux method) (pyemma.msm.models.msm.MSM method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.MEMM method) (pyemma.thermo.MultiThermModel method) (pyemma.thermo.StationaryModel method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method) (pyemma.thermo.models.memm.MEMM method), [1], [2], [3] (pyemma.thermo.models.multi_therm.MultiThermModel method), [1], [2], [3]

use_trajectory_lengths_cache (pyemma.util._config.Config attribute) used_filenames (pyemma.util._config.Config attribute)

V

V (pyemma.coordinates.transform.VAMPModel attribute) VAMP (class in pyemma.coordinates.transform) vamp() (in module pyemma.coordinates)

VAMPChapmanKolmogorovValidator (class in pyemma.coordinates.transform) VAMPModel (class in pyemma.coordinates.transform) var_cutoff (pyemma.coordinates.transform.TICA attribute) (pyemma.coordinates.transform.tica.TICA attribute)

W

WHAM (class in pyemma.thermo) wham() (in module pyemma.thermo) write_to_csv() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method)

write_to_hdf5() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.kmeans.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method)