LICENSE.txt
MANIFEST.in
README.rst
setup.cfg
setup.py
setup_util.py
versioneer.py
doc/Makefile
doc/README.rst
doc/jupyter_nbconvert_config.py
doc/requirements-build-doc.txt
doc/source/CHANGELOG.rst
doc/source/Configuration.rst
doc/source/DEVELOPMENT.rst
doc/source/INSTALL.rst
doc/source/conf.py
doc/source/index.rst
doc/source/ipython.rst
doc/source/_static/emma-logo.png
doc/source/_static/pyemma_paper_doi.svg
doc/source/api/coordinates.clustering.rst
doc/source/api/coordinates.data.rst
doc/source/api/coordinates.pipelines.rst
doc/source/api/coordinates.transform.rst
doc/source/api/index.rst
doc/source/api/index_coor.rst
doc/source/api/index_msm.rst
doc/source/api/index_plots.rst
doc/source/api/index_thermo.rst
doc/source/api/msm.analysis.rst
doc/source/api/msm.dtraj.rst
doc/source/api/msm.estimation.rst
doc/source/api/msm.flux.rst
doc/source/api/msm.generation.rst
pyEMMA.egg-info/PKG-INFO
pyEMMA.egg-info/SOURCES.txt
pyEMMA.egg-info/dependency_links.txt
pyEMMA.egg-info/not-zip-safe
pyEMMA.egg-info/pbr.json
pyEMMA.egg-info/requires.txt
pyEMMA.egg-info/top_level.txt
pyemma/__init__.py
pyemma/_version.py
pyemma/logging.yml
pyemma/pyemma.cfg
pyemma/_base/__init__.py
pyemma/_base/estimator.py
pyemma/_base/logging.py
pyemma/_base/model.py
pyemma/_base/progress/__init__.py
pyemma/_base/progress/reporter.py
pyemma/_base/progress/bar/__init__.py
pyemma/_base/progress/bar/_impl.py
pyemma/_base/progress/bar/gui.py
pyemma/_base/progress/bar/misc.py
pyemma/_base/tests/__init__.py
pyemma/_base/tests/test_progress.py
pyemma/_ext/__init__.py
pyemma/_ext/sklearn/__init__.py
pyemma/_ext/sklearn/base.py
pyemma/_ext/sklearn/parameter_search.py
pyemma/coordinates/__init__.py
pyemma/coordinates/acf.py
pyemma/coordinates/api.py
pyemma/coordinates/pipelines.py
pyemma/coordinates/clustering/__init__.py
pyemma/coordinates/clustering/assign.py
pyemma/coordinates/clustering/interface.py
pyemma/coordinates/clustering/kmeans.py
pyemma/coordinates/clustering/regspace.py
pyemma/coordinates/clustering/uniform_time.py
pyemma/coordinates/clustering/include/clustering.h
pyemma/coordinates/clustering/src/clustering.c
pyemma/coordinates/clustering/src/kmeans.c
pyemma/coordinates/clustering/src/regspatial.c
pyemma/coordinates/data/__init__.py
pyemma/coordinates/data/data_in_memory.py
pyemma/coordinates/data/feature_reader.py
pyemma/coordinates/data/fragmented_trajectory_reader.py
pyemma/coordinates/data/numpy_filereader.py
pyemma/coordinates/data/py_csv_reader.py
pyemma/coordinates/data/_base/__init__.py
pyemma/coordinates/data/_base/datasource.py
pyemma/coordinates/data/_base/iterable.py
pyemma/coordinates/data/_base/random_accessible.py
pyemma/coordinates/data/featurization/__init__.py
pyemma/coordinates/data/featurization/_base.py
pyemma/coordinates/data/featurization/angles.py
pyemma/coordinates/data/featurization/distances.py
pyemma/coordinates/data/featurization/featurizer.py
pyemma/coordinates/data/featurization/misc.py
pyemma/coordinates/data/featurization/util.py
