Updated website for the 2023.5.1 release

OpenBioSim · Jan 2, 2024 · 370de06 · 370de06
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diff --git a/_modules/index.html b/_modules/index.html
@@ -517,7 +517,7 @@ <h1>All modules for which code is available</h1>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -532,7 +532,7 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire.html b/_modules/sire.html
@@ -1153,7 +1153,7 @@ <h1>Source code for sire</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -1168,7 +1168,7 @@ <h1>Source code for sire</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/_load.html b/_modules/sire/_load.html
@@ -1335,7 +1335,7 @@ <h1>Source code for sire._load</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -1350,7 +1350,7 @@ <h1>Source code for sire._load</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/_match.html b/_modules/sire/_match.html
@@ -440,7 +440,7 @@ <h1>Source code for sire._match</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -455,7 +455,7 @@ <h1>Source code for sire._match</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/_measure.html b/_modules/sire/_measure.html
@@ -647,7 +647,7 @@ <h1>Source code for sire._measure</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -662,7 +662,7 @@ <h1>Source code for sire._measure</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/_parallel.html b/_modules/sire/_parallel.html
@@ -479,7 +479,7 @@ <h1>Source code for sire._parallel</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -494,7 +494,7 @@ <h1>Source code for sire._parallel</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/_pythonize.html b/_modules/sire/_pythonize.html
@@ -904,7 +904,7 @@ <h1>Source code for sire._pythonize</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -919,7 +919,7 @@ <h1>Source code for sire._pythonize</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/base.html b/_modules/sire/base.html
@@ -618,7 +618,7 @@ <h1>Source code for sire.base</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -633,7 +633,7 @@ <h1>Source code for sire.base</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/convert.html b/_modules/sire/convert.html
@@ -752,7 +752,7 @@ <h1>Source code for sire.convert</h1><div class="highlight"><pre>
     <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
         <span class="k">raise</span> <span class="ne">ModuleNotFoundError</span><span class="p">(</span>
             <span class="s2">&quot;openmm is not available. Please install via &quot;</span>
-            <span class="s2">&quot;&#39;mamba install -c conda-forge openmm&#39;&quot;</span>
+            <span class="s2">&quot;&#39;conda install -c conda-forge openmm&#39;&quot;</span>
         <span class="p">)</span>
 
     <span class="kn">from</span> <span class="nn">..base</span> <span class="kn">import</span> <span class="n">create_map</span>
@@ -806,7 +806,7 @@ <h1>Source code for sire.convert</h1><div class="highlight"><pre>
     <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
         <span class="k">raise</span> <span class="ne">ModuleNotFoundError</span><span class="p">(</span>
             <span class="s2">&quot;openmm is not available. Please install via &quot;</span>
-            <span class="s2">&quot;&#39;mamba install -c conda-forge openmm&#39;&quot;</span>
+            <span class="s2">&quot;&#39;conda install -c conda-forge openmm&#39;&quot;</span>
         <span class="p">)</span>
 
     <span class="n">mols</span> <span class="o">=</span> <span class="n">_sire_to_openmm</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="nb">map</span><span class="o">=</span><span class="nb">map</span><span class="p">)</span>
@@ -830,7 +830,7 @@ <h1>Source code for sire.convert</h1><div class="highlight"><pre>
     <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
         <span class="k">raise</span> <span class="ne">ModuleNotFoundError</span><span class="p">(</span>
             <span class="s2">&quot;rdkit is not available. Please install via &quot;</span>
-            <span class="s2">&quot;&#39;mamba install -c conda-forge rdkit&#39;&quot;</span>
+            <span class="s2">&quot;&#39;conda install -c conda-forge rdkit&#39;&quot;</span>
         <span class="p">)</span>
 
