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<!DOCTYPE html>
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<title>Accessing the results — gorder "1.2.0" documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="gorder.html">Performing the analysis</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis_types.html">Analysis types</a></li>
<li class="toctree-l1"><a class="reference internal" href="leaflets.html">Order parameters for individual leaflets</a></li>
<li class="toctree-l1"><a class="reference internal" href="ordermap.html">Maps of order parameters</a></li>
<li class="toctree-l1"><a class="reference internal" href="estimate_error.html">Estimating error</a></li>
<li class="toctree-l1"><a class="reference internal" href="geometry.html">Order parameters for specific membrane region</a></li>
<li class="toctree-l1"><a class="reference internal" href="membrane_normal.html">Specifying membrane normal</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Accessing the results</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#gorder.results.AnalysisResults"><code class="docutils literal notranslate"><span class="pre">AnalysisResults</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AnalysisResults.average_order"><code class="docutils literal notranslate"><span class="pre">AnalysisResults.average_order()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AnalysisResults.average_ordermaps"><code class="docutils literal notranslate"><span class="pre">AnalysisResults.average_ordermaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AnalysisResults.get_molecule"><code class="docutils literal notranslate"><span class="pre">AnalysisResults.get_molecule()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AnalysisResults.leaflets_data"><code class="docutils literal notranslate"><span class="pre">AnalysisResults.leaflets_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AnalysisResults.molecules"><code class="docutils literal notranslate"><span class="pre">AnalysisResults.molecules()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AnalysisResults.n_analyzed_frames"><code class="docutils literal notranslate"><span class="pre">AnalysisResults.n_analyzed_frames()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AnalysisResults.normals_data"><code class="docutils literal notranslate"><span class="pre">AnalysisResults.normals_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AnalysisResults.write"><code class="docutils literal notranslate"><span class="pre">AnalysisResults.write()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#gorder.results.AtomResults"><code class="docutils literal notranslate"><span class="pre">AtomResults</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AtomResults.atom"><code class="docutils literal notranslate"><span class="pre">AtomResults.atom()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AtomResults.bonds"><code class="docutils literal notranslate"><span class="pre">AtomResults.bonds()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AtomResults.get_bond"><code class="docutils literal notranslate"><span class="pre">AtomResults.get_bond()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AtomResults.molecule"><code class="docutils literal notranslate"><span class="pre">AtomResults.molecule()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AtomResults.order"><code class="docutils literal notranslate"><span class="pre">AtomResults.order()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.AtomResults.ordermaps"><code class="docutils literal notranslate"><span class="pre">AtomResults.ordermaps()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.results.BondResults"><code class="docutils literal notranslate"><span class="pre">BondResults</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.BondResults.atoms"><code class="docutils literal notranslate"><span class="pre">BondResults.atoms()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.BondResults.molecule"><code class="docutils literal notranslate"><span class="pre">BondResults.molecule()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.BondResults.order"><code class="docutils literal notranslate"><span class="pre">BondResults.order()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.BondResults.ordermaps"><code class="docutils literal notranslate"><span class="pre">BondResults.ordermaps()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.results.Convergence"><code class="docutils literal notranslate"><span class="pre">Convergence</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Convergence.frames"><code class="docutils literal notranslate"><span class="pre">Convergence.frames()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Convergence.lower"><code class="docutils literal notranslate"><span class="pre">Convergence.lower()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Convergence.total"><code class="docutils literal notranslate"><span class="pre">Convergence.total()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Convergence.upper"><code class="docutils literal notranslate"><span class="pre">Convergence.upper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.results.LeafletsData"><code class="docutils literal notranslate"><span class="pre">LeafletsData</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.LeafletsData.frames"><code class="docutils literal notranslate"><span class="pre">LeafletsData.frames()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.LeafletsData.get_molecule"><code class="docutils literal