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<title>Analysis types — gorder "1.2.0" documentation</title>
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<li class="toctree-l2"><a class="reference internal" href="#gorder.analysis_types.AAOrder"><code class="docutils literal notranslate"><span class="pre">AAOrder</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.analysis_types.CGOrder"><code class="docutils literal notranslate"><span class="pre">CGOrder</span></code></a></li>
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<section id="module-gorder.analysis_types">
<span id="analysis-types"></span><h1>Analysis types<a class="headerlink" href="#module-gorder.analysis_types" title="Link to this heading"></a></h1>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.analysis_types.AAOrder">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.analysis_types.</span></span><span class="sig-name descname"><span class="pre">AAOrder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">heavy_atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hydrogens</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.analysis_types.AAOrder" title="Link to this definition"></a></dt>
<dd><p>Request the calculation of atomistic order parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>heavy_atoms</strong> (<em>str</em>) – Selection query specifying the heavy atoms to be used in the analysis (typically carbon atoms in lipid tails).</p></li>
<li><p><strong>hydrogens</strong> (<em>str</em>) – Selection query specifiying the hydrogen atoms to be used in the analysis (only those bonded to heavy atoms will be considered).</p></li>
</ul>
</dd>
</dl>
<p class="rubric">Notes</p>
<ul class="simple">
<li><p>Atoms should be specified using the <a class="reference external" href="https://ladme.github.io/gsl-guide">groan selection language</a>.</p></li>
<li><p>Order parameters are calculated for bonds between <cite>heavy_atoms</cite> and <cite>hydrogens</cite>. These bonds are detected automatically.</p></li>
<li><p>The order parameters for heavy atoms are determined by averaging the order parameters of the corresponding bonds.</p></li>
</ul>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.analysis_types.CGOrder">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.analysis_types.</span></span><span class="sig-name descname"><span class="pre">CGOrder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">beads</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.analysis_types.CGOrder" title="Link to this definition"></a></dt>
<dd><p>Request the calculation of coarse-grained order parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>beads</strong> (<em>str</em>) – Selection query specifying the coarse-grained beads to be used in the analysis.</p>
</dd>
</dl>
<p class="rubric">Notes</p>
<ul class="simple">
<li><p>Beads should be specified using the <a class="reference external" href="https://ladme.github.io/gsl-guide">groan selection language</a>.</p></li>
<li><p>Order parameters are calculated for bonds between individual <cite>beads</cite>. These bonds are detected automatically.</p></li>
</ul>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.analysis_types.UAOrder">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.analysis_types.</span></span><span class="sig-name descname"><span class="pre">UAOrder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">saturated</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unsaturated</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.analysis_types.UAOrder" title="Link to this definition"></a></dt>
<dd><p>Request the calculation of united-atom order parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>saturated</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>default=None</em>) – Selection query specifying saturated carbons which order parameters should be calculated.</p></li>
<li><p><strong>unsaturated</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>default=None</em>) – Selection query specifying unsaturated carbons which order parameters should be calculated.</p></li>
<li><p><strong>ignore</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>default=None</em>) – Selection query specifying atoms to be completely ignored when performing the analysis.</p></li>
</ul>
</dd>
</dl>
<p class="rubric">Notes</p>
<ul class="simple">
<li><p>To specify atoms, use the <a class="reference external" href="https://ladme.github.io/gsl-guide">groan selection language</a>.</p></li>
<li><p>The positions of hydrogens will be predicted for the respective carbons and order parameters will be calculated
for the individual carbon-hydrogen bonds.</p></li>
<li><p>Only carbons are supported. If you need to predict hydrogens for other elements, look elsewhere!</p></li>
<li><p>When calculating the number of bonds, <cite>gorder</cite> does not distinguish between single and double bonds.
This means it will attempt to add one hydrogen to a carboxyl atom if specified.
A simple solution to this issue is to exclude such atoms from the analysis.</p></li>
</ul>
</dd></dl>
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