MANIFEST.in
basesetup.py
setup.py
examples/.gitignore
examples/bayesian-msm.ipynb
examples/cluster-comparison.ipynb
examples/gmrq-model-selection.ipynb
examples/hmm-and-msm.ipynb
examples/implied-timescales.ipynb
examples/plot-tica-heatmap.ipynb
examples/quadwell-n-states.ipynb
examples/quadwell.ipynb
examples/tica-example.ipynb
examples/uncertainty.ipynb
msmbuilder/__init__.py
msmbuilder/base.py
msmbuilder/cmdline.py
msmbuilder/dataset.py
msmbuilder/libdistance.cpython-34m.so
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/__pycache__/__init__.cpython-34.pyc
msmbuilder/__pycache__/base.cpython-34.pyc
msmbuilder/__pycache__/cmdline.cpython-34.pyc
msmbuilder/__pycache__/dataset.cpython-34.pyc
msmbuilder/__pycache__/version.cpython-34.pyc
msmbuilder/cluster/.gitignore
msmbuilder/cluster/__init__.py
msmbuilder/cluster/_kmedoids.cpp
msmbuilder/cluster/_kmedoids.cpython-34m.so
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/__pycache__/__init__.cpython-34.pyc
msmbuilder/cluster/__pycache__/agglomerative.cpython-34.pyc
msmbuilder/cluster/__pycache__/base.cpython-34.pyc
msmbuilder/cluster/__pycache__/kcenters.cpython-34.pyc
msmbuilder/cluster/__pycache__/kmedoids.cpython-34.pyc
msmbuilder/cluster/__pycache__/minibatchkmedoids.cpython-34.pyc
msmbuilder/cluster/__pycache__/ndgrid.cpython-34.pyc
msmbuilder/cluster/__pycache__/regularspatial.cpython-34.pyc
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/transform.py
msmbuilder/commands/__pycache__/__init__.cpython-34.pyc
msmbuilder/commands/__pycache__/atom_indices.cpython-34.pyc
msmbuilder/commands/__pycache__/convert_chunked_project.cpython-34.pyc
msmbuilder/commands/__pycache__/example_datasets.cpython-34.pyc
msmbuilder/commands/__pycache__/featurizer.cpython-34.pyc
msmbuilder/commands/__pycache__/fit.cpython-34.pyc
msmbuilder/commands/__pycache__/fit_transform.cpython-34.pyc
msmbuilder/commands/__pycache__/implied_timescales.cpython-34.pyc
msmbuilder/commands/__pycache__/transform.cpython-34.pyc
msmbuilder/decomposition/__init__.py
msmbuilder/decomposition/base.py
msmbuilder/decomposition/pca.py
msmbuilder/decomposition/sparsetica.py
msmbuilder/decomposition/speigh.py
msmbuilder/decomposition/tica.py
msmbuilder/decomposition/utils.py
msmbuilder/decomposition/__pycache__/__init__.cpython-34.pyc
msmbuilder/decomposition/__pycache__/base.cpython-34.pyc
msmbuilder/decomposition/__pycache__/pca.cpython-34.pyc
msmbuilder/decomposition/__pycache__/sparsetica.cpython-34.pyc
msmbuilder/decomposition/__pycache__/speigh.cpython-34.pyc
msmbuilder/decomposition/__pycache__/tica.cpython-34.pyc
msmbuilder/decomposition/__pycache__/utils.cpython-34.pyc
msmbuilder/example_datasets/.gitignore
msmbuilder/example_datasets/__init__.py
msmbuilder/example_datasets/_muller.c
msmbuilder/example_datasets/_muller.cpython-34m.so
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/example_datasets/__pycache__/__init__.cpython-34.pyc
msmbuilder/example_datasets/__pycache__/alanine_dipeptide.cpython-34.pyc
msmbuilder/example_datasets/__pycache__/base.cpython-34.pyc
msmbuilder/example_datasets/__pycache__/brownian1d.cpython-34.pyc
msmbuilder/example_datasets/__pycache__/fs_peptide.cpython-34.pyc
msmbuilder/example_datasets/__pycache__/met_enkephalin.cpython-34.pyc
msmbuilder/example_datasets/__pycache__/muller.cpython-34.pyc
msmbuilder/featurizer/__init__.py
msmbuilder/featurizer/featurizer.py
