Index

_

__call__() (deeptime.base.Transformer method) (deeptime.basis.Concatenation method) (deeptime.basis.Identity method) (deeptime.basis.Monomials method) (deeptime.basis.Observable method) (deeptime.clustering.BoxDiscretizationModel method) (deeptime.clustering.ClusterModel method) (deeptime.clustering.KMeans method) (deeptime.clustering.KMeansModel method) (deeptime.clustering.MiniBatchKMeans method) (deeptime.covariance.KoopmanWeightingEstimator method) (deeptime.covariance.KoopmanWeightingModel method) (deeptime.covariance.WhiteningTransform method) (deeptime.data.BickleyJet method) (deeptime.data.CustomSystem method) (deeptime.data.TimeDependentSystem method) (deeptime.data.TimeIndependentSystem method) (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TAEModel method) (deeptime.decomposition.deep.TVAE method) (deeptime.decomposition.deep.TVAEEncoder method) (deeptime.decomposition.deep.TVAEModel method) (deeptime.decomposition.deep.VAMPNet method) (deeptime.decomposition.deep.VAMPNetModel method) (deeptime.decomposition.DMD method) (deeptime.decomposition.DMDModel method) (deeptime.decomposition.EDMD method) (deeptime.decomposition.EDMDModel method) (deeptime.decomposition.KernelCCAModel method) (deeptime.decomposition.KernelEDMD method) (deeptime.decomposition.KernelEDMDModel method) (deeptime.decomposition.KVAD method) (deeptime.decomposition.KVADModel method) (deeptime.decomposition.TICA method) (deeptime.decomposition.TransferOperatorModel method) (deeptime.decomposition.VAMP method) (deeptime.kernels.GaussianKernel method) (deeptime.kernels.GeneralizedGaussianKernel method) (deeptime.kernels.Kernel method) (deeptime.kernels.LaplacianKernel method) (deeptime.kernels.PolynomialKernel method) (deeptime.kernels.TorchGaussianKernel method) (deeptime.markov.TransitionCountEstimator method) (deeptime.util.callbacks.ProgressCallback method)

A

abc_flow() (in module deeptime.data) accuracy (deeptime.markov.hmm.MaximumLikelihoodHMM property) add_barrier() (deeptime.data.DrunkardsWalk method) add_module() (deeptime.decomposition.deep.TVAEEncoder method) adjacency_matrix (deeptime.plots.Network property) allow_disconnected (deeptime.markov.msm.MaximumLikelihoodMSM property) analytic_msm (deeptime.data.DoubleWellDiscrete property) apply() (deeptime.decomposition.deep.TVAEEncoder method) (deeptime.kernels.GaussianKernel method) (deeptime.kernels.GeneralizedGaussianKernel method) (deeptime.kernels.Kernel method) (deeptime.kernels.LaplacianKernel method) (deeptime.kernels.PolynomialKernel method) (deeptime.kernels.TorchGaussianKernel method)

apply_periodic_boundary_conditions() (deeptime.data.BickleyJet static method) assignments (deeptime.markov.PCCAModel property) astype() (deeptime.util.data.TimeLaggedDataset method) (deeptime.util.data.TrajectoryDataset method) atleast_nd() (in module deeptime.util.types) AugmentedMSM (class in deeptime.markov.msm) AugmentedMSMEstimator (class in deeptime.markov.msm) available (deeptime.clustering.MetricRegistry property) available_drivers (deeptime.decomposition.DMD attribute) available_modes (deeptime.decomposition.DMD attribute) available_operators (deeptime.decomposition.EDMD attribute)

B

backward() (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.decomposition.EDMDModel method) (deeptime.decomposition.KernelCCAModel method) (deeptime.decomposition.KernelEDMDModel method) (deeptime.decomposition.KVADModel method) (deeptime.decomposition.TransferOperatorModel method) backward_committor (deeptime.markov.ReactiveFlux property) BayesianHMM (class in deeptime.markov.hmm) BayesianHMMPosterior (class in deeptime.markov.hmm) BayesianMSM (class in deeptime.markov.msm) BayesianMSMPosterior (class in deeptime.markov.msm) bessels_correction (deeptime.covariance.Covariance property) (deeptime.covariance.CovarianceModel property)

bfloat16() (deeptime.decomposition.deep.TVAEEncoder method) biased_conf_energies (deeptime.markov.msm.TRAMModel property) bickley_jet() (in module deeptime.data) BickleyJet (class in deeptime.data) birth_death_chain() (in module deeptime.data) BirthDeathChain (class in deeptime.data) blocksplit_trajs() (in module deeptime.decomposition) bootstrap_counts() (in module deeptime.markov.tools.estimation) bootstrap_trajectories() (in module deeptime.markov.tools.estimation) bounds (deeptime.plots.Network property) BoxDiscretization (class in deeptime.clustering) BoxDiscretizationModel (class in deeptime.clustering) buffers() (deeptime.decomposition.deep.TVAEEncoder method)

C

c (deeptime.data.BickleyJet property) cached_property (class in deeptime.util.decorators) ChapmanKolmogorovTest (class in deeptime.util.validation) check_against_model() (deeptime.markov.msm.TRAMDataset method) children() (deeptime.decomposition.deep.TVAEEncoder method) ck_test() (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.hmm.HiddenMarkovModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.BayesianMSMPosterior method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.util.validation) cluster_centers (deeptime.clustering.BoxDiscretizationModel property) (deeptime.clustering.ClusterModel property) (deeptime.clustering.KMeansModel property) ClusterModel (class in deeptime.clustering) cmap (deeptime.plots.Network property) coarse_grain() (deeptime.markov.ReactiveFlux method) coarse_grained_stationary_probability (deeptime.markov.PCCAModel property) coarse_grained_transition_matrix (deeptime.markov.PCCAModel property) coarsegrain() (in module deeptime.markov.tools.flux) coefficients (deeptime.sindy.SINDyModel property) collect_observations_in_state() (deeptime.markov.hmm.HiddenMarkovModel method) committor() (in module deeptime.markov.tools.analysis) committor_backward() (deeptime.data.BirthDeathChain method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) committor_forward() (deeptime.data.BirthDeathChain method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) committor_sensitivity() (in module deeptime.markov.tools.analysis) compute_c00 (deeptime.covariance.Covariance property) compute_c0t (deeptime.covariance.Covariance property) compute_connected_sets() (in module deeptime.markov) compute_ctt (deeptime.covariance.Covariance property) compute_dtrajs_effective() (in module deeptime.markov) compute_effective_stride() (in module deeptime.markov) compute_index_states() (in module deeptime.markov.sample) compute_log_likelihood() (deeptime.markov.msm.TRAMModel method) compute_observable() (deeptime.markov.msm.TRAMModel method) compute_observation_likelihood() (deeptime.markov.hmm.HiddenMarkovModel method) compute_PMF() (deeptime.markov.msm.TRAMModel method) compute_sample_weights_log() (deeptime.markov.msm.TRAMModel method) compute_state_indices() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) compute_trajectory_weights() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) compute_viterbi_paths() (deeptime.markov.hmm.HiddenMarkovModel method) ConcatDataset (class in deeptime.util.data) Concatenation (class in deeptime.basis) confidence_interval() (in module deeptime.util) connected_sets() (deeptime.markov.TransitionCountModel method) (in module deeptime.markov.tools.estimation) connectivity_options (deeptime.markov.msm.TRAMDataset attribute) const_weight_input (deeptime.covariance.KoopmanWeightingModel property) converged (deeptime.clustering.BoxDiscretizationModel property) (deeptime.clustering.ClusterModel property) (deeptime.clustering.KMeansModel property) convergence_criterion_lagrange (deeptime.markov.msm.AugmentedMSMEstimator property) coordinate_to_state() (deeptime.data.DrunkardsWalk method) copy() (deeptime.base.Model method) (deeptime.clustering.BoxDiscretizationModel method) (deeptime.clustering.ClusterModel method) (deeptime.clustering.KMeansModel method) (deeptime.covariance.CovarianceModel method) (deeptime.covariance.KoopmanWeightingModel method) (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.decomposition.deep.TAEModel method) (deeptime.decomposition.deep.TVAEModel method) (deeptime.decomposition.deep.VAMPNetModel method) (deeptime.decomposition.DMDModel method) (deeptime.decomposition.EDMDModel method) (deeptime.decomposition.KernelCCAModel method) (deeptime.decomposition.KernelEDMDModel method) (deeptime.decomposition.KVADModel method) (deeptime.decomposition.TransferOperatorModel method) (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.hmm.DiscreteOutputModel method) (deeptime.markov.hmm.GaussianOutputModel method) (deeptime.markov.hmm.HiddenMarkovModel method) (deeptime.markov.hmm.OutputModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.BayesianMSMPosterior method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (deeptime.markov.msm.TRAMModel method) (deeptime.markov.PCCAModel method) (deeptime.markov.ReactiveFlux method) (deeptime.markov.TransitionCountModel method) (deeptime.sindy.SINDyModel method)

