rebuilt html docs for version 2.8.0-dev0 from branch develop with sph…

…inx at 1e95ff7

2.8.0-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="39e091c102e442148eb0d6025d718c72" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="5d7ee1365b08472d8692eb48addd8237" 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>

2.8.0-dev0/formats/auxiliary.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 0x7fe1136b7190&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f3350c5dc00&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 0x7fe11833b5e0&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f33515d3490&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="nn">matplotlib.pyplot</span> <span class="k">as</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 0x7fe113be2680&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f334bdfad10&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>

2.8.0-dev0/formats/index.html

@@ -604,12 +604,12 @@
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/data.html#data-format"><span class="std std-ref">DATA</span></a></p></td>
 <td><p>LAMMPS data file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, types</p></td>
 <td></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="reference/dms.html#dms-format"><span class="std std-ref">DMS</span></a></p></td>
 <td><p>DESRES Molecular Structure file</p></td>
-<td><p>atomnums, bonds, chainIDs, charges, names, resnames</p></td>
+<td><p>atomnums, bonds, chainIDs, charges, masses, names, resnames</p></td>
 <td><p>types</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/gms.html#gms-format"><span class="std std-ref">GMS</span></a></p></td>
@@ -624,7 +624,7 @@
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/gsd.html#gsd-format"><span class="std std-ref">GSD</span></a></p></td>
 <td><p>HOOMD GSD file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers, names, radii, resnames</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, names, radii, resnames, types</p></td>
 <td></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="reference/config.html#history-format"><span class="std std-ref">HISTORY</span></a></p></td>
@@ -639,17 +639,17 @@
 </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>
 <td><p>LAMMPS ascii dump file</p></td>
+<td><p>masses, types</p></td>
 <td></td>
-<td><p>masses</p></td>
 </tr>
 <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><p>altLocs, bonds, charges, icodes, models, names, occupancies, resnames, tempfactors</p></td>
+<td><p>altLocs, bonds, charges, icodes, models, names, occupancies, resnames, tempfactors, types</p></td>
 <td><p>masses</p></td>
 </tr>
 <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><p>bonds, charges, elements, names, resnames</p></td>
+<td><p>bonds, charges, elements, names, resnames, types</p></td>
 <td><p>masses</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/pdb.html#pdb-format"><span class="std std-ref">PDB, ENT</span></a></p></td>
@@ -659,7 +659,7 @@
 </tr>
 <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><p>altLocs, chainIDs, charges, icodes, names, occupancies, record_types, resnames, tempfactors</p></td>
+<td><p>altLocs, chainIDs, charges, icodes, names, occupancies, record_types, resnames, tempfactors, types</p></td>
 <td><p>masses</p></td>
 </tr>
 <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>
@@ -669,27 +669,27 @@
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="reference/psf.html#psf-format"><span class="std std-ref">PSF</span></a></p></td>
 <td><p>CHARMM, NAMD, or XPLOR PSF file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers, names, resnames</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, names, resnames, types</p></td>
 <td></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/top.html#top-format"><span class="std std-ref">TOP, PRMTOP, PARM7</span></a></p></td>
 <td><p>AMBER topology file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, names, resnames, type_indices, types</p></td>
 <td></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>
 <td><p>GROMACS run topology file</p></td>
-<td><p>angles, bonds, chainIDs, charges, dihedrals, elements, impropers, molnums, moltypes, names, resnames</p></td>
+<td><p>angles, bonds, chainIDs, charges, dihedrals, elements, impropers, masses, molnums, moltypes, names, resnames, types</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, ARC</span></a></p></td>
 <td><p>Tinker file</p></td>
-<td><p>bonds, elements, names</p></td>
+<td><p>bonds, elements, names, types</p></td>
 <td><p>masses</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="reference/xml.html#xml-format"><span class="std std-ref">XML</span></a></p></td>
 <td><p>HOOMD XML file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers, radii</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, radii, types</p></td>
 <td></td>
 </tr>
 <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>