notranslate"><span class="pre">LeafletsData.get_molecule()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.results.Map"><code class="docutils literal notranslate"><span class="pre">Map</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Map.extract"><code class="docutils literal notranslate"><span class="pre">Map.extract()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Map.get_at"><code class="docutils literal notranslate"><span class="pre">Map.get_at()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Map.span_x"><code class="docutils literal notranslate"><span class="pre">Map.span_x()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Map.span_y"><code class="docutils literal notranslate"><span class="pre">Map.span_y()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Map.tile_dim"><code class="docutils literal notranslate"><span class="pre">Map.tile_dim()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.results.MoleculeResults"><code class="docutils literal notranslate"><span class="pre">MoleculeResults</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.MoleculeResults.atoms"><code class="docutils literal notranslate"><span class="pre">MoleculeResults.atoms()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.MoleculeResults.average_order"><code class="docutils literal notranslate"><span class="pre">MoleculeResults.average_order()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.MoleculeResults.average_ordermaps"><code class="docutils literal notranslate"><span class="pre">MoleculeResults.average_ordermaps()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.MoleculeResults.bonds"><code class="docutils literal notranslate"><span class="pre">MoleculeResults.bonds()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.MoleculeResults.convergence"><code class="docutils literal notranslate"><span class="pre">MoleculeResults.convergence()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.MoleculeResults.get_atom"><code class="docutils literal notranslate"><span class="pre">MoleculeResults.get_atom()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.MoleculeResults.get_bond"><code class="docutils literal notranslate"><span class="pre">MoleculeResults.get_bond()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.MoleculeResults.molecule"><code class="docutils literal notranslate"><span class="pre">MoleculeResults.molecule()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.results.Order"><code class="docutils literal notranslate"><span class="pre">Order</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Order.error"><code class="docutils literal notranslate"><span class="pre">Order.error()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.Order.value"><code class="docutils literal notranslate"><span class="pre">Order.value()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.results.OrderCollection"><code class="docutils literal notranslate"><span class="pre">OrderCollection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.OrderCollection.lower"><code class="docutils literal notranslate"><span class="pre">OrderCollection.lower()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.OrderCollection.total"><code class="docutils literal notranslate"><span class="pre">OrderCollection.total()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.OrderCollection.upper"><code class="docutils literal notranslate"><span class="pre">OrderCollection.upper()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.results.OrderMapsCollection"><code class="docutils literal notranslate"><span class="pre">OrderMapsCollection</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.OrderMapsCollection.lower"><code class="docutils literal notranslate"><span class="pre">OrderMapsCollection.lower()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.OrderMapsCollection.total"><code class="docutils literal notranslate"><span class="pre">OrderMapsCollection.total()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="#gorder.results.OrderMapsCollection.upper"><code class="docutils literal notranslate"><span class="pre">OrderMapsCollection.upper()</span></code></a></li>
</ul>
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</ul>
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<li class="toctree-l1"><a class="reference internal" href="exceptions.html">Errors you can encounter</a></li>
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<section id="module-gorder.results">
<span id="accessing-the-results"></span><h1>Accessing the results<a class="headerlink" href="#module-gorder.results" title="Link to this heading"></a></h1>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.AnalysisResults">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">AnalysisResults</span></span><a class="headerlink" href="#gorder.results.AnalysisResults" title="Link to this definition"></a></dt>
<dd><p>Container for all results of an analysis.</p>
<p>Provides access to overall results, per-molecule results, average order
parameters, average order maps, and optionally collected leaflet classification data.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AnalysisResults.average_order">
<span class="sig-name descname"><span class="pre">average_order</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AnalysisResults.average_order" title="Link to this definition"></a></dt>
<dd><p>Get average order parameters across all bond types of all molecules.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Collection of average order parameters.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.OrderCollection" title="gorder.results.OrderCollection">OrderCollection</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AnalysisResults.average_ordermaps">