correlation() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov.tools.analysis) correlation_obs() (deeptime.markov.hmm.HiddenMarkovModel method) count() (deeptime.markov.TransitionCountEstimator static method) count_fraction (deeptime.markov.msm.MarkovStateModelCollection property) count_fractions (deeptime.markov.msm.MarkovStateModelCollection property) count_matrix (deeptime.markov.TransitionCountModel property) count_matrix() (in module deeptime.markov.tools.estimation) count_matrix_full (deeptime.markov.TransitionCountModel property) count_matrix_histogram() (deeptime.markov.TransitionCountModel method) count_mode (deeptime.markov.TransitionCountEstimator property) count_model (deeptime.markov.hmm.HiddenMarkovModel property) (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) count_states() (in module deeptime.markov) counting_mode (deeptime.markov.TransitionCountModel property) cov (deeptime.decomposition.CovarianceKoopmanModel property) cov_00 (deeptime.covariance.CovarianceModel property) (deeptime.decomposition.CovarianceKoopmanModel property) cov_0t (deeptime.covariance.CovarianceModel property) (deeptime.decomposition.CovarianceKoopmanModel property) cov_tt (deeptime.covariance.CovarianceModel property) (deeptime.decomposition.CovarianceKoopmanModel property) covar() (in module deeptime.covariance) Covariance (class in deeptime.covariance) covariance_estimator() (deeptime.decomposition.TICA class method) (deeptime.decomposition.VAMP class method) covariance_matrix (deeptime.data.Ellipsoids property) CovarianceKoopmanModel (class in deeptime.decomposition) CovarianceModel (class in deeptime.covariance) covariances (deeptime.covariance.KoopmanWeightingModel property) covariances() (in module deeptime.decomposition.deep) covars() (in module deeptime.covariance) cpu() (deeptime.decomposition.deep.TVAEEncoder method) cuda() (deeptime.decomposition.deep.TVAEEncoder method) cumulative_kinetic_variance (deeptime.decomposition.CovarianceKoopmanModel property) current_model (deeptime.markov.msm.MarkovStateModelCollection property) custom_ode() (in module deeptime.data) custom_sde() (in module deeptime.data) CustomSystem (class in deeptime.data) cvsplit_trajs() (in module deeptime.decomposition)

D

d_x (deeptime.plots.Network property) d_y (deeptime.plots.Network property) data (deeptime.util.data.TimeLaggedDataset property) (deeptime.util.data.TrajectoryDataset property) data_lagged (deeptime.util.data.TimeLaggedDataset property) (deeptime.util.data.TrajectoryDataset property) data_mean_removed (deeptime.covariance.CovarianceModel property) Dataset (class in deeptime.base) decoder (deeptime.decomposition.deep.TAEModel property) (deeptime.decomposition.deep.TVAEModel property) deeptime.basis module deeptime.clustering module deeptime.covariance module deeptime.data module deeptime.decomposition module deeptime.kernels module deeptime.markov.tools.analysis module deeptime.markov.tools.estimation module deeptime.markov.tools.flux module deeptime.numeric module deeptime.plots module deeptime.sindy module deeptime.util module

default() (deeptime.markov.hmm.BayesianHMM static method) deleter() (deeptime.util.decorators.cached_property method) deprecated_argument() (in module deeptime.util.decorators) device (deeptime.decomposition.deep.TAE property) (deeptime.decomposition.deep.TVAE property) (deeptime.decomposition.deep.VAMPNet property) diag_only (deeptime.covariance.Covariance property) dim (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.KVAD property) (deeptime.decomposition.TICA property) (deeptime.decomposition.VAMP property) dimension (deeptime.data.BickleyJet property) (deeptime.data.CustomSystem property) (deeptime.data.TimeDependentSystem property) (deeptime.data.TimeIndependentSystem property) discrete_trajectory() (deeptime.data.Ellipsoids method) DiscreteOutputModel (class in deeptime.markov.hmm) DMD (class in deeptime.decomposition) DMDModel (class in deeptime.decomposition) dmin (deeptime.clustering.RegularSpace property) domain_size (deeptime.data.PBFSimulator property) double() (deeptime.decomposition.deep.TVAEEncoder method) double_well_2d() (in module deeptime.data) double_well_discrete() (in module deeptime.data) DoubleWellDiscrete (class in deeptime.data) drop_nan_rows() (in module deeptime.numeric) drunkards_walk() (in module deeptime.data) DrunkardsWalk (class in deeptime.data) dtraj (deeptime.data.DoubleWellDiscrete property) dtraj_n() (deeptime.data.DoubleWellDiscrete method) dtraj_n2() (deeptime.data.DoubleWellDiscrete method) dtraj_n2bad (deeptime.data.DoubleWellDiscrete property) dtraj_n2good (deeptime.data.DoubleWellDiscrete property) dtraj_n6good (deeptime.data.DoubleWellDiscrete property) dtype (deeptime.decomposition.deep.TAE property) (deeptime.decomposition.deep.TVAE property) (deeptime.decomposition.deep.VAMPNet property)

E

edge_base_scale (deeptime.plots.Network property) edge_label() (deeptime.plots.Network method) edge_labels (deeptime.plots.Network property) EDMD (class in deeptime.decomposition) EDMDModel (class in deeptime.decomposition) effective_output_dimension() (deeptime.decomposition.CovarianceKoopmanModel static method) eig_corr() (in module deeptime.numeric) eigenvalue_sensitivity() (in module deeptime.markov.tools.analysis) eigenvalues() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov.tools.analysis) eigenvector_sensitivity() (in module deeptime.markov.tools.analysis) eigenvectors() (in module deeptime.markov.tools.analysis) eigenvectors_left() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) eigenvectors_left_obs (deeptime.markov.hmm.HiddenMarkovModel property) eigenvectors_right() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) eigenvectors_right_obs (deeptime.markov.hmm.HiddenMarkovModel property) eigs() (in module deeptime.numeric) Ellipsoids (class in deeptime.data) ellipsoids() (in module deeptime.data) empirical_koopman_model (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) encoder (deeptime.decomposition.deep.TAEModel property) (deeptime.decomposition.deep.TVAEModel property)

energy2d() (in module deeptime.util) Energy2dPlot (class in deeptime.plots) EnergyLandscape2d (class in deeptime.util) eps (deeptime.data.BickleyJet property) epsilon (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.deep.VAMPNet property) (deeptime.decomposition.KVAD property) (deeptime.decomposition.TICA property) (deeptime.decomposition.VAMP property) equations() (deeptime.sindy.SINDyModel method) err_est (deeptime.util.validation.ChapmanKolmogorovTest property) error_perturbation() (in module deeptime.markov.tools.estimation) estimates (deeptime.util.validation.ChapmanKolmogorovTest property) estimates_samples (deeptime.util.validation.ChapmanKolmogorovTest property) Estimator (class in deeptime.base) estimator_from_feature_trajectories() (deeptime.markov.msm.AugmentedMSMEstimator static method) eval() (deeptime.decomposition.deep.TVAEEncoder method) evaluate_loss() (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TVAE method) evaluate_samples() (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.msm.BayesianMSMPosterior method) expectation() (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov.tools.analysis) expectation_obs() (deeptime.markov.hmm.HiddenMarkovModel method) expectation_sensitivity() (in module deeptime.markov.tools.analysis) expectations_by_state (deeptime.markov.msm.AugmentedMSMEstimator property) expected_counts() (in module deeptime.markov.tools.analysis) expected_counts_stationary() (in module deeptime.markov.tools.analysis) experimental_measurement_weights (deeptime.markov.msm.AugmentedMSMEstimator property) experimental_measurements (deeptime.markov.msm.AugmentedMSMEstimator property) extra_repr() (deeptime.decomposition.deep.TVAEEncoder method)

