├── .github └── PULL_REQUEST_TEMPLATE.md ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── appveyor.yml ├── basesetup.py ├── devtools ├── README.md ├── conda-recipe-win │ ├── bld.bat │ └── meta.yaml ├── conda-recipe │ ├── bld.bat │ ├── build.sh │ └── meta.yaml └── travis-ci │ ├── build_docs.sh │ ├── install_miniconda.sh │ ├── set_doc_version.py │ └── update_versions_json.py ├── docs ├── .gitignore ├── Makefile ├── _static │ ├── msmexplorer.png │ ├── msmexplorer_notext.png │ └── msmexplorer_notext.svg ├── api.rst ├── bibparse.py ├── changelog.rst ├── conf.py ├── contributing.rst ├── index.rst ├── installing.rst ├── notebooks │ ├── Fs-Peptide.rst │ └── index.rst ├── papers.bib ├── papers_templ.rst ├── requirements.txt └── sphinxext │ ├── color_generator.py │ ├── embed.tpl │ ├── ipython_console_highlighting.py │ ├── ipython_directive.py │ ├── notebook_sphinxext.py │ ├── plot_directive.py │ └── plot_generator.py ├── examples ├── colors.py ├── plot_angles.py ├── plot_chord.py ├── plot_decomp_grid.py ├── plot_free_energy_1d.py ├── plot_free_energy_2d.py ├── plot_histogram.py ├── plot_implied_timescales.py ├── plot_msm_network.py ├── plot_pop_resids.py ├── plot_stackdist.py ├── plot_timescales.py ├── plot_tpaths.py ├── plot_trace.py ├── plot_trace2d.py └── plot_voronoi.py ├── msmexplorer ├── __init__.py ├── palettes │ ├── __init__.py │ └── custom.py ├── plots │ ├── __init__.py │ ├── cluster.py │ ├── misc.py │ ├── msm.py │ ├── projection.py │ └── tpt.py ├── tests │ ├── __init__.py │ ├── test_cluster_plot.py │ ├── test_misc_plot.py │ ├── test_msm_plot.py │ ├── test_projection_plot.py │ ├── test_timeseries_plot.py │ ├── test_tpt_plot.py │ └── test_utils.py └── utils.py ├── notebooks └── Fs-Peptide-Example.ipynb ├── paper ├── compile_paper.sh ├── paper.bib ├── paper.md ├── paper.pdf └── paper.template ├── requirements.txt └── setup.py /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- 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