<span class="sig-name descname"><span class="pre">average_ordermaps</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AnalysisResults.average_ordermaps" title="Link to this definition"></a></dt>
<dd><p>Get average order parameter maps across all bond types of all molecules.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Collection of average order maps.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.OrderMapsCollection" title="gorder.results.OrderMapsCollection">OrderMapsCollection</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AnalysisResults.get_molecule">
<span class="sig-name descname"><span class="pre">get_molecule</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AnalysisResults.get_molecule" title="Link to this definition"></a></dt>
<dd><p>Get results for a molecule type with the specified name.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>name</strong> (<em>str</em>) – Name of the molecule type.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Results for the specified molecule type.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#gorder.results.MoleculeResults" title="gorder.results.MoleculeResults">MoleculeResults</a></p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="exceptions.html#gorder.exceptions.APIError" title="gorder.exceptions.APIError"><strong>APIError</strong></a> – If no molecule type with the given name exists.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AnalysisResults.leaflets_data">
<span class="sig-name descname"><span class="pre">leaflets_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AnalysisResults.leaflets_data" title="Link to this definition"></a></dt>
<dd><p>Get collected leaflet classification data.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Leaflet classification data if stored; otherwise <cite>None</cite>.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.LeafletsData" title="gorder.results.LeafletsData">LeafletsData</a></p>
</dd>
</dl>
<p class="rubric">Notes</p>
<p>Leaflet classification data are not stored by default. To store them,
you must explicitly request collection during analysis.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AnalysisResults.molecules">
<span class="sig-name descname"><span class="pre">molecules</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AnalysisResults.molecules" title="Link to this definition"></a></dt>
<dd><p>Get results for all individual molecule types.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>A list of results for each molecule type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[<a class="reference internal" href="#gorder.results.MoleculeResults" title="gorder.results.MoleculeResults">MoleculeResults</a>]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AnalysisResults.n_analyzed_frames">
<span class="sig-name descname"><span class="pre">n_analyzed_frames</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AnalysisResults.n_analyzed_frames" title="Link to this definition"></a></dt>
<dd><p>Get the total number of analyzed frames.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Number of frames processed in the analysis.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>int</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AnalysisResults.normals_data">
<span class="sig-name descname"><span class="pre">normals_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AnalysisResults.normals_data" title="Link to this definition"></a></dt>
<dd><p>Get collected membrane normals.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Membrane normals data if stored; otherwise <cite>None</cite>.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>NormalsData</p>
</dd>
</dl>
<p class="rubric">Notes</p>
<p>Membrane normals are not stored by default. To store them,
you must explicitly request collection during analysis.
Collecting membrane normals is only supported when they are dynamically calculated.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AnalysisResults.write">
<span class="sig-name descname"><span class="pre">write</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AnalysisResults.write" title="Link to this definition"></a></dt>
<dd><p>Write the results into output files.</p>
<dl class="field-list simple">
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="exceptions.html#gorder.exceptions.WriteError" title="gorder.exceptions.WriteError"><strong>WriteError</strong></a> – If writing fails due to file system or internal errors.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.AtomResults">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">AtomResults</span></span><a class="headerlink" href="#gorder.results.AtomResults" title="Link to this definition"></a></dt>
<dd><p>Results of the analysis for a single atom type.</p>
<p>Provides access to per-atom type order parameters, order maps, and the bond results
associated with this atom type.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AtomResults.atom">
<span class="sig-name descname"><span class="pre">atom</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AtomResults.atom" title="Link to this definition"></a></dt>
<dd><p>Get the type of the atom for which these results were calculated.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>The atom type for which these results were calculated.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>AtomType</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AtomResults.bonds">