F

f (deeptime.data.BickleyJet property) (deeptime.data.CustomSystem property) (deeptime.data.TimeDependentSystem property) (deeptime.data.TimeIndependentSystem property) feature_component_correlation (deeptime.decomposition.CovarianceKoopmanModel property) fetch_model() (deeptime.base.Estimator method) (deeptime.clustering.BoxDiscretization method) (deeptime.clustering.KMeans method) (deeptime.clustering.MiniBatchKMeans method) (deeptime.clustering.RegularSpace method) (deeptime.covariance.Covariance method) (deeptime.covariance.KoopmanWeightingEstimator method) (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TVAE method) (deeptime.decomposition.deep.VAMPNet method) (deeptime.decomposition.DMD method) (deeptime.decomposition.EDMD method) (deeptime.decomposition.KernelCCA method) (deeptime.decomposition.KernelEDMD method) (deeptime.decomposition.KVAD method) (deeptime.decomposition.TICA method) (deeptime.decomposition.VAMP method) (deeptime.markov.hmm.BayesianHMM method) (deeptime.markov.hmm.MaximumLikelihoodHMM method) (deeptime.markov.msm.AugmentedMSMEstimator method) (deeptime.markov.msm.BayesianMSM method) (deeptime.markov.msm.MaximumLikelihoodMSM method) (deeptime.markov.msm.OOMReweightedMSM method) (deeptime.markov.msm.TRAM method) (deeptime.markov.TransitionCountEstimator method) (deeptime.sindy.SINDy method) fingerprint_correlation() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov.tools.analysis) fingerprint_correlation_obs() (deeptime.markov.hmm.HiddenMarkovModel method) fingerprint_relaxation() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov.tools.analysis) fingerprint_relaxation_obs() (deeptime.markov.hmm.HiddenMarkovModel method) finite_difference_coefficients() (in module deeptime.util.diff) finite_difference_operator_midpoints() (in module deeptime.util.diff) fit() (deeptime.base.Estimator method) (deeptime.clustering.BoxDiscretization method) (deeptime.clustering.KMeans method) (deeptime.clustering.MiniBatchKMeans method) (deeptime.clustering.RegularSpace method) (deeptime.covariance.Covariance method) (deeptime.covariance.KoopmanWeightingEstimator method) (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TVAE method) (deeptime.decomposition.deep.VAMPNet method) (deeptime.decomposition.DMD method) (deeptime.decomposition.EDMD method) (deeptime.decomposition.KernelCCA method) (deeptime.decomposition.KernelEDMD method) (deeptime.decomposition.KVAD method) (deeptime.decomposition.TICA method) (deeptime.decomposition.VAMP method) (deeptime.markov.hmm.BayesianHMM method) (deeptime.markov.hmm.DiscreteOutputModel method) (deeptime.markov.hmm.GaussianOutputModel method) (deeptime.markov.hmm.MaximumLikelihoodHMM method) (deeptime.markov.hmm.OutputModel method) (deeptime.markov.msm.AugmentedMSMEstimator method) (deeptime.markov.msm.BayesianMSM method) (deeptime.markov.msm.MaximumLikelihoodMSM method) (deeptime.markov.msm.OOMReweightedMSM method) (deeptime.markov.msm.TRAM method) (deeptime.markov.TransitionCountEstimator method) (deeptime.sindy.SINDy method) (deeptime.sindy.STLSQ method)

fit_fetch() (deeptime.base.Estimator method) (deeptime.clustering.BoxDiscretization method) (deeptime.clustering.KMeans method) (deeptime.clustering.MiniBatchKMeans method) (deeptime.clustering.RegularSpace method) (deeptime.covariance.Covariance method) (deeptime.covariance.KoopmanWeightingEstimator method) (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TVAE method) (deeptime.decomposition.deep.VAMPNet method) (deeptime.decomposition.DMD method) (deeptime.decomposition.EDMD method) (deeptime.decomposition.KernelCCA method) (deeptime.decomposition.KernelEDMD method) (deeptime.decomposition.KVAD method) (deeptime.decomposition.TICA method) (deeptime.decomposition.VAMP method) (deeptime.markov.hmm.BayesianHMM method) (deeptime.markov.hmm.MaximumLikelihoodHMM method) (deeptime.markov.msm.AugmentedMSMEstimator method) (deeptime.markov.msm.BayesianMSM method) (deeptime.markov.msm.MaximumLikelihoodMSM method) (deeptime.markov.msm.OOMReweightedMSM method) (deeptime.markov.msm.TRAM method) (deeptime.markov.TransitionCountEstimator method) (deeptime.sindy.SINDy method) fit_from_counts() (deeptime.markov.msm.BayesianMSM method) (deeptime.markov.msm.MaximumLikelihoodMSM method) fit_from_covariances() (deeptime.decomposition.TICA method) (deeptime.decomposition.VAMP method) fit_from_discrete_timeseries() (deeptime.markov.msm.BayesianMSM method) (deeptime.markov.msm.MaximumLikelihoodMSM method) fit_from_msm() (deeptime.markov.msm.BayesianMSM method) fit_from_timeseries() (deeptime.decomposition.TICA method) (deeptime.decomposition.VAMP method) fit_transform() (deeptime.clustering.KMeans method) (deeptime.clustering.MiniBatchKMeans method) (deeptime.covariance.KoopmanWeightingEstimator method) (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TVAE method) (deeptime.decomposition.deep.VAMPNet method) (deeptime.decomposition.DMD method) (deeptime.decomposition.EDMD method) (deeptime.decomposition.KernelEDMD method) (deeptime.decomposition.KVAD method) (deeptime.decomposition.TICA method) (deeptime.decomposition.VAMP method) (deeptime.markov.TransitionCountEstimator method) fixed_initial_distribution (deeptime.markov.hmm.MaximumLikelihoodHMM property) fixed_seed (deeptime.clustering.KMeans property) (deeptime.clustering.MiniBatchKMeans property) fixed_stationary_distribution (deeptime.markov.hmm.MaximumLikelihoodHMM property) float() (deeptime.decomposition.deep.TVAEEncoder method) flux() (deeptime.data.BirthDeathChain method) flux_consumers() (in module deeptime.markov.tools.flux) flux_matrix() (in module deeptime.markov.tools.flux) flux_producers() (in module deeptime.markov.tools.flux) flux_production() (in module deeptime.markov.tools.flux) forward() (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.decomposition.deep.TVAEEncoder method) (deeptime.decomposition.EDMDModel method) (deeptime.decomposition.KernelCCAModel method) (deeptime.decomposition.KernelEDMDModel method) (deeptime.decomposition.KVADModel method) (deeptime.decomposition.TransferOperatorModel method) forward_committor (deeptime.markov.ReactiveFlux property) from_data() (in module deeptime.markov.hmm.init.gaussian) from_numpy() (deeptime.util.data.TrajectoriesDataset static method) from_trajectories() (deeptime.util.data.TrajectoryDataset static method)

G

gather() (deeptime.util.QuantityStatistics static method) gather_stats() (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.msm.BayesianMSMPosterior method) GaussianKernel (class in deeptime.kernels) GaussianOutputModel (class in deeptime.markov.hmm) GeneralizedGaussianKernel (class in deeptime.kernels) generate() (deeptime.data.BickleyJet method) generate_observation_trajectory() (deeptime.markov.hmm.DiscreteOutputModel method) (deeptime.markov.hmm.GaussianOutputModel method) (deeptime.markov.hmm.OutputModel method) get_buffer() (deeptime.decomposition.deep.TVAEEncoder method) get_extra_state() (deeptime.decomposition.deep.TVAEEncoder method) get_feature_names() (deeptime.basis.Monomials method) get_feature_names_out() (deeptime.basis.Monomials method) get_parameter() (deeptime.decomposition.deep.TVAEEncoder method) get_params() (deeptime.base.Estimator method) (deeptime.base.Model method) (deeptime.clustering.BoxDiscretization method) (deeptime.clustering.BoxDiscretizationModel method) (deeptime.clustering.ClusterModel method) (deeptime.clustering.KMeans method) (deeptime.clustering.KMeansModel method) (deeptime.clustering.MiniBatchKMeans method) (deeptime.clustering.RegularSpace method) (deeptime.covariance.Covariance method) (deeptime.covariance.CovarianceModel method) (deeptime.covariance.KoopmanWeightingEstimator method) (deeptime.covariance.KoopmanWeightingModel method) (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TAEModel method) (deeptime.decomposition.deep.TVAE method) (deeptime.decomposition.deep.TVAEModel method) (deeptime.decomposition.deep.VAMPNet method) (deeptime.decomposition.deep.VAMPNetModel method) (deeptime.decomposition.DMD method) (deeptime.decomposition.DMDModel method) (deeptime.decomposition.EDMD method) (deeptime.decomposition.EDMDModel method) (deeptime.decomposition.KernelCCA method) (deeptime.decomposition.KernelCCAModel method) (deeptime.decomposition.KernelEDMD method) (deeptime.decomposition.KernelEDMDModel method) (deeptime.decomposition.KVAD method) (deeptime.decomposition.KVADModel method) (deeptime.decomposition.TICA method) (deeptime.decomposition.TransferOperatorModel method) (deeptime.decomposition.VAMP method) (deeptime.markov.hmm.BayesianHMM method) (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.hmm.DiscreteOutputModel method) (deeptime.markov.hmm.GaussianOutputModel method) (deeptime.markov.hmm.HiddenMarkovModel method) (deeptime.markov.hmm.MaximumLikelihoodHMM method) (deeptime.markov.hmm.OutputModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.AugmentedMSMEstimator method) (deeptime.markov.msm.BayesianMSM method) (deeptime.markov.msm.BayesianMSMPosterior method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (deeptime.markov.msm.MaximumLikelihoodMSM method) (deeptime.markov.msm.OOMReweightedMSM method) (deeptime.markov.msm.TRAM method) (deeptime.markov.msm.TRAMModel method) (deeptime.markov.PCCAModel method) (deeptime.markov.ReactiveFlux method) (deeptime.markov.TransitionCountEstimator method) (deeptime.markov.TransitionCountModel method) (deeptime.sindy.SINDy method) (deeptime.sindy.SINDyModel method) (deeptime.sindy.STLSQ method)