     <span class="kn">from</span> <span class="nn">..base</span> <span class="kn">import</span> <span class="n">create_map</span>
@@ -864,7 +864,7 @@ <h1>Source code for sire.convert</h1><div class="highlight"><pre>
     <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
         <span class="k">raise</span> <span class="ne">ModuleNotFoundError</span><span class="p">(</span>
             <span class="s2">&quot;rdkit is not available. Please install via &quot;</span>
-            <span class="s2">&quot;&#39;mamba install -c conda-forge rdkit&#39;&quot;</span>
+            <span class="s2">&quot;&#39;conda install -c conda-forge rdkit&#39;&quot;</span>
         <span class="p">)</span>
 
     <span class="kn">from</span> <span class="nn">..base</span> <span class="kn">import</span> <span class="n">create_map</span>
@@ -891,7 +891,7 @@ <h1>Source code for sire.convert</h1><div class="highlight"><pre>
     <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
         <span class="k">raise</span> <span class="ne">ModuleNotFoundError</span><span class="p">(</span>
             <span class="s2">&quot;gemmi is not available. Please install via &quot;</span>
-            <span class="s2">&quot;&#39;mamba install -c conda-forge gemmi&#39;&quot;</span>
+            <span class="s2">&quot;&#39;conda install -c conda-forge gemmi&#39;&quot;</span>
         <span class="p">)</span>
 
     <span class="kn">from</span> <span class="nn">..base</span> <span class="kn">import</span> <span class="n">create_map</span>
@@ -949,7 +949,7 @@ <h1>Source code for sire.convert</h1><div class="highlight"><pre>
     <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
         <span class="k">raise</span> <span class="ne">ModuleNotFoundError</span><span class="p">(</span>
             <span class="s2">&quot;rdkit is not available. Please install via &quot;</span>
-            <span class="s2">&quot;&#39;mamba install -c conda-forge rdkit&#39;&quot;</span>
+            <span class="s2">&quot;&#39;conda install -c conda-forge rdkit&#39;&quot;</span>
         <span class="p">)</span>
 
     <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
@@ -1010,7 +1010,7 @@ <h1>Source code for sire.convert</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -1025,7 +1025,7 @@ <h1>Source code for sire.convert</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/io.html b/_modules/sire/io.html
@@ -518,7 +518,7 @@ <h1>Source code for sire.io</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -533,7 +533,7 @@ <h1>Source code for sire.io</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/legacy/Base.html b/_modules/sire/legacy/Base.html
@@ -541,7 +541,7 @@ <h1>Source code for sire.legacy.Base</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -556,7 +556,7 @@ <h1>Source code for sire.legacy.Base</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/maths.html b/_modules/sire/maths.html
@@ -766,7 +766,7 @@ <h1>Source code for sire.maths</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -781,7 +781,7 @@ <h1>Source code for sire.maths</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/maths/_sphere.html b/_modules/sire/maths/_sphere.html
@@ -576,7 +576,7 @@ <h1>Source code for sire.maths._sphere</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -591,7 +591,7 @@ <h1>Source code for sire.maths._sphere</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/maths/_vector.html b/_modules/sire/maths/_vector.html
@@ -701,7 +701,7 @@ <h1>Source code for sire.maths._vector</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -716,7 +716,7 @@ <h1>Source code for sire.maths._vector</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/mol.html b/_modules/sire/mol.html
@@ -2921,7 +2921,7 @@ <h1>Source code for sire.mol</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -2936,7 +2936,7 @@ <h1>Source code for sire.mol</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/sire/mol/_cursor.html b/_modules/sire/mol/_cursor.html
@@ -4634,7 +4634,7 @@ <h1>Source code for sire.mol._cursor</h1><div class="highlight"><pre>
             Made with 
             <a href="https://github.com/pradyunsg/furo">Furo</a>
             <div class="last-updated">
-              Last updated on Dec 15, 2023</div>
+              Last updated on Jan 02, 2024</div>
           </div>
           <div class="right-details">
 
@@ -4649,7 +4649,7 @@ <h1>Source code for sire.mol._cursor</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=1b6071b6"></script>
+</div><script src="../../../_static/documentation_options.js?v=bf18f5af"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=32e29ea5"></script>