MANIFEST.in
basesetup.py
setup.cfg
setup.py
examples/.gitignore
examples/Clustering-Comparison.ipynb
examples/Fs-Peptide-command-line.ipynb
examples/Fs-Peptide-in-RAM.ipynb
examples/Fs-Peptide-with-Pipeline.ipynb
examples/Fs-Peptide-with-dataset.ipynb
examples/GMRQ-Model-Selection.ipynb
examples/LICENSE.md
examples/Ward-Clustering.ipynb
examples/tICA-vs-PCA.ipynb
examples/advanced/bayesian-msm.ipynb
examples/advanced/hmm-and-msm.ipynb
examples/advanced/implied-timescales.ipynb
examples/advanced/plot-tica-heatmap.ipynb
examples/advanced/quadwell-n-states.ipynb
examples/advanced/quadwell.ipynb
examples/advanced/uncertainty.ipynb
msmbuilder/__init__.py
msmbuilder/base.py
msmbuilder/cmdline.py
msmbuilder/dataset.py
msmbuilder/version.py
msmbuilder.egg-info/PKG-INFO
msmbuilder.egg-info/SOURCES.txt
msmbuilder.egg-info/dependency_links.txt
msmbuilder.egg-info/entry_points.txt
msmbuilder.egg-info/not-zip-safe
msmbuilder.egg-info/top_level.txt
msmbuilder/cluster/.gitignore
msmbuilder/cluster/__init__.py
msmbuilder/cluster/_kmedoids.pyx
msmbuilder/cluster/agglomerative.py
msmbuilder/cluster/apm.py
msmbuilder/cluster/base.py
msmbuilder/cluster/kcenters.py
msmbuilder/cluster/kmedoids.py
msmbuilder/cluster/minibatchkmedoids.py
msmbuilder/cluster/ndgrid.py
msmbuilder/cluster/regularspatial.py
msmbuilder/cluster/src/kmedoids.cc
msmbuilder/cluster/src/kmedoids.h
msmbuilder/commands/__init__.py
msmbuilder/commands/atom_indices.py
msmbuilder/commands/convert_chunked_project.py
msmbuilder/commands/example_datasets.py
msmbuilder/commands/featurizer.py
msmbuilder/commands/fit.py
msmbuilder/commands/fit_transform.py
msmbuilder/commands/implied_timescales.py
msmbuilder/commands/template_project.py
msmbuilder/commands/transform.py
msmbuilder/decomposition/.gitignore
msmbuilder/decomposition/__init__.py
msmbuilder/decomposition/_speigh.pyx
msmbuilder/decomposition/base.py
msmbuilder/decomposition/kernel_approximation.py
msmbuilder/decomposition/ktica.py
msmbuilder/decomposition/pca.py
msmbuilder/decomposition/sparsetica.py
msmbuilder/decomposition/tica.py
msmbuilder/decomposition/utils.py
msmbuilder/example_datasets/.gitignore
msmbuilder/example_datasets/__init__.py
msmbuilder/example_datasets/_muller.pyx
msmbuilder/example_datasets/alanine_dipeptide.py
msmbuilder/example_datasets/base.py
msmbuilder/example_datasets/brownian1d.py
msmbuilder/example_datasets/fs_peptide.py
msmbuilder/example_datasets/met_enkephalin.py
msmbuilder/example_datasets/muller.py
msmbuilder/feature_extraction/__init__.py
msmbuilder/feature_selection/__init__.py
msmbuilder/feature_selection/base.py
msmbuilder/feature_selection/featureselector.py
msmbuilder/featurizer/__init__.py
msmbuilder/featurizer/feature_union.py
msmbuilder/featurizer/featurizer.py
msmbuilder/featurizer/indices.py
msmbuilder/featurizer/subset.py
msmbuilder/hmm/.gitignore
msmbuilder/hmm/__init__.py
msmbuilder/hmm/discrete_approx.py
msmbuilder/hmm/gaussian.pyx
msmbuilder/hmm/vonmises.pyx
msmbuilder/hmm/cephes/README.md
msmbuilder/hmm/cephes/cephes.h
msmbuilder/hmm/cephes/cephes_names.h
msmbuilder/hmm/cephes/chbevl.c
msmbuilder/hmm/cephes/gamma.c