<span class="sig-name descname"><span class="pre">bonds</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AtomResults.bonds" title="Link to this definition"></a></dt>
<dd><p>Get the results for each bond type of this atom type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Results for all bond types involving this atom type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[<a class="reference internal" href="#gorder.results.BondResults" title="gorder.results.BondResults">BondResults</a>]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AtomResults.get_bond">
<span class="sig-name descname"><span class="pre">get_bond</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">relative_index</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AtomResults.get_bond" title="Link to this definition"></a></dt>
<dd><p>Get the results for a bond types between this atom type and a hydrogen type (AA) or virtual hydrogen type (UA).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>relative_index</strong> (<em>int</em>) – Relative index (zero-based) of the bonded hydrogen atom type.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Results for the specified bond type.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#gorder.results.BondResults" title="gorder.results.BondResults">BondResults</a></p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="exceptions.html#gorder.exceptions.APIError" title="gorder.exceptions.APIError"><strong>APIError</strong></a> – If the specified (virtual) hydrogen type does not exist.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AtomResults.molecule">
<span class="sig-name descname"><span class="pre">molecule</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AtomResults.molecule" title="Link to this definition"></a></dt>
<dd><p>Get the name of the molecule type for this atom type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Name of the molecule containing this atom type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AtomResults.order">
<span class="sig-name descname"><span class="pre">order</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AtomResults.order" title="Link to this definition"></a></dt>
<dd><p>Get order parameters calculated for this atom type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Collection of order parameters for this atom type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.OrderCollection" title="gorder.results.OrderCollection">OrderCollection</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.AtomResults.ordermaps">
<span class="sig-name descname"><span class="pre">ordermaps</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.AtomResults.ordermaps" title="Link to this definition"></a></dt>
<dd><p>Get order maps calculated for this atom type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Collection of order maps for this atom type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.OrderMapsCollection" title="gorder.results.OrderMapsCollection">OrderMapsCollection</a></p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.BondResults">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">BondResults</span></span><a class="headerlink" href="#gorder.results.BondResults" title="Link to this definition"></a></dt>
<dd><p>Results of the analysis for a single bond type.</p>
<p>Provides access to the molecule name, the atom types involved (if available),
and the order parameters and order maps for this bond type.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.BondResults.atoms">
<span class="sig-name descname"><span class="pre">atoms</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.BondResults.atoms" title="Link to this definition"></a></dt>
<dd><p>Get the atom types involved in this bond type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>The two atom types forming this bond type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[AtomType, AtomType]</p>
</dd>
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="exceptions.html#gorder.exceptions.APIError" title="gorder.exceptions.APIError"><strong>APIError</strong></a> – If the bond type is a virtual united-atom bond type (UA), where only one real atom type exists.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.BondResults.molecule">
<span class="sig-name descname"><span class="pre">molecule</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.BondResults.molecule" title="Link to this definition"></a></dt>
<dd><p>Get the name of the molecule type for this bond type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Name of the molecule containing this bond type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.BondResults.order">
<span class="sig-name descname"><span class="pre">order</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.BondResults.order" title="Link to this definition"></a></dt>
<dd><p>Get order parameters calculated for this bond type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Collection of order parameters for this bond type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.OrderCollection" title="gorder.results.OrderCollection">OrderCollection</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.BondResults.ordermaps">
<span class="sig-name descname"><span class="pre">ordermaps</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.BondResults.ordermaps" title="Link to this definition"></a></dt>
