LICENSE.txt
MANIFEST.in
README.rst
setup.cfg
setup.py
setup_util.py
versioneer.py
msmtools/__init__.py
msmtools/_version.py
msmtools.egg-info/PKG-INFO
msmtools.egg-info/SOURCES.txt
msmtools.egg-info/dependency_links.txt
msmtools.egg-info/not-zip-safe
msmtools.egg-info/pbr.json
msmtools.egg-info/requires.txt
msmtools.egg-info/top_level.txt
msmtools/analysis/__init__.py
msmtools/analysis/api.py
msmtools/analysis/dense/__init__.py
msmtools/analysis/dense/assessment.py
msmtools/analysis/dense/assessment_test.py
msmtools/analysis/dense/birth_death_chain.py
msmtools/analysis/dense/committor.py
msmtools/analysis/dense/committor_test.py
msmtools/analysis/dense/correlations.py
msmtools/analysis/dense/correlations_test.py
msmtools/analysis/dense/decomposition.py
msmtools/analysis/dense/decomposition_test.py
msmtools/analysis/dense/expectations.py
msmtools/analysis/dense/expectations_test.py
msmtools/analysis/dense/fingerprints.py
msmtools/analysis/dense/fingerprints_test.py
msmtools/analysis/dense/hitting_probability.py
msmtools/analysis/dense/hitting_probability_test.py
msmtools/analysis/dense/mean_first_passage_time.py
msmtools/analysis/dense/mean_first_passage_time_test.py
msmtools/analysis/dense/pcca.py
msmtools/analysis/dense/pcca_test.py
msmtools/analysis/dense/sensitivity.py
msmtools/analysis/dense/sensitivity_test.py
msmtools/analysis/dense/stationary_vector.py
msmtools/analysis/dense/stationary_vector_test.py
msmtools/analysis/sparse/__init__.py
msmtools/analysis/sparse/assessment.py
msmtools/analysis/sparse/assessment_test.py
msmtools/analysis/sparse/birth_death_chain.py
msmtools/analysis/sparse/committor.py
msmtools/analysis/sparse/committor_test.py
msmtools/analysis/sparse/decomposition.py
msmtools/analysis/sparse/decomposition_test.py
msmtools/analysis/sparse/expectations.py
msmtools/analysis/sparse/expectations_test.py
msmtools/analysis/sparse/fingerprints.py
msmtools/analysis/sparse/fingerprints_test.py
msmtools/analysis/sparse/mean_first_passage_time.py
msmtools/analysis/sparse/mean_first_passage_time_test.py
msmtools/analysis/sparse/stationary_vector.py
msmtools/analysis/sparse/stationary_vector_test.py
msmtools/analysis/tests/P_rev_251x251.dat
msmtools/analysis/tests/birth_death_chain.py
msmtools/analysis/tests/test_assessment.py
msmtools/analysis/tests/test_committor.py
msmtools/analysis/tests/test_decomposition.py
msmtools/analysis/tests/test_expectations.py
msmtools/analysis/tests/test_fingerprints.py
msmtools/analysis/tests/test_mfpt.py
msmtools/analysis/tests/test_sensitivity.py
msmtools/dtraj/__init__.py
msmtools/dtraj/api.py
msmtools/dtraj/tests/test_trajectory.py
msmtools/dtraj/tests/testfiles/dtraj.dat
msmtools/dtraj/tests/testfiles/dtraj.npy
msmtools/estimation/__init__.py
msmtools/estimation/api.py
msmtools/estimation/dense/__init__.py
msmtools/estimation/dense/_mle_trev.c
msmtools/estimation/dense/_mle_trev.h
msmtools/estimation/dense/_mle_trev_given_pi.c
msmtools/estimation/dense/_mle_trev_given_pi.h
msmtools/estimation/dense/_ranlib.c
msmtools/estimation/dense/_ranlib.h
msmtools/estimation/dense/_rnglib.c
msmtools/estimation/dense/_rnglib.h
msmtools/estimation/dense/bootstrapping.py
msmtools/estimation/dense/covariance.py
msmtools/estimation/dense/covariance_test.py
msmtools/estimation/dense/mle_trev.c
msmtools/estimation/dense/mle_trev.pyx
msmtools/estimation/dense/mle_trev_given_pi.c
msmtools/estimation/dense/mle_trev_given_pi.pyx
msmtools/estimation/dense/ratematrix.py
msmtools/estimation/dense/sample_rev.c
msmtools/estimation/dense/sample_rev.h
msmtools/estimation/dense/sample_revpi.c
msmtools/estimation/dense/sample_revpi.h
msmtools/estimation/dense/sampler_nrev.py
msmtools/estimation/dense/sampler_rev.c
msmtools/estimation/dense/sampler_rev.pyx
msmtools/estimation/dense/sampler_revpi.c
