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‎.buildinfo‎

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# Sphinx build info version 1
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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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‎CG_fiber.html‎

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<script src="_static/doctools.js"></script>
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<link rel="search" type="application/opensearchdescription+xml"
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title="Search within MDAnalysisData 0.8.1 documentation"
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<div itemprop="articleBody">
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<section id="module-MDAnalysisData.CG_fiber">
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<span id="cg-fiber-dataset"></span><span id="cg-fiber"></span><h1>CG fiber dataset<a class="headerlink" href="#module-MDAnalysisData.CG_fiber" title="Permalink to this headline"></a></h1>
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<span id="cg-fiber-dataset"></span><span id="cg-fiber"></span><h1>CG fiber dataset<a class="headerlink" href="#module-MDAnalysisData.CG_fiber" title="Permalink to this headline"></a></h1>
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<p>The <a class="reference internal" href="#module-MDAnalysisData.CG_fiber" title="MDAnalysisData.CG_fiber"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysisData.CG_fiber</span></code></a> module contains a coarse-grained
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MD trajectory showing the self-assembly of an amphiphilic molecule.</p>
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<table class="longtable docutils align-default">
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</table>
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<section id="id1">
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<span id="id2"></span><h2>CG fiber dataset<a class="headerlink" href="#id1" title="Permalink to this headline"></a></h2>
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<span id="id2"></span><h2>CG fiber dataset<a class="headerlink" href="#id1" title="Permalink to this headline"></a></h2>
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<p>MD trajectory showing the self-assembly of an amphiphilic molecule.</p>
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<p>The topology is contained in the PSF file (CHARMM format). The
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trajectory is contained in the DCD file (CHARMM/NAMD format).</p>
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<section id="notes">
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<h3>Notes<a class="headerlink" href="#notes" title="Permalink to this headline"></a></h3>
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<h3>Notes<a class="headerlink" href="#notes" title="Permalink to this headline"></a></h3>
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<p>Data set characteristics:</p>
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<blockquote>
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<div><dl class="field-list simple">
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</div></blockquote>
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<dl class="py function">
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<dt class="sig sig-object py" id="MDAnalysisData.CG_fiber.fetch_CG_fiber">
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<span class="sig-prename descclassname"><span class="pre">MDAnalysisData.CG_fiber.</span></span><span class="sig-name descname"><span class="pre">fetch_CG_fiber</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_home</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">download_if_missing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MDAnalysisData/CG_fiber.html#fetch_CG_fiber"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#MDAnalysisData.CG_fiber.fetch_CG_fiber" title="Permalink to this definition"></a></dt>
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<span class="sig-prename descclassname"><span class="pre">MDAnalysisData.CG_fiber.</span></span><span class="sig-name descname"><span class="pre">fetch_CG_fiber</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_home</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">download_if_missing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MDAnalysisData/CG_fiber.html#fetch_CG_fiber"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#MDAnalysisData.CG_fiber.fetch_CG_fiber" title="Permalink to this definition"></a></dt>
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<dd><p>Load the CG fiber self-assembly trajectory</p>
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<dl class="field-list simple">
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<dt class="field-odd">Parameters</dt>
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<dd class="field-odd"><ul class="simple">
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<li><p><strong>data_home</strong> (<em>optional</em><em>, </em><em>default: None</em>) – Specify another download and cache folder for the datasets. By default
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all MDAnalysisData data is stored in ‘~/MDAnalysis_data’ subfolders.
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This dataset is stored in <code class="docutils literal notranslate"><span class="pre">&lt;data_home&gt;/CG_fiber</span></code>.</p></li>
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<li><p><strong>download_if_missing</strong> (<em>optional</em><em>, </em><em>default=True</em>) – If <code class="docutils literal notranslate"><span class="pre">False</span></code>, raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IOError" title="(in Python v3.9)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">IOError</span></code></a> if the data is not locally available
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<li><p><strong>download_if_missing</strong> (<em>optional</em><em>, </em><em>default=True</em>) – If <code class="docutils literal notranslate"><span class="pre">False</span></code>, raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IOError" title="(in Python v3.10)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">IOError</span></code></a> if the data is not locally available
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instead of trying to download the data from the source site.</p></li>
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</ul>
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‎PEG_1chain.html‎

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<section id="module-MDAnalysisData.PEG_1chain">
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<p>The <a class="reference internal" href="#module-MDAnalysisData.PEG_1chain" title="MDAnalysisData.PEG_1chain"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysisData.PEG_1chain</span></code></a> module contains a coarse-grained
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<span id="id1"></span><h2>PEG polymer dataset<a class="headerlink" href="#peg-1chain-dataset" title="Permalink to this headline"></a></h2>
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<p>MD trajectory showing the self-assembly of an amphiphilic molecule.</p>
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<p>The topology is contained in the PRMTOP file (AMBER format). The
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trajectory is contained in the NETCDF (.nc) file (AMBER format).</p>
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<h3>Notes<a class="headerlink" href="#notes" title="Permalink to this headline"></a></h3>
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<h3>Notes<a class="headerlink" href="#notes" title="Permalink to this headline"></a></h3>
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<p>Data set characteristics:</p>
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<dl class="py function">
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<dt class="sig sig-object py" id="MDAnalysisData.PEG_1chain.fetch_PEG_1chain">
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<span class="sig-prename descclassname"><span class="pre">MDAnalysisData.PEG_1chain.</span></span><span class="sig-name descname"><span class="pre">fetch_PEG_1chain</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_home</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">download_if_missing</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MDAnalysisData/PEG_1chain.html#fetch_PEG_1chain"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#MDAnalysisData.PEG_1chain.fetch_PEG_1chain" title="Permalink to this definition"></a></dt>
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<dd><p>Load the PEG polymer trajectory</p>
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<dl class="field-list simple">
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<dt class="field-odd">Parameters</dt>
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<dd class="field-odd"><ul class="simple">
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<li><p><strong>data_home</strong> (<em>optional</em><em>, </em><em>default: None</em>) – Specify another download and cache folder for the datasets. By default
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all MDAnalysisData data is stored in ‘~/MDAnalysis_data’ subfolders.
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This dataset is stored in <code class="docutils literal notranslate"><span class="pre">&lt;data_home&gt;/CG_fiber</span></code>.</p></li>
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<li><p><strong>download_if_missing</strong> (<em>optional</em><em>, </em><em>default=True</em>) – If <code class="docutils literal notranslate"><span class="pre">False</span></code>, raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IOError" title="(in Python v3.9)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">IOError</span></code></a> if the data is not locally available
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<li><p><strong>download_if_missing</strong> (<em>optional</em><em>, </em><em>default=True</em>) – If <code class="docutils literal notranslate"><span class="pre">False</span></code>, raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IOError" title="(in Python v3.10)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">IOError</span></code></a> if the data is not locally available
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instead of trying to download the data from the source site.</p></li>
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‎_modules/MDAnalysisData/CG_fiber.html‎

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‎_modules/MDAnalysisData/PEG_1chain.html‎

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‎_modules/MDAnalysisData/adk_equilibrium.html‎

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‎_modules/MDAnalysisData/adk_transitions.html‎

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‎_modules/MDAnalysisData/base.html‎

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‎_modules/MDAnalysisData/ifabp_water.html‎

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