rebuilt html docs for version 2.7.0-dev0 from branch develop with sph…

…inx at 698e083

2.7.0-dev0/_sources/preparing_releases_and_hotfixes.rst.txt

@@ -67,7 +67,7 @@ Summary of tasks
 Getting the develop branch ready for a release
 ----------------------------------------------
 
-#. Declare feature freeze on ``develop`` via `discord` and `GitHub Discussions (Anouncement)`_
+#. Declare feature freeze on ``develop`` via `discord` and `GitHub Discussions (Announcement)`_
 
 #. Create a pre-release feature branch from ``develop``
 

2.7.0-dev0/advanced_topology.html

@@ -197,7 +197,7 @@
 <span id="advanced-topology"></span><h1>Advanced topology concepts<a class="headerlink" href="#advanced-topology-concepts" title="Permalink to this heading"></a></h1>
 <section id="adding-a-residue-or-segment-to-a-universe">
 <span id="adding-residue"></span><h2>Adding a Residue or Segment to a Universe<a class="headerlink" href="#adding-a-residue-or-segment-to-a-universe" title="Permalink to this heading"></a></h2>
-<p>To add a <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/core/groups.html#MDAnalysis.core.groups.Residue" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Residue</span></code></a> or <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/core/groups.html#MDAnalysis.core.groups.Segment" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Segment</span></code></a> to a topology, use the <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/core/universe.html#MDAnalysis.core.universe.Universe.add_Residue" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Universe.add_Residue</span></code></a> or <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/core/universe.html#MDAnalysis.core.universe.Universe.add_Segment" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Universe.add_Segment</span></code></a> methods.</p>
+<p>To add a <code class="xref py py-class docutils literal notranslate"><span class="pre">Residue</span></code> or <code class="xref py py-class docutils literal notranslate"><span class="pre">Segment</span></code> to a topology, use the <code class="xref py py-meth docutils literal notranslate"><span class="pre">Universe.add_Residue</span></code> or <code class="xref py py-meth docutils literal notranslate"><span class="pre">Universe.add_Segment</span></code> methods.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">u</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="n">PSF</span><span class="p">,</span> <span class="n">DCD</span><span class="p">)</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">u</span><span class="o">.</span><span class="n">segments</span>
 <span class="go">&lt;SegmentGroup with 1 segment&gt;</span>
@@ -210,7 +210,7 @@
 <span class="go">&lt;AtomGroup with 0 atoms&gt;</span>
 </pre></div>
 </div>
-<p>To assign the last 100 residues from the <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/core/universe.html#MDAnalysis.core.universe.Universe" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Universe</span></code></a> to this new Segment:</p>
+<p>To assign the last 100 residues from the <code class="xref py py-class docutils literal notranslate"><span class="pre">Universe</span></code> to this new Segment:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">u</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="o">-</span><span class="mi">100</span><span class="p">:]</span><span class="o">.</span><span class="n">segments</span> <span class="o">=</span> <span class="n">newseg</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">newseg</span><span class="o">.</span><span class="n">atoms</span>
 <span class="go">&lt;AtomGroup with 1600 atoms&gt;</span>

2.7.0-dev0/contributing_code.html

@@ -991,15 +991,15 @@ <h3>Documenting changes<a class="headerlink" href="#documenting-changes" title="
 </section>
 <section id="writing-docs-for-abstract-base-classes">
 <h3>Writing docs for abstract base classes<a class="headerlink" href="#writing-docs-for-abstract-base-classes" title="Permalink to this heading"></a></h3>
-<p>MDAnalysis contains a number of abstract base classes, such as <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnalysisBase</span></code></a>. Developers who define new base classes, or modify existing ones, should follow these rules:</p>
+<p>MDAnalysis contains a number of abstract base classes, such as <code class="xref py py-class docutils literal notranslate"><span class="pre">AnalysisBase</span></code>. Developers who define new base classes, or modify existing ones, should follow these rules:</p>
 <blockquote>
 <div><ul class="simple">
 <li><p>The <em>class docstring</em> needs to contain a list of methods that can be overwritten by inheritance from the base class. Distinguish and document methods as required or optional.</p></li>
 <li><p>The class docstring should contain a minimal example for how to derive this class. This demonstrates best practices, documents ideas and intentions behind the specific choices in the API, helps to promote a unified code base, and is useful for developers as a concise summary of the API.</p></li>
 <li><p>A more detailed description of methods should come in the <em>method docstring</em>, with a note specifying if the method is required or optional to overwrite.</p></li>
 </ul>
 </div></blockquote>
-<p>See the documentation of <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a> for an example of this documentation.</p>
+<p>See the documentation of <code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code> for an example of this documentation.</p>
 </section>
 <section id="adding-your-documentation-to-mdanalysis">
 <h3>Adding your documentation to MDAnalysis<a class="headerlink" href="#adding-your-documentation-to-mdanalysis" title="Permalink to this heading"></a></h3>