get_submodule() (deeptime.decomposition.deep.TVAEEncoder method) getter() (deeptime.util.decorators.cached_property method) gram() (deeptime.kernels.GaussianKernel method) (deeptime.kernels.GeneralizedGaussianKernel method) (deeptime.kernels.Kernel method) (deeptime.kernels.LaplacianKernel method) (deeptime.kernels.PolynomialKernel method) (deeptime.kernels.TorchGaussianKernel method) gross_flux (deeptime.markov.ReactiveFlux property)

H

h (deeptime.data.BickleyJet property) (deeptime.data.CustomSystem property) (deeptime.data.TimeDependentSystem property) (deeptime.data.TimeIndependentSystem property) half() (deeptime.decomposition.deep.TVAEEncoder method) handle_n_jobs() (in module deeptime.util.parallel) handle_progress_bar() (in module deeptime.util.platform) has_count_model (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) has_errors (deeptime.util.validation.ChapmanKolmogorovTest property) has_model (deeptime.base.Estimator property) (deeptime.clustering.BoxDiscretization property) (deeptime.clustering.KMeans property) (deeptime.clustering.MiniBatchKMeans property) (deeptime.clustering.RegularSpace property) (deeptime.covariance.Covariance property) (deeptime.covariance.KoopmanWeightingEstimator property) (deeptime.decomposition.deep.TAE property) (deeptime.decomposition.deep.TVAE property) (deeptime.decomposition.deep.VAMPNet property) (deeptime.decomposition.DMD property) (deeptime.decomposition.EDMD property) (deeptime.decomposition.KernelCCA property) (deeptime.decomposition.KernelEDMD property) (deeptime.decomposition.KVAD property) (deeptime.decomposition.TICA property) (deeptime.decomposition.VAMP property) (deeptime.markov.hmm.BayesianHMM property) (deeptime.markov.hmm.MaximumLikelihoodHMM property) (deeptime.markov.msm.AugmentedMSMEstimator property) (deeptime.markov.msm.BayesianMSM property) (deeptime.markov.msm.MaximumLikelihoodMSM property) (deeptime.markov.msm.OOMReweightedMSM property) (deeptime.markov.msm.TRAM property) (deeptime.markov.TransitionCountEstimator property) (deeptime.sindy.SINDy property)

has_potential_function (deeptime.data.BickleyJet property) (deeptime.data.CustomSystem property) (deeptime.data.TimeDependentSystem property) (deeptime.data.TimeIndependentSystem property) has_samples (deeptime.util.validation.ImpliedTimescales property) hidden_state_trajectories (deeptime.markov.hmm.HiddenMarkovModel property) hidden_state_trajectories_samples (deeptime.markov.hmm.BayesianHMMPosterior property) HiddenMarkovModel (class in deeptime.markov.hmm) hitting_probability() (in module deeptime.markov.tools.analysis) hmm() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method)

I

Identity (class in deeptime.basis) ignore_outliers (deeptime.markov.hmm.DiscreteOutputModel property) (deeptime.markov.hmm.GaussianOutputModel property) (deeptime.markov.hmm.OutputModel property) implied_timescales() (in module deeptime.util.validation) ImpliedTimescales (class in deeptime.util.validation) indices_by_distribution() (in module deeptime.markov.sample) indices_by_sequence() (in module deeptime.markov.sample) indices_by_state() (in module deeptime.markov.sample) inertia (deeptime.clustering.KMeansModel property) inertias (deeptime.clustering.KMeansModel property) init_strategy (deeptime.clustering.KMeans property) (deeptime.clustering.MiniBatchKMeans property) initial_centers (deeptime.clustering.KMeans property) (deeptime.clustering.MiniBatchKMeans property) initial_count (deeptime.markov.hmm.HiddenMarkovModel property) initial_distribution (deeptime.markov.hmm.HiddenMarkovModel property) initial_distribution_prior (deeptime.markov.hmm.BayesianHMM property) initial_hmm (deeptime.markov.hmm.BayesianHMM property) initial_model (deeptime.markov.hmm.MaximumLikelihoodHMM property) instantaneous_coefficients (deeptime.decomposition.CovarianceKoopmanModel property) instantaneous_obs (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.EDMDModel property) (deeptime.decomposition.KernelCCAModel property) (deeptime.decomposition.KernelEDMDModel property) (deeptime.decomposition.KVADModel property) (deeptime.decomposition.TransferOperatorModel property)

integrator (deeptime.data.BickleyJet property) (deeptime.data.CustomSystem property) (deeptime.data.TimeDependentSystem property) (deeptime.data.TimeIndependentSystem property) intercept (deeptime.sindy.SINDyModel property) intermediate_states (deeptime.markov.ReactiveFlux property) ipu() (deeptime.decomposition.deep.TVAEEncoder method) is_connected() (deeptime.markov.TransitionCountModel method) (in module deeptime.markov.tools.analysis) (in module deeptime.markov.tools.estimation) is_diagonal_matrix() (in module deeptime.numeric) is_full_model (deeptime.markov.TransitionCountModel property) is_lagged (deeptime.covariance.Covariance property) is_rate_matrix() (in module deeptime.markov.tools.analysis) is_real (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) is_reversible() (in module deeptime.markov.tools.analysis) is_square_matrix() (in module deeptime.numeric) is_timelagged_dataset() (in module deeptime.util.types) is_torch_kernel() (in module deeptime.kernels) is_transition_matrix() (in module deeptime.markov.tools.analysis) is_valid_coordinate() (deeptime.data.DrunkardsWalk method)

K

k (deeptime.data.BickleyJet property) Kernel (class in deeptime.kernels) kernel (deeptime.decomposition.KernelCCAModel property) KernelCCA (class in deeptime.decomposition) KernelCCAModel (class in deeptime.decomposition) KernelEDMD (class in deeptime.decomposition) KernelEDMDModel (class in deeptime.decomposition) KMeans (class in deeptime.clustering) kmeans_plusplus() (in module deeptime.clustering) KMeansModel (class in deeptime.clustering) koopman_matrix (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.EDMDModel property) (deeptime.decomposition.KernelCCAModel property) (deeptime.decomposition.KernelEDMDModel property) (deeptime.decomposition.KVADModel property) (deeptime.decomposition.TransferOperatorModel property)

koopman_matrix() (in module deeptime.decomposition.deep) koopman_model (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) koopman_operator (deeptime.covariance.KoopmanWeightingModel property) KoopmanReweightedMSM (class in deeptime.markov.msm) KoopmanWeightingEstimator (class in deeptime.covariance) KoopmanWeightingModel (class in deeptime.covariance) KVAD (class in deeptime.decomposition) kvad_score() (in module deeptime.decomposition.deep) KVADModel (class in deeptime.decomposition)

