diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index f95dd340f1d29ae6e4c110a2948d8468d4218089..c17396d63f79bdf26a29d16e85d25dc278ef95b4 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Building ProMod3" href="../buildsystem.html" />
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 8e6ea4b3b1480d42a1db1c030243b470763c4737..408223d63c3356f2cbddee7f22175516ff007228 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="ProMod3’s Share Of CMake" href="../cmake/index.html" />
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 05fc1b2e750fedfb23f3d188c3c24e70c1ae8c72..d013cbc79d4fb5dd10f9d668518e7e7ce0e40c8b 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="ProMod3 and Containers" href="container/index.html" />
@@ -36,7 +37,7 @@
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
<p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-2.2.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to
+2.3.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to
use <a class="reference external" href="https://github.com/openmm/openmm">OpenMM</a>. To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required. The same
versions of <a class="reference external" href="https://www.python.org/">Python</a> and <a class="reference external" href="https://www.boost.org/">Boost</a> are needed as used in OST. For <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a>
we need at least version 3.3.0. To build the documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> is
@@ -45,7 +46,7 @@ release supporting Python 2.7 is 2.1.0 which also requires OST to be
compiled with Python 2.7.</p>
<p>The currently preferred versions are:</p>
<ul class="simple">
-<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.2.0</li>
+<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.3.0</li>
<li><a class="reference external" href="https://github.com/openmm/openmm">OpenMM</a> 7.1.1</li>
<li><a class="reference external" href="https://cmake.org/">CMake</a> 3.12.1</li>
<li><a class="reference external" href="https://www.python.org/">Python</a> 3.6.0</li>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 0b80d30ae3dd19f7b8e1a0de8461ab13325d194a..9f00e07757540e4ddd5bc2b3b7a0a744fcda935f 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="References" href="references.html" />
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index d23eb193c7f9f7936d0559954876eeee439dae7b..a18b6c781a3bb93cdd4087606e9e03e918e0d8be 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Using Binary Files In ProMod3" href="../portableIO.html" />
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index 577d8f353ccc1742a2873ee4b2783363bba657dd..efd454dae0676f9373d8fcb8a97239da4e4397d9 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Singularity" href="singularity.html" />
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
index b2acf949f8275d519e0518cc12e39e329e5c7c38..1cd6fb1b509d6a2aa6e8002a02d8a2d63b57c3af 100644
--- a/doc/html/container/index.html
+++ b/doc/html/container/index.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Docker" href="docker.html" />
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index 822589adbb3c09a516e85dc329741a558ccb71ac..61c1dc21108f9c9bc370ce4264333beb34a73f94 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="modelling - Protein Modelling" href="../modelling/index.html" />
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 9a91958ba05680843048a7a2c1952181a19ecb6d..9f612109a6e472105c26df477282cb25ce8cbf50 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="test_actions - Testing Actions" href="actions/index_dev.html" />
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index 0bd556db022d0bf906076a4efb559a6ac5390cbc..4db119f6e43fd07a28ca388d8630770c5f964dda 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Runtime profiling" href="runtime_profiling.html" />
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index 67f27f5c150058fd589e025c9ac439ce322e67c3..1d1d0b3a00098296d63b6421e6f39cdc5e26e41c 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index f3c67939eabe27bcb932fd392f5ea247e48bef30..6abb2303e27b455c68ba34793f62d6acebf77093 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Geometry functions" href="geometry.html" />
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index c004384d95e2e1c34185044e6a3cf87c1dad335d..551c891176d54176d2663a43965cb80a1a739b21 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 03f4e0f52a428fe1abc517c85e25a47190a3d863..ad588482c05bbd2192e5f094c543e73abc327ccb 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index 73327fdf03047a788ae356769a287d3203fdd9e1..795b6c9fad6daab07814879961cac843f5caba8e 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index e8be91c6babffd21629566b134c0a2101f7fcb9b..f6cbb73e8d60cf848b57bb6bf6609d49473eb9d2 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Contributing" href="../user_contributions.html" />