2.7.0-dev0/examples/analysis/README.html

@@ -272,7 +272,7 @@ <h2>Imports and dependencies<a class="headerlink" href="#imports-and-dependencie
 </section>
 <section id="alignments-and-rms-fitting">
 <span id="alignment-and-rms"></span><h1>Alignments and RMS fitting<a class="headerlink" href="#alignments-and-rms-fitting" title="Permalink to this heading"></a></h1>
-<p>The <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/align.html#module-MDAnalysis.analysis.align" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.align</span></code></a> and <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/rms.html#module-MDAnalysis.analysis.rms" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.rms</span></code></a>
+<p>The <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.align</span></code> and <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.rms</span></code>
 modules contain the functions used for aligning structures,
 aligning trajectories, and calculating root mean squared quantities.</p>
 <p>Demonstrations of alignment are in <a class="reference external" href="/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb">align_structure</a>,
@@ -300,7 +300,7 @@ <h2>Imports and dependencies<a class="headerlink" href="#imports-and-dependencie
 </section>
 <section id="distances-and-contacts">
 <h1>Distances and contacts<a class="headerlink" href="#distances-and-contacts" title="Permalink to this heading"></a></h1>
-<p>The <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/distances.html#module-MDAnalysis.analysis.distances" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.distances</span></code></a> module provides functions to rapidly compute distances. These largely take in coordinate arrays.</p>
+<p>The <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.distances</span></code> module provides functions to rapidly compute distances. These largely take in coordinate arrays.</p>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="distances_and_contacts/distances_between_atomgroups.html">Atom-wise distances between matching AtomGroups</a></li>
@@ -309,7 +309,7 @@ <h1>Distances and contacts<a class="headerlink" href="#distances-and-contacts" t
 </ul>
 </div>
 <p>Residues can be determined to be in contact if atoms from the two residues are within a certain distance. Analysing the fraction of contacts retained by a protein over at trajectory, as compared to the number of contacts in a reference frame or structure, can give insight into folding processes and domain movements.</p>
-<p><a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/contacts.html#module-MDAnalysis.analysis.contacts" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.contacts</span></code></a> contains functions and a class to analyse the fraction of native contacts over a trajectory.</p>
+<p><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.contacts</span></code> contains functions and a class to analyse the fraction of native contacts over a trajectory.</p>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="distances_and_contacts/contacts_native_fraction.html">Fraction of native contacts over a trajectory</a></li>

2.7.0-dev0/examples/analysis/alignment_and_rms/README.html

@@ -212,7 +212,7 @@
 
   <section id="alignments-and-rms-fitting">
 <span id="alignment-and-rms"></span><h1>Alignments and RMS fitting<a class="headerlink" href="#alignments-and-rms-fitting" title="Permalink to this heading"></a></h1>
-<p>The <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/align.html#module-MDAnalysis.analysis.align" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.align</span></code></a> and <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/rms.html#module-MDAnalysis.analysis.rms" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.rms</span></code></a>
+<p>The <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.align</span></code> and <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.rms</span></code>
 modules contain the functions used for aligning structures,
 aligning trajectories, and calculating root mean squared quantities.</p>
 <p>Demonstrations of alignment are in <a class="reference external" href="/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb">align_structure</a>,

2.7.0-dev0/examples/analysis/distances_and_contacts/README.html

@@ -213,7 +213,7 @@
 
   <section id="distances-and-contacts">
 <h1>Distances and contacts<a class="headerlink" href="#distances-and-contacts" title="Permalink to this heading"></a></h1>
-<p>The <a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/distances.html#module-MDAnalysis.analysis.distances" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.distances</span></code></a> module provides functions to rapidly compute distances. These largely take in coordinate arrays.</p>
+<p>The <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.distances</span></code> module provides functions to rapidly compute distances. These largely take in coordinate arrays.</p>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="distances_between_atomgroups.html">Atom-wise distances between matching AtomGroups</a></li>
@@ -222,7 +222,7 @@ <h1>Distances and contacts<a class="headerlink" href="#distances-and-contacts" t
 </ul>
 </div>
 <p>Residues can be determined to be in contact if atoms from the two residues are within a certain distance. Analysing the fraction of contacts retained by a protein over at trajectory, as compared to the number of contacts in a reference frame or structure, can give insight into folding processes and domain movements.</p>
-<p><a class="reference external" href="https://docs.mdanalysis.org/2.7.0-dev0/documentation_pages/analysis/contacts.html#module-MDAnalysis.analysis.contacts" title="(in MDAnalysis v2.7.0-dev0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.contacts</span></code></a> contains functions and a class to analyse the fraction of native contacts over a trajectory.</p>
+<p><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.analysis.contacts</span></code> contains functions and a class to analyse the fraction of native contacts over a trajectory.</p>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="contacts_native_fraction.html">Fraction of native contacts over a trajectory</a></li>

2.7.0-dev0/examples/constructing_universe.html

@@ -715,7 +715,7 @@ <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title
 <li><p>NMP: residues 30-59 (blue)</p></li>
 <li><p>LID: residues 122-159 (yellow)</p></li>
 </ul>
-<p><img alt="921134b37b3441e8bc55d6c7f8087dd3" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="5be1c0ca020d4d488bf22abef2f32e82" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
 <div class="nbinput docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[26]:
 </pre></div>