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  <h3><a href="#">Table Of Contents</a></h3>
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<li><a class="reference internal" href="#">OpenStructure documentation</a><ul>
<li><a class="reference internal" href="#introduction">Introduction</a><ul>
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<li><a class="reference internal" href="#modules">Modules</a><ul>
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<li><a class="reference internal" href="#extending-openstructure">Extending OpenStructure</a><ul>
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  <div class="section" id="openstructure-documentation">
<h1>OpenStructure documentation<a class="headerlink" href="#openstructure-documentation" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
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<li class="toctree-l1"><a class="reference internal" href="intro.html">A gentle introduction to OpenStructure</a><ul>
<li class="toctree-l2"><a class="reference internal" href="intro.html#what-will-be-covered-in-this-tutorial">What will be covered in this tutorial?</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#getting-ready-to-rumble">Getting ready to rumble</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#loading-and-inspecting-a-protein-structure">Loading and inspecting a protein structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#let-there-be-shiny-graphics">Let There Be Shiny Graphics</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#introduction-to-views">Introduction to Views</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#the-query-language">The Query Language</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#constructing-views-manually">Constructing Views Manually</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#saving-an-entity">Saving an Entity</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#loading-images-and-density-maps">Loading &nbsp;images and density maps</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#manipulating-images-and-density-maps">Manipulating &nbsp;images and density maps</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#displaying-images-and-density-maps">Displaying images and density maps</a></li>
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<li class="toctree-l1"><a class="reference internal" href="install.html">Installing OpenStructure</a><ul>
<li class="toctree-l2"><a class="reference internal" href="install.html#installing-the-dependencies">Installing the Dependencies</a></li>
<li class="toctree-l2"><a class="reference internal" href="install.html#checking-out-the-source">Checking out the Source</a></li>
<li class="toctree-l2"><a class="reference internal" href="install.html#configuring">Configuring</a></li>
<li class="toctree-l2"><a class="reference internal" href="install.html#building-the-project">Building the Project</a></li>
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<div class="section" id="modules">
<h2>Modules<a class="headerlink" href="#modules" title="Permalink to this headline">¶</a></h2>
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<li class="toctree-l1"><a class="reference internal" href="base/generic.html">Storing Custom Data</a><ul>
<li class="toctree-l2"><a class="reference internal" href="base/generic.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="base/generic.html#storing-and-accessing-data">Storing and Accessing Data</a></li>
<li class="toctree-l2"><a class="reference internal" href="base/generic.html#use-of-generic-properties-in-queries">Use of Generic Properties in Queries</a></li>
<li class="toctree-l2"><a class="reference internal" href="base/generic.html#api-documentation">API documentation</a></li>
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<li class="toctree-l1"><a class="reference internal" href="img/base/img.html"><tt class="docutils literal"><span class="pre">img</span></tt> Images and Density Maps</a><ul>
<li class="toctree-l2"><a class="reference internal" href="img/base/img.html#introduction-the-imagehandle">Introduction : The ImageHandle</a></li>
<li class="toctree-l2"><a class="reference internal" href="img/base/img.html#creating-and-visualizing-imagehandles">Creating  and visualizing ImageHandles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="img/base/img.html#applying-a-fourier-transform">Applying a Fourier Transform</a></li>
<li class="toctree-l2"><a class="reference internal" href="img/base/img.html#extracting-and-pasting-images">Extracting and Pasting Images</a></li>
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<li class="toctree-l1"><a class="reference internal" href="img/alg/alg.html"><tt class="docutils literal"><span class="pre">alg</span></tt> - Image Processing Algorithms</a><ul>
<li class="toctree-l2"><a class="reference internal" href="img/alg/alg.html#usage-of-image-algorithms">Usage of Image Algorithms</a></li>