msmbuilder/hmm/cephes/i0.c
msmbuilder/hmm/cephes/i1.c
msmbuilder/hmm/cephes/mconf.h
msmbuilder/hmm/cephes/mtherr.c
msmbuilder/hmm/cephes/polevl.c
msmbuilder/hmm/cephes/psi.c
msmbuilder/hmm/cephes/zeta.c
msmbuilder/hmm/src/GaussianHMMFitter.cpp
msmbuilder/hmm/src/VonMisesHMMFitter.cpp
msmbuilder/hmm/src/logsumexp.hpp
msmbuilder/hmm/src/include/GaussianHMMFitter.h
msmbuilder/hmm/src/include/HMMFitter.h
msmbuilder/hmm/src/include/Trajectory.h
msmbuilder/hmm/src/include/VonMisesHMMFitter.h
msmbuilder/hmm/src/include/sse_mathfun.h
msmbuilder/io/__init__.py
msmbuilder/io/gather_metadata.py
msmbuilder/io/io.py
msmbuilder/io/project_template.py
msmbuilder/io/sampling/__init__.py
msmbuilder/io/sampling/sampling.py
msmbuilder/io_templates/twitter-bootstrap.html
msmbuilder/libdistance/.gitignore
msmbuilder/libdistance/libdistance.pyx
msmbuilder/libdistance/src/assign.hpp
msmbuilder/libdistance/src/cdist.hpp
msmbuilder/libdistance/src/dist.hpp
msmbuilder/libdistance/src/distance_kernels.h
msmbuilder/libdistance/src/pdist.hpp
msmbuilder/libdistance/src/sumdist.hpp
msmbuilder/lumping/__init__.py
msmbuilder/lumping/pcca.py
msmbuilder/lumping/pcca_plus.py
msmbuilder/msm/.gitignore
msmbuilder/msm/__init__.py
msmbuilder/msm/_markovstatemodel.pyx
msmbuilder/msm/_metzner_mcmc_fast.pyx
msmbuilder/msm/_metzner_mcmc_slow.py
msmbuilder/msm/_ratematrix.pyx
msmbuilder/msm/_ratematrix_priors.pyx
msmbuilder/msm/_ratematrix_support.pyx
msmbuilder/msm/bayes_ratematrix.py
msmbuilder/msm/bayesmsm.py
msmbuilder/msm/core.py
msmbuilder/msm/implied_timescales.py
msmbuilder/msm/markov_appreciation.py
msmbuilder/msm/msm.py
msmbuilder/msm/ratematrix.py
msmbuilder/msm/src/metzner_mcmc.c
msmbuilder/msm/src/metzner_mcmc.h
msmbuilder/msm/src/transmat_mle_prinz.c
msmbuilder/msm/src/transmat_mle_prinz.h
msmbuilder/msm/validation/__init__.py
msmbuilder/msm/validation/bootstrapmsm.py
msmbuilder/preprocessing/__init__.py
msmbuilder/preprocessing/base.py
msmbuilder/preprocessing/timeseries.py
msmbuilder/project_templates/0-test-install.py
msmbuilder/project_templates/1-get-example-data.py
msmbuilder/project_templates/LICENSE.md
msmbuilder/project_templates/README.md
msmbuilder/project_templates/plot_header.template
msmbuilder/project_templates/plot_macros.template
msmbuilder/project_templates/analysis/gather-metadata-plot.py
msmbuilder/project_templates/analysis/gather-metadata.py
msmbuilder/project_templates/cluster/cluster-plot.py
msmbuilder/project_templates/cluster/cluster.py
msmbuilder/project_templates/cluster/sample-clusters-plot.py
msmbuilder/project_templates/cluster/sample-clusters.py
msmbuilder/project_templates/dihedrals/featurize-plot.py
msmbuilder/project_templates/dihedrals/featurize.py
msmbuilder/project_templates/landmarks/featurize-plot.py
msmbuilder/project_templates/landmarks/featurize.py
msmbuilder/project_templates/landmarks/find-landmarks.py
msmbuilder/project_templates/msm/microstate-plot.py
msmbuilder/project_templates/msm/microstate-traj.py
msmbuilder/project_templates/msm/microstate.py
msmbuilder/project_templates/msm/timescales-plot.py
msmbuilder/project_templates/msm/timescales.py