L

L (deeptime.util.QuantityStatistics property) L0 (deeptime.data.BickleyJet property) lagrangian_mult_log (deeptime.markov.msm.TRAMModel property) lagtime (deeptime.covariance.Covariance property) (deeptime.covariance.CovarianceModel property) (deeptime.covariance.KoopmanWeightingEstimator property) (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.TICA property) (deeptime.decomposition.VAMP property) (deeptime.markov.hmm.BayesianHMMPosterior property) (deeptime.markov.hmm.HiddenMarkovModel property) (deeptime.markov.hmm.MaximumLikelihoodHMM property) (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.BayesianMSMPosterior property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) (deeptime.markov.TransitionCountEstimator property) (deeptime.markov.TransitionCountModel property) (deeptime.util.data.TrajectoriesDataset property)

lagtimes (deeptime.util.validation.ChapmanKolmogorovTest property) (deeptime.util.validation.ImpliedTimescales property) LaplacianKernel (class in deeptime.kernels) largest_connected_set() (in module deeptime.markov.tools.estimation) largest_connected_submatrix() (in module deeptime.markov.tools.estimation) learning_rate (deeptime.decomposition.deep.TAE property) (deeptime.decomposition.deep.TVAE property) (deeptime.decomposition.deep.VAMPNet property) lifetimes (deeptime.markov.hmm.HiddenMarkovModel property) likelihood (deeptime.markov.hmm.HiddenMarkovModel property) likelihoods (deeptime.markov.hmm.HiddenMarkovModel property) load_state_dict() (deeptime.decomposition.deep.TVAEEncoder method) lobe (deeptime.decomposition.deep.VAMPNet property) (deeptime.decomposition.deep.VAMPNetModel property) lobe_timelagged (deeptime.decomposition.deep.VAMPNet property) (deeptime.decomposition.deep.VAMPNetModel property) log_likelihood() (in module deeptime.markov.tools.estimation) lorenz_system() (in module deeptime.data)

M

major_flux() (deeptime.markov.ReactiveFlux method) make_animation() (deeptime.data.PBFSimulator method) map_discrete_to_observations() (deeptime.data.Ellipsoids method) map_observations_to_submodel() (deeptime.markov.hmm.DiscreteOutputModel method) markov_state_energies (deeptime.markov.msm.TRAMModel property) MarkovStateModel (class in deeptime.markov.msm) MarkovStateModelCollection (class in deeptime.markov.msm) max_cache (deeptime.markov.msm.AugmentedMSMEstimator property) max_centers (deeptime.clustering.RegularSpace property) max_iter (deeptime.clustering.KMeans property) (deeptime.clustering.MiniBatchKMeans property) max_n_processes (deeptime.util.validation.ImpliedTimescales property) max_n_samples (deeptime.util.validation.ImpliedTimescales property) MaximumLikelihoodHMM (class in deeptime.markov.hmm) MaximumLikelihoodMSM (class in deeptime.markov.msm) maxit (deeptime.markov.hmm.MaximumLikelihoodHMM property) maxit_reversible (deeptime.markov.hmm.MaximumLikelihoodHMM property) maxiter (deeptime.markov.msm.AugmentedMSMEstimator property) mean (deeptime.util.QuantityStatistics property) mean_0 (deeptime.covariance.CovarianceModel property) (deeptime.decomposition.CovarianceKoopmanModel property) mean_t (deeptime.covariance.CovarianceModel property) (deeptime.decomposition.CovarianceKoopmanModel property) means (deeptime.markov.hmm.GaussianOutputModel property) memberships (deeptime.markov.PCCAModel property) metastable_assignments (deeptime.markov.hmm.HiddenMarkovModel property) metastable_distributions (deeptime.markov.hmm.HiddenMarkovModel property) (deeptime.markov.PCCAModel property) metastable_from_data() (in module deeptime.markov.hmm.init.discrete) metastable_from_msm() (in module deeptime.markov.hmm.init.discrete) metastable_memberships (deeptime.markov.hmm.HiddenMarkovModel property) metastable_sets (deeptime.markov.hmm.HiddenMarkovModel property) metric (deeptime.clustering.BoxDiscretizationModel property) (deeptime.clustering.ClusterModel property) (deeptime.clustering.KMeans property) (deeptime.clustering.KMeansModel property) (deeptime.clustering.MiniBatchKMeans property) (deeptime.clustering.RegularSpace property) MetricRegistry (class in deeptime.clustering) metrics (in module deeptime.clustering) mfpt (deeptime.markov.ReactiveFlux property) mfpt() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov.tools.analysis) (in module deeptime.markov.tools.flux) mfpt_sensitivity() (in module deeptime.markov.tools.analysis) MiniBatchKMeans (class in deeptime.clustering) Model (class in deeptime.base)

model (deeptime.base.Estimator property) (deeptime.clustering.BoxDiscretization property) (deeptime.clustering.KMeans property) (deeptime.clustering.MiniBatchKMeans property) (deeptime.clustering.RegularSpace property) (deeptime.covariance.Covariance property) (deeptime.covariance.KoopmanWeightingEstimator property) (deeptime.decomposition.deep.TAE property) (deeptime.decomposition.deep.TVAE property) (deeptime.decomposition.deep.VAMPNet property) (deeptime.decomposition.DMD property) (deeptime.decomposition.EDMD property) (deeptime.decomposition.KernelCCA property) (deeptime.decomposition.KernelEDMD property) (deeptime.decomposition.KVAD property) (deeptime.decomposition.TICA property) (deeptime.decomposition.VAMP property) (deeptime.markov.hmm.BayesianHMM property) (deeptime.markov.hmm.MaximumLikelihoodHMM property) (deeptime.markov.msm.AugmentedMSMEstimator property) (deeptime.markov.msm.BayesianMSM property) (deeptime.markov.msm.MaximumLikelihoodMSM property) (deeptime.markov.msm.OOMReweightedMSM property) (deeptime.markov.msm.TRAM property) (deeptime.markov.TransitionCountEstimator property) (deeptime.sindy.SINDy property) modified_state_counts_log (deeptime.markov.msm.TRAMModel property) module deeptime.basis deeptime.clustering deeptime.covariance deeptime.data deeptime.decomposition deeptime.kernels deeptime.markov.tools.analysis deeptime.markov.tools.estimation deeptime.markov.tools.flux deeptime.numeric deeptime.plots deeptime.sindy deeptime.util module_available() (in module deeptime.util.platform) modules() (deeptime.decomposition.deep.TVAEEncoder method) moments_block() (in module deeptime.covariance) moments_XX() (in module deeptime.covariance) moments_XXXY() (in module deeptime.covariance) Monomials (class in deeptime.basis) msm (deeptime.data.BirthDeathChain property) (deeptime.data.DrunkardsWalk property) (deeptime.data.Ellipsoids property) msm_collection (deeptime.markov.msm.TRAMModel property)

N

n_clusters (deeptime.clustering.BoxDiscretizationModel property) (deeptime.clustering.ClusterModel property) (deeptime.clustering.KMeans property) (deeptime.clustering.KMeansModel property) (deeptime.clustering.MiniBatchKMeans property) (deeptime.clustering.RegularSpace property) n_connected_msms (deeptime.markov.msm.MarkovStateModelCollection property) n_eigenvalues (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) n_hidden_states (deeptime.markov.hmm.DiscreteOutputModel property) (deeptime.markov.hmm.GaussianOutputModel property) (deeptime.markov.hmm.HiddenMarkovModel property) (deeptime.markov.hmm.MaximumLikelihoodHMM property) (deeptime.markov.hmm.OutputModel property) n_jobs (deeptime.clustering.KMeans property) (deeptime.clustering.MiniBatchKMeans property) (deeptime.clustering.RegularSpace property) n_lagtimes (deeptime.util.validation.ImpliedTimescales property) n_markov_states (deeptime.markov.msm.TRAMDataset property) n_metastable (deeptime.markov.PCCAModel property) n_nodes (deeptime.plots.Network property) n_observable_states (deeptime.markov.hmm.DiscreteOutputModel property) (deeptime.markov.hmm.GaussianOutputModel property) (deeptime.markov.hmm.OutputModel property) n_observation_states (deeptime.markov.hmm.HiddenMarkovModel property) n_particles (deeptime.data.PBFSimulator property) n_samples (deeptime.markov.hmm.BayesianHMM property)

n_samples() (deeptime.util.validation.ImpliedTimescales method) n_states (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) (deeptime.markov.ReactiveFlux property) (deeptime.markov.TransitionCountEstimator property) (deeptime.markov.TransitionCountModel property) n_states_full (deeptime.markov.TransitionCountModel property) n_steps (deeptime.data.BickleyJet property) (deeptime.data.CustomSystem property) (deeptime.data.TimeDependentSystem property) (deeptime.data.TimeIndependentSystem property) n_therm_states (deeptime.markov.msm.TRAMDataset property) named_buffers() (deeptime.decomposition.deep.TVAEEncoder method) named_children() (deeptime.decomposition.deep.TVAEEncoder method) named_modules() (deeptime.decomposition.deep.TVAEEncoder method) named_parameters() (deeptime.decomposition.deep.TVAEEncoder method) ncov (deeptime.covariance.Covariance property) ncv (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) net_flux (deeptime.markov.ReactiveFlux property) netflux() (deeptime.data.BirthDeathChain method) Network (class in deeptime.plots) node_sizes (deeptime.plots.Network property) nonempty_obs() (deeptime.markov.hmm.HiddenMarkovModel method) normalize() (deeptime.markov.hmm.DiscreteOutputModel method) number_of_states() (in module deeptime.markov)

