Merge pull request #3 from isambard-uob/get_ss_regions

Get Secondary Structure Regions
isambard-uob · Sep 27, 2018 · 906e2af · 906e2af
2 parents f10682a + ccab394
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diff --git a/README.md b/README.md
@@ -54,6 +54,12 @@ complex selections and performing analysis. Take a look at the
 
 ## Release Notes
 
+## v1.4.0
+
+* **Adds `get_ss_regions` to `ampal.dssp`.** This function can be used to
+  extract all regions of a protein in a particular secondary structure.
+* **Fixes bug with DSSP `ss_region` tagging.** End residues used to be missed.
+
 ## v1.3.0
 
 * **Adds an interface for NACCESS.** Functions for using NACCESS to calculate

diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 3affbacc5a3153bb7f37e7835b45de66
+config: e70e5006c821c99214503c163a30b1cc
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/.doctrees/AMPAL_Introduction_and_Selections.doctree b/docs/.doctrees/AMPAL_Introduction_and_Selections.doctree
diff --git a/docs/.doctrees/Advanced_Selections_and_Analysis.doctree b/docs/.doctrees/Advanced_Selections_and_Analysis.doctree
diff --git a/docs/.doctrees/ampal.doctree b/docs/.doctrees/ampal.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/installation.doctree b/docs/.doctrees/installation.doctree
diff --git a/docs/.doctrees/modules.doctree b/docs/.doctrees/modules.doctree
diff --git a/docs/AMPAL_Introduction_and_Selections.html b/docs/AMPAL_Introduction_and_Selections.html
@@ -6,14 +6,14 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>An Introduction to the AMPAL Framework &#8212; AMPAL 1.0.0 documentation</title>
+    <title>An Introduction to the AMPAL Framework &#8212; AMPAL 1.4.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-    <script type="text/javascript" src="_static/documentation_options.js"></script>
+    <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
     <script type="text/javascript" src="_static/jquery.js"></script>
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Advanced Selections and Analysis" href="Advanced_Selections_and_Analysis.html" />
@@ -30,6 +30,8 @@
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
+
+
           <div class="body" role="main">
 
   <div class="section" id="an-introduction-to-the-ampal-framework">
@@ -47,7 +49,7 @@ <h1>An Introduction to the AMPAL Framework<a class="headerlink" href="#an-introd
 objects, but they are just protein-specific versions of <code class="docutils literal notranslate"><span class="pre">Polymer</span></code>
 and <code class="docutils literal notranslate"><span class="pre">Monomer</span></code>. We wanted to keep the base objects as generic as
 possible to allow other biomolecules (like DNA or RNA), or even
-unnatural polymers (like <span class="math notranslate">\(\beta\)</span>-amino acids) to be
+unnatural polymers (like <span class="math notranslate nohighlight">\(\beta\)</span>-amino acids) to be
 represented using this architecture. While some these features are
 not currently implemented in ISAMBARD, this will lead to more
 scalable code with reduced duplication in the future.</div></blockquote>
@@ -255,7 +257,7 @@ <h2>4. Selecting Residues<a class="headerlink" href="#selecting-residues" title=
 <div class="section" id="selecting-atoms">
 <h2>5. Selecting Atoms<a class="headerlink" href="#selecting-atoms" title="Permalink to this headline">¶</a></h2>
 <p>Atoms can be selected using a string of their PDB atom type, for example
-the C<span class="math notranslate">\(\alpha\)</span> atom of the residue can be selected like this:</p>
+the C<span class="math notranslate nohighlight">\(\alpha\)</span> atom of the residue can be selected like this:</p>
 <div class="code ipython3 highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">my_residue_A23</span><span class="p">[</span><span class="s1">&#39;CA&#39;</span><span class="p">]</span>
 </pre></div>
 </div>
@@ -483,24 +485,39 @@ <h2>8. Summary and activities<a class="headerlink" href="#summary-and-activities
 
 
           </div>
+
         </div>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
-  <h3><a href="index.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">An Introduction to the AMPAL Framework</a><ul>
-<li><a class="reference internal" href="#converting-pdb-files-to-ampal-objects">1. Converting PDB files to AMPAL Objects</a></li>
-<li><a class="reference internal" href="#basic-analysis">2. Basic Analysis</a></li>
-<li><a class="reference internal" href="#selecting-chains">3. Selecting Chains</a></li>
-<li><a class="reference internal" href="#selecting-residues">4. Selecting Residues</a></li>
-<li><a class="reference internal" href="#selecting-atoms">5. Selecting Atoms</a></li>
-<li><a class="reference internal" href="#ampal-parents">6. AMPAL Parents</a></li>
-<li><a class="reference internal" href="#ligands">7. Ligands</a></li>
-<li><a class="reference internal" href="#summary-and-activities">8. Summary and activities</a></li>
+<h1 class="logo"><a href="index.html">AMPAL</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<p class="caption"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Introduction to AMPAL</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#converting-pdb-files-to-ampal-objects">1. Converting PDB files to AMPAL Objects</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#basic-analysis">2. Basic Analysis</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#selecting-chains">3. Selecting Chains</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#selecting-residues">4. Selecting Residues</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#selecting-atoms">5. Selecting Atoms</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#ampal-parents">6. AMPAL Parents</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#ligands">7. Ligands</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#summary-and-activities">8. Summary and activities</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Advanced_Selections_and_Analysis.html">Advanced Selections</a></li>
+<li class="toctree-l1"><a class="reference internal" href="modules.html">API Reference</a></li>
 </ul>
+
 <div class="relations">
 <h3>Related Topics</h3>
 <ul>
@@ -510,13 +527,6 @@ <h3>Related Topics</h3>
   </ul></li>
 </ul>
 </div>
-  <div role="note" aria-label="source link">
-    <h3>This Page</h3>
-    <ul class="this-page-menu">
-      <li><a href="_sources/AMPAL_Introduction_and_Selections.rst.txt"
-            rel="nofollow">Show Source</a></li>
-    </ul>
-   </div>
 <div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <div class="searchformwrapper">
@@ -537,8 +547,8 @@ <h3>Quick search</h3>
       &copy;2018, Woolfson Group, UoB.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.7.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.10</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.1</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.11</a>
 