<dd><p>Get order maps calculated for this bond type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Collection of order maps for this bond type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.OrderMapsCollection" title="gorder.results.OrderMapsCollection">OrderMapsCollection</a></p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.Convergence">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">Convergence</span></span><a class="headerlink" href="#gorder.results.Convergence" title="Link to this definition"></a></dt>
<dd><p>Stores information about the convergence of order parameter calculations
for a single molecule.</p>
<p>Provides cumulative averages over time for the full membrane and for
individual leaflets.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Convergence.frames">
<span class="sig-name descname"><span class="pre">frames</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Convergence.frames" title="Link to this definition"></a></dt>
<dd><p>Get the indices of trajectory frames for which order parameters were calculated.</p>
<p>The first analyzed frame is assigned an index of 1. For example,
if the analysis starts at 200 ns, the frame at or just after 200 ns
is indexed as 1.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Indices of the analyzed frames.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[int]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Convergence.lower">
<span class="sig-name descname"><span class="pre">lower</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Convergence.lower" title="Link to this definition"></a></dt>
<dd><p>Get cumulative average order parameters for the lower leaflet.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Cumulative averages for the lower leaflet, or <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Convergence.total">
<span class="sig-name descname"><span class="pre">total</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Convergence.total" title="Link to this definition"></a></dt>
<dd><p>Get cumulative average order parameters for the entire membrane.</p>
<p>Each element represents the cumulative average up to that frame.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Cumulative averages for the full membrane, or <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Convergence.upper">
<span class="sig-name descname"><span class="pre">upper</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Convergence.upper" title="Link to this definition"></a></dt>
<dd><p>Get cumulative average order parameters for the upper leaflet.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Cumulative averages for the upper leaflet, or <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[float]</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.LeafletsData">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">LeafletsData</span></span><a class="headerlink" href="#gorder.results.LeafletsData" title="Link to this definition"></a></dt>
<dd><p>Stores collected leaflet classification data.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.LeafletsData.frames">
<span class="sig-name descname"><span class="pre">frames</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.LeafletsData.frames" title="Link to this definition"></a></dt>
<dd><p>Get the indices of trajectory frames for which leaflet classification was performed.</p>
<p>The first analyzed frame is assigned an index of 1. For example,
if the analysis starts at 200 ns, the frame at or just after 200 ns
is indexed as 1.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Indices of the frames for which leaflet classification was performed.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[int]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.LeafletsData.get_molecule">
<span class="sig-name descname"><span class="pre">get_molecule</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.LeafletsData.get_molecule" title="Link to this definition"></a></dt>
<dd><p>Get leaflet classification data for the specified molecule type.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>molecule</strong> (<em>str</em>) – Name of the molecule type to query.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A 2D array where rows correspond to analyzed trajectory frames and columns to
individual molecules. Values are <cite>1</cite> for molecules in the upper leaflet
and <cite>0</cite> for molecules in the lower leaflet. Returns <cite>None</cite> if no leaflet
classification data exists for the specified molecule type.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>numpy.ndarray of shape (n_frames, n_molecules), dtype=uint8</p>
</dd>
</dl>
<p class="rubric">Notes</p>
<p>This is a potentially expensive operation, as it involves copying and
converting from the internal Rust representation into a NumPy array.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.Map">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">Map</span></span><a class="headerlink" href="#gorder.results.Map" title="Link to this definition"></a></dt>
<dd><p>Map of order parameters.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Map.extract">
<span class="sig-name descname"><span class="pre">extract</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Map.extract" title="Link to this definition"></a></dt>
<dd><p>Extract the order map into NumPy arrays.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>A tuple of NumPy arrays:
- The first array (1D) contains positions of the grid tiles along the first dimension of the map (typically <cite>x</cite>).
- The second array (1D) contains positions of the grid tiles along the second dimension of the map (typically <cite>y</cite>).