O

Observable (class in deeptime.basis) observable_transform (deeptime.decomposition.KVAD property) observation_symbols (deeptime.markov.hmm.HiddenMarkovModel property) observation_symbols_full (deeptime.markov.hmm.HiddenMarkovModel property) observations() (deeptime.data.Ellipsoids method) oom_components (deeptime.markov.msm.KoopmanReweightedMSM property) oom_eigenvalues (deeptime.markov.msm.KoopmanReweightedMSM property) oom_evaluator (deeptime.markov.msm.KoopmanReweightedMSM property) oom_information_state_vector (deeptime.markov.msm.KoopmanReweightedMSM property) oom_rank (deeptime.markov.msm.KoopmanReweightedMSM property) oom_timescales (deeptime.markov.msm.KoopmanReweightedMSM property) OOMReweightedMSM (class in deeptime.markov.msm) operator (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.EDMDModel property) (deeptime.decomposition.KernelCCAModel property) (deeptime.decomposition.KernelEDMDModel property) (deeptime.decomposition.KVADModel property) (deeptime.decomposition.TransferOperatorModel property) operator_inverse (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.EDMDModel property) (deeptime.decomposition.KernelCCAModel property) (deeptime.decomposition.KernelEDMDModel property) (deeptime.decomposition.KVADModel property) (deeptime.decomposition.TransferOperatorModel property)

optimizer (deeptime.decomposition.deep.TAE property) (deeptime.decomposition.deep.TVAE property) (deeptime.decomposition.deep.VAMPNet property) optimizer_state (deeptime.markov.msm.AugmentedMSM property) ornstein_uhlenbeck() (in module deeptime.data) output_dimension (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.EDMDModel property) (deeptime.decomposition.KernelCCAModel property) (deeptime.decomposition.KernelEDMDModel property) (deeptime.decomposition.KVADModel property) (deeptime.decomposition.TransferOperatorModel property) output_model (deeptime.markov.hmm.HiddenMarkovModel property) output_probabilities (deeptime.markov.hmm.DiscreteOutputModel property) (deeptime.markov.hmm.HiddenMarkovModel property) OutputModel (class in deeptime.markov.hmm)

P

parameters() (deeptime.decomposition.deep.TVAEEncoder method) partial_fit() (deeptime.clustering.MiniBatchKMeans method) (deeptime.clustering.RegularSpace method) (deeptime.covariance.Covariance method) (deeptime.covariance.KoopmanWeightingEstimator method) (deeptime.decomposition.deep.VAMPNet method) (deeptime.decomposition.TICA method) (deeptime.decomposition.VAMP method) pathways() (deeptime.markov.ReactiveFlux method) (in module deeptime.markov.tools.flux) PBFSimulator (class in deeptime.data) pcca() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov) pcca_memberships() (in module deeptime.markov.tools.analysis) PCCAModel (class in deeptime.markov) periodic_bc (deeptime.data.BickleyJet property) plot() (deeptime.plots.Network method) (deeptime.util.EnergyLandscape2d method) (deeptime.util.validation.ChapmanKolmogorovTest method) (deeptime.util.validation.ImpliedTimescales method) plot_2d_map() (deeptime.data.DrunkardsWalk method) plot_adjacency() (in module deeptime.plots) plot_ck_test() (in module deeptime.plots) plot_contour2d_from_xyz() (in module deeptime.plots) plot_density() (in module deeptime.plots) plot_energy2d() (in module deeptime.plots) plot_flux() (in module deeptime.plots)

plot_implied_timescales() (in module deeptime.plots) plot_markov_model() (in module deeptime.plots) plot_network() (deeptime.data.DrunkardsWalk method) plot_path() (deeptime.data.DrunkardsWalk static method) plotting_function() (in module deeptime.util.decorators) PolynomialKernel (class in deeptime.kernels) pos (deeptime.plots.Network property) position_based_fluids() (in module deeptime.data) potential() (deeptime.data.BickleyJet method) (deeptime.data.CustomSystem method) (deeptime.data.TimeDependentSystem method) (deeptime.data.TimeIndependentSystem method) predict() (deeptime.sindy.SINDyModel method) (deeptime.sindy.STLSQ method) predictions (deeptime.util.validation.ChapmanKolmogorovTest property) predictions_samples (deeptime.util.validation.ChapmanKolmogorovTest property) print() (deeptime.sindy.SINDyModel method) prinz_potential() (in module deeptime.data) prior (deeptime.markov.hmm.BayesianHMMPosterior property) (deeptime.markov.hmm.DiscreteOutputModel property) (deeptime.markov.msm.BayesianMSMPosterior property) prior_const() (in module deeptime.markov.tools.estimation) prior_neighbor() (in module deeptime.markov.tools.estimation) prior_rev() (in module deeptime.markov.tools.estimation) ProgressCallback (class in deeptime.util.callbacks) propagate() (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.markov.hmm.HiddenMarkovModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method)

Q

quadruple_well() (in module deeptime.data)

quadruple_well_asymmetric() (in module deeptime.data) QuantityStatistics (class in deeptime.util)

R

R (deeptime.util.QuantityStatistics property) r0 (deeptime.data.BickleyJet property) random_guess() (in module deeptime.markov.hmm.init.discrete) random_state (deeptime.data.Ellipsoids property) rate (deeptime.markov.ReactiveFlux property) rate() (deeptime.data.BirthDeathChain method) (in module deeptime.markov.tools.flux) rate_matrix() (in module deeptime.markov.tools.estimation) rdl_decomposition() (in module deeptime.markov.tools.analysis) reactive_flux() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov) ReactiveFlux (class in deeptime.markov) register() (deeptime.clustering.MetricRegistry method) register_backward_hook() (deeptime.decomposition.deep.TVAEEncoder method) register_buffer() (deeptime.decomposition.deep.TVAEEncoder method) register_forward_hook() (deeptime.decomposition.deep.TVAEEncoder method) register_forward_pre_hook() (deeptime.decomposition.deep.TVAEEncoder method) register_full_backward_hook() (deeptime.decomposition.deep.TVAEEncoder method) register_load_state_dict_post_hook() (deeptime.decomposition.deep.TVAEEncoder method) register_module() (deeptime.decomposition.deep.TVAEEncoder method) register_parameter() (deeptime.decomposition.deep.TVAEEncoder method)

RegularSpace (class in deeptime.clustering) relaxation() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov.tools.analysis) relaxation_obs() (deeptime.markov.hmm.HiddenMarkovModel method) remove_data_mean (deeptime.covariance.Covariance property) requires_grad_() (deeptime.decomposition.deep.TVAEEncoder method) restrict_to_largest_connected_set() (deeptime.markov.msm.TRAMDataset method) restrict_to_submodel() (deeptime.markov.msm.TRAMDataset method) reversible (deeptime.covariance.Covariance property) (deeptime.markov.hmm.BayesianHMM property) (deeptime.markov.hmm.MaximumLikelihoodHMM property) (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.AugmentedMSMEstimator property) (deeptime.markov.msm.BayesianMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) (deeptime.markov.msm.MaximumLikelihoodMSM property) (deeptime.markov.msm.OOMReweightedMSM property) (deeptime.markov.msm.TRAM property) run() (deeptime.data.PBFSimulator method)