pyemma/coordinates/data/util/__init__.py
pyemma/coordinates/data/util/frames_from_file.py
pyemma/coordinates/data/util/reader_utils.py
pyemma/coordinates/data/util/traj_info_cache.py
pyemma/coordinates/estimators/__init__.py
pyemma/coordinates/estimators/covar/__init__.py
pyemma/coordinates/estimators/covar/moments.py
pyemma/coordinates/estimators/covar/running_moments.py
pyemma/coordinates/estimators/covar/covar_c/__init__.py
pyemma/coordinates/estimators/covar/covar_c/_covartools.c
pyemma/coordinates/estimators/covar/covar_c/_covartools.h
pyemma/coordinates/estimators/covar/covar_c/covartools.c
pyemma/coordinates/estimators/covar/covar_c/covartools.pyx
pyemma/coordinates/tests/__init__.py
pyemma/coordinates/tests/pyemma.log
pyemma/coordinates/tests/test_acf.py
pyemma/coordinates/tests/test_api_load.py
pyemma/coordinates/tests/test_api_source.py
pyemma/coordinates/tests/test_assign.py
pyemma/coordinates/tests/test_cluster.py
pyemma/coordinates/tests/test_cluster_samples.py
pyemma/coordinates/tests/test_coordinates_iterator.py
pyemma/coordinates/tests/test_csvreader.py
pyemma/coordinates/tests/test_datainmemory.py
pyemma/coordinates/tests/test_discretizer.py
pyemma/coordinates/tests/test_featurereader.py
pyemma/coordinates/tests/test_featurereader_and_tica.py
pyemma/coordinates/tests/test_featurereader_and_tica_projection.py
pyemma/coordinates/tests/test_featurizer.py
pyemma/coordinates/tests/test_fragmented_trajectory.py
pyemma/coordinates/tests/test_frames_from_file.py
pyemma/coordinates/tests/test_kmeans.py
pyemma/coordinates/tests/test_mini_batch_kmeans.py
pyemma/coordinates/tests/test_numpyfilereader.py
pyemma/coordinates/tests/test_pca.py
pyemma/coordinates/tests/test_pipeline.py
pyemma/coordinates/tests/test_random_access_stride.py
pyemma/coordinates/tests/test_regspace.py
pyemma/coordinates/tests/test_save_traj.py
pyemma/coordinates/tests/test_save_trajs.py
pyemma/coordinates/tests/test_source.py
pyemma/coordinates/tests/test_stride.py
pyemma/coordinates/tests/test_tica.py
pyemma/coordinates/tests/test_traj_info_cache.py
pyemma/coordinates/tests/test_uniform_time.py
pyemma/coordinates/tests/util.py
pyemma/coordinates/tests/data/bpti_001-033.xtc
pyemma/coordinates/tests/data/bpti_034-066.xtc
pyemma/coordinates/tests/data/bpti_067-100.xtc
pyemma/coordinates/tests/data/bpti_ca.pdb
pyemma/coordinates/tests/data/bpti_mini.binpos
pyemma/coordinates/tests/data/bpti_mini.dcd
pyemma/coordinates/tests/data/bpti_mini.h5
pyemma/coordinates/tests/data/bpti_mini.lh5
pyemma/coordinates/tests/data/bpti_mini.nc
pyemma/coordinates/tests/data/bpti_mini.netcdf
pyemma/coordinates/tests/data/bpti_mini.trr
pyemma/coordinates/tests/data/bpti_mini.xtc
pyemma/coordinates/tests/data/opsin_Ca_1_frame.pdb.gz
pyemma/coordinates/tests/data/opsin_aa_1_frame.pdb.gz
pyemma/coordinates/tests/data/test.pdb
pyemma/coordinates/transform/__init__.py
pyemma/coordinates/transform/pca.py
pyemma/coordinates/transform/tica.py
pyemma/coordinates/transform/transformer.py