2.8.0-dev0/formats/topology.html

@@ -210,12 +210,12 @@ <h1>Topology<a class="headerlink" href="#topology" title="Link to this heading">
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/data.html#data-format"><span class="std std-ref">DATA</span></a></p></td>
 <td><p>LAMMPS data file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, types</p></td>
 <td></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="reference/dms.html#dms-format"><span class="std std-ref">DMS</span></a></p></td>
 <td><p>DESRES Molecular Structure file</p></td>
-<td><p>atomnums, bonds, chainIDs, charges, names, resnames</p></td>
+<td><p>atomnums, bonds, chainIDs, charges, masses, names, resnames</p></td>
 <td><p>types</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/gms.html#gms-format"><span class="std std-ref">GMS</span></a></p></td>
@@ -230,7 +230,7 @@ <h1>Topology<a class="headerlink" href="#topology" title="Link to this heading">
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/gsd.html#gsd-format"><span class="std std-ref">GSD</span></a></p></td>
 <td><p>HOOMD GSD file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers, names, radii, resnames</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, names, radii, resnames, types</p></td>
 <td></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="reference/config.html#history-format"><span class="std std-ref">HISTORY</span></a></p></td>
@@ -245,17 +245,17 @@ <h1>Topology<a class="headerlink" href="#topology" title="Link to this heading">
 </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>
 <td><p>LAMMPS ascii dump file</p></td>
+<td><p>masses, types</p></td>
 <td></td>
-<td><p>masses</p></td>
 </tr>
 <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><p>altLocs, bonds, charges, icodes, models, names, occupancies, resnames, tempfactors</p></td>
+<td><p>altLocs, bonds, charges, icodes, models, names, occupancies, resnames, tempfactors, types</p></td>
 <td><p>masses</p></td>
 </tr>
 <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><p>bonds, charges, elements, names, resnames</p></td>
+<td><p>bonds, charges, elements, names, resnames, types</p></td>
 <td><p>masses</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/pdb.html#pdb-format"><span class="std std-ref">PDB, ENT</span></a></p></td>
@@ -265,7 +265,7 @@ <h1>Topology<a class="headerlink" href="#topology" title="Link to this heading">
 </tr>
 <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><p>altLocs, chainIDs, charges, icodes, names, occupancies, record_types, resnames, tempfactors</p></td>
+<td><p>altLocs, chainIDs, charges, icodes, names, occupancies, record_types, resnames, tempfactors, types</p></td>
 <td><p>masses</p></td>
 </tr>
 <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>
@@ -275,27 +275,27 @@ <h1>Topology<a class="headerlink" href="#topology" title="Link to this heading">
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="reference/psf.html#psf-format"><span class="std std-ref">PSF</span></a></p></td>
 <td><p>CHARMM, NAMD, or XPLOR PSF file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers, names, resnames</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, names, resnames, types</p></td>
 <td></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="reference/top.html#top-format"><span class="std std-ref">TOP, PRMTOP, PARM7</span></a></p></td>
 <td><p>AMBER topology file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, names, resnames, type_indices, types</p></td>
 <td></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>
 <td><p>GROMACS run topology file</p></td>
-<td><p>angles, bonds, chainIDs, charges, dihedrals, elements, impropers, molnums, moltypes, names, resnames</p></td>
+<td><p>angles, bonds, chainIDs, charges, dihedrals, elements, impropers, masses, molnums, moltypes, names, resnames, types</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, ARC</span></a></p></td>
 <td><p>Tinker file</p></td>
-<td><p>bonds, elements, names</p></td>
+<td><p>bonds, elements, names, types</p></td>
 <td><p>masses</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="reference/xml.html#xml-format"><span class="std std-ref">XML</span></a></p></td>
 <td><p>HOOMD XML file</p></td>
-<td><p>angles, bonds, charges, dihedrals, impropers, radii</p></td>
+<td><p>angles, bonds, charges, dihedrals, impropers, masses, radii, types</p></td>
 <td></td>
 </tr>
 <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>

