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<title>Performing the analysis — gorder "1.2.0" documentation</title>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Performing the analysis</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#gorder.Analysis"><code class="docutils literal notranslate"><span class="pre">Analysis</span></code></a><ul>
<li class="toctree-l3"><a class="reference internal" href="#gorder.Analysis.from_file"><code class="docutils literal notranslate"><span class="pre">Analysis.from_file()</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="leaflets.html">Order parameters for individual leaflets</a></li>
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<li class="toctree-l1"><a class="reference internal" href="estimate_error.html">Estimating error</a></li>
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<li class="toctree-l1"><a class="reference internal" href="membrane_normal.html">Specifying membrane normal</a></li>
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<section id="module-gorder">
<span id="performing-the-analysis"></span><h1>Performing the analysis<a class="headerlink" href="#module-gorder" title="Link to this heading"></a></h1>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.Analysis">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.</span></span><span class="sig-name descname"><span class="pre">Analysis</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trajectory</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">analysis_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bonds</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">index</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">output_yaml</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">output_tab</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">output_xvg</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">output_csv</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">membrane_normal</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">begin</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">end</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">step</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">min_samples</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">n_threads</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">leaflets</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">ordermap</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">estimate_error</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">geometry</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">handle_pbc</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">silent</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">overwrite</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" title="Link to this definition"></a></dt>
<dd><p>Class describing all the parameters of the analysis.</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>structure</strong> (<em>str</em>) – Path to a TPR (recommended), PDB, GRO, or PQR file containing the structure and topology of the system.</p></li>
<li><p><strong>trajectory</strong> (<em>Union</em><em>[</em><em>str</em><em>, </em><em>Sequence</em><em>[</em><em>str</em><em>]</em><em>]</em>) – Path to an XTC (recommended), TRR, or GRO trajectory file to be analyzed.
You can provide multiple XTC or TRR trajectories and these will be seamlessly concatenated.</p></li>
<li><p><strong>analysis_type</strong> (<em>Union</em><em>[</em><a class="reference internal" href="analysis_types.html#gorder.analysis_types.AAOrder" title="gorder.analysis_types.AAOrder"><em>AAOrder</em></a><em>, </em><a class="reference internal" href="analysis_types.html#gorder.analysis_types.CGOrder" title="gorder.analysis_types.CGOrder"><em>CGOrder</em></a><em>, </em><a class="reference internal" href="analysis_types.html#gorder.analysis_types.UAOrder" title="gorder.analysis_types.UAOrder"><em>UAOrder</em></a><em>]</em>) – Type of analysis to perform (e.g., AAOrder or CGOrder).</p></li>
<li><p><strong>bonds</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>default=None</em>) – Path to a file containing bonding information. If specified, this overrides bonds from the structure file.</p></li>
<li><p><strong>index</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>default=None</em>) – Path to an NDX file specifying groups in the system.</p></li>
<li><p><strong>output_yaml</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>default=None</em>) – Path to an output YAML file containing the full analysis results.</p></li>
<li><p><strong>output_tab</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>default=None</em>) – Path to an output TABLE file with human-readable results.</p></li>
<li><p><strong>output_xvg</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>default=None</em>) – Filename pattern for output XVG files storing results. Each molecule type gets a separate file.</p></li>
<li><p><strong>output_csv</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em><em>, </em><em>default=None</em>) – Path to an output CSV file containing analysis results.</p></li>
<li><p><strong>membrane_normal</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><em>str</em><em>, </em><em>Mapping</em><em>[</em><em>str</em><em>, </em><em>ndarray</em><em>[</em><em>float32</em><em>]</em><em>]</em><em>, </em><a class="reference internal" href="membrane_normal.html#gorder.membrane_normal.DynamicNormal" title="gorder.membrane_normal.DynamicNormal"><em>DynamicNormal</em></a><em>]</em><em>]</em><em>, </em><em>default=None</em>) – Direction of the membrane normal.
Allowed values are <cite>x</cite>, <cite>y</cite>, <cite>z</cite>, path to file, dictionary specifying manual membrane normals or an instance of <cite>DynamicNormal</cite>.
