setup.py
msmbuilder/__init__.py
msmbuilder/base.py
msmbuilder/cmdline.py
msmbuilder/dataset.py
msmbuilder/markovstatemodel.py
msmbuilder/tica.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/__init__.py
msmbuilder/cluster/_kmedoids.pyx
msmbuilder/cluster/agglomerative.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/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/transform.py
msmbuilder/decomposition/__init__.py
msmbuilder/decomposition/base.py
msmbuilder/decomposition/pca.py
msmbuilder/decomposition/sparsetica.py
msmbuilder/decomposition/tica.py
msmbuilder/example_datasets/__init__.py
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/featurizer/__init__.py
msmbuilder/featurizer/featurizer.py
msmbuilder/featurizer/subset_featurizer.py
msmbuilder/hmm/__init__.py
msmbuilder/hmm/discrete_approx.py
msmbuilder/hmm/ghmm.py
msmbuilder/hmm/vmhmm.py
msmbuilder/hmm/cephes/chbevl.c
msmbuilder/hmm/cephes/i0.c
msmbuilder/hmm/src/gaussian_likelihood.c
msmbuilder/hmm/vonmises/spleval.c
msmbuilder/hmm/vonmises/vmhmm.c
msmbuilder/hmm/vonmises/vmhmmwrap.pyx
msmbuilder/hmm/wrappers/GaussianHMMCPUImpl.pyx
msmbuilder/libdistance/libdistance.pyx
msmbuilder/lumping/__init__.py
msmbuilder/lumping/pcca.py
msmbuilder/lumping/pcca_plus.py
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/bayesmsm.py
msmbuilder/msm/core.py
msmbuilder/msm/implied_timescales.py
msmbuilder/msm/msm.py
msmbuilder/msm/ratematrix.py
msmbuilder/msm/src/metzner_mcmc.c
msmbuilder/msm/src/transmat_mle_prinz.c
msmbuilder/scripts/__init__.py
msmbuilder/scripts/msmb.py
msmbuilder/tests/__init__.py
msmbuilder/tests/test_GaussianHMMCPUImpl.py
msmbuilder/tests/test_agglomerative.py
msmbuilder/tests/test_clustering.py
msmbuilder/tests/test_commands.py
msmbuilder/tests/test_cyblas.pyx
msmbuilder/tests/test_cyblas_wrapper.py
msmbuilder/tests/test_dataset.py
msmbuilder/tests/test_estimator_subclassing.py
msmbuilder/tests/test_featurizer.py
msmbuilder/tests/test_ghmm.py
msmbuilder/tests/test_kcenters.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_ndgrid.py
msmbuilder/tests/test_param_sweep.py
msmbuilder/tests/test_pca.py
msmbuilder/tests/test_ratematrix.py
msmbuilder/tests/test_sasa_featurizer.py
msmbuilder/tests/test_strongly_connected_subgraph.py
msmbuilder/tests/test_tica.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/test_1.sh
msmbuilder/tests/workflows/test_2.sh
msmbuilder/tests/workflows/test_3.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/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