msmbuilder/featurizer/subset_featurizer.py
msmbuilder/featurizer/__pycache__/__init__.cpython-34.pyc
msmbuilder/featurizer/__pycache__/featurizer.cpython-34.pyc
msmbuilder/featurizer/__pycache__/subset_featurizer.cpython-34.pyc
msmbuilder/hmm/.gitignore
msmbuilder/hmm/__init__.py
msmbuilder/hmm/_ghmm.cpython-34m.so
msmbuilder/hmm/_vmhmm.cpython-34m.so
msmbuilder/hmm/discrete_approx.py
msmbuilder/hmm/ghmm.py
msmbuilder/hmm/vmhmm.py
msmbuilder/hmm/__pycache__/__init__.cpython-34.pyc
msmbuilder/hmm/__pycache__/discrete_approx.cpython-34.pyc
msmbuilder/hmm/__pycache__/ghmm.cpython-34.pyc
msmbuilder/hmm/__pycache__/vmhmm.cpython-34.pyc
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/backward.hpp
msmbuilder/hmm/src/forward.hpp
msmbuilder/hmm/src/gaussian_likelihood.c
msmbuilder/hmm/src/ghmm_estep.hpp
msmbuilder/hmm/src/logsumexp.hpp
msmbuilder/hmm/src/posteriors.hpp
msmbuilder/hmm/src/transitioncounts.hpp
msmbuilder/hmm/src/include/gaussian_likelihood.h
msmbuilder/hmm/src/include/sse_mathfun.h
msmbuilder/hmm/vonmises/aligned_malloc.h
msmbuilder/hmm/vonmises/build_spline.py
msmbuilder/hmm/vonmises/spleval.c
msmbuilder/hmm/vonmises/spleval.h
msmbuilder/hmm/vonmises/vmhmm.c
msmbuilder/hmm/vonmises/vmhmmwrap.c
msmbuilder/hmm/vonmises/vmhmmwrap.pyx
msmbuilder/hmm/vonmises/data/inv_mbessel_deriv.dat
msmbuilder/hmm/vonmises/data/inv_mbessel_x.dat
msmbuilder/hmm/vonmises/data/inv_mbessel_y.dat
msmbuilder/hmm/wrappers/GaussianHMMCPUImpl.cpp
msmbuilder/hmm/wrappers/GaussianHMMCPUImpl.pyx
msmbuilder/hmm/wrappers/headers.pxd
msmbuilder/libdistance/.gitignore
msmbuilder/libdistance/libdistance.cpp
msmbuilder/libdistance/libdistance.pyx
msmbuilder/libdistance/src/assign.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/lumping/__pycache__/__init__.cpython-34.pyc
msmbuilder/lumping/__pycache__/pcca.cpython-34.pyc
msmbuilder/lumping/__pycache__/pcca_plus.cpython-34.pyc
msmbuilder/msm/.gitignore
msmbuilder/msm/__init__.py
msmbuilder/msm/_markovstatemodel.c
msmbuilder/msm/_markovstatemodel.cpython-34m.so
msmbuilder/msm/_markovstatemodel.pyx
msmbuilder/msm/_metzner_mcmc_fast.c
msmbuilder/msm/_metzner_mcmc_fast.cpython-34m.so
msmbuilder/msm/_metzner_mcmc_fast.pyx
msmbuilder/msm/_metzner_mcmc_slow.py
msmbuilder/msm/_ratematrix.c
msmbuilder/msm/_ratematrix.cpython-34m.so
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/msm.py
msmbuilder/msm/ratematrix.py
msmbuilder/msm/__pycache__/__init__.cpython-34.pyc
msmbuilder/msm/__pycache__/_metzner_mcmc_slow.cpython-34.pyc
msmbuilder/msm/__pycache__/bayes_ratematrix.cpython-34.pyc
msmbuilder/msm/__pycache__/bayesmsm.cpython-34.pyc
msmbuilder/msm/__pycache__/core.cpython-34.pyc
msmbuilder/msm/__pycache__/implied_timescales.cpython-34.pyc
msmbuilder/msm/__pycache__/msm.cpython-34.pyc
msmbuilder/msm/__pycache__/ratematrix.cpython-34.pyc
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/scripts/__init__.py
msmbuilder/scripts/msmb.py
msmbuilder/scripts/__pycache__/__init__.cpython-34.pyc
msmbuilder/scripts/__pycache__/msmb.cpython-34.pyc
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_GaussianHMMCPUImpl.py
msmbuilder/tests/test_agglomerative.py
msmbuilder/tests/test_bayes_ratematrix.py
msmbuilder/tests/test_clustering.py
msmbuilder/tests/test_commands.py
msmbuilder/tests/test_cyblas.c
msmbuilder/tests/test_cyblas.cpython-34m.so
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_msm_uncertainty.py
