├── .gitignore ├── .travis.yml ├── AUTHORS ├── LICENSE.md ├── Makefile ├── README.md ├── _build ├── doctrees │ ├── diffusion_analysis.doctree │ ├── environment.pickle │ ├── index.doctree │ └── test_diffusion_analysis.doctree └── html │ ├── .buildinfo │ ├── _sources │ ├── diffusion_analysis.txt │ ├── index.txt │ └── test_diffusion_analysis.txt │ ├── _static │ ├── ajax-loader.gif │ ├── basic.css │ ├── comment-bright.png │ ├── comment-close.png │ ├── comment.png │ ├── default.css │ ├── doctools.js │ ├── down-pressed.png │ ├── down.png │ ├── file.png │ ├── jquery.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── sidebar.js │ ├── underscore.js │ ├── up-pressed.png │ ├── up.png │ └── websupport.js │ ├── diffusion_analysis.html │ ├── genindex.html │ ├── index.html │ ├── objects.inv │ ├── py-modindex.html │ ├── search.html │ ├── searchindex.js │ └── test_diffusion_analysis.html ├── conf.py ├── diffusion_analysis.py ├── diffusion_analysis.rst ├── diffusion_analysis_sim126_extended.ipynb ├── doctesting.py ├── example_MSD_extraction.png ├── example_linear.png ├── example_nonlinear.png ├── index.rst ├── requirements.txt ├── setup.py ├── test_data ├── diffusion_testing.xtc ├── dummy.gro ├── generate_artificial_xtc_diffusion_testing.py ├── test_multiple_protein.gro └── test_multiple_protein.xtc └── test_diffusion_analysis.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | *.pkl 3 | *.swp 4 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tylerjereddy/diffusion_analysis_MD_simulations/HEAD/.travis.yml -------------------------------------------------------------------------------- /AUTHORS: -------------------------------------------------------------------------------- 1 | Anna Duncan 2 | Laura Domicevica 3 | 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