- The third array (2D) contains the calculated order parameters.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[np.ndarray[float32], np.ndarray[float32], np.ndarray[float32]]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Map.get_at">
<span class="sig-name descname"><span class="pre">get_at</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Map.get_at" title="Link to this definition"></a></dt>
<dd><p>Get the order parameter at the specified coordinates.</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>x</strong> (<em>float</em>) – Coordinate along the first dimension of the map.</p></li>
<li><p><strong>y</strong> (<em>float</em>) – Coordinate along the second dimension of the map.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Order parameter at the given coordinates, or <cite>None</cite> if out of bounds.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Map.span_x">
<span class="sig-name descname"><span class="pre">span_x</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Map.span_x" title="Link to this definition"></a></dt>
<dd><p>Get the span of the map along the first dimension of the map.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Minimum and maximum coordinates along the first dimension of the map.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[float, float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Map.span_y">
<span class="sig-name descname"><span class="pre">span_y</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Map.span_y" title="Link to this definition"></a></dt>
<dd><p>Get the span of the map along the second dimension of the map.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Minimum and maximum coordinates along the second dimension of the map.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[float, float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Map.tile_dim">
<span class="sig-name descname"><span class="pre">tile_dim</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Map.tile_dim" title="Link to this definition"></a></dt>
<dd><p>Get the dimensions of a single grid tile in the map.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Width and height of a single tile of the map.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[float, float]</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.MoleculeResults">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">MoleculeResults</span></span><a class="headerlink" href="#gorder.results.MoleculeResults" title="Link to this definition"></a></dt>
<dd><p>Results of the analysis for a single molecule type.</p>
<p>Provides access to average order parameters, average order maps, and per-atom or
per-bond results, as well as convergence data when available.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.MoleculeResults.atoms">
<span class="sig-name descname"><span class="pre">atoms</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.MoleculeResults.atoms" title="Link to this definition"></a></dt>
<dd><p>Get results for each heavy atom type of the molecule.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Per-atom type results.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[<a class="reference internal" href="#gorder.results.AtomResults" title="gorder.results.AtomResults">AtomResults</a>]</p>
</dd>
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="exceptions.html#gorder.exceptions.APIError" title="gorder.exceptions.APIError"><strong>APIError</strong></a> – If results are obtained for a coarse-grained system (atom-level results unavailable).</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.MoleculeResults.average_order">
<span class="sig-name descname"><span class="pre">average_order</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.MoleculeResults.average_order" title="Link to this definition"></a></dt>
<dd><p>Get average order parameters for this molecule type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Collection of average order parameters across all bond types.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.OrderCollection" title="gorder.results.OrderCollection">OrderCollection</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.MoleculeResults.average_ordermaps">
<span class="sig-name descname"><span class="pre">average_ordermaps</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.MoleculeResults.average_ordermaps" title="Link to this definition"></a></dt>
<dd><p>Get average order parameter maps for this molecule type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Collection of average order maps across all bond types.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.OrderMapsCollection" title="gorder.results.OrderMapsCollection">OrderMapsCollection</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.MoleculeResults.bonds">
<span class="sig-name descname"><span class="pre">bonds</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.MoleculeResults.bonds" title="Link to this definition"></a></dt>
<dd><p>Get results for each bond type of the molecule.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Per-bond type results.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[<a class="reference internal" href="#gorder.results.BondResults" title="gorder.results.BondResults">BondResults</a>]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.MoleculeResults.convergence">
<span class="sig-name descname"><span class="pre">convergence</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.MoleculeResults.convergence" title="Link to this definition"></a></dt>
<dd><p>Get convergence data for the molecule.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Convergence data if available; otherwise <cite>None</cite>.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.Convergence" title="gorder.results.Convergence">Convergence</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.MoleculeResults.get_atom">
<span class="sig-name descname"><span class="pre">get_atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">relative_index</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.MoleculeResults.get_atom" title="Link to this definition"></a></dt>
<dd><p>Get results for a heavy atom type with the specified relative index.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>relative_index</strong> (<em>int</em>) – Relative index (zero-based) of the atom type within the molecule type.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Results for the specified atom type.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#gorder.results.AtomResults" title="gorder.results.AtomResults">AtomResults</a></p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="exceptions.html#gorder.exceptions.APIError" title="gorder.exceptions.APIError"><strong>APIError</strong></a> – If the atom type does not exist or results are obtained for a coarse-grained system.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.MoleculeResults.get_bond">