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 2f8b193bd5108337b83f3c7c930bae2f93e9e398..2a060c73826e7fe234a7ce2a43e024b9755ff058 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Contributing" href="contributing.html" />
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 992e567b6b62be24b4461f44d73bc0fd934e1844..7084fedebc67848cc80f6bd2f5f058fe931016ed 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 35f7a0f49f858d702f4a19510e1b84261c7df64d..5ef68c4bd5228d4b81369271fa83fc79b7cf5f62 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -15,6 +15,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index 5c0c457fde4071d540983bba817bd677ac2713f6..80a23c32bac0dd7b3a391415c5fe91aa5ffc6e88 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="ProMod3 Actions" href="actions/index.html" />
diff --git a/doc/html/index.html b/doc/html/index.html
index 8d76841ad0a419376c61c6187022e0992f47358e..48736a0c783604f8b6d4ffc81ebfacd942b36dd3 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Documentation For Users" href="users.html" />
diff --git a/doc/html/license.html b/doc/html/license.html
index c403448ee9eddf31f03e19f6c73666e7c6c51907..2fa7eaf1e51cfcc2ccd9a981b902d1ebfdb7e3f8 100644
--- a/doc/html/license.html
+++ b/doc/html/license.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="References" href="references.html" />
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index 60fcbb1292f4dcf3de7e0d3e301723da5ebda429..f27b4188bdce492b5a6be0d1175442ff9542ba6a 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index ef05adc472d91759067a50f6f61c52d7b2fd3ad0..bc203c9950665a139f17eae99ff48700adbec51c 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 152ee112cc030646a382a303bb0cc8e6707be97b..5ea7d7d40d1528fe32dde6b8137749297f3b63e4 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Representing Loops" href="backbone.html" />
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index 091526cee6ceb21c67944a0596393eae2192a40d..3d5bd43d253ffba41578c413e00a7ba26a6c8b0e 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="core - ProMod3 Core Functionality" href="../core/index.html" />
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index d6eb58249c1f0a59f6b7bdd1b5185f6324e8dfb4..5110342b60f1cb3c51960fa24cbda974c559bf5c 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Loading Precomputed Objects" href="load_loop_objects.html" />
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 412e4d223771009c8b38759eee8e8969e9773539..2ce5f6faeef242db1fc6f37ff534d74c46380d12 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Handling All Atom Positions" href="all_atom.html" />
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index dd8ae5ba64e673aa91edfff803f909669779334c..fa34d776bc15cf23340f75e569d3dbc290de5bc1 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Structural Data" href="structure_db.html" />
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 6dbc29808ddd18f3002e1e33b75fe592a5031f49..b50786148354be50f4cf7124d841b262debf706d 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="sidechain - Sidechain Modelling" href="../sidechain/index.html" />
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 78fdaac53cb4968f9321afdf9a2df4700bd85aa9..33480a71923b4579ff5e5d80d23a55595592cbc6 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Handling Loop Candidates" href="loop_candidates.html" />
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index b9427e4295d0169f3a3a6523572c04ce71a131de..72df0c020ef76b044551de040d7a72cfdd0944e8 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Modelling Pipeline" href="pipeline.html" />
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index a0cdc58b29b83e9594f731490e8b479ba0844130..a04ae292b2ed52770a63c7d47eed174fbcce7f13 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Fitting Loops Into Gaps" href="loop_closing.html" />
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index c15b2587fdf642cffe36472bc5d3412184f7da3b..dfab8aa39dbb0a60f7f0322aea794238a08ceb65 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" />
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index f6e0434429496a6011c12d07e9b516a66c482471..04ece5d3cd50301e608eaf4d6bde84499b465b51 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Handling Gaps" href="gap_handling.html" />
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 828169d20cac4964062530ff477078750f7c4b9b..e05d228440ebf6a0b28b68d3315ff15fd858cc20 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index fc1b426cb2d944bd5dde74cc4b81ce7922ed771d..184688346f49e5b7d8d9cfdeec85da76417ef6d5 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Model Checking" href="model_checking.html" />
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index 9d8f425be45a2c42cdb26cd54981bfeb0310b7c9..980622fd937d01d81b7fc7169cbaa996af57c06d 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Modelling Algorithms" href="algorithms.html" />
