rebuilt html docs for version 2.11.0-dev0 from branch develop with sphinx at 528b512

Author: github-actions

2.11.0-dev0/_modules/MDAnalysis/analysis/msd.html

@@ -212,7 +212,34 @@ <h1>Source code for MDAnalysis.analysis.msd</h1><div class="highlight"><pre>
 <span class="sd">   </span>
 <span class="sd">   In MDAnalysis you can use the </span>
 <span class="sd">   :class:`~MDAnalysis.transformations.nojump.NoJump`</span>
-<span class="sd">   transformation. </span>
+<span class="sd">   transformation to unwrap coordinates on-the-fly.</span>
+<span class="sd">    </span>
+<span class="sd">   A minimal example:</span>
+
+<span class="sd">   .. code-block:: python</span>
+<span class="sd">      </span>
+<span class="sd">      import MDAnalysis as mda</span>
+<span class="sd">      from MDAnalysis.transformations import NoJump</span>
+<span class="sd">      </span>
+<span class="sd">      u = mda.Universe(TOP, TRAJ)</span>
+<span class="sd">      </span>
+<span class="sd">      # Apply NoJump transformation to unwrap coordinates</span>
+<span class="sd">      u.trajectory.add_transformations(NoJump(u))</span>
+<span class="sd">       </span>
+<span class="sd">      # Now the trajectory is unwrapped and MSD can be computed normally:</span>
+<span class="sd">      from MDAnalysis.analysis.msd import EinsteinMSD</span>
+<span class="sd">      MSD = EinsteinMSD(u, select=&quot;all&quot;, msd_type=&quot;xyz&quot;)</span>
+<span class="sd">      MSD.run()</span>
+
+<span class="sd">   This example assumes that the trajectory contains periodic box</span>
+<span class="sd">   dimensions. If no periodic boundary information is present, box</span>
+<span class="sd">   dimensions must be defined before applying ``NoJump``, which can</span>
+<span class="sd">   be accomplished by applying the</span>
+<span class="sd">   :class:`~MDAnalysis.transformations.boxdimensions.set_dimensions`</span>
+<span class="sd">   transformation *before* the </span>
+<span class="sd">   :class:`~MDAnalysis.transformations.nojump.NoJump` transformation.</span>
+<span class="sd">   </span>
+<span class="sd">   This replaces the need to preprocess trajectories externally.</span>
 <span class="sd">   </span>
 <span class="sd">   In GROMACS, for example, this can be done using `gmx trjconv`_ with the</span>
 <span class="sd">   ``-pbc nojump`` flag.</span>

2.11.0-dev0/documentation_pages/analysis/msd.html

@@ -214,7 +214,30 @@
 back into the primary simulation cell.</p>
 <p>In MDAnalysis you can use the
 <a class="reference internal" href="../transformations/nojump.html#MDAnalysis.transformations.nojump.NoJump" title="MDAnalysis.transformations.nojump.NoJump"><code class="xref py py-class docutils literal notranslate"><span class="pre">NoJump</span></code></a>
-transformation.</p>
+transformation to unwrap coordinates on-the-fly.</p>
+<p>A minimal example:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">MDAnalysis</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">mda</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">MDAnalysis.transformations</span><span class="w"> </span><span class="kn">import</span> <span class="n">NoJump</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">TOP</span><span class="p">,</span> <span class="n">TRAJ</span><span class="p">)</span>
+
+<span class="c1"># Apply NoJump transformation to unwrap coordinates</span>
+<span class="n">u</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">add_transformations</span><span class="p">(</span><span class="n">NoJump</span><span class="p">(</span><span class="n">u</span><span class="p">))</span>
+
+<span class="c1"># Now the trajectory is unwrapped and MSD can be computed normally:</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">MDAnalysis.analysis.msd</span><span class="w"> </span><span class="kn">import</span> <span class="n">EinsteinMSD</span>
+<span class="n">MSD</span> <span class="o">=</span> <span class="n">EinsteinMSD</span><span class="p">(</span><span class="n">u</span><span class="p">,</span> <span class="n">select</span><span class="o">=</span><span class="s2">&quot;all&quot;</span><span class="p">,</span> <span class="n">msd_type</span><span class="o">=</span><span class="s2">&quot;xyz&quot;</span><span class="p">)</span>
+<span class="n">MSD</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>This example assumes that the trajectory contains periodic box
+dimensions. If no periodic boundary information is present, box
+dimensions must be defined before applying <code class="docutils literal notranslate"><span class="pre">NoJump</span></code>, which can
+be accomplished by applying the
+<a class="reference internal" href="../transformations/boxdimensions.html#MDAnalysis.transformations.boxdimensions.set_dimensions" title="MDAnalysis.transformations.boxdimensions.set_dimensions"><code class="xref py py-class docutils literal notranslate"><span class="pre">set_dimensions</span></code></a>
+transformation <em>before</em> the
+<a class="reference internal" href="../transformations/nojump.html#MDAnalysis.transformations.nojump.NoJump" title="MDAnalysis.transformations.nojump.NoJump"><code class="xref py py-class docutils literal notranslate"><span class="pre">NoJump</span></code></a> transformation.</p>
+<p>This replaces the need to preprocess trajectories externally.</p>
 <p>In GROMACS, for example, this can be done using <a class="reference external" href="https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html">gmx trjconv</a> with the
 <code class="docutils literal notranslate"><span class="pre">-pbc</span> <span class="pre">nojump</span></code> flag.</p>
 </div>