       |
       <a href="_sources/AMPAL_Introduction_and_Selections.rst.txt"

diff --git a/docs/Advanced_Selections_and_Analysis.html b/docs/Advanced_Selections_and_Analysis.html
@@ -6,14 +6,14 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Advanced Selections and Analysis &#8212; AMPAL 1.0.0 documentation</title>
+    <title>Advanced Selections and Analysis &#8212; AMPAL 1.4.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-    <script type="text/javascript" src="_static/documentation_options.js"></script>
+    <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
     <script type="text/javascript" src="_static/jquery.js"></script>
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="ampal" href="modules.html" />
@@ -30,6 +30,8 @@
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
+
+
           <div class="body" role="main">
 
   <div class="section" id="advanced-selections-and-analysis">
@@ -462,8 +464,8 @@ <h2>5. Geometry in AMPAL<a class="headerlink" href="#geometry-in-ampal" title="P
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">-</span><span class="mf">179.8002001034783</span> <span class="o">-</span><span class="mf">64.10861163046212</span> <span class="o">-</span><span class="mf">45.84373968479124</span>
 </pre></div>
 </div>
-<p>We can use it to calculate the <span class="math notranslate">\(\chi\)</span> torsion angles too. R2 is
-leucine, so we can calculate the <span class="math notranslate">\(\chi_1\)</span> and <span class="math notranslate">\(\chi_2\)</span>
+<p>We can use it to calculate the <span class="math notranslate nohighlight">\(\chi\)</span> torsion angles too. R2 is
+leucine, so we can calculate the <span class="math notranslate nohighlight">\(\chi_1\)</span> and <span class="math notranslate nohighlight">\(\chi_2\)</span>
 angles:</p>
 <div class="code ipython3 highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">r2</span><span class="o">.</span><span class="n">atoms</span>
 </pre></div>
@@ -518,22 +520,37 @@ <h2>6. Summary and activities<a class="headerlink" href="#summary-and-activities
 
 
           </div>
+
         </div>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
-  <h3><a href="index.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Advanced Selections and Analysis</a><ul>
-<li><a class="reference internal" href="#selecting-all-residues-or-atoms">1. Selecting All Residues or Atoms</a></li>
-<li><a class="reference internal" href="#analysing-composition">2. Analysing Composition</a></li>
-<li><a class="reference internal" href="#distance-analysis">3. Distance Analysis</a></li>
-<li><a class="reference internal" href="#is-within">4. Is Within</a></li>
-<li><a class="reference internal" href="#geometry-in-ampal">5. Geometry in AMPAL</a></li>
-<li><a class="reference internal" href="#summary-and-activities">6. Summary and activities</a></li>
+<h1 class="logo"><a href="index.html">AMPAL</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<p class="caption"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="AMPAL_Introduction_and_Selections.html">Introduction to AMPAL</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Advanced Selections</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#selecting-all-residues-or-atoms">1. Selecting All Residues or Atoms</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#analysing-composition">2. Analysing Composition</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#distance-analysis">3. Distance Analysis</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#is-within">4. Is Within</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#geometry-in-ampal">5. Geometry in AMPAL</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#summary-and-activities">6. Summary and activities</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="modules.html">API Reference</a></li>
 </ul>
+
 <div class="relations">
 <h3>Related Topics</h3>
 <ul>
@@ -543,13 +560,6 @@ <h3>Related Topics</h3>
   </ul></li>
 </ul>
 </div>
-  <div role="note" aria-label="source link">
-    <h3>This Page</h3>
-    <ul class="this-page-menu">
-      <li><a href="_sources/Advanced_Selections_and_Analysis.rst.txt"
-            rel="nofollow">Show Source</a></li>
-    </ul>
-   </div>
 <div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
     <div class="searchformwrapper">
@@ -570,8 +580,8 @@ <h3>Quick search</h3>
       &copy;2018, Woolfson Group, UoB.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.7.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.10</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.1</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.11</a>
 
       |
       <a href="_sources/Advanced_Selections_and_Analysis.rst.txt"