<li class="toctree-l2"><a class="reference internal" href="img/alg/alg.html#filters-in-fourier-space">Filters in Fourier Space</a></li>
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<li class="toctree-l1"><a class="reference internal" href="geom/geom.html"><tt class="docutils literal"><span class="pre">geom</span></tt> &#8211; vectors, matrices and geometrical objects</a><ul>
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<li class="toctree-l1"><a class="reference internal" href="conop/conop.html"><tt class="docutils literal"><span class="pre">conop</span></tt> &#8211; Connectivity and Topology of Molecules</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="conop/conop.html#the-builder-interface">The Builder interface</a></li>
<li class="toctree-l2"><a class="reference internal" href="conop/conop.html#connecting-atoms">Connecting atoms</a></li>
<li class="toctree-l2"><a class="reference internal" href="conop/conop.html#convert-mm-cif-dictionary">Convert MM CIF dictionary</a></li>
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<li class="toctree-l1"><a class="reference internal" href="mol/base/mol.html"><tt class="docutils literal"><span class="pre">mol</span></tt> &#8211; Molecular structures and surfaces</a><ul>
<li class="toctree-l2"><a class="reference internal" href="mol/base/entity.html">The Molecular Entity</a></li>
<li class="toctree-l2"><a class="reference internal" href="mol/base/editors.html">Editors</a></li>
<li class="toctree-l2"><a class="reference internal" href="mol/base/query.html">Queries</a></li>
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<li class="toctree-l1"><a class="reference internal" href="seq/base/seq.html"><tt class="docutils literal"><span class="pre">seq</span></tt> &#8211; Sequences and Alignments</a><ul>
<li class="toctree-l2"><a class="reference internal" href="seq/base/seq.html#attaching-structures-to-sequences">Attaching Structures to Sequences</a></li>
<li class="toctree-l2"><a class="reference internal" href="seq/base/seq.html#loading-and-saving-sequences-and-alignments">Loading and Saving Sequences and Alignments</a></li>
<li class="toctree-l2"><a class="reference internal" href="seq/base/seq.html#the-sequencehandle">The SequenceHandle</a></li>
<li class="toctree-l2"><a class="reference internal" href="seq/base/seq.html#the-sequencelist">The SequenceList</a></li>
<li class="toctree-l2"><a class="reference internal" href="seq/base/seq.html#the-alignmenthandle">The AlignmentHandle</a></li>
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<li class="toctree-l1"><a class="reference internal" href="base/base.html"><tt class="docutils literal"><span class="pre">ost.settings</span></tt> - Locate Files and Retrieve Preferences</a></li>
<li class="toctree-l1"><a class="reference internal" href="io/io.html"><tt class="docutils literal"><span class="pre">io</span></tt> - Input and Output of Sequences, Structures and Maps</a><ul>
<li class="toctree-l2"><a class="reference internal" href="io/io.html#molecular-structures">Molecular Structures</a></li>
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<li class="toctree-l1"><a class="reference internal" href="gui/gui.html"><tt class="docutils literal"><span class="pre">gui</span></tt> &#8211; Graphical User Interface</a></li>
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<div class="section" id="extending-openstructure">
<h2>Extending OpenStructure<a class="headerlink" href="#extending-openstructure" title="Permalink to this headline">¶</a></h2>
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<li class="toctree-l1"><a class="reference internal" href="newmodule.html">Creating a New Module</a><ul>
<li class="toctree-l2"><a class="reference internal" href="newmodule.html#directory-structure">Directory Structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="newmodule.html#the-module-code">The Module Code</a></li>
<li class="toctree-l2"><a class="reference internal" href="newmodule.html#the-testing-framework">The Testing Framework</a></li>
<li class="toctree-l2"><a class="reference internal" href="newmodule.html#the-python-wrapper">The Python Wrapper</a></li>
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<li class="toctree-l1"><a class="reference internal" href="external.html">Using External Programs within OpenStructure</a><ul>
<li class="toctree-l2"><a class="reference internal" href="external.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="external.html#locating-the-executable">Locating the Executable</a></li>
<li class="toctree-l2"><a class="reference internal" href="external.html#prepare-all-files">Prepare All Files</a></li>
<li class="toctree-l2"><a class="reference internal" href="external.html#execute-the-external-program">Execute the External Program</a></li>
<li class="toctree-l2"><a class="reference internal" href="external.html#read-generated-output">Read Generated Output</a></li>
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