S

sample() (deeptime.markov.hmm.DiscreteOutputModel method) (deeptime.markov.hmm.GaussianOutputModel method) (deeptime.markov.hmm.OutputModel method) (deeptime.markov.msm.BayesianMSM method) sample_by_observation_probabilities() (deeptime.markov.hmm.HiddenMarkovModel method) samples (deeptime.markov.hmm.BayesianHMMPosterior property) (deeptime.markov.msm.BayesianMSMPosterior property) samples_for_process() (deeptime.util.validation.ImpliedTimescales method) scaling (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.TICA property) (deeptime.decomposition.VAMP property) schatten_norm() (in module deeptime.numeric) score() (deeptime.clustering.KMeansModel method) (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (deeptime.sindy.SINDyModel method) (deeptime.sindy.STLSQ method) score_method (deeptime.decomposition.deep.VAMPNet property) seed (deeptime.data.Ellipsoids property) select() (deeptime.markov.msm.MarkovStateModelCollection method) selected_count_fraction (deeptime.markov.TransitionCountModel property) selected_state_fraction (deeptime.markov.TransitionCountModel property) set_extra_state() (deeptime.decomposition.deep.TVAEEncoder method) set_params() (deeptime.base.Estimator method) (deeptime.base.Model method) (deeptime.clustering.BoxDiscretization method) (deeptime.clustering.BoxDiscretizationModel method) (deeptime.clustering.ClusterModel method) (deeptime.clustering.KMeans method) (deeptime.clustering.KMeansModel method) (deeptime.clustering.MiniBatchKMeans method) (deeptime.clustering.RegularSpace method) (deeptime.covariance.Covariance method) (deeptime.covariance.CovarianceModel method) (deeptime.covariance.KoopmanWeightingEstimator method) (deeptime.covariance.KoopmanWeightingModel method) (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TAEModel method) (deeptime.decomposition.deep.TVAE method) (deeptime.decomposition.deep.TVAEModel method) (deeptime.decomposition.deep.VAMPNet method) (deeptime.decomposition.deep.VAMPNetModel method) (deeptime.decomposition.DMD method) (deeptime.decomposition.DMDModel method) (deeptime.decomposition.EDMD method) (deeptime.decomposition.EDMDModel method) (deeptime.decomposition.KernelCCA method) (deeptime.decomposition.KernelCCAModel method) (deeptime.decomposition.KernelEDMD method) (deeptime.decomposition.KernelEDMDModel method) (deeptime.decomposition.KVAD method) (deeptime.decomposition.KVADModel method) (deeptime.decomposition.TICA method) (deeptime.decomposition.TransferOperatorModel method) (deeptime.decomposition.VAMP method) (deeptime.markov.hmm.BayesianHMM method) (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.hmm.DiscreteOutputModel method) (deeptime.markov.hmm.GaussianOutputModel method) (deeptime.markov.hmm.HiddenMarkovModel method) (deeptime.markov.hmm.MaximumLikelihoodHMM method) (deeptime.markov.hmm.OutputModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.AugmentedMSMEstimator method) (deeptime.markov.msm.BayesianMSM method) (deeptime.markov.msm.BayesianMSMPosterior method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (deeptime.markov.msm.MaximumLikelihoodMSM method) (deeptime.markov.msm.OOMReweightedMSM method) (deeptime.markov.msm.TRAM method) (deeptime.markov.msm.TRAMModel method) (deeptime.markov.PCCAModel method) (deeptime.markov.ReactiveFlux method) (deeptime.markov.TransitionCountEstimator method) (deeptime.markov.TransitionCountModel method) (deeptime.sindy.SINDy method) (deeptime.sindy.SINDyModel method) (deeptime.sindy.STLSQ method) setflags() (deeptime.base.Dataset method) (deeptime.markov.msm.TRAMDataset method) (deeptime.util.data.ConcatDataset method) (deeptime.util.data.TimeLaggedConcatDataset method) (deeptime.util.data.TimeLaggedDataset method) (deeptime.util.data.TrajectoriesDataset method) (deeptime.util.data.TrajectoryDataset method) sets (deeptime.markov.PCCAModel property) setter() (deeptime.util.decorators.cached_property method) setup_optimizer() (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TVAE method) (deeptime.decomposition.deep.VAMPNet method) share_memory() (deeptime.decomposition.deep.TVAEEncoder method) sigma (deeptime.kernels.GaussianKernel property) (deeptime.kernels.TorchGaussianKernel property) sigmas (deeptime.markov.hmm.GaussianOutputModel property)

simulate() (deeptime.markov.hmm.HiddenMarkovModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (deeptime.sindy.SINDyModel method) simulate_oscillatory_force() (deeptime.data.PBFSimulator method) simulate_trajectories() (deeptime.data.DoubleWellDiscrete method) simulate_trajectory() (deeptime.data.DoubleWellDiscrete method) SINDy (class in deeptime.sindy) SINDyModel (class in deeptime.sindy) singular_values (deeptime.decomposition.CovarianceKoopmanModel property) singular_vectors_left (deeptime.decomposition.CovarianceKoopmanModel property) singular_vectors_right (deeptime.decomposition.CovarianceKoopmanModel property) sliding_window() (in module deeptime.util.data) sort_eigs() (in module deeptime.numeric) source_states (deeptime.markov.ReactiveFlux property) sparse (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.AugmentedMSMEstimator property) (deeptime.markov.msm.BayesianMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) (deeptime.markov.msm.MaximumLikelihoodMSM property) (deeptime.markov.msm.OOMReweightedMSM property) (deeptime.markov.msm.TRAM property) (deeptime.markov.TransitionCountEstimator property) sparse_mode (deeptime.covariance.Covariance property) spd_eig() (in module deeptime.numeric) spd_inv() (in module deeptime.numeric) spd_inv_split() (in module deeptime.numeric) spd_inv_sqrt() (in module deeptime.numeric) spd_truncated_svd() (in module deeptime.numeric) sqrt_model() (in module deeptime.data) state_colors (deeptime.plots.Network property) state_counts (deeptime.markov.msm.TRAMDataset property) state_dict() (deeptime.decomposition.deep.TVAEEncoder method) state_fraction (deeptime.markov.msm.MarkovStateModelCollection property) state_fractions (deeptime.markov.msm.MarkovStateModelCollection property) state_histogram (deeptime.markov.TransitionCountModel property) state_histogram_full (deeptime.markov.TransitionCountModel property) state_labels (deeptime.plots.Network property) state_probabilities (deeptime.markov.hmm.HiddenMarkovModel property) state_sizes (deeptime.plots.Network property) state_symbols (deeptime.markov.TransitionCountModel property) state_symbols() (deeptime.markov.msm.MarkovStateModelCollection method) state_symbols_with_blank (deeptime.markov.TransitionCountModel property) state_to_coordinate() (deeptime.data.DrunkardsWalk method) states (deeptime.markov.TransitionCountModel property) states_largest() (deeptime.markov.hmm.HiddenMarkovModel method) states_populous() (deeptime.markov.hmm.HiddenMarkovModel method) states_to_symbols() (deeptime.markov.TransitionCountModel method) stationary (deeptime.markov.hmm.BayesianHMM property) (deeptime.markov.hmm.MaximumLikelihoodHMM property) (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) stationary_distribution (deeptime.data.BirthDeathChain property) (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) (deeptime.markov.ReactiveFlux property) stationary_distribution() (in module deeptime.markov.tools.analysis) stationary_distribution_constraint (deeptime.markov.msm.BayesianMSM property) (deeptime.markov.msm.MaximumLikelihoodMSM property) stationary_distribution_obs (deeptime.markov.hmm.HiddenMarkovModel property) stationary_distribution_sensitivity() (in module deeptime.markov.tools.analysis) std (deeptime.util.QuantityStatistics property) STLSQ (class in deeptime.sindy) store_hidden (deeptime.markov.hmm.BayesianHMM property) stride (deeptime.markov.hmm.HiddenMarkovModel property) (deeptime.markov.hmm.MaximumLikelihoodHMM property) submodel() (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.hmm.DiscreteOutputModel method) (deeptime.markov.hmm.GaussianOutputModel method) (deeptime.markov.hmm.HiddenMarkovModel method) (deeptime.markov.hmm.OutputModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.BayesianMSMPosterior method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (deeptime.markov.TransitionCountModel method) submodel_disconnect() (deeptime.markov.hmm.HiddenMarkovModel method) submodel_largest() (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.hmm.HiddenMarkovModel method) (deeptime.markov.TransitionCountModel method) submodel_populous() (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.hmm.HiddenMarkovModel method) subsets (deeptime.util.data.ConcatDataset property) (deeptime.util.data.TimeLaggedConcatDataset property) (deeptime.util.data.TrajectoriesDataset property) support_confidence (deeptime.markov.msm.AugmentedMSMEstimator property) supports_progress_interface() (in module deeptime.util.callbacks) swissroll_model() (in module deeptime.data) sym_inverse() (in module deeptime.decomposition.deep) symbols_to_states() (deeptime.markov.TransitionCountModel method) symmetrized (deeptime.covariance.CovarianceModel property)

