rebuilt html docs for version 2.6.0-dev0 from branch develop with sph…

…inx at bd3c14c

2.6.0-dev0/_modules/MDAnalysis/units.html

@@ -269,6 +269,23 @@ <h1>Source code for MDAnalysis.units</h1><div class="highlight"><pre>
 
 <span class="sd">&quot;&quot;&quot;</span>
 
+<span class="kn">import</span> <span class="nn">warnings</span>
+
+
+<span class="c1"># Remove in 2.8.0</span>
+<span class="k">class</span> <span class="nc">DeprecatedKeyAccessDict</span><span class="p">(</span><span class="nb">dict</span><span class="p">):</span>
+    <span class="n">deprecated_kB</span> <span class="o">=</span> <span class="s1">&#39;Boltzman_constant&#39;</span>
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">key</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">deprecated_kB</span><span class="p">:</span>
+            <span class="n">wmsg</span> <span class="o">=</span> <span class="p">(</span><span class="s2">&quot;Please use &#39;Boltzmann_constant&#39; henceforth. The key &quot;</span>
+                    <span class="s2">&quot;&#39;Boltzman_constant&#39; was a typo and will be removed &quot;</span>
+                    <span class="s2">&quot;in MDAnalysis 2.8.0.&quot;</span><span class="p">)</span>
+            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="n">wmsg</span><span class="p">,</span> <span class="ne">DeprecationWarning</span><span class="p">)</span>
+            <span class="n">key</span> <span class="o">=</span> <span class="s1">&#39;Boltzmann_constant&#39;</span>
+        <span class="k">return</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__getitem__</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+
 <span class="c1">#</span>
 <span class="c1"># NOTE: Whenever a constant is added to the constants dict, you also</span>
 <span class="c1">#       MUST add an appropriate entry to</span>
@@ -286,13 +303,13 @@ <h1>Source code for MDAnalysis.units</h1><div class="highlight"><pre>
 <span class="c1">#:    http://physics.nist.gov/Pubs/SP811/appenB8.html#C</span>
 <span class="c1">#:</span>
 <span class="c1">#: .. versionadded:: 0.9.0</span>
-<span class="n">constants</span> <span class="o">=</span> <span class="p">{</span>
+<span class="n">constants</span> <span class="o">=</span> <span class="n">DeprecatedKeyAccessDict</span><span class="p">({</span>
     <span class="s1">&#39;N_Avogadro&#39;</span><span class="p">:</span> <span class="mf">6.02214129e+23</span><span class="p">,</span>          <span class="c1"># mol**-1</span>
     <span class="s1">&#39;elementary_charge&#39;</span><span class="p">:</span> <span class="mf">1.602176565e-19</span><span class="p">,</span>  <span class="c1"># As</span>
     <span class="s1">&#39;calorie&#39;</span><span class="p">:</span> <span class="mf">4.184</span><span class="p">,</span>                      <span class="c1"># J</span>
     <span class="s1">&#39;Boltzmann_constant&#39;</span><span class="p">:</span> <span class="mf">8.314462159e-3</span><span class="p">,</span>   <span class="c1"># KJ (mol K)**-1</span>
     <span class="s1">&#39;electric_constant&#39;</span><span class="p">:</span> <span class="mf">5.526350e-3</span><span class="p">,</span>      <span class="c1"># As (Angstroms Volts)**-1</span>
-<span class="p">}</span>
+<span class="p">})</span>
 
 <span class="c1">#: The basic unit of *length* in MDAnalysis is the Angstrom.</span>
 <span class="c1">#: Conversion factors between the base unit and other lengthUnits *x* are stored.</span>

