├── .gitattributes ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── OpenSMOG ├── OpenSMOG.py ├── OpenSMOG_Reporter.py ├── __init__.py ├── oscheck.py └── share │ ├── OpenSMOG.xsd │ └── tests │ ├── 2ci2.AA.CD1 │ ├── SBM_AA_dihe │ │ ├── dihetest.b │ │ ├── dihetest.bif │ │ ├── dihetest.nb │ │ └── dihetest.sif │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── 2ci2.AA.CD4 │ ├── SBM_AA_dihe │ │ ├── dihetest.b │ │ ├── dihetest.bif │ │ ├── dihetest.nb │ │ └── dihetest.sif │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── 2ci2.AA.CustomDihedrals │ ├── SBM_AA+CustomDihedrals │ │ ├── test.b │ │ ├── test.bif │ │ ├── test.nb │ │ └── test.sif │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── 2ci2.AA.PBC │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── 2ci2.AA.gaussian │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── 2ci2.AA.noxml │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.gro │ ├── opentest.top │ └── smogcommands │ ├── 2ci2.AA │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── 2ci2.CA.gaussian │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── 2ci2.CA │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── DNA-BMG.AA.CD1 │ ├── SBM_AA_dihe │ │ ├── dihetest.b │ │ ├── dihetest.bif │ │ ├── dihetest.nb │ │ └── dihetest.sif │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.10.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── DNA-BMG.AA.CD4 │ ├── SBM_AA_dihe │ │ ├── dihetest.b │ │ ├── dihetest.bif │ │ ├── dihetest.nb │ │ └── dihetest.sif │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.10.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── DNA-BMG.AA.CustomDihedrals │ ├── SBM_AA+CustomDihedrals │ │ ├── test.b │ │ ├── test.bif │ │ ├── test.nb │ │ └── test.sif │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.10.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── DNA-BMG.AA.CustomDihedrals2 │ ├── SBM_AA+CustomDihedrals │ │ ├── test.b │ │ ├── test.bif │ │ ├── test.nb │ │ └── test.sif │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.10.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── DNA-BMG.AA │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.10.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── opentest.top │ ├── opentest.xml │ └── smogcommands │ ├── PDBs │ ├── 2ci2.adj.pdb │ ├── 2ci2.split.pdb │ ├── DNA.terminal.BMG.pdb │ ├── RNA.adj.pdb │ └── RNA.adj2.pdb │ ├── RNAion.PBC │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.10.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── notes │ ├── opentest.top │ ├── opentest.xml │ ├── sbm.test │ │ ├── test.b │ │ ├── test.bif │ │ ├── test.extras │ │ ├── test.ions.def │ │ ├── test.nb │ │ └── test.sif │ └── smogcommands │ ├── RNAion2.PBC │ ├── energies │ ├── frame.0.gro │ ├── frame.1.gro │ ├── frame.10.gro │ ├── frame.2.gro │ ├── frame.3.gro │ ├── frame.4.gro │ ├── frame.5.gro │ ├── frame.6.gro │ ├── frame.7.gro │ ├── frame.8.gro │ ├── frame.9.gro │ ├── notes │ ├── opentest.gro │ ├── opentest.top │ ├── opentest.xml │ ├── sbm.test │ │ ├── test.b │ │ ├── test.bif │ │ ├── test.extras │ │ ├── test.ions.def │ │ ├── test.nb │ │ └── test.sif │ └── smogcommands │ └── listoftests ├── README.rst ├── Tutorials ├── SBM_AA.ipynb ├── SBM_CA.ipynb ├── SMOG2_AA_CI2 │ ├── 2ci2.AA.contacts │ ├── 2ci2.AA.gro │ ├── 2ci2.AA.ndx │ ├── 2ci2.AA.top │ ├── 2ci2.AA.xml │ ├── 2ci2.adj.pdb │ ├── 2ci2.atoms.pdb │ └── 2ci2.pdb └── SMOG2_CA_CI2 │ ├── 2ci2.CA.contacts │ ├── 2ci2.CA.contacts.CG │ ├── 2ci2.CA.gro │ ├── 2ci2.CA.ndx │ ├── 2ci2.CA.top │ ├── 2ci2.CA.xml │ ├── 2ci2.CA4SCM.gro │ ├── 2ci2.adj.pdb │ ├── 2ci2.atoms.pdb │ └── 2ci2.pdb ├── docs ├── Makefile ├── build │ ├── doctrees │ │ ├── GettingStarted │ │ │ ├── install.doctree │ │ │ └── intro.doctree │ │ ├── OpenSMOG.doctree │ │ ├── Reference │ │ │ ├── citing.doctree │ │ │ ├── license.doctree │ │ │ └── references.doctree │ │ ├── Tutorials │ │ │ └── SBM_CA.