rebuilt html docs for version 2.10.0-dev0 from branch develop with sphinx at b280419

Author: github-actions

2.10.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf

@@ -717,7 +717,7 @@ <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="0723bdab80af44d88fddb30016bb1b23" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="3182edb047ba4659a63f4bd472dfc714" 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>

2.10.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html

@@ -261,7 +261,7 @@ <h2>Reading data directly<a class="headerlink" href="#reading-data-directly" tit
 <span class="gp">In [3]: </span><span class="n">aux</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="n">XVG_BZ2</span><span class="p">)</span>
 
 <span class="gp">In [4]: </span><span class="n">aux</span>
-<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7ff336284130&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe15a847310&gt;</span>
 </pre></div>
 </div>
 <p>In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.</p>
@@ -460,7 +460,7 @@ <h2>Recreating auxiliaries<a class="headerlink" href="#recreating-auxiliaries" t
 <span class="gp">In [30]: </span><span class="k">del</span> <span class="n">aux</span>
 
 <span class="gp">In [31]: </span><span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="o">**</span><span class="n">description</span><span class="p">)</span>
-<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7ff336f197e0&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe15a943430&gt;</span>
 </pre></div>
 </div>
 <p>The ‘description’ of any or all the auxiliaries added to a trajectory can be
@@ -575,7 +575,7 @@ <h2>Standalone Usage<a class="headerlink" href="#standalone-usage" title="Link t
 <div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [45]: </span><span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span>
 
 <span class="gp">In [46]: </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Time&quot;</span><span class="p">],</span> <span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Temperature&quot;</span><span class="p">])</span>
-<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7ff336e2e260&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7fe15ad71390&gt;]</span>
 
 <span class="gp">In [47]: </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;Temperature [K]&quot;</span><span class="p">)</span>
 <span class="gh">Out[47]: </span><span class="go">Text(0, 0.5, &#39;Temperature [K]&#39;)</span>