2.6.0-dev0/documentation_pages/analysis/wbridge_analysis.html

@@ -1017,15 +1017,15 @@ <h2><span class="section-number">4.3.3.8. </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">('OD1',</span> <span class="pre">'OD2',</span> <span class="pre">'SD',</span> <span class="pre">'OC2',</span> <span class="pre">'OW',</span> <span class="pre">'ND1',</span> <span class="pre">'OG1',</span> <span class="pre">'OE1',</span> <span class="pre">'SG',</span> <span class="pre">'OH2',</span> <span class="pre">'OE2',</span> <span class="pre">'O',</span> <span class="pre">'NE2',</span> <span class="pre">'OH',</span> <span class="pre">'OC1',</span> <span class="pre">'OG'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('O2',</span> <span class="pre">'OY',</span> <span class="pre">'O',</span> <span class="pre">'OW',</span> <span class="pre">'OH',</span> <span class="pre">'NT',</span> <span class="pre">'SM',</span> <span class="pre">'N',</span> <span class="pre">'OS'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Permalink 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">('SG',</span> <span class="pre">'OD2',</span> <span class="pre">'OE1',</span> <span class="pre">'OE2',</span> <span class="pre">'OC1',</span> <span class="pre">'OC2',</span> <span class="pre">'OG',</span> <span class="pre">'OG1',</span> <span class="pre">'O',</span> <span class="pre">'OH2',</span> <span class="pre">'OW',</span> <span class="pre">'NE2',</span> <span class="pre">'OH',</span> <span class="pre">'OD1',</span> <span class="pre">'SD',</span> <span class="pre">'ND1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OY',</span> <span class="pre">'O2',</span> <span class="pre">'OS',</span> <span class="pre">'NT',</span> <span class="pre">'N',</span> <span class="pre">'OW',</span> <span class="pre">'SM',</span> <span class="pre">'OH',</span> <span class="pre">'O'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Permalink 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">('NE',</span> <span class="pre">'NZ',</span> <span class="pre">'OH2',</span> <span class="pre">'ND2',</span> <span class="pre">'NH1',</span> <span class="pre">'NE2',</span> <span class="pre">'OW',</span> <span class="pre">'NE1',</span> <span class="pre">'ND1',</span> <span class="pre">'OG1',</span> <span class="pre">'NH2',</span> <span class="pre">'OH',</span> <span class="pre">'N',</span> <span class="pre">'OG',</span> <span class="pre">'SG'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OW',</span> <span class="pre">'OH',</span> <span class="pre">'NT',</span> <span class="pre">'N',</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="Permalink 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">('SG',</span> <span class="pre">'OH2',</span> <span class="pre">'NE',</span> <span class="pre">'NE1',</span> <span class="pre">'ND2',</span> <span class="pre">'N',</span> <span class="pre">'NZ',</span> <span class="pre">'OW',</span> <span class="pre">'NE2',</span> <span class="pre">'OG',</span> <span class="pre">'NH2',</span> <span class="pre">'OH',</span> <span class="pre">'NH1',</span> <span class="pre">'OG1',</span> <span class="pre">'ND1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N',</span> <span class="pre">'OW',</span> <span class="pre">'OH',</span> <span class="pre">'N3',</span> <span class="pre">'NT'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS" title="Permalink 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>

2.6.0-dev0/index.html

@@ -103,7 +103,7 @@ <h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentatio
 <dd class="field-odd"><p>2.6.0-dev0</p>
 </dd>
 <dt class="field-even">Date</dt>
-<dd class="field-even"><p>Aug 09, 2023</p>
+<dd class="field-even"><p>Aug 10, 2023</p>
 </dd>
 </dl>
 <p><strong>MDAnalysis</strong> (<a class="reference external" href="https://www.mdanalysis.org">www.mdanalysis.org</a>) is an object-oriented python

dev/_modules/MDAnalysis/units.html

@@ -269,6 +269,23 @@ <h1>Source code for MDAnalysis.units</h1><div class="highlight"><pre>
 
 <span class="sd">&quot;&quot;&quot;</span>
 
+<span class="kn">import</span> <span class="nn">warnings</span>
+
+
+<span class="c1"># Remove in 2.8.0</span>
+<span class="k">class</span> <span class="nc">DeprecatedKeyAccessDict</span><span class="p">(</span><span class="nb">dict</span><span class="p">):</span>
+    <span class="n">deprecated_kB</span> <span class="o">=</span> <span class="s1">&#39;Boltzman_constant&#39;</span>
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">key</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">deprecated_kB</span><span class="p">:</span>
+            <span class="n">wmsg</span> <span class="o">=</span> <span class="p">(</span><span class="s2">&quot;Please use &#39;Boltzmann_constant&#39; henceforth. The key &quot;</span>
+                    <span class="s2">&quot;&#39;Boltzman_constant&#39; was a typo and will be removed &quot;</span>
+                    <span class="s2">&quot;in MDAnalysis 2.8.0.&quot;</span><span class="p">)</span>
+            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="n">wmsg</span><span class="p">,</span> <span class="ne">DeprecationWarning</span><span class="p">)</span>
+            <span class="n">key</span> <span class="o">=</span> <span class="s1">&#39;Boltzmann_constant&#39;</span>
+        <span class="k">return</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__getitem__</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+
 <span class="c1">#</span>
 <span class="c1"># NOTE: Whenever a constant is added to the constants dict, you also</span>
 <span class="c1">#       MUST add an appropriate entry to</span>
@@ -286,13 +303,13 @@ <h1>Source code for MDAnalysis.units</h1><div class="highlight"><pre>
 <span class="c1">#:    http://physics.nist.gov/Pubs/SP811/appenB8.html#C</span>
 <span class="c1">#:</span>
 <span class="c1">#: .. versionadded:: 0.9.0</span>
-<span class="n">constants</span> <span class="o">=</span> <span class="p">{</span>
+<span class="n">constants</span> <span class="o">=</span> <span class="n">DeprecatedKeyAccessDict</span><span class="p">({</span>
     <span class="s1">&#39;N_Avogadro&#39;</span><span class="p">:</span> <span class="mf">6.02214129e+23</span><span class="p">,</span>          <span class="c1"># mol**-1</span>
     <span class="s1">&#39;elementary_charge&#39;</span><span class="p">:</span> <span class="mf">1.602176565e-19</span><span class="p">,</span>  <span class="c1"># As</span>
     <span class="s1">&#39;calorie&#39;</span><span class="p">:</span> <span class="mf">4.184</span><span class="p">,</span>                      <span class="c1"># J</span>
     <span class="s1">&#39;Boltzmann_constant&#39;</span><span class="p">:</span> <span class="mf">8.314462159e-3</span><span class="p">,</span>   <span class="c1"># KJ (mol K)**-1</span>
     <span class="s1">&#39;electric_constant&#39;</span><span class="p">:</span> <span class="mf">5.526350e-3</span><span class="p">,</span>      <span class="c1"># As (Angstroms Volts)**-1</span>
-<span class="p">}</span>
+<span class="p">})</span>
 