msmtools/estimation/dense/sampler_revpi.pyx
msmtools/estimation/dense/tmatrix_sampler.py
msmtools/estimation/dense/tmatrix_sampler_test.py
msmtools/estimation/dense/transition_matrix.py
msmtools/estimation/dense/util.h
msmtools/estimation/sparse/__init__.py
msmtools/estimation/sparse/_mle_trev.c
msmtools/estimation/sparse/_mle_trev.h
msmtools/estimation/sparse/_mle_trev_given_pi.c
msmtools/estimation/sparse/_mle_trev_given_pi.h
msmtools/estimation/sparse/connectivity.py
msmtools/estimation/sparse/connectivity_test.py
msmtools/estimation/sparse/count_matrix.py
msmtools/estimation/sparse/effective_counts.py
msmtools/estimation/sparse/likelihood.py
msmtools/estimation/sparse/likelihood_test.py
msmtools/estimation/sparse/mle_trev.c
msmtools/estimation/sparse/mle_trev.pyx
msmtools/estimation/sparse/mle_trev_given_pi.c
msmtools/estimation/sparse/mle_trev_given_pi.pyx
msmtools/estimation/sparse/prior.py
msmtools/estimation/sparse/prior_test.py
msmtools/estimation/sparse/transition_matrix.py
msmtools/estimation/sparse/transition_matrix_test.py
msmtools/estimation/tests/test_bootstrapping.py
msmtools/estimation/tests/test_connectivity.py
msmtools/estimation/tests/test_count_matrix.py
msmtools/estimation/tests/test_effective_count_matrix.py
msmtools/estimation/tests/test_likelihood.py
msmtools/estimation/tests/test_mle_trev.py
msmtools/estimation/tests/test_mle_trev_given_pi.py
msmtools/estimation/tests/test_prior.py
msmtools/estimation/tests/test_ratematrix.py
msmtools/estimation/tests/test_tmatrix_sampling.py
msmtools/estimation/tests/test_transition_matrix.py
msmtools/estimation/tests/testfiles/C_13_lag.dat
msmtools/estimation/tests/testfiles/C_13_sliding.dat
msmtools/estimation/tests/testfiles/C_1_lag.dat
msmtools/estimation/tests/testfiles/C_1_sliding.dat
msmtools/estimation/tests/testfiles/C_7_lag.dat
msmtools/estimation/tests/testfiles/C_7_sliding.dat
msmtools/estimation/tests/testfiles/dtraj.dat
msmtools/estimation/tests/testfiles/pi.dat
msmtools/flux/__init__.py
msmtools/flux/api.py
msmtools/flux/reactive_flux.py
msmtools/flux/reactive_flux_test.py
msmtools/flux/dense/__init__.py
msmtools/flux/dense/tpt.py
msmtools/flux/dense/tpt_test.py
msmtools/flux/sparse/__init__.py
msmtools/flux/sparse/pathways.py
msmtools/flux/sparse/pathways_test.py
msmtools/flux/sparse/tpt.py
msmtools/flux/sparse/tpt_test.py
msmtools/flux/tests/birth_death_chain.py
msmtools/flux/tests/test_pathways.py
msmtools/flux/tests/test_tpt.py
msmtools/generation/__init__.py
msmtools/generation/api.py
msmtools/generation/tests/test_generation.py
msmtools/util/__init__.py
msmtools/util/annotators.py
msmtools/util/exceptions.py
msmtools/util/numeric.py
msmtools/util/sigint_handler.h
msmtools/util/statistics.py
msmtools/util/types.py
msmtools/util/kahandot_src/_kahandot.c
msmtools/util/kahandot_src/_kahandot.h
msmtools/util/kahandot_src/kahandot.c
msmtools/util/kahandot_src/kahandot.pyx
msmtools/util/matrix/__init__.py
msmtools/util/matrix/matrix.py
msmtools/util/matrix/matrix_test.py
msmtools/util/matrix/testfiles/matrix_complex.dat
msmtools/util/matrix/testfiles/matrix_complex.npy
msmtools/util/matrix/testfiles/matrix_float.dat
msmtools/util/matrix/testfiles/matrix_float.npy
msmtools/util/matrix/testfiles/matrix_int.dat
msmtools/util/matrix/testfiles/matrix_int.npy
msmtools/util/matrix/testfiles/spmatrix_complex.coo.dat
msmtools/util/matrix/testfiles/spmatrix_complex.coo.npy
msmtools/util/matrix/testfiles/spmatrix_complex_reference.dat
msmtools/util/matrix/testfiles/spmatrix_float.coo.dat
msmtools/util/matrix/testfiles/spmatrix_float.coo.npy
msmtools/util/matrix/testfiles/spmatrix_float_reference.dat
msmtools/util/matrix/testfiles/spmatrix_int.coo.dat
msmtools/util/matrix/testfiles/spmatrix_int.coo.npy
msmtools/util/matrix/testfiles/spmatrix_int_reference.dat