2.10.0-dev0/examples/constructing_universe.html

@@ -278,142 +278,147 @@
 <td><p>✓</p></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/in.html#in-format"><span class="std std-ref">IN</span></a></p></td>
+<tr class="row-even"><td><p><span class="xref std std-ref">IMD</span></p></td>
+<td><p>Stream data using the IMDv3 protocol</p></td>
+<td></td>
+<td></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/in.html#in-format"><span class="std std-ref">IN</span></a></p></td>
 <td><p>FHI-aims input file</p></td>
 <td><p>✓</p></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/inpcrd.html#inpcrd-format"><span class="std std-ref">INPCRD</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/inpcrd.html#inpcrd-format"><span class="std std-ref">INPCRD</span></a></p></td>
 <td><p>AMBER restart file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/dcd_lammps.html#lammps-format"><span class="std std-ref">LAMMPS</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/dcd_lammps.html#lammps-format"><span class="std std-ref">LAMMPS</span></a></p></td>
 <td><p>a LAMMPS DCD trajectory</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/lammpsdump.html#lammpsdump-format"><span class="std std-ref">LAMMPSDUMP</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/lammpsdump.html#lammpsdump-format"><span class="std std-ref">LAMMPSDUMP</span></a></p></td>
 <td><p>LAMMPS ascii dump file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/trj.html#trj-format"><span class="std std-ref">MDCRD</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/trj.html#trj-format"><span class="std std-ref">MDCRD</span></a></p></td>
 <td><p>AMBER ASCII trajectories</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/mmtf.html#mmtf-format"><span class="std std-ref">MMTF</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/mmtf.html#mmtf-format"><span class="std std-ref">MMTF</span></a></p></td>
 <td><p>MMTF file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/mol2.html#mol2-format"><span class="std std-ref">MOL2</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/mol2.html#mol2-format"><span class="std std-ref">MOL2</span></a></p></td>
 <td><p>Tripos MOL2 file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/coor.html#coor-format"><span class="std std-ref">NAMDBIN</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/coor.html#coor-format"><span class="std std-ref">NAMDBIN</span></a></p></td>
 <td><p>NAMD binary restart file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/ncdf.html#ncdf-format"><span class="std std-ref">NC</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/ncdf.html#ncdf-format"><span class="std std-ref">NC</span></a></p></td>
 <td><p>AMBER NETCDF format</p></td>
 <td><p>✓</p></td>
 <td><p>✓</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/ncdf.html#ncdf-format"><span class="std std-ref">NCDF</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/ncdf.html#ncdf-format"><span class="std std-ref">NCDF</span></a></p></td>
 <td><p>AMBER NETCDF format</p></td>
 <td><p>✓</p></td>
 <td><p>✓</p></td>
 </tr>
-<tr class="row-even"><td><p><span class="xref std std-ref">OPENMMAPP</span></p></td>
+<tr class="row-odd"><td><p><span class="xref std std-ref">OPENMMAPP</span></p></td>
 <td><p><a class="reference external" href="https://openmm.org/">OpenMM</a> Application layer objects</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><span class="xref std std-ref">OPENMMSIMULATION</span></p></td>
+<tr class="row-even"><td><p><span class="xref std std-ref">OPENMMSIMULATION</span></p></td>
 <td><p><a class="reference external" href="https://openmm.org/">OpenMM</a> Simulation objects</p></td>
 <td><p>✓</p></td>
 <td><p>✓</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/parmed.html#parmed-format"><span class="std std-ref">PARMED</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/parmed.html#parmed-format"><span class="std std-ref">PARMED</span></a></p></td>
 <td><p><a class="reference external" href="http://parmed.github.io/ParmEd/html/index.html">ParmEd</a> Structure</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/pdb.html#pdb-format"><span class="std std-ref">PDB</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/pdb.html#pdb-format"><span class="std std-ref">PDB</span></a></p></td>
 <td><p>Standard PDB file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/pdbqt.html#pdbqt-format"><span class="std std-ref">PDBQT</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/pdbqt.html#pdbqt-format"><span class="std std-ref">PDBQT</span></a></p></td>
 <td><p>PDBQT file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/pqr.html#pqr-format"><span class="std std-ref">PQR</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/pqr.html#pqr-format"><span class="std std-ref">PQR</span></a></p></td>
 <td><p>PQR file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><span class="xref std std-ref">RDKIT</span></p></td>
+<tr class="row-odd"><td><p><span class="xref std std-ref">RDKIT</span></p></td>
 <td><p><a class="reference external" href="https://www.rdkit.org/">RDKit</a> Molecule</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/inpcrd.html#inpcrd-format"><span class="std std-ref">RESTRT</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/inpcrd.html#inpcrd-format"><span class="std std-ref">RESTRT</span></a></p></td>
 <td><p>AMBER restart file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/tng.html#tng-format"><span class="std std-ref">TNG</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/tng.html#tng-format"><span class="std std-ref">TNG</span></a></p></td>
 <td><p>Trajectory Next Generation file</p></td>
 <td><p>✓</p></td>
 <td><p>✓</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/tpr.html#tpr-format"><span class="std std-ref">TPR</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/tpr.html#tpr-format"><span class="std std-ref">TPR</span></a></p></td>
 <td><p>GROMACS run topology file</p></td>
 <td><p>✓</p></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><span class="xref std std-ref">TRC</span></p></td>
+<tr class="row-odd"><td><p><span class="xref std std-ref">TRC</span></p></td>
 <td><p>GROMOS11 trajectory file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/trj.html#trj-format"><span class="std std-ref">TRJ</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/trj.html#trj-format"><span class="std std-ref">TRJ</span></a></p></td>
 <td><p>AMBER ASCII trajectories</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/trr.html#trr-format"><span class="std std-ref">TRR</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/trr.html#trr-format"><span class="std std-ref">TRR</span></a></p></td>
 <td><p>GROMACS TRR trajectory</p></td>
 <td><p>✓</p></td>
 <td><p>✓</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/trz.html#trz-format"><span class="std std-ref">TRZ</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/trz.html#trz-format"><span class="std std-ref">TRZ</span></a></p></td>
 <td><p>IBIsCO or YASP binary trajectory</p></td>
 <td><p>✓</p></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/txyz.html#txyz-format"><span class="std std-ref">TXYZ</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/txyz.html#txyz-format"><span class="std std-ref">TXYZ</span></a></p></td>
 <td><p>Tinker file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/xpdb.html#xpdb-format"><span class="std std-ref">XPDB</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/xpdb.html#xpdb-format"><span class="std std-ref">XPDB</span></a></p></td>
 <td><p>Extended PDB file</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="reference/xtc.html#xtc-format"><span class="std std-ref">XTC</span></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="reference/xtc.html#xtc-format"><span class="std std-ref">XTC</span></a></p></td>
 <td><p>GROMACS compressed trajectory</p></td>
 <td></td>
 <td></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="reference/xyz.html#xyz-format"><span class="std std-ref">XYZ</span></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="reference/xyz.html#xyz-format"><span class="std std-ref">XYZ</span></a></p></td>
 <td><p>XYZ file</p></td>
 <td></td>
 <td></td>