msmbuilder/project_templates/rmsd/rmsd-plot.py
msmbuilder/project_templates/rmsd/rmsd.py
msmbuilder/project_templates/tica/tica-plot.py
msmbuilder/project_templates/tica/tica-sample-coordinate-plot.py
msmbuilder/project_templates/tica/tica-sample-coordinate.py
msmbuilder/project_templates/tica/tica.py
msmbuilder/scripts/__init__.py
msmbuilder/scripts/msmb.py
msmbuilder/src/config.pxi
msmbuilder/src/cy_blas.pyx
msmbuilder/src/scipy_lapack.h
msmbuilder/src/triu_utils.pyx
msmbuilder/src/f2py/f2pyptr.h
msmbuilder/tests/.gitignore
msmbuilder/tests/__init__.py
msmbuilder/tests/native.pdb
msmbuilder/tests/test_agglomerative.py
msmbuilder/tests/test_alphaanglefeaturizer.py
msmbuilder/tests/test_apm.py
msmbuilder/tests/test_bayes_ratematrix.py
msmbuilder/tests/test_bootstrap_msm.py
msmbuilder/tests/test_build_counts.py
msmbuilder/tests/test_clustering.py
msmbuilder/tests/test_commands.py
msmbuilder/tests/test_commands_exist.py
msmbuilder/tests/test_contactfeaturizers.py
msmbuilder/tests/test_cyblas.pyx
msmbuilder/tests/test_cyblas_wrapper.py
msmbuilder/tests/test_dataset.py
msmbuilder/tests/test_decomposition.py
msmbuilder/tests/test_estimator_subclassing.py
msmbuilder/tests/test_feature_descriptor.py
msmbuilder/tests/test_feature_selection.py
msmbuilder/tests/test_featureunion.py
msmbuilder/tests/test_featurizer.py
msmbuilder/tests/test_featurizer_subset.py
msmbuilder/tests/test_gather_metadata.py
msmbuilder/tests/test_ghmm.py
msmbuilder/tests/test_kcenters.py
msmbuilder/tests/test_kernel_approximation.py
msmbuilder/tests/test_kmedoids.py
msmbuilder/tests/test_libdistance.py
msmbuilder/tests/test_lumping.py
msmbuilder/tests/test_metzner_mcmc.py
msmbuilder/tests/test_msm.py
msmbuilder/tests/test_msm_uncertainty.py
msmbuilder/tests/test_muller.py
msmbuilder/tests/test_ndgrid.py
msmbuilder/tests/test_nearest.py
msmbuilder/tests/test_param_sweep.py
msmbuilder/tests/test_preprocessing.py
msmbuilder/tests/test_ratematrix.py
msmbuilder/tests/test_rmsdfeaturizer.py
msmbuilder/tests/test_sampling.py
msmbuilder/tests/test_sasa_featurizer.py
msmbuilder/tests/test_sparsetica.py
msmbuilder/tests/test_speigh.py
msmbuilder/tests/test_strongly_connected_subgraph.py
msmbuilder/tests/test_template_project.py
msmbuilder/tests/test_tpt.py
msmbuilder/tests/test_transition_counts.py
msmbuilder/tests/test_transmat_mle_prinz.py
msmbuilder/tests/test_utils.py
msmbuilder/tests/test_vmhmm.py
msmbuilder/tests/test_workflows.py
msmbuilder/tests/workflows/basic.sh
msmbuilder/tests/workflows/ghmm.sh
msmbuilder/tests/workflows/rmsd.sh
msmbuilder/tpt/__init__.py
msmbuilder/tpt/committor.py
msmbuilder/tpt/flux.py
msmbuilder/tpt/hub.py
msmbuilder/tpt/mfpt.py
msmbuilder/tpt/path.py
msmbuilder/utils/__init__.py
msmbuilder/utils/compat.py
msmbuilder/utils/draw_samples.py
msmbuilder/utils/io.py
msmbuilder/utils/nearest.py
msmbuilder/utils/param_sweep.py
msmbuilder/utils/probability.py
msmbuilder/utils/subsampler.py
msmbuilder/utils/validation.py
msmbuilder/utils/progressbar/__init__.py
msmbuilder/utils/progressbar/compat.py
msmbuilder/utils/progressbar/progressbar.py
msmbuilder/utils/progressbar/widgets.py