T

TAE (class in deeptime.decomposition.deep) TAEModel (class in deeptime.decomposition.deep) target_states (deeptime.markov.ReactiveFlux property) therm_state_energies (deeptime.markov.msm.TRAMModel property) thomas_attractor() (in module deeptime.data) TICA (class in deeptime.decomposition) time_dependent (deeptime.data.BickleyJet property) (deeptime.data.CustomSystem property) (deeptime.data.TimeDependentSystem property) (deeptime.data.TimeIndependentSystem property) time_dependent_quintuple_well() (in module deeptime.data) TimeDependentSystem (class in deeptime.data) TimeIndependentSystem (class in deeptime.data) timelagged_coefficients (deeptime.decomposition.CovarianceKoopmanModel property) timelagged_obs (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.EDMDModel property) (deeptime.decomposition.KernelCCAModel property) (deeptime.decomposition.KernelEDMDModel property) (deeptime.decomposition.KVADModel property) (deeptime.decomposition.TransferOperatorModel property) TimeLaggedConcatDataset (class in deeptime.util.data) TimeLaggedDataset (class in deeptime.util.data) timescale_sensitivity() (in module deeptime.markov.tools.analysis) timescales() (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.markov.hmm.BayesianHMMPosterior method) (deeptime.markov.hmm.HiddenMarkovModel method) (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.BayesianMSMPosterior method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) (in module deeptime.markov.tools.analysis) timescales_for_process() (deeptime.util.validation.ImpliedTimescales method) timeshifted_split() (in module deeptime.util.data) tmatrix_cov() (in module deeptime.markov.tools.estimation) tmatrix_metropolis1d() (in module deeptime.data) tmatrix_sampler() (in module deeptime.markov.tools.estimation) to() (deeptime.decomposition.deep.TVAEEncoder method) to_3d() (deeptime.data.BickleyJet static method) to_dataset() (in module deeptime.util.types) to_empty() (deeptime.decomposition.deep.TVAEEncoder method) to_koopman_model() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method) to_netflux() (in module deeptime.markov.tools.flux) to_state_probability_trajectory() (deeptime.markov.hmm.DiscreteOutputModel method) (deeptime.markov.hmm.GaussianOutputModel method) (deeptime.markov.hmm.OutputModel method) tolerance (deeptime.clustering.KMeans property) (deeptime.clustering.KMeansModel property) (deeptime.clustering.MiniBatchKMeans property) TorchGaussianKernel (class in deeptime.kernels) total_count (deeptime.markov.TransitionCountModel property) total_flux (deeptime.markov.ReactiveFlux property) total_flux() (in module deeptime.markov.tools.flux) totalflux() (deeptime.data.BirthDeathChain method) train() (deeptime.decomposition.deep.TVAEEncoder method) train_losses (deeptime.decomposition.deep.TAE property) (deeptime.decomposition.deep.TVAE property) train_scores (deeptime.decomposition.deep.VAMPNet property) trajectories (deeptime.util.data.TrajectoriesDataset property) TrajectoriesDataset (class in deeptime.util.data) trajectory() (deeptime.data.BickleyJet method) (deeptime.data.CustomSystem method) (deeptime.data.TimeDependentSystem method) (deeptime.data.TimeIndependentSystem method) TrajectoryDataset (class in deeptime.util.data) TRAM (class in deeptime.markov.msm)

tram_input (deeptime.markov.msm.TRAMDataset property) TRAMDataset (class in deeptime.markov.msm) TRAMModel (class in deeptime.markov.msm) TransferOperatorModel (class in deeptime.decomposition) transform() (deeptime.base.Transformer method) (deeptime.basis.Concatenation method) (deeptime.basis.Identity method) (deeptime.basis.Monomials method) (deeptime.basis.Observable method) (deeptime.clustering.BoxDiscretizationModel method) (deeptime.clustering.ClusterModel method) (deeptime.clustering.KMeans method) (deeptime.clustering.KMeansModel method) (deeptime.clustering.MiniBatchKMeans method) (deeptime.covariance.KoopmanWeightingEstimator method) (deeptime.covariance.KoopmanWeightingModel method) (deeptime.covariance.WhiteningTransform method) (deeptime.decomposition.CovarianceKoopmanModel method) (deeptime.decomposition.deep.TAE method) (deeptime.decomposition.deep.TAEModel method) (deeptime.decomposition.deep.TVAE method) (deeptime.decomposition.deep.TVAEModel method) (deeptime.decomposition.deep.VAMPNet method) (deeptime.decomposition.deep.VAMPNetModel method) (deeptime.decomposition.DMD method) (deeptime.decomposition.DMDModel method) (deeptime.decomposition.EDMD method) (deeptime.decomposition.EDMDModel method) (deeptime.decomposition.KernelCCAModel method) (deeptime.decomposition.KernelEDMD method) (deeptime.decomposition.KernelEDMDModel method) (deeptime.decomposition.KVAD method) (deeptime.decomposition.KVADModel method) (deeptime.decomposition.TICA method) (deeptime.decomposition.TransferOperatorModel method) (deeptime.decomposition.VAMP method) (deeptime.markov.TransitionCountEstimator method) (deeptime.sindy.SINDyModel method) transform_discrete_trajectories_to_observed_symbols() (deeptime.markov.hmm.HiddenMarkovModel method) transform_discrete_trajectories_to_submodel() (deeptime.markov.TransitionCountModel method) transform_onehot() (deeptime.clustering.BoxDiscretizationModel method) transform_to_density() (deeptime.data.PBFSimulator method) Transformer (class in deeptime.base) transition_counts (deeptime.markov.hmm.HiddenMarkovModel property) (deeptime.markov.msm.TRAMDataset property) transition_matrix (deeptime.data.BirthDeathChain property) (deeptime.data.DoubleWellDiscrete property) (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) transition_matrix() (in module deeptime.markov.tools.estimation) transition_matrix_obs() (deeptime.markov.hmm.HiddenMarkovModel method) transition_matrix_prior (deeptime.markov.hmm.BayesianHMM property) transition_matrix_tolerance (deeptime.markov.msm.AugmentedMSM property) (deeptime.markov.msm.KoopmanReweightedMSM property) (deeptime.markov.msm.MarkovStateModel property) (deeptime.markov.msm.MarkovStateModelCollection property) transition_model (deeptime.markov.hmm.HiddenMarkovModel property) TransitionCountEstimator (class in deeptime.markov) TransitionCountModel (class in deeptime.markov) triple_well_1d() (in module deeptime.data) triple_well_2d() (in module deeptime.data) tv_derivative() (in module deeptime.util.diff) TVAE (class in deeptime.decomposition.deep) TVAEEncoder (class in deeptime.decomposition.deep) TVAEModel (class in deeptime.decomposition.deep) twostep_count_matrices (deeptime.markov.msm.KoopmanReweightedMSM property) type() (deeptime.decomposition.deep.TVAEEncoder method)

U

U0 (deeptime.data.BickleyJet property) uncertainties (deeptime.markov.msm.AugmentedMSMEstimator property) update_stationary_distribution() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method)

update_transition_matrix() (deeptime.markov.msm.AugmentedMSM method) (deeptime.markov.msm.KoopmanReweightedMSM method) (deeptime.markov.msm.MarkovStateModel method) (deeptime.markov.msm.MarkovStateModelCollection method)

V

valid_impls (deeptime.kernels.GaussianKernel attribute) (deeptime.kernels.TorchGaussianKernel attribute) validate() (deeptime.decomposition.deep.VAMPNet method) validation_losses (deeptime.decomposition.deep.TAE property) (deeptime.decomposition.deep.TVAE property) validation_scores (deeptime.decomposition.deep.VAMPNet property) VAMP (class in deeptime.decomposition) vamp_score() (in module deeptime.decomposition) (in module deeptime.decomposition.deep) vamp_score_cv() (in module deeptime.decomposition) vamp_score_data() (in module deeptime.decomposition)

VAMPNet (class in deeptime.decomposition.deep) vampnet_loss() (in module deeptime.decomposition.deep) VAMPNetModel (class in deeptime.decomposition.deep) var_cutoff (deeptime.decomposition.CovarianceKoopmanModel property) (deeptime.decomposition.TICA property) (deeptime.decomposition.VAMP property) vectorized_f (deeptime.data.BickleyJet property) (deeptime.data.CustomSystem property) (deeptime.data.TimeDependentSystem property) (deeptime.data.TimeIndependentSystem property) visited_set (deeptime.markov.TransitionCountModel property)

W

walk() (deeptime.data.DrunkardsWalk method) weights() (deeptime.covariance.KoopmanWeightingModel method) weights_input (deeptime.covariance.KoopmanWeightingModel property) whiten() (deeptime.covariance.CovarianceModel method)

whitening_rank_0 (deeptime.decomposition.CovarianceKoopmanModel property) whitening_rank_t (deeptime.decomposition.CovarianceKoopmanModel property) whitening_transformation (deeptime.covariance.KoopmanWeightingModel property) WhiteningTransform (class in deeptime.covariance) with_traceback() (deeptime.numeric.ZeroRankError method)

X

xpu() (deeptime.decomposition.deep.TVAEEncoder method)

Z

zero_grad() (deeptime.decomposition.deep.TVAEEncoder method)

ZeroRankError