 <span class="c1">#: The basic unit of *length* in MDAnalysis is the Angstrom.</span>
 <span class="c1">#: Conversion factors between the base unit and other lengthUnits *x* are stored.</span>

dev/documentation_pages/analysis/wbridge_analysis.html

@@ -1017,15 +1017,15 @@ <h2><span class="section-number">4.3.3.8. </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">('OD1',</span> <span class="pre">'OD2',</span> <span class="pre">'SD',</span> <span class="pre">'OC2',</span> <span class="pre">'OW',</span> <span class="pre">'ND1',</span> <span class="pre">'OG1',</span> <span class="pre">'OE1',</span> <span class="pre">'SG',</span> <span class="pre">'OH2',</span> <span class="pre">'OE2',</span> <span class="pre">'O',</span> <span class="pre">'NE2',</span> <span class="pre">'OH',</span> <span class="pre">'OC1',</span> <span class="pre">'OG'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('O2',</span> <span class="pre">'OY',</span> <span class="pre">'O',</span> <span class="pre">'OW',</span> <span class="pre">'OH',</span> <span class="pre">'NT',</span> <span class="pre">'SM',</span> <span class="pre">'N',</span> <span class="pre">'OS'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Permalink 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">('SG',</span> <span class="pre">'OD2',</span> <span class="pre">'OE1',</span> <span class="pre">'OE2',</span> <span class="pre">'OC1',</span> <span class="pre">'OC2',</span> <span class="pre">'OG',</span> <span class="pre">'OG1',</span> <span class="pre">'O',</span> <span class="pre">'OH2',</span> <span class="pre">'OW',</span> <span class="pre">'NE2',</span> <span class="pre">'OH',</span> <span class="pre">'OD1',</span> <span class="pre">'SD',</span> <span class="pre">'ND1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OY',</span> <span class="pre">'O2',</span> <span class="pre">'OS',</span> <span class="pre">'NT',</span> <span class="pre">'N',</span> <span class="pre">'OW',</span> <span class="pre">'SM',</span> <span class="pre">'OH',</span> <span class="pre">'O'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Permalink 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">('NE',</span> <span class="pre">'NZ',</span> <span class="pre">'OH2',</span> <span class="pre">'ND2',</span> <span class="pre">'NH1',</span> <span class="pre">'NE2',</span> <span class="pre">'OW',</span> <span class="pre">'NE1',</span> <span class="pre">'ND1',</span> <span class="pre">'OG1',</span> <span class="pre">'NH2',</span> <span class="pre">'OH',</span> <span class="pre">'N',</span> <span class="pre">'OG',</span> <span class="pre">'SG'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OW',</span> <span class="pre">'OH',</span> <span class="pre">'NT',</span> <span class="pre">'N',</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="Permalink 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">('SG',</span> <span class="pre">'OH2',</span> <span class="pre">'NE',</span> <span class="pre">'NE1',</span> <span class="pre">'ND2',</span> <span class="pre">'N',</span> <span class="pre">'NZ',</span> <span class="pre">'OW',</span> <span class="pre">'NE2',</span> <span class="pre">'OG',</span> <span class="pre">'NH2',</span> <span class="pre">'OH',</span> <span class="pre">'NH1',</span> <span class="pre">'OG1',</span> <span class="pre">'ND1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N',</span> <span class="pre">'OW',</span> <span class="pre">'OH',</span> <span class="pre">'N3',</span> <span class="pre">'NT'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS" title="Permalink 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>

dev/index.html

@@ -103,7 +103,7 @@ <h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentatio
 <dd class="field-odd"><p>2.6.0-dev0</p>
 </dd>
 <dt class="field-even">Date</dt>
-<dd class="field-even"><p>Aug 09, 2023</p>
+<dd class="field-even"><p>Aug 10, 2023</p>
 </dd>
 </dl>
 <p><strong>MDAnalysis</strong> (<a class="reference external" href="https://www.mdanalysis.org">www.mdanalysis.org</a>) is an object-oriented python