msmbuilder/tests/test_muller.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_sparsetica.py
msmbuilder/tests/test_speigh.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/__pycache__/__init__.cpython-34.pyc
msmbuilder/tests/__pycache__/test_GaussianHMMCPUImpl.cpython-34.pyc
msmbuilder/tests/__pycache__/test_agglomerative.cpython-34.pyc
msmbuilder/tests/__pycache__/test_bayes_ratematrix.cpython-34.pyc
msmbuilder/tests/__pycache__/test_clustering.cpython-34.pyc
msmbuilder/tests/__pycache__/test_commands.cpython-34.pyc
msmbuilder/tests/__pycache__/test_cyblas_wrapper.cpython-34.pyc
msmbuilder/tests/__pycache__/test_dataset.cpython-34.pyc
msmbuilder/tests/__pycache__/test_estimator_subclassing.cpython-34.pyc
msmbuilder/tests/__pycache__/test_featurizer.cpython-34.pyc
msmbuilder/tests/__pycache__/test_ghmm.cpython-34.pyc
msmbuilder/tests/__pycache__/test_kcenters.cpython-34.pyc
msmbuilder/tests/__pycache__/test_kmedoids.cpython-34.pyc
msmbuilder/tests/__pycache__/test_libdistance.cpython-34.pyc
msmbuilder/tests/__pycache__/test_lumping.cpython-34.pyc
msmbuilder/tests/__pycache__/test_metzner_mcmc.cpython-34.pyc
msmbuilder/tests/__pycache__/test_msm.cpython-34.pyc
msmbuilder/tests/__pycache__/test_msm_uncertainty.cpython-34.pyc
msmbuilder/tests/__pycache__/test_muller.cpython-34.pyc
msmbuilder/tests/__pycache__/test_ndgrid.cpython-34.pyc
msmbuilder/tests/__pycache__/test_param_sweep.cpython-34.pyc
msmbuilder/tests/__pycache__/test_pca.cpython-34.pyc
msmbuilder/tests/__pycache__/test_ratematrix.cpython-34.pyc
msmbuilder/tests/__pycache__/test_sasa_featurizer.cpython-34.pyc
msmbuilder/tests/__pycache__/test_sparsetica.cpython-34.pyc
msmbuilder/tests/__pycache__/test_speigh.cpython-34.pyc
msmbuilder/tests/__pycache__/test_strongly_connected_subgraph.cpython-34.pyc
msmbuilder/tests/__pycache__/test_tica.cpython-34.pyc
msmbuilder/tests/__pycache__/test_tpt.cpython-34.pyc
msmbuilder/tests/__pycache__/test_transition_counts.cpython-34.pyc
msmbuilder/tests/__pycache__/test_transmat_mle_prinz.cpython-34.pyc
msmbuilder/tests/__pycache__/test_utils.cpython-34.pyc
msmbuilder/tests/__pycache__/test_vmhmm.cpython-34.pyc
msmbuilder/tests/__pycache__/test_workflows.cpython-34.pyc
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/tpt/__pycache__/__init__.cpython-34.pyc
msmbuilder/tpt/__pycache__/committor.cpython-34.pyc
msmbuilder/tpt/__pycache__/flux.cpython-34.pyc
msmbuilder/tpt/__pycache__/hub.cpython-34.pyc
msmbuilder/tpt/__pycache__/mfpt.cpython-34.pyc
msmbuilder/tpt/__pycache__/path.cpython-34.pyc
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/__pycache__/__init__.cpython-34.pyc
msmbuilder/utils/__pycache__/compat.cpython-34.pyc
msmbuilder/utils/__pycache__/draw_samples.cpython-34.pyc
msmbuilder/utils/__pycache__/io.cpython-34.pyc
msmbuilder/utils/__pycache__/param_sweep.cpython-34.pyc
msmbuilder/utils/__pycache__/probability.cpython-34.pyc
msmbuilder/utils/__pycache__/subsampler.cpython-34.pyc
msmbuilder/utils/__pycache__/validation.cpython-34.pyc
msmbuilder/utils/progressbar/__init__.py
msmbuilder/utils/progressbar/compat.py
msmbuilder/utils/progressbar/progressbar.py
msmbuilder/utils/progressbar/widgets.py
msmbuilder/utils/progressbar/__pycache__/__init__.cpython-34.pyc
msmbuilder/utils/progressbar/__pycache__/compat.cpython-34.pyc
msmbuilder/utils/progressbar/__pycache__/progressbar.cpython-34.pyc
msmbuilder/utils/progressbar/__pycache__/widgets.cpython-34.pyc