Defaults to the z-axis if not specified.</p></li>
<li><p><strong>begin</strong> (<em>Optional</em><em>[</em><em>float</em><em>]</em><em>, </em><em>default=None</em>) – Starting time of the trajectory analysis in picoseconds (ps). Defaults to the beginning of the trajectory.</p></li>
<li><p><strong>end</strong> (<em>Optional</em><em>[</em><em>float</em><em>]</em><em>, </em><em>default=None</em>) – Ending time of the trajectory analysis in picoseconds (ps). Defaults to the end of the trajectory.</p></li>
<li><p><strong>step</strong> (<em>Optional</em><em>[</em><em>int</em><em>]</em><em>, </em><em>default=None</em>) – Step size for analysis. Every Nth frame will be analyzed. Defaults to 1.</p></li>
<li><p><strong>min_samples</strong> (<em>Optional</em><em>[</em><em>int</em><em>]</em><em>, </em><em>default=None</em>) – Minimum number of samples required for each heavy atom or bond type to compute its order parameter. Defaults to 1.</p></li>
<li><p><strong>n_threads</strong> (<em>Optional</em><em>[</em><em>int</em><em>]</em><em>, </em><em>default=None</em>) – Number of threads to use for analysis. Defaults to 1.</p></li>
<li><p><strong>leaflets</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><a class="reference internal" href="leaflets.html#gorder.leaflets.GlobalClassification" title="gorder.leaflets.GlobalClassification"><em>GlobalClassification</em></a><em>, </em><a class="reference internal" href="leaflets.html#gorder.leaflets.LocalClassification" title="gorder.leaflets.LocalClassification"><em>LocalClassification</em></a><em>, </em><a class="reference internal" href="leaflets.html#gorder.leaflets.IndividualClassification" title="gorder.leaflets.IndividualClassification"><em>IndividualClassification</em></a><em>, </em><a class="reference internal" href="leaflets.html#gorder.leaflets.ClusteringClassification" title="gorder.leaflets.ClusteringClassification"><em>ClusteringClassification</em></a><em>, </em><a class="reference internal" href="leaflets.html#gorder.leaflets.SphericalClusteringClassification" title="gorder.leaflets.SphericalClusteringClassification"><em>SphericalClusteringClassification</em></a><em>, </em><a class="reference internal" href="leaflets.html#gorder.leaflets.ManualClassification" title="gorder.leaflets.ManualClassification"><em>ManualClassification</em></a><em>, </em><a class="reference internal" href="leaflets.html#gorder.leaflets.NdxClassification" title="gorder.leaflets.NdxClassification"><em>NdxClassification</em></a><em>]</em><em>]</em><em>, </em><em>default=None</em>) – Defines how lipids are assigned to membrane leaflets. If provided, order parameters are calculated per leaflet.</p></li>
<li><p><strong>ordermap</strong> (<em>Optional</em><em>[</em><a class="reference internal" href="ordermap.html#gorder.ordermap.OrderMap" title="gorder.ordermap.OrderMap"><em>OrderMap</em></a><em>]</em><em>, </em><em>default=None</em>) – Specifies parameters for ordermap calculations. If not provided, ordermaps are not generated.</p></li>
<li><p><strong>estimate_error</strong> (<em>Optional</em><em>[</em><a class="reference internal" href="estimate_error.html#gorder.estimate_error.EstimateError" title="gorder.estimate_error.EstimateError"><em>EstimateError</em></a><em>]</em><em>, </em><em>default=None</em>) – Enables error estimation for each bond if specified.</p></li>
<li><p><strong>geometry</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><a class="reference internal" href="geometry.html#gorder.geometry.Cuboid" title="gorder.geometry.Cuboid"><em>Cuboid</em></a><em>, </em><a class="reference internal" href="geometry.html#gorder.geometry.Cylinder" title="gorder.geometry.Cylinder"><em>Cylinder</em></a><em>, </em><a class="reference internal" href="geometry.html#gorder.geometry.Sphere" title="gorder.geometry.Sphere"><em>Sphere</em></a><em>]</em><em>]</em><em>, </em><em>default=None</em>) – Defines a specific region in the simulation box for order parameter calculations. Defaults to the entire system.</p></li>
<li><p><strong>handle_pbc</strong> (<em>Optional</em><em>[</em><em>bool</em><em>]</em><em>, </em><em>default=True</em>) – If False, ignores periodic boundary conditions (PBC). Defaults to True.</p></li>
<li><p><strong>silent</strong> (<em>Optional</em><em>[</em><em>bool</em><em>]</em><em>, </em><em>default=False</em>) – If True, suppresses standard output messages during analysis.</p></li>
<li><p><strong>overwrite</strong> (<em>Optional</em><em>[</em><em>bool</em><em>]</em><em>, </em><em>default=False</em>) – If True, overwrites existing output files and directories without backups.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.Analysis.from_file">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.Analysis.from_file" title="Link to this definition"></a></dt>
<dd><p>Read analysis options from a YAML configuration file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>file</strong> (<em>str</em>) – Path to the YAML configuration file.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Analysis instance initialized from the file.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#gorder.Analysis" title="gorder.Analysis">Analysis</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.ConfigError" title="gorder.exceptions.ConfigError"><strong>ConfigError</strong></a> – If the file cannot be read or parsed.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="gorder.Analysis.run">
<span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#gorder.Analysis.run" title="Link to this definition"></a></dt>
<dd><p>Run the analysis.</p>
<p>Executes the configured analysis on the input data and returns the results.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Results of the analysis.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference internal" href="results.html#gorder.results.AnalysisResults" title="gorder.results.AnalysisResults">AnalysisResults</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.AnalysisError" title="gorder.exceptions.AnalysisError"><strong>AnalysisError</strong></a> – If the analysis fails.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
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