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ └── nbsphinx │ │ │ └── Tutorials │ │ │ └── SBM_CA.ipynb │ └── html │ │ ├── .buildinfo │ │ ├── GettingStarted │ │ ├── install.html │ │ └── intro.html │ │ ├── OpenSMOG.html │ │ ├── Reference │ │ ├── citing.html │ │ ├── license.html │ │ └── references.html │ │ ├── Tutorials │ │ ├── SBM_CA.html │ │ └── SBM_CA.ipynb │ │ ├── _images │ │ └── OpenSMOG_pipeline.jpg │ │ ├── _modules │ │ ├── OpenSMOG.html │ │ └── index.html │ │ ├── _sources │ │ ├── GettingStarted │ │ │ ├── install.rst.txt │ │ │ └── intro.rst.txt │ │ ├── OpenSMOG.rst.txt │ │ ├── Reference │ │ │ ├── citing.rst.txt │ │ │ ├── license.rst.txt │ │ │ └── references.rst.txt │ │ ├── Tutorials │ │ │ └── SBM_CA.ipynb.txt │ │ └── index.rst.txt │ │ ├── _static │ │ ├── basic.css │ │ ├── css │ │ │ ├── badge_only.css │ │ │ ├── fonts │ │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ ├── fontawesome-webfont.woff │ │ │ │ ├── fontawesome-webfont.woff2 │ │ │ │ ├── lato-bold-italic.woff │ │ │ │ ├── lato-bold-italic.woff2 │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-normal-italic.woff │ │ │ │ ├── lato-normal-italic.woff2 │ │ │ │ ├── lato-normal.woff │ │ │ │ └── lato-normal.woff2 │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── 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 │ │ ├── jquery-3.5.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── badge_only.js │ │ │ ├── html5shiv-printshiv.min.js │ │ │ ├── html5shiv.min.js │ │ │ └── theme.js │ │ ├── jupyter-sphinx.css │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.12.0.js │ │ └── underscore.js │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ └── searchindex.js ├── environment.yml ├── make.bat ├── requirements.txt └── source │ ├── .readthedocs.yml │ ├── GettingStarted │ ├── install.rst │ └── intro.rst │ ├── OpenSMOG.rst │ ├── Reference │ ├── OpenSMOG.bib │ ├── citing.rst │ ├── license.rst │ └── references.rst │ ├── Tutorials │ ├── SBM_AA.ipynb │ ├── SBM_CA.ipynb │ └── SMOG2_usage.rst │ ├── _build │ └── html │ │ ├── .buildinfo │ │ ├── .doctrees │ │ ├── GettingStarted │ │ │ ├── install.doctree │ │ │ └── intro.doctree │ │ ├── OpenSMOG.doctree │ │ ├── Reference │ │ │ ├── citing.doctree │ │ │ ├── license.doctree │ │ │ └── references.doctree │ │ ├── Tutorials │ │ │ ├── SBM_AA.doctree │ │ │ ├── SBM_CA.doctree │ │ │ ├── SMOG2_usage.doctree │ │ │ └── gen_CA.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ └── nbsphinx │ │ │ └── Tutorials │ │ │ ├── SBM_AA.ipynb │ │ │ └── SBM_CA.ipynb │ │ ├── GettingStarted │ │ ├── install.html │ │ └── intro.html │ │ ├── OpenSMOG.html │ │ ├── Reference │ │ ├── citing.html │ │ ├── license.html │ │ └── references.html │ │ ├── Tutorials │ │ ├── SBM_AA.html │ │ ├── SBM_AA.ipynb │ │ ├── SBM_CA.html │ │ ├── SBM_CA.ipynb │ │ ├── SMOG2_usage.html │ │ └── gen_CA.html │ │ ├── _images │ │ └── OpenSMOG_pipeline.jpg │ │ ├── _modules │ │ ├── OpenSMOG.html │ │ └── index.html │ │ ├── _sources │ │ ├── GettingStarted │ │ │ ├── install.rst.txt │ │ │ └── intro.rst.txt │ │ ├── OpenSMOG.rst.txt │ │ ├── Reference │ │ │ ├── citing.rst.txt │ │ │ ├── license.rst.txt │ │ │ └── references.rst.txt │ │ ├── Tutorials │ │ │ ├── SBM_AA.ipynb.txt │ │ │ ├── SBM_CA.ipynb.txt │ │ │ ├── SMOG2_usage.rst.txt │ │ │ └── gen_CA.rst.txt │ │ └── index.rst.txt │ │ ├── _static │ │ ├── basic.css │ │ ├── css │ │ │ ├── badge_only.css │ │ │ ├── fonts │ │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ ├── fontawesome-webfont.woff │ │ │ │ ├── fontawesome-webfont.woff2 │ │ │ │ ├── lato-bold-italic.woff │ │ │ │ ├── lato-bold-italic.woff2 │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-normal-italic.woff │ │ │ │ ├── lato-normal-italic.woff2 │ │ │ │ ├── lato-normal.woff │ │ │ │ └── lato-normal.woff2 │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── 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 │ │ ├── jquery-3.5.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── badge_only.js │ │ │ ├── html5shiv-printshiv.min.js │ │ │ ├── html5shiv.min.js │ │ │ └── theme.js │ │ ├── jupyter-sphinx.css │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.12.0.js │ │ └── underscore.js │ │ 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