pyemma/coordinates/util/__init__.py
pyemma/coordinates/util/change_notification.py
pyemma/coordinates/util/patches.py
pyemma/coordinates/util/stat.py
pyemma/datasets/__init__.py
pyemma/datasets/api.py
pyemma/datasets/double_well_discrete.npz
pyemma/datasets/double_well_discrete.py
pyemma/msm/__init__.py
pyemma/msm/api.py
pyemma/msm/estimators/__init__.py
pyemma/msm/estimators/_dtraj_stats.py
pyemma/msm/estimators/bayesian_hmsm.py
pyemma/msm/estimators/bayesian_msm.py
pyemma/msm/estimators/implied_timescales.py
pyemma/msm/estimators/lagged_model_validators.py
pyemma/msm/estimators/maximum_likelihood_hmsm.py
pyemma/msm/estimators/maximum_likelihood_msm.py
pyemma/msm/models/__init__.py
pyemma/msm/models/hmsm.py
pyemma/msm/models/hmsm_sampled.py
pyemma/msm/models/msm.py
pyemma/msm/models/msm_sampled.py
pyemma/msm/models/reactive_flux.py
pyemma/msm/tests/__init__.py
pyemma/msm/tests/birth_death_chain.py
pyemma/msm/tests/test_bayesian_hmsm.py
pyemma/msm/tests/test_bayesian_msm.py
pyemma/msm/tests/test_cktest.py
pyemma/msm/tests/test_estimator.py
pyemma/msm/tests/test_hmsm.py
pyemma/msm/tests/test_its.py
pyemma/msm/tests/test_msm.py
pyemma/msm/tests/test_msm_lowlevel_deprecation.py
pyemma/msm/tests/test_reactive_flux.py
pyemma/msm/tests/test_tpt.py
pyemma/plots/__init__.py
pyemma/plots/markovtests.py
pyemma/plots/networks.py
pyemma/plots/plots2d.py
pyemma/plots/thermoplots.py
pyemma/plots/timescales.py
pyemma/plots/_ext/__init__.py
pyemma/plots/_ext/fruchterman_reingold.py
pyemma/plots/tests/__init__.py
pyemma/plots/tests/test_its.py
pyemma/plots/tests/test_markovtests.py
pyemma/plots/tests/test_networks.py
pyemma/thermo/__init__.py
pyemma/thermo/api.py
pyemma/thermo/estimators/DTRAM_estimator.py
pyemma/thermo/estimators/TRAM_estimator.py
pyemma/thermo/estimators/WHAM_estimator.py
pyemma/thermo/estimators/__init__.py
pyemma/thermo/estimators/_callback.py
pyemma/thermo/models/__init__.py
pyemma/thermo/models/multi_therm.py
pyemma/thermo/models/stationary.py
pyemma/thermo/tests/test_TRAM.py
pyemma/thermo/tests/test_api.py
pyemma/thermo/tests/test_util.py
pyemma/thermo/util/__init__.py
pyemma/thermo/util/util.py
pyemma/util/__init__.py
pyemma/util/annotators.py
pyemma/util/config.py
pyemma/util/contexts.py
pyemma/util/debug.py
pyemma/util/discrete_trajectories.py
pyemma/util/exceptions.py
pyemma/util/files.py
pyemma/util/indices.py
pyemma/util/linalg.py
pyemma/util/log.py
pyemma/util/numeric.py
pyemma/util/reflection.py
pyemma/util/statistics.py
pyemma/util/testing_tools.py
pyemma/util/types.py
pyemma/util/units.py
pyemma/util/_ext/__init__.py
pyemma/util/_ext/shimmodule.py
pyemma/util/tests/__init__.py
pyemma/util/tests/statistics_test.py
pyemma/util/tests/test_config.py
pyemma/util/tests/test_discrete_trajectories.py
pyemma/util/tests/test_estimation_required_decorator.py
pyemma/util/tests/test_log.py
pyemma/util/tests/test_shortcut.py
pyemma/util/tests/test_units.py
pyemma/util/tests/data/dtraj.dat
pyemma/util/tests/data/dtraj.npy