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index 8673a178b72ec37b44a21944549be38496afe5df..53ee73f38cf93faae4a3eaef0a682ed27f29dc3c 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="License" href="license.html" />
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index f8ab5e923cc125254ff44284775f242f5306afff..06632bdef08109eb6898181cc0df6a7ebb72ba1c 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
diff --git a/doc/html/references.html b/doc/html/references.html
index b62376523726e32439c68a6f01d26ab12bda9c0e..c5cfde451fc538649c62098da9c73dc3434b22f5 100644
--- a/doc/html/references.html
+++ b/doc/html/references.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Changelog" href="changelog.html" />
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index e28bc2d03f3f4ae0c54781ed7262cc26f6cf8245..3e3d467e790f5bf411b0328dc7ff1466db12cd59 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index 23d39eeb9f648b95efeaeaf339ce5f00ab371bc0..ab4bc1a2ce98e5afc7b5073c5ed553defd7fa3ca 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Backbone Scorers" href="backbone_scorers.html" />
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index 77966293fc27acea90a27fafb7cb0a1f80beec5c..ff76e572ea550aa83438163d2af9440503f6bfbe 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="All Atom Scorers" href="all_atom_scorers.html" />
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index 3bed039fe9190f5a023bb0f504126a01cff958f1..ebc4d6c9bffda1a6c3c14b758a59734dec80e3aa 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Backbone Score Environment" href="backbone_score_env.html" />
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index 803eb26293b8a3449ebd1120eefc19ca7f68578d..0de14121fe084c5aea2c6ace5fcaf4684ed7c45a 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
diff --git a/doc/html/search.html b/doc/html/search.html
index 70aed32d90596e754a0afe56ee21fc1399703cdd..a60fd4630084ef95efe75cbfb5c15432c6e4eb59 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -15,6 +15,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<script type="text/javascript" src="_static/searchtools.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="#" />
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index fc12a56c25423340bbb4e17b2e5a1f5cde191352..3d8e50950092529e4ae9bd789e0e12de31fbe8e2 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Loading Rotamer Libraries" href="loading.html" />
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index 1959e0362501160d7878f411295625db9ec37ae2..e85a1e8ff373c6e2aaf478b1af6ed7691f9c7397 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index c9dbd450da516075dca9c35e6e67b913159928ad..61732485dc5627272f1857dcc88e22d4d5619ba1 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Disulfid Bond Evaluation" href="disulfid.html" />
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index ca935f97a60f72f2fc70c46b145c6d8bbb1a4a0e..e6e40a3b78011f7f26bea103c0f5ac16172bc58b 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Representing Sidechains - Rotamers & Co." href="rotamer.html" />
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index 09c6257d65c354b8d370f22ebf8dae3037a6c135..d54af5fd4e741da4b8dad8ae3bb522993a715f17 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Subrotamer Optimization" href="subrotamer_optimizer.html" />
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index a3e419a1b31a0a8611130744c4ccc6296cf4dd20..e33eb6e988202302ca3ad1bef062b3fb14235bb4 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Frame - The Rigid Part" href="frame.html" />
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 4d2c9141281160d28ba802e63b3daa219f95d6af..3e5431c2715fae4618854aff7f6ecaed7223de42 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 5e459c5e507378dcc0b09436fa159f358a521d15..6dd76800bccb8370dbcd92c5bda8d59d0b3edeb4 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Rotamer Graph" href="graph.html" />
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index f46fb69b46a485045fa31445b122ee10af71343c..241f685e465a346f918d7686995e4e0c4d5b4194 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="scoring - Loop Scoring" href="../scoring/index.html" />
diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html
index d42afe63211e062b211dabd868e38f42a0c69f6d..44fd3f6c307cb7180f9da374afbe04099aeb5b42 100644
--- a/doc/html/user_contributions.html
+++ b/doc/html/user_contributions.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Documentation For Developers" href="developers.html" />
diff --git a/doc/html/users.html b/doc/html/users.html
index c7cbf01143addc506c3ed5010cd8f69ae3f74175..81a37ae06ac1e75b57de228030d9f22fde448332 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -14,6 +14,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Getting Started" href="gettingstarted.html" />