├── .github ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── build-code.yml │ └── build-wheels.yml ├── .gitignore ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── appveyor.yml ├── basesetup.py ├── devtools ├── README.md ├── conda-recipe │ ├── bld.bat │ ├── build.sh │ └── meta.yaml └── travis-ci │ ├── build_docs.sh │ ├── install_miniconda.sh │ ├── set_doc_version.py │ └── update_versions_json.py ├── docs ├── LICENSE ├── Makefile ├── _static │ ├── flow-chart.png │ ├── fspeptide.png │ ├── kde-vs-histogram.png │ ├── lengths-hist.png │ ├── logo-200px.png │ ├── logo.png │ ├── msm-microstates.png │ ├── tica-heatmap.png │ ├── tica-movie.gif │ └── tica_vs_pca.png ├── _templates │ └── class.rst ├── advanced_examples │ ├── bayesian-msm.rst │ ├── gmrq-model-selection.rst │ ├── hmm-and-msm.rst │ ├── implied-timescales.rst │ ├── index.rst │ ├── plot-tica-heatmap.rst │ ├── quadwell-n-states.rst │ ├── quadwell.rst │ ├── tica-1.rst │ └── uncertainty.rst ├── apipatterns.rst ├── background.rst ├── bibparse.py ├── changelog.rst ├── cluster.rst ├── conf.py ├── contributing.rst ├── datasets.rst ├── decomposition.rst ├── examples │ ├── Clustering-Comparison.rst │ ├── Fs-Peptide-command-line.rst │ ├── Fs-Peptide-in-RAM.rst │ ├── Fs-Peptide-with-dataset.rst │ ├── GMRQ-Model-Selection.rst │ ├── Ligand-Featurization.rst │ ├── Ward-Clustering.rst │ ├── index.rst │ └── tICA-vs-PCA.rst ├── faq.rst ├── feature_selection.rst ├── featurization.rst ├── figures │ └── kde-vs-histogram.py ├── gmrq.rst ├── hmm.rst ├── index.rst ├── installation.rst ├── io.rst ├── make.bat ├── msm.rst ├── plugins.rst ├── preprocessing.rst ├── publications.bib ├── publications_templ.rst ├── ratematrix.rst ├── requirements.txt ├── sphinxext │ ├── embed.tpl │ └── notebook_sphinxext.py ├── tpt.rst └── tutorial.rst ├── examples ├── Clustering-Comparison.ipynb ├── Fs-Peptide-command-line.ipynb ├── Fs-Peptide-in-RAM.ipynb ├── Fs-Peptide-with-Pipeline.ipynb ├── Fs-Peptide-with-dataset.ipynb ├── GMRQ-Model-Selection.ipynb ├── LICENSE.md ├── Ligand-Featurization.ipynb ├── Ward-Clustering.ipynb ├── advanced │ ├── bayesian-msm.ipynb │ ├── hmm-and-msm.ipynb │ ├── implied-timescales.ipynb │ ├── plot-tica-heatmap.ipynb │ ├── quadwell-n-states.ipynb │ ├── quadwell.ipynb │ └── uncertainty.ipynb └── tICA-vs-PCA.ipynb ├── msmbuilder ├── __init__.py ├── base.py ├── cluster │ ├── .gitignore │ ├── __init__.py │ ├── _kmedoids.pyx │ ├── agglomerative.py │ ├── apm.py │ ├── base.py │ ├── kcenters.py │ ├── kmedoids.py │ ├── minibatchkmedoids.py │ ├── ndgrid.py │ ├── regularspatial.py │ └── src │ │ ├── kmedoids.cc │ │ └── kmedoids.h ├── cmdline.py ├── commands │ ├── __init__.py │ ├── atom_indices.py │ ├── convert_chunked_project.py │ ├── example_datasets.py │ ├── featurizer.py │ ├── fit.py │ ├── fit_transform.py │ ├── implied_timescales.py │ ├── template_project.py │ └── transform.py ├── dataset.py ├── decomposition │ ├── .gitignore │ ├── __init__.py │ ├── _speigh.pyx │ ├── base.py │ ├── kernel_approximation.py │ ├── ksparsetica.py │ ├── ktica.py │ ├── pca.py │ ├── sparsetica.py │ ├── tica.py │ └── utils.py ├── example_datasets │ ├── .gitignore │ ├── __init__.py │ ├── _muller.pyx │ ├── alanine_dipeptide.py │ ├── base.py │ ├── brownian1d.py │ ├── fs_peptide.py │ ├── met_enkephalin.py │ └── muller.py ├── feature_extraction │ └── __init__.py ├── feature_selection │ ├── __init__.py │ ├── base.py │ └── featureselector.py ├── featurizer │ ├── __init__.py │ ├── feature_union.py │ ├── featurizer.py │ ├── indices.py │ ├── multichain.py │ ├── multiseq_featuizer.py │ └── subset.py ├── hmm │ ├── .gitignore │ ├── __init__.py │ ├── cephes │ │ ├── README.md │ │ ├── cephes.h │ │ ├── cephes_names.h │ │ ├── chbevl.c │ │ ├── gamma.c │ │ ├── i0.c │ │ ├── i1.c │ │ ├── mconf.h │ │ ├── mtherr.c │ │ ├── polevl.c │ │ ├── psi.c │ │ └── zeta.c │ ├── discrete_approx.py │ ├── gaussian.pyx │ ├── src │ │ ├── GaussianHMMFitter.cpp │ │ ├── VonMisesHMMFitter.cpp │ │ ├── include │ │ │ ├── GaussianHMMFitter.h │ │ │ ├── HMMFitter.h │ │ │ ├── Trajectory.h │ │ │ ├── VonMisesHMMFitter.h │ │ │ ├── sse2neon.h │ │ │ └── sse_mathfun.h │ │ └── logsumexp.hpp │ └── vonmises.pyx ├── io │ ├── __init__.py │ ├── gather_metadata.py │ ├── io.py │ ├── project_template.py │ └── sampling │ │ ├── __init__.py │ │ └── sampling.py ├── io_templates │ └── twitter-bootstrap.html ├── libdistance │ ├── .gitignore │ ├── libdistance.pyx │ └── src │ │ ├── assign.hpp │ │ ├── cdist.hpp │ │ ├── dist.hpp │ │ ├── distance_kernels.h │ │ ├── pdist.hpp │ │ └── sumdist.hpp ├── lumping │ ├── __init__.py │ ├── bace.py │ ├── mvca.py │ ├── pcca.py │ └── pcca_plus.py ├── msm │ ├── .gitignore │ ├── __init__.py │ ├── _markovstatemodel.pyx │ ├── _metzner_mcmc_fast.pyx │ ├── _metzner_mcmc_slow.py │ ├── _ratematrix.pyx │ ├── _ratematrix_priors.pyx │ ├── _ratematrix_support.pyx │ ├── bayes_ratematrix.py │ ├── bayesmsm.py │ ├── core.py │ ├── implied_timescales.py │ ├── markov_appreciation.py │ ├── msm.py │ ├── ratematrix.py │ ├── src │ │ ├── metzner_mcmc.c │ │ ├── metzner_mcmc.h │ │ ├── transmat_mle_prinz.c │ │ └── transmat_mle_prinz.h │ └── validation │ │ ├── __init__.py │ │ └── bootstrapmsm.py ├── preprocessing │ ├── __init__.py │ ├── base.py │ └── timeseries.py ├── project_templates │ ├── 0-test-install.py │ ├── 1-get-example-data.py │ ├── LICENSE.md │ ├── README.md │ ├── analysis │ │ ├── gather-metadata-plot.py │ │ └── gather-metadata.py │ ├── cluster │ │ ├── cluster-plot.py │ │ ├── cluster.py │ │ ├── sample-clusters-plot.py │ │ └── sample-clusters.py │ ├── dihedrals │ │ ├── featurize-plot.py │ │ └── featurize.py │ ├── landmarks │ │ ├── featurize-plot.py │ │ ├── featurize.py │ │ └── find-landmarks.py │ ├── msm │ │ ├── microstate-plot.py │ │ ├── microstate-traj.py │ │ ├── microstate.py │ │ ├── timescales-plot.py │ │ └── timescales.py │ ├── plot_header.template │ ├── plot_macros.template │ ├── rmsd │ │ ├── rmsd-plot.py │ │ └── rmsd.py │ └── tica │ │ ├── tica-plot.py │ │ ├── tica-sample-coordinate-plot.py │ │ ├── tica-sample-coordinate.py │ │ └── tica.py ├── scripts │ ├── __init__.py │ └── msmb.py ├── src │ ├── cy_blas.pyx │ ├── f2py │ │ └── f2pyptr.h │ ├── scipy_lapack.h │ └── triu_utils.pyx ├── tests │ ├── .gitignore │ ├── __init__.py │ ├── data_init.py │ ├── native.pdb │ ├── test_agglomerative.py │ ├── test_alphaanglefeaturizer.py │ ├── test_apm.py │ ├── test_bayes_ratematrix.py │ ├── test_bootstrap_msm.py │ ├── test_build_counts.py │ ├── test_clustering.py │ ├── test_commands.py │ ├── test_commands_exist.py │ ├── test_contactfeaturizers.py │ ├── test_cyblas.pyx │ ├── test_cyblas_wrapper.py │ ├── test_dataset.py │ ├── test_decomposition.py │ ├── test_estimator_subclassing.py │ ├── test_feature_descriptor.py │ ├── test_feature_selection.py │ ├── test_featureunion.py │ ├── test_featurizer.py │ ├── test_featurizer_subset.py │ ├── test_gather_metadata.py │ ├── test_ghmm.py │ ├── test_kcenters.py │ ├── test_kernel_approximation.py │ ├── test_kmedoids.py │ ├── test_ksparsetica.py │ ├── test_libdistance.py │ ├── test_ligandfeaturizers.py │ ├── test_lumping.py │ ├── test_metzner_mcmc.py │ ├── test_mfpt_error.py │ ├── test_msm.py │ ├── test_msm_uncertainty.py │ ├── test_muller.py │ ├── test_ndgrid.py │ ├── test_nearest.py │ ├── test_param_sweep.py │ ├── test_preprocessing.py │ ├── test_ratematrix.py │ ├── test_rmsdfeaturizer.py │ ├── test_sampling.py │ ├── test_sasa_featurizer.py │ ├── test_sparsetica.py │ ├── test_speigh.py │ ├── test_strongly_connected_subgraph.py │ ├── test_template_project.py │ ├── test_tpt.py │ ├── test_transition_counts.py │ ├── test_transmat_mle_prinz.py │ ├── test_utils.py │ ├── test_vmhmm.py │ ├── test_workflows.py │ └── workflows │ │ ├── basic.sh │ │ ├── ghmm.sh │ │ └── rmsd.sh ├── tpt │ ├── __init__.py │ ├── committor.py │ ├── flux.py │ ├── hub.py │ ├── mfpt.py │ └── path.py └── utils │ ├── __init__.py │ ├── compat.py │ ├── divergence.py │ ├── draw_samples.py │ ├── io.py │ ├── nearest.py │ ├── param_sweep.py │ 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