2.11.0-dev0/documentation_pages/analysis/wbridge_analysis.html

@@ -1048,15 +1048,15 @@ <h2><span class="section-number">4.4.3.8. </span>Classes<a class="headerlink" hr
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS">
-<span class="sig-name descname"><span class="pre">DEFAULT_ACCEPTORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('SD',</span> <span class="pre">'SG',</span> <span class="pre">'OH2',</span> <span class="pre">'OH',</span> <span class="pre">'OE1',</span> <span class="pre">'O',</span> <span class="pre">'ND1',</span> <span class="pre">'OC2',</span> <span class="pre">'OG1',</span> <span class="pre">'OE2',</span> <span class="pre">'OC1',</span> <span class="pre">'NE2',</span> <span class="pre">'OW',</span> <span class="pre">'OD2',</span> <span class="pre">'OG',</span> <span class="pre">'OD1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'O2',</span> <span class="pre">'OW',</span> <span class="pre">'O',</span> <span class="pre">'OS',</span> <span class="pre">'NT',</span> <span class="pre">'OY',</span> <span class="pre">'SM',</span> <span class="pre">'N'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">DEFAULT_ACCEPTORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('OE2',</span> <span class="pre">'OD2',</span> <span class="pre">'SD',</span> <span class="pre">'OG1',</span> <span class="pre">'OD1',</span> <span class="pre">'O',</span> <span class="pre">'OW',</span> <span class="pre">'OH',</span> <span class="pre">'OC2',</span> <span class="pre">'OC1',</span> <span class="pre">'NE2',</span> <span class="pre">'ND1',</span> <span class="pre">'OH2',</span> <span class="pre">'SG',</span> <span class="pre">'OG',</span> <span class="pre">'OE1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'OS',</span> <span class="pre">'SM',</span> <span class="pre">'N',</span> <span class="pre">'OY',</span> <span class="pre">'OW',</span> <span class="pre">'O',</span> <span class="pre">'NT',</span> <span class="pre">'O2'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Link to this definition"></a></dt>
 <dd><p>default atom names that are treated as hydrogen <em>acceptors</em>
 (see <a class="reference internal" href="#default-atom-names-for-water-bridge-analysis"><span class="std std-ref">Default heavy atom names for CHARMM27 force field.</span></a>);
 use the keyword <cite>acceptors</cite> to add a list of additional acceptor names.</p>
 </dd></dl>
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS">
-<span class="sig-name descname"><span class="pre">DEFAULT_DONORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('SG',</span> <span class="pre">'OH2',</span> <span class="pre">'NH1',</span> <span class="pre">'OH',</span> <span class="pre">'NE',</span> <span class="pre">'NE2',</span> <span class="pre">'OW',</span> <span class="pre">'NH2',</span> <span class="pre">'OG',</span> <span class="pre">'NZ',</span> <span class="pre">'NE1',</span> <span class="pre">'ND2',</span> <span class="pre">'ND1',</span> <span class="pre">'N',</span> <span class="pre">'OG1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'OH',</span> <span class="pre">'N',</span> <span class="pre">'OW',</span> <span class="pre">'N3'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">DEFAULT_DONORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('OH',</span> <span class="pre">'OG1',</span> <span class="pre">'NE2',</span> <span class="pre">'NH2',</span> <span class="pre">'NE',</span> <span class="pre">'ND2',</span> <span class="pre">'ND1',</span> <span class="pre">'OH2',</span> <span class="pre">'SG',</span> <span class="pre">'N',</span> <span class="pre">'NH1',</span> <span class="pre">'NZ',</span> <span class="pre">'NE1',</span> <span class="pre">'OG',</span> <span class="pre">'OW'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N',</span> <span class="pre">'N3',</span> <span class="pre">'OH',</span> <span class="pre">'NT',</span> <span class="pre">'OW'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS" title="Link to this definition"></a></dt>
 <dd><p>default heavy atom names whose hydrogens are treated as <em>donors</em>
 (see <a class="reference internal" href="#default-atom-names-for-water-bridge-analysis"><span class="std std-ref">Default heavy atom names for CHARMM27 force field.</span></a>);
 use the keyword <cite>donors</cite> to add a list of additional donor names.</p>

