├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── docs ├── .nojekyll ├── Makefile ├── _build │ ├── doctrees │ │ ├── environment.pickle │ │ ├── index.doctree │ │ └── source │ │ │ ├── _autosummary │ │ │ ├── janus.driver.doctree │ │ │ ├── janus.initializer.doctree │ │ │ ├── janus.mm_wrapper.MMWrapper.doctree │ │ │ ├── janus.mm_wrapper.OpenMMWrapper.doctree │ │ │ ├── janus.qm_wrapper.Psi4Wrapper.doctree │ │ │ ├── janus.qm_wrapper.QMWrapper.doctree │ │ │ ├── janus.qmmm.AQMMM.doctree │ │ │ ├── janus.qmmm.DAS.doctree │ │ │ ├── janus.qmmm.HotSpot.doctree │ │ │ ├── janus.qmmm.OniomXS.doctree │ │ │ ├── janus.qmmm.PAP.doctree │ │ │ ├── janus.qmmm.QMMM.doctree │ │ │ ├── janus.qmmm.SAP.doctree │ │ │ └── janus.system.doctree │ │ │ ├── intro.doctree │ │ │ ├── janus.doctree │ │ │ ├── janus_mm_wrapper.doctree │ │ │ ├── janus_qm_wrapper.doctree │ │ │ ├── janus_qmmm.doctree │ │ │ ├── modules.doctree │ │ │ ├── running-janus.doctree │ │ │ └── setting-up-janus.doctree │ └── html │ │ ├── .buildinfo │ │ ├── .nojekyll │ │ ├── _sources │ │ ├── index.rst.txt │ │ └── source │ │ │ ├── _autosummary │ │ │ ├── janus.driver.rst.txt │ │ │ ├── janus.initializer.rst.txt │ │ │ ├── janus.mm_wrapper.MMWrapper.rst.txt │ │ │ ├── janus.mm_wrapper.OpenMMWrapper.rst.txt │ │ │ ├── janus.qm_wrapper.Psi4Wrapper.rst.txt │ │ │ ├── janus.qm_wrapper.QMWrapper.rst.txt │ │ │ ├── janus.qmmm.AQMMM.rst.txt │ │ │ ├── janus.qmmm.DAS.rst.txt │ │ │ ├── janus.qmmm.HotSpot.rst.txt │ │ │ ├── janus.qmmm.OniomXS.rst.txt │ │ │ ├── janus.qmmm.PAP.rst.txt │ │ │ ├── janus.qmmm.QMMM.rst.txt │ │ │ ├── janus.qmmm.SAP.rst.txt │ │ │ └── janus.system.rst.txt │ │ │ ├── intro.rst.txt │ │ │ ├── janus.rst.txt │ │ │ ├── janus_mm_wrapper.rst.txt │ │ │ ├── janus_qm_wrapper.rst.txt │ │ │ ├── janus_qmmm.rst.txt │ │ │ ├── modules.rst.txt │ │ │ ├── running-janus.rst.txt │ │ │ └── setting-up-janus.rst.txt │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ └── fontawesome-webfont.woff2 │ │ ├── jquery-3.2.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── source │ │ ├── _autosummary │ │ ├── janus.driver.html │ │ ├── janus.initializer.html │ │ ├── janus.mm_wrapper.MMWrapper.html │ │ ├── janus.mm_wrapper.OpenMMWrapper.html │ │ ├── janus.qm_wrapper.Psi4Wrapper.html │ │ ├── janus.qm_wrapper.QMWrapper.html │ │ ├── janus.qmmm.AQMMM.html │ │ ├── janus.qmmm.DAS.html │ │ ├── janus.qmmm.HotSpot.html │ │ ├── janus.qmmm.OniomXS.html │ │ ├── janus.qmmm.PAP.html │ │ ├── janus.qmmm.QMMM.html │ │ ├── janus.qmmm.SAP.html │ │ └── janus.system.html │ │ ├── intro.html │ │ ├── janus.html │ │ ├── janus_mm_wrapper.html │ │ ├── janus_qm_wrapper.html │ │ ├── janus_qmmm.html │ │ ├── modules.html │ │ ├── running-janus.html │ │ └── setting-up-janus.html ├── conf.py ├── index.html ├── index.rst └── source │ ├── _autosummary │ ├── janus.driver.rst │ ├── janus.initializer.rst │ ├── janus.mm_wrapper.MMWrapper.rst │ ├── janus.mm_wrapper.OpenMMWrapper.rst │ ├── janus.qm_wrapper.Psi4Wrapper.rst │ ├── janus.qm_wrapper.QMWrapper.rst │ ├── janus.qmmm.AQMMM.rst │ ├── janus.qmmm.DAS.rst │ ├── janus.qmmm.HotSpot.rst │ ├── janus.qmmm.OniomXS.rst │ ├── janus.qmmm.PAP.rst │ ├── janus.qmmm.QMMM.rst │ ├── janus.qmmm.SAP.rst │ └── janus.system.rst │ ├── intro.rst │ ├── janus.rst │ ├── janus_mm_wrapper.rst │ ├── janus_qm_wrapper.rst │ ├── janus_qmmm.rst │ ├── modules.rst │ ├── running-janus.rst │ └── setting-up-janus.rst ├── examples ├── oniomxs_example.py └── sample_input.json ├── images ├── janus_logo_final.pdf └── janus_logo_final.png ├── janus ├── __init__.py ├── driver.py ├── initializer.py ├── janus.py ├── mm_wrapper │ ├── __init__.py │ ├── mm_wrapper.py │ └── openmm_wrapper.py ├── partition │ ├── __init__.py │ ├── distance.py │ ├── hysteretic.py │ └── partition.py ├── qm_wrapper │ ├── __init__.py │ ├── psi4_wrapper.py │ └── qm_wrapper.py ├── qmmm │ ├── __init__.py │ ├── aqmmm.py │ ├── buffered_force.py │ ├── das.py │ ├── hot_spot.py │ ├── oniom_xs.py │ ├── pap.py │ ├── qmmm.py │ └── sap.py └── system.py ├── setup.py └── tests ├── files ├── test_initializer │ └── input.json └── test_openmm │ ├── ala_ala_ala.pdb │ ├── ala_water.pdb │ ├── input.pdb │ ├── input_protein.pdb │ └── water.pdb ├── test_das.py ├── test_distance_partition.py ├── test_hot_spot.py ├── test_initializer.py ├── test_oniom_xs.py ├── test_openmm.py ├── test_pap.py ├── test_psi4.py ├── test_qmmm.py ├── test_sap.py └── test_system.py /.gitignore: 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