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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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config: 9ebbbdd7422349856bbc9649af0dee0c
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tags: 645f666f9bcd5a90fca523b33c5a78b7

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‎CG_fiber.html‎

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<!DOCTYPE html>
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head>
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<meta charset="utf-8" />
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<title>CG fiber dataset &#8212; MDAnalysisData 0.8.0 documentation</title>
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<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
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<script type="text/javascript" src="_static/jquery.js"></script>
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<script type="text/javascript" src="_static/doctools.js"></script>
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<script type="text/javascript" src="_static/language_data.js"></script>
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<link rel="search" type="application/opensearchdescription+xml"
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title="Search within MDAnalysisData 0.8.0 documentation"
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href="_static/opensearch.xml"/>
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<link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="search" title="Search" href="search.html" />
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<link rel="prev" title="Vesicles datasets" href="vesicles.html" />
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<link rel="stylesheet" href="_static/custom.css" type="text/css" />
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<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
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</head><body>
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<div class="document">
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<div class="documentwrapper">
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<div class="bodywrapper">
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<div class="body" role="main">
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<div class="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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<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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<colgroup>
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<col style="width: 10%" />
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<col style="width: 90%" />
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</colgroup>
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<tbody>
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<tr class="row-odd"><td><p><a class="reference internal" href="#MDAnalysisData.CG_fiber.fetch_CG_fiber" title="MDAnalysisData.CG_fiber.fetch_CG_fiber"><code class="xref py py-obj docutils literal notranslate"><span class="pre">fetch_CG_fiber</span></code></a>([data_home, download_if_missing])</p></td>
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<td><p>Load the CG fiber self-assembly trajectory</p></td>
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</tr>
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</tbody>
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</table>
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<div class="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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<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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<div class="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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<p>Data set characteristics:</p>
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<blockquote>
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<div><dl class="field-list simple">
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<dt class="field-odd">size</dt>
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<dd class="field-odd"><p>213 MB</p>
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</dd>
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<dt class="field-even">number of trajectories</dt>
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<dd class="field-even"><p>1</p>
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</dd>
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<dt class="field-odd">creator</dt>
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<dd class="field-odd"><p>Aysenur Iscen</p>
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</dd>
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<dt class="field-even">URL</dt>
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<dd class="field-even"><p><a class="reference external" href="https://figshare.com/articles/126chains_dcd/7259915">https://figshare.com/articles/126chains_dcd/7259915</a></p>
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</dd>
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<dt class="field-odd">license</dt>
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<dd class="field-odd"><p><a class="reference external" href="https://creativecommons.org/licenses/by/4.0/legalcode">CC-BY 4.0</a></p>
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</dd>
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</dl>
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</div></blockquote>
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<dl class="function">
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<dt id="MDAnalysisData.CG_fiber.fetch_CG_fiber">
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<code class="sig-prename descclassname">MDAnalysisData.CG_fiber.</code><code class="sig-name descname">fetch_CG_fiber</code><span class="sig-paren">(</span><em class="sig-param">data_home=None</em>, <em class="sig-param">download_if_missing=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/MDAnalysisData/CG_fiber.html#fetch_CG_fiber"><span class="viewcode-link">[source]</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 v3.7)"><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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</dd>
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<dt class="field-even">Returns</dt>
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<dd class="field-even"><p><ul class="simple">
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<li><p><strong>dataset</strong> (<em>dict-like object with the following attributes:</em>)</p></li>
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<li><p><strong>dataset.topology</strong> (<em>filename</em>) – Filename of the topology file</p></li>
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<li><p><strong>dataset.trajectory</strong> (<em>filename</em>) – Filename of the trajectory file</p></li>
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<li><p><strong>dataset.DESCR</strong> (<em>string</em>) – Description of the trajectory.</p></li>
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</ul>
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</p>
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</dd>
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</dl>
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<p>See <a class="reference internal" href="#id1"><span class="std std-ref">CG fiber dataset</span></a> for description.</p>
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</dd></dl>
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</div>
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</div>
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</div>
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</div>
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</div>
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</div>
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<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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<div class="sphinxsidebarwrapper">
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<p class="logo">
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<a href="index.html">
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<img class="logo" src="_static/logos/MDAnalysisData-logo.png" alt="Logo"/>
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<h1 class="logo logo-name">MDAnalysisData</h1>
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</a>
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</p>
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<p class="blurb">Biomolecular simulation datasets</p>
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<h3>Navigation</h3>
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<p class="caption"><span class="caption-text">Overview</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="install.html">Installing</a></li>
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<li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
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<li class="toctree-l1"><a class="reference internal" href="helpers.html">Helpers</a></li>
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<li class="toctree-l1"><a class="reference internal" href="credits.html">Credits</a></li>
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</ul>
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<p class="caption"><span class="caption-text">Datasets</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="adk_equilibrium.html">AdK equilibrium dataset</a></li>
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<li class="toctree-l1"><a class="reference internal" href="adk_transitions.html">AdK transitions datasets</a></li>
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<li class="toctree-l1"><a class="reference internal" href="PEG_1chain.html">PEG polymer dataset</a></li>
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<li class="toctree-l1"><a class="reference internal" href="ifabp_water.html">I-FABP dataset</a></li>
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<li class="toctree-l1"><a class="reference internal" href="nhaa_equilibrium.html">NhaA equilibrium dataset</a></li>
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<li class="toctree-l1"><a class="reference internal" href="yiip_equilibrium.html">YiiP equilibrium dataset</a></li>
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<li class="toctree-l1"><a class="reference internal" href="membrane_peptide.html">Membrane peptide dataset</a></li>
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<li class="toctree-l1"><a class="reference internal" href="vesicles.html">Vesicles datasets</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">CG fiber dataset</a></li>
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</ul>
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<hr />
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<ul>
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<li class="toctree-l1"><a href="https://www.mdanalysis.org/">MDAnalysis</a></li>
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<li class="toctree-l1"><a href="https://alchemtest.readthedocs.io/">alchemtest</a></li>
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</ul>
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<div class="relations">
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<h3>Related Topics</h3>
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<ul>
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<li><a href="index.html">Documentation overview</a><ul>
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<li>Previous: <a href="vesicles.html" title="previous chapter">Vesicles datasets</a></li>
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&copy;2018, Oliver Beckstein, Shujie Fan, Micaela Matta, Richard J. Gowers.
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