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<h1>Documentation For Users<a class="headerlink" href="#documentation-for-users" title="Permalink to this headline">¶</a></h1>
<p>This section is for users of ProMod3. It describes how to compile and run
scripts using the functionality of this library.</p>
<p>Contents:</p>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="gettingstarted.html">Getting Started</a><ul>
<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html#get-and-run-project">Get and Run ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html#modelling-pipeline">Modelling pipeline</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="actions/index.html#building-models">Building models</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="buildsystem.html">Building ProMod3</a><ul>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html#dependencies">Dependencies</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html#using-cmake">Using CMake</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html#running-make">Running Make</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html#installing-project">Installing ProMod3</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="modelling/index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="modelling/pipeline.html">Modelling Pipeline</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/model_checking.html">Model Checking</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/gap_handling.html">Handling Gaps</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/loop_candidates.html">Handling Loop Candidates</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/loop_closing.html">Fitting Loops Into Gaps</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/monte_carlo.html">Generating Loops De Novo</a></li><li class="toctree-l2"><a class="reference internal" href="modelling/sidechain_reconstruction.html">Sidechain Reconstruction</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/algorithms.html">Modelling Algorithms</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_id.html">RotamerID</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer.html">Rotamers</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/frame.html">Frame</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_lib.html">Rotamer Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_constructor.html">Rotamer Constructor</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/graph.html">Rotamer Graph</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/disulfid.html">Disulfid Bond Evaluation</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/loading.html">Loading Rotamer Libraries</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/subrotamer_optimizer.html">Subrotamer Optimization</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="scoring/index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li class="toctree-l2"><a class="reference internal" href="scoring/backbone_score_env.html">Backbone Score Environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/backbone_scorers.html">Backbone Scorers</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/all_atom_scorers.html">All Atom Scorers</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="loop/index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="loop/backbone.html">Representing Loops</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/torsion_sampler.html">Sampling Dihedral Angles</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/structure_db.html">Structural Data</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/all_atom.html">Handling All Atom Positions</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/mm_system_creation.html">Generate <code class="docutils literal"><span class="pre">ost.mol.mm</span></code> systems</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/load_loop_objects.html">Loading Precomputed Objects</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="core/index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
<li class="toctree-l2"><a class="reference internal" href="core/pm3argparse.html"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/geometry.html">Geometry functions</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/runtime_profiling.html">Runtime profiling</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
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<li>Previous: <a href="index.html" title="previous chapter">Welcome To ProMod3’s Documentation!</a></li>
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