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Getting Started
Motivation
Installation
Tutorial
Examples
Reference
Featurization
Decomposition
Clustering
Markov state models (MSMs)
Model Selection using GMRQ
Continuous-time MSMs
Hidden Markov models (HMMs)
Transition Path Theory
Datasets
I/O
Ancillary
FAQs
API Patterns
Writing Plugins
Changelog
Version 3.6.1
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Other versions
Reference
ΒΆ
Featurization
Featurizations
msmbuilder.featurizer.AtomPairsFeaturizer
msmbuilder.featurizer.ContactFeaturizer
msmbuilder.featurizer.DRIDFeaturizer
msmbuilder.featurizer.DihedralFeaturizer
msmbuilder.featurizer.GaussianSolventFeaturizer
msmbuilder.featurizer.RMSDFeaturizer
msmbuilder.featurizer.RawPositionsFeaturizer
msmbuilder.featurizer.SuperposeFeaturizer
Alternative to Featurization
Decomposition
tICA
PCA
Algorithms
msmbuilder.decomposition.tICA
msmbuilder.decomposition.SparseTICA
msmbuilder.decomposition.PCA
Theory
PCA
tICA
Hyperparameters
Drawbacks
Combination with MSM
References
Clustering
Algorithms
References
Markov state models (MSMs)
Algorithms
msmbuilder.msm.MarkovStateModel
msmbuilder.msm.BayesianMarkovStateModel
Maximum Likelihood and Bayesian Estimation
Tradeoffs and Parameter Selection
References
Model Selection using GMRQ
Algorithms
msmbuilder.decomposition.tICA.score
msmbuilder.msm.MarkovStateModel.score
msmbuilder.msm.ContinuousTimeMSM.score
References
Continuous-time MSMs
Theory
Uncertainties
Algorithms
msmbuilder.msm.ContinuousTimeMSM
References
Hidden Markov models (HMMs)
HMMs for Biophysics
Algorithms
msmbuilder.hmm.GaussianHMM
msmbuilder.hmm.VonMisesHMM
References
Transition Path Theory
References
Functions
msmbuilder.tpt.fluxes
msmbuilder.tpt.net_fluxes
msmbuilder.tpt.fraction_visited
msmbuilder.tpt.hub_scores
msmbuilder.tpt.paths
msmbuilder.tpt.top_path
msmbuilder.tpt.committors
msmbuilder.tpt.conditional_committors
msmbuilder.tpt.mfpts
Datasets
Datasets
Datasets on Disk
Trajectory Datasets - Read only
Provenance Information
Models
Functions
I/O
Dictionary of trajectories
Mapping keys to filenames
Metadata
Estimators
Saving and loading
Gathering Metadata
Project Templates