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<div class="section" id="workflow">
<h1>Workflow<a class="headerlink" href="#workflow" title="Permalink to this headline">¶</a></h1>
<p>The whole workflow of reverse mapping of molecules is divided into two parts as well as code. We will describe it on the example of dodecane.
The files are available in <cite>example/dodecane</cite> directory that is attached to the code source.</p>
<p><strong>Input files</strong></p>
<blockquote>
<div><ul class="simple">
<li><code class="docutils literal notranslate"><span class="pre">cg_conf.gro</span></code>: input CG coordinate file</li>
<li><code class="docutils literal notranslate"><span class="pre">dodecane_settings.xml</span></code>: input XML settings file</li>
<li><code class="docutils literal notranslate"><span class="pre">dodecane_single.gro</span></code>: input atomistic coordinate file</li>
</ul>
</div></blockquote>
<p><strong>Steps</strong></p>
<blockquote>
<div><ol class="arabic simple">
<li><code class="docutils literal notranslate"><span class="pre">cd</span> <span class="pre">example/dodecane</span></code></li>
<li><code class="docutils literal notranslate"><span class="pre">../../src/prepare_files.py</span> <span class="pre">--options</span> <span class="pre">dodecane_settings.xml</span></code> - prepare hybrid configuration files</li>
<li><code class="docutils literal notranslate"><span class="pre">../../src/start_backmapping.py</span> <span class="pre">--conf</span> <span class="pre">hyb_conf.gro</span> <span class="pre">--topology</span> <span class="pre">hyb_topology.top</span> <span class="pre">--alpha</span> <span class="pre">0.00001</span> <span class="pre">--exclusion_list</span> <span class="pre">exclusion_hyb_topol.list</span></code> - run reverse mapping procedure</li>
</ol>
</div></blockquote>
<p>In the end we will get two files:</p>
<blockquote>
<div><ul class="simple">
<li>atomistic coordinate file: <code class="docutils literal notranslate"><span class="pre">sim0confout_final_aa_0.0001_12345.gro</span></code></li>
<li>atomistic topology file: <code class="docutils literal notranslate"><span class="pre">sim0topol_aa_0.0001_12345.top`</span></code>.</li>
</ul>
</div></blockquote>
<p>If the atomistic topology file still containst CG information, you can clean it by the tool <cite>reorder_topology</cite> from <a class="reference external" href="https://github.com/md-lab-tools/lab-tools">LabTools</a></p>
<p>Example of usage:
<code class="docutils literal notranslate"><span class="pre">reorder_topology</span> <span class="pre">--coord</span> <span class="pre">sim0confout_final_aa_0.0001_12345.gro</span> <span class="pre">--in_top</span> <span class="pre">../hyb_topol.top</span> <span class="pre">--out_top</span> <span class="pre">aa_topol.top</span> <span class="pre">--clean</span> <span class="pre">--remove_cross</span></code></p>
<p>which will produce <cite>aa_topol.top</cite> file.</p>
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