<span class="sig-name descname"><span class="pre">get_bond</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">relative_index_1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">relative_index_2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.MoleculeResults.get_bond" title="Link to this definition"></a></dt>
<dd><p>Get results for a bond type involving atom types with the specified relative indices.</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>relative_index_1</strong> (<em>int</em>)</p></li>
<li><p><strong>relative_index_2</strong> (<em>int</em>) – Relative indices (zero-based) of the bonded atom types.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Results for the specified bond type.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#gorder.results.BondResults" title="gorder.results.BondResults">BondResults</a></p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="exceptions.html#gorder.exceptions.APIError" title="gorder.exceptions.APIError"><strong>APIError</strong></a> – If the bond type does not exist or the results are obtained for a united-atom system.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.MoleculeResults.molecule">
<span class="sig-name descname"><span class="pre">molecule</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.MoleculeResults.molecule" title="Link to this definition"></a></dt>
<dd><p>Get the name of the molecule type.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Name of the molecule type.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>str</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.Order">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">Order</span></span><a class="headerlink" href="#gorder.results.Order" title="Link to this definition"></a></dt>
<dd><p>Single order parameter value, optionally with its estimated error.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Order.error">
<span class="sig-name descname"><span class="pre">error</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Order.error" title="Link to this definition"></a></dt>
<dd><p>Get the estimated error for this order parameter.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Estimated error of the order parameter, or <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.Order.value">
<span class="sig-name descname"><span class="pre">value</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.Order.value" title="Link to this definition"></a></dt>
<dd><p>Get the value of the order parameter (mean from the analyzed frames).</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Mean value of the order parameter.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>float</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.OrderCollection">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">OrderCollection</span></span><a class="headerlink" href="#gorder.results.OrderCollection" title="Link to this definition"></a></dt>
<dd><p>Order parameters for a single object (atom type, bond type, molecule type, system)
calculated for the full membrane, the upper leaflet, and the lower leaflet.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.OrderCollection.lower">
<span class="sig-name descname"><span class="pre">lower</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.OrderCollection.lower" title="Link to this definition"></a></dt>
<dd><p>Get the order parameter calculated from the lower leaflet.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Order parameter for the lower leaflet. Returns <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.Order" title="gorder.results.Order">Order</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.OrderCollection.total">
<span class="sig-name descname"><span class="pre">total</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.OrderCollection.total" title="Link to this definition"></a></dt>
<dd><p>Get the order parameter calculated from the whole membrane.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Order parameter for the whole membrane. Returns <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.Order" title="gorder.results.Order">Order</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.OrderCollection.upper">
<span class="sig-name descname"><span class="pre">upper</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.OrderCollection.upper" title="Link to this definition"></a></dt>
<dd><p>Get the order parameter calculated from the upper leaflet.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Order parameter for the upper leaflet. Returns <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.Order" title="gorder.results.Order">Order</a></p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.results.OrderMapsCollection">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.results.</span></span><span class="sig-name descname"><span class="pre">OrderMapsCollection</span></span><a class="headerlink" href="#gorder.results.OrderMapsCollection" title="Link to this definition"></a></dt>
<dd><p>Order maps for a single object (atom type, bond type, molecule type, system)
calculated for the full membrane, the upper leaflet, and the lower leaflet.</p>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.OrderMapsCollection.lower">
<span class="sig-name descname"><span class="pre">lower</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.OrderMapsCollection.lower" title="Link to this definition"></a></dt>
<dd><p>Get the order map calculated from the lower leaflet.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Order map for the lower leaflet, or <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.Map" title="gorder.results.Map">Map</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.OrderMapsCollection.total">
<span class="sig-name descname"><span class="pre">total</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.OrderMapsCollection.total" title="Link to this definition"></a></dt>
<dd><p>Get the order map calculated from the whole membrane.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Order map for the whole membrane, or <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.Map" title="gorder.results.Map">Map</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.results.OrderMapsCollection.upper">
<span class="sig-name descname"><span class="pre">upper</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.results.OrderMapsCollection.upper" title="Link to this definition"></a></dt>
<dd><p>Get the order map calculated from the upper leaflet.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Order map for the upper leaflet, or <cite>None</cite> if not available.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="#gorder.results.Map" title="gorder.results.Map">Map</a></p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
</div>
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