2.11.0-dev0/searchindex.js

@@ -212,7 +212,34 @@ <h1>Source code for MDAnalysis.analysis.msd</h1><div class="highlight"><pre>
 <span class="sd">   </span>
 <span class="sd">   In MDAnalysis you can use the </span>
 <span class="sd">   :class:`~MDAnalysis.transformations.nojump.NoJump`</span>
-<span class="sd">   transformation. </span>
+<span class="sd">   transformation to unwrap coordinates on-the-fly.</span>
+<span class="sd">    </span>
+<span class="sd">   A minimal example:</span>
+
+<span class="sd">   .. code-block:: python</span>
+<span class="sd">      </span>
+<span class="sd">      import MDAnalysis as mda</span>
+<span class="sd">      from MDAnalysis.transformations import NoJump</span>
+<span class="sd">      </span>
+<span class="sd">      u = mda.Universe(TOP, TRAJ)</span>
+<span class="sd">      </span>
+<span class="sd">      # Apply NoJump transformation to unwrap coordinates</span>
+<span class="sd">      u.trajectory.add_transformations(NoJump(u))</span>
+<span class="sd">       </span>
+<span class="sd">      # Now the trajectory is unwrapped and MSD can be computed normally:</span>
+<span class="sd">      from MDAnalysis.analysis.msd import EinsteinMSD</span>
+<span class="sd">      MSD = EinsteinMSD(u, select=&quot;all&quot;, msd_type=&quot;xyz&quot;)</span>
+<span class="sd">      MSD.run()</span>
+
+<span class="sd">   This example assumes that the trajectory contains periodic box</span>
+<span class="sd">   dimensions. If no periodic boundary information is present, box</span>
+<span class="sd">   dimensions must be defined before applying ``NoJump``, which can</span>
+<span class="sd">   be accomplished by applying the</span>
+<span class="sd">   :class:`~MDAnalysis.transformations.boxdimensions.set_dimensions`</span>
+<span class="sd">   transformation *before* the </span>
+<span class="sd">   :class:`~MDAnalysis.transformations.nojump.NoJump` transformation.</span>
+<span class="sd">   </span>
+<span class="sd">   This replaces the need to preprocess trajectories externally.</span>
 <span class="sd">   </span>
 <span class="sd">   In GROMACS, for example, this can be done using `gmx trjconv`_ with the</span>
 <span class="sd">   ``-pbc nojump`` flag.</span>

dev/_modules/MDAnalysis/analysis/msd.html

@@ -214,7 +214,30 @@
 back into the primary simulation cell.</p>
 <p>In MDAnalysis you can use the
 <a class="reference internal" href="../transformations/nojump.html#MDAnalysis.transformations.nojump.NoJump" title="MDAnalysis.transformations.nojump.NoJump"><code class="xref py py-class docutils literal notranslate"><span class="pre">NoJump</span></code></a>
-transformation.</p>
+transformation to unwrap coordinates on-the-fly.</p>
+<p>A minimal example:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">MDAnalysis</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">mda</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">MDAnalysis.transformations</span><span class="w"> </span><span class="kn">import</span> <span class="n">NoJump</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">TOP</span><span class="p">,</span> <span class="n">TRAJ</span><span class="p">)</span>
+
+<span class="c1"># Apply NoJump transformation to unwrap coordinates</span>
+<span class="n">u</span><span class="o">.</span><span class="n">trajectory</span><span class="o">.</span><span class="n">add_transformations</span><span class="p">(</span><span class="n">NoJump</span><span class="p">(</span><span class="n">u</span><span class="p">))</span>
+
+<span class="c1"># Now the trajectory is unwrapped and MSD can be computed normally:</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">MDAnalysis.analysis.msd</span><span class="w"> </span><span class="kn">import</span> <span class="n">EinsteinMSD</span>
+<span class="n">MSD</span> <span class="o">=</span> <span class="n">EinsteinMSD</span><span class="p">(</span><span class="n">u</span><span class="p">,</span> <span class="n">select</span><span class="o">=</span><span class="s2">&quot;all&quot;</span><span class="p">,</span> <span class="n">msd_type</span><span class="o">=</span><span class="s2">&quot;xyz&quot;</span><span class="p">)</span>
+<span class="n">MSD</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>This example assumes that the trajectory contains periodic box
+dimensions. If no periodic boundary information is present, box
+dimensions must be defined before applying <code class="docutils literal notranslate"><span class="pre">NoJump</span></code>, which can
+be accomplished by applying the
+<a class="reference internal" href="../transformations/boxdimensions.html#MDAnalysis.transformations.boxdimensions.set_dimensions" title="MDAnalysis.transformations.boxdimensions.set_dimensions"><code class="xref py py-class docutils literal notranslate"><span class="pre">set_dimensions</span></code></a>
+transformation <em>before</em> the
+<a class="reference internal" href="../transformations/nojump.html#MDAnalysis.transformations.nojump.NoJump" title="MDAnalysis.transformations.nojump.NoJump"><code class="xref py py-class docutils literal notranslate"><span class="pre">NoJump</span></code></a> transformation.</p>
+<p>This replaces the need to preprocess trajectories externally.</p>
 <p>In GROMACS, for example, this can be done using <a class="reference external" href="https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html">gmx trjconv</a> with the
 <code class="docutils literal notranslate"><span class="pre">-pbc</span> <span class="pre">nojump</span></code> flag.</p>
 </div>