2.8.0-dev0/index.html

@@ -192,7 +192,7 @@
   <section id="welcome-to-mdanalysis-user-guide-s-documentation">
 <h1>Welcome to MDAnalysis User Guide’s documentation!<a class="headerlink" href="#welcome-to-mdanalysis-user-guide-s-documentation" title="Link to this heading"></a></h1>
 <p><strong>MDAnalysis version:</strong> 2.8.0-dev0</p>
-<p><strong>Last updated:</strong> Oct 18, 2024</p>
+<p><strong>Last updated:</strong> Oct 22, 2024</p>
 <p><strong>MDAnalysis</strong> (<a class="reference external" href="https://www.mdanalysis.org">www.mdanalysis.org</a>) is a Python
 toolkit to analyse molecular dynamics files and trajectories in <a class="reference internal" href="formats/index.html#formats"><span class="std std-ref">many popular formats</span></a>. MDAnalysis can write
 most of these formats, too, together with atom selections for use in <a class="reference internal" href="formats/selection_exporters.html#selection-exporters"><span class="std std-ref">visualisation tools or other analysis programs</span></a>.

2.8.0-dev0/reading_and_writing.html

@@ -320,27 +320,27 @@ <h4>Building trajectories in memory<a class="headerlink" href="#building-traject
 
 <span class="gp">In [16]: </span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
 <span class="gh">Out[16]: </span>
-<span class="go">array([[0.03684666, 0.8914058 , 0.75454605],</span>
-<span class="go">       [0.08306053, 0.8529569 , 0.8825315 ],</span>
-<span class="go">       [0.29624537, 0.49249718, 0.9363721 ],</span>
+<span class="go">array([[0.5550874 , 0.47308663, 0.672447  ],</span>
+<span class="go">       [0.45735562, 0.7299391 , 0.09616397],</span>
+<span class="go">       [0.64312583, 0.36355793, 0.68103373],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.19385266, 0.30602154, 0.2795746 ],</span>
-<span class="go">       [0.8865553 , 0.11298756, 0.6689483 ],</span>
-<span class="go">       [0.36228254, 0.42016888, 0.03131042]], dtype=float32)</span>
+<span class="go">       [0.13389875, 0.16191345, 0.38977104],</span>
+<span class="go">       [0.78060484, 0.12310851, 0.11195699],</span>
+<span class="go">       [0.8411623 , 0.918963  , 0.60834426]], dtype=float32)</span>
 </pre></div>
 </div>
 <p>or they can be directly passed in when creating a Universe.</p>
 <div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [17]: </span><span class="n">universe2</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">PDB</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="n">MemoryReader</span><span class="p">)</span>
 
 <span class="gp">In [18]: </span><span class="n">universe2</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
 <span class="gh">Out[18]: </span>
-<span class="go">array([[0.03684666, 0.8914058 , 0.75454605],</span>
-<span class="go">       [0.08306053, 0.8529569 , 0.8825315 ],</span>
-<span class="go">       [0.29624537, 0.49249718, 0.9363721 ],</span>
+<span class="go">array([[0.5550874 , 0.47308663, 0.672447  ],</span>
+<span class="go">       [0.45735562, 0.7299391 , 0.09616397],</span>
+<span class="go">       [0.64312583, 0.36355793, 0.68103373],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.19385266, 0.30602154, 0.2795746 ],</span>
-<span class="go">       [0.8865553 , 0.11298756, 0.6689483 ],</span>
-<span class="go">       [0.36228254, 0.42016888, 0.03131042]], dtype=float32)</span>
+<span class="go">       [0.13389875, 0.16191345, 0.38977104],</span>
+<span class="go">       [0.78060484, 0.12310851, 0.11195699],</span>
+<span class="go">       [0.8411623 , 0.918963  , 0.60834426]], dtype=float32)</span>
 </pre></div>
 </div>
 </section>