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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>AnyPyTools’ documentation! — AnyPyTools 1.9.0 documentation</title>
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<h1>AnyPyTools’ documentation!<a class="headerlink" href="#anypytools-documentation" title="Permalink to this headline">¶</a></h1>
<p>AnyPyTools is a toolkit for working with the AnyBody Modeling System (AMS) from
Python.</p>
<div class="figure align-center" id="id1">
<a class="reference internal image-reference" href="_images/relax.png"><img alt="don't panic" src="_images/relax.png" style="width: 80%;" /></a>
<p class="caption"><span class="caption-text">Don’t panic</span><a class="headerlink" href="#id1" title="Permalink to this image">¶</a></p>
</div>
<p>Its main purpose is to launch AnyBody simulations and collect results. It has a
scheduler to launch multiple instances of AMS utilising computers with multiple
cores. AnyPyTools makes it easy to do parameter and sensitivity and many other
things which is not possible directly within the AnyBody Modeling System.</p>
<div class="section" id="installation">
<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h2>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="dependencies.html">Dependencies</a></li>
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</ul>
</div>
</div>
<div class="section" id="guides">
<h2>Guides<a class="headerlink" href="#guides" title="Permalink to this headline">¶</a></h2>
<p>The tutorials below are also available as a set of
<a class="reference external" href="http://nbviewer.jupyter.org/github/AnyBody-Research-Group/AnyPyTools/blob/master/docs/Tutorial/00_AnyPyTools_tutorial.ipynb">Jupyter Notebooks</a></p>
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<li class="toctree-l1"><a class="reference internal" href="Tutorial/01_Getting_started_with_anypytools.html">Getting Started with AnyPyTools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Tutorial/02_Generating_macros.html">Creating AnyScript Macros</a></li>
<li class="toctree-l1"><a class="reference internal" href="Tutorial/03_Working_with_output_from_Anybody.html">Working with data from AnyBody</a></li>
<li class="toctree-l1"><a class="reference internal" href="Tutorial/04_Batch_processing_multiple_models.html">Batch processing</a></li>
<li class="toctree-l1"><a class="reference internal" href="Tutorial/05_Monte_Carlo_studies_etc.html">Advanced Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="Tutorial/06_Tips%26Tricks.html">Tips & Trics for anypytools</a></li>
</ul>
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<div class="section" id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h2>
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<li class="toctree-l1"><a class="reference internal" href="api/index.html">AnyPyTools API</a></li>
<li class="toctree-l1"><a class="reference internal" href="pytest_plugin.html">PyTest plugin.</a></li>
</ul>
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<div class="section" id="how-to-cite">
<h2>How to cite?<a class="headerlink" href="#how-to-cite" title="Permalink to this headline">¶</a></h2>
<p>If you use the library for publications please cite as:</p>
<div class="without-title admonition seealso">
<p class="admonition-title">See also</p>
<p>Lund et al., (2019). AnyPyTools: A Python package for reproducible research with the AnyBody Modeling System. Journal of Open Source Software, 4(33), 1108, <a class="reference external" href="https://doi.org/10.21105/joss.01108">https://doi.org/10.21105/joss.01108</a></p>
</div>
</div>
<div class="section" id="development">
<h2>Development<a class="headerlink" href="#development" title="Permalink to this headline">¶</a></h2>
<p>I greatly appreciate any contributions to AnyPyTools! If you would like to contribute,
it is as easy as forking the repository on GitHub, making your changes, and
issuing a pull request. If you have any questions about this process don’t
hesitate to ask.</p>
<p>See the <a class="reference internal" href="devguide.html#devguide"><span class="std std-ref">Developer’s Guide</span></a> for more information about contributing.</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="devguide.html">Developer’s Guide</a></li>
<li class="toctree-l1"><a class="reference internal" href="changelog.html">AnyPyTools Change Log</a></li>
</ul>
</div>
</div>
<div class="section" id="usefull-links">
<h2>Usefull links<a class="headerlink" href="#usefull-links" title="Permalink to this headline">¶</a></h2>
<p>If you have questions or comments, please contact the author directly, or
open a <a class="reference external" href="https://github.com/AnyBody-Research-Group/AnyPyTools/issues/new">new issue on GitHub</a></p>
<ul class="simple">
<li><p><a class="reference external" href="https://nbviewer.jupyter.org/github/AnyBody-Research-Group/AnyPyTools/blob/master/docs/Tutorial/00_AnyPyTools_tutorial.ipynb">Jupyter Notebook tutorial</a></p></li>
<li><p><a class="reference external" href="https://anybody-research-group.github.io/anypytools-docs">Documentation</a></p></li>
<li><p><a class="reference external" href="https://gitter.im/AnyBody-Research-Group/AnyPyTools">Gitter</a></p></li>
<li><p><a class="reference external" href="https://github.com/AnyBody-Research-Group/AnyPyTools">GitHub Repository</a></p></li>
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