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MDAnalysis · Aug 28, 2023 · 8555354 · 8555354
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diff --git a/.doctrees/ProLIF.doctree b/.doctrees/ProLIF.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/mdakits.doctree b/.doctrees/mdakits.doctree
diff --git a/ProLIF.html b/ProLIF.html
@@ -25,8 +25,8 @@
     <link rel="author" title="About these documents" href="about.html" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="propkatraj" href="propkatraj.html" />
-    <link rel="prev" title="lipyds" href="lipyds.html" /> 
+    <link rel="next" title="lipyds" href="lipyds.html" />
+    <link rel="prev" title="mdachecker" href="mdachecker.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -52,16 +52,16 @@
               <p class="caption" role="heading"><span class="caption-text">Table of Contents</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="mdakits.html">Registry of MDAnalysis Toolkits (MDAKits)</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="lipyds.html">lipyds</a></li>
+<li class="toctree-l2"><a class="reference internal" href="openmm-mdanalysis-reporter.html">openmm-mdanalysis-reporter</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mdachecker.html">mdachecker</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">ProLIF</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#installation-instructions">Installation instructions</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="propkatraj.html">propkatraj</a></li>
+<li class="toctree-l2"><a class="reference internal" href="lipyds.html">lipyds</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hole2-mdakit.html">hole2-mdakit</a></li>
-<li class="toctree-l2"><a class="reference internal" href="mdachecker.html">mdachecker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="propkatraj.html">propkatraj</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mdacli.html">mdacli</a></li>
-<li class="toctree-l2"><a class="reference internal" href="openmm-mdanalysis-reporter.html">openmm-mdanalysis-reporter</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About MDAKits</a></li>
@@ -109,7 +109,7 @@
 <div class="line">* <a class="reference external" href="https://zenodo.org/record/7332369">https://zenodo.org/record/7332369</a></div>
 </div>
 <div class="line">🧪 <strong>Tests (latest):</strong> <a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="ProLIF develop CI status" src="https://img.shields.io/badge/latest-passed-green.svg" /></a></div>
-<div class="line">🧪 <strong>Tests (develop):</strong> <a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="ProLIF develop CI status" src="https://img.shields.io/badge/develop-passed-green.svg" /></a></div>
+<div class="line">🧪 <strong>Tests (develop):</strong> <a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="ProLIF develop CI status" src="https://img.shields.io/badge/develop-failed-red.svg" /></a></div>
 <div class="line"><strong>Description:</strong></div>
 <div class="line"><em>Interaction Fingerprints for protein-ligand complexes and more</em></div>
 </div>
@@ -131,8 +131,8 @@ <h2>Installation instructions<a class="headerlink" href="#installation-instructi
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="lipyds.html" class="btn btn-neutral float-left" title="lipyds" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="propkatraj.html" class="btn btn-neutral float-right" title="propkatraj" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="mdachecker.html" class="btn btn-neutral float-left" title="mdachecker" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="lipyds.html" class="btn btn-neutral float-right" title="lipyds" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>

diff --git a/_sources/ProLIF.rst.txt b/_sources/ProLIF.rst.txt
@@ -39,7 +39,7 @@ The source code of ProLIF can be installed using the following:
    :alt: ProLIF develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. |ProLIF_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+.. |ProLIF_develop| image:: https://img.shields.io/badge/develop-failed-red.svg
    :alt: ProLIF develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
diff --git a/_sources/mdakits.rst.txt b/_sources/mdakits.rst.txt
@@ -16,74 +16,82 @@ Each of the MDAKits in the following table links to a page with more details abo
       - Keywords
       - Authors
       - CI badges
-    * - :ref:`lipyds`
-      - lipids, membranes
-      - lilyminium
-      - |lipyds_latest| |lipyds_develop|
+    * - :ref:`openmm-mdanalysis-reporter`
+      - OpenMM, Reporters
+      - `openmm-mdanalysis-reporter authors`_
+      - |openmm-mdanalysis-reporter_latest| |openmm-mdanalysis-reporter_develop|
+    * - :ref:`mdachecker`
+      - structure analysis, conformation checks
+      - IAlibay
+      - |mdachecker_latest| |mdachecker_develop|
     * - :ref:`ProLIF`
       - drug-design, cheminformatics, molecular-dynamics
       - Cédric Bouysset
       - |ProLIF_latest| |ProLIF_develop|
-    * - :ref:`propkatraj`
-      - pKa, protein
-      - `propkatraj authors`_
-      - |propkatraj_latest| |propkatraj_develop|
+    * - :ref:`lipyds`
+      - lipids, membranes
+      - lilyminium
+      - |lipyds_latest| |lipyds_develop|
     * - :ref:`hole2-mdakit`
       - pores, ion channels, transporters, HOLE
       - `hole2-mdakit authors`_
       - |hole2-mdakit_latest| |hole2-mdakit_develop|
-    * - :ref:`mdachecker`
-      - structure analysis, conformation checks
-      - IAlibay
-      - |mdachecker_latest| |mdachecker_develop|
+    * - :ref:`propkatraj`
+      - pKa, protein
+      - `propkatraj authors`_
+      - |propkatraj_latest| |propkatraj_develop|
     * - :ref:`mdacli`
       - command line interface, molecular-dynamics
       - `mdacli authors`_
       - |mdacli_latest| |mdacli_develop|
-    * - :ref:`openmm-mdanalysis-reporter`
-      - OpenMM, Reporters
-      - `openmm-mdanalysis-reporter authors`_
-      - |openmm-mdanalysis-reporter_latest| |openmm-mdanalysis-reporter_develop|
 
 
 .. toctree::
    :maxdepth: 1
    :hidden:
 
-   lipyds
+   openmm-mdanalysis-reporter
+   mdachecker
    ProLIF
-   propkatraj
+   lipyds
    hole2-mdakit
-   mdachecker
+   propkatraj
    mdacli
-   openmm-mdanalysis-reporter
 
 
-.. |lipyds_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
-   :alt: lipyds develop CI status
+.. _`openmm-mdanalysis-reporter authors`:
+   https://github.com/sef43/openmm-mdanalysis-reporter/blob/main/AUTHORS.md
+
+.. |openmm-mdanalysis-reporter_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
+   :alt: openmm-mdanalysis-reporter develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. |lipyds_develop| image:: https://img.shields.io/badge/develop-unavailable-inactive.svg
-   :alt: lipyds develop CI status
+.. |openmm-mdanalysis-reporter_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+   :alt: openmm-mdanalysis-reporter develop CI status
+   :target: https://github.com/MDAnalysis/MDAKits/actions
+
+.. |mdachecker_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
+   :alt: mdachecker develop CI status
+   :target: https://github.com/MDAnalysis/MDAKits/actions
+
+.. |mdachecker_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+   :alt: mdachecker develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
 .. |ProLIF_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
    :alt: ProLIF develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. |ProLIF_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+.. |ProLIF_develop| image:: https://img.shields.io/badge/develop-failed-red.svg
    :alt: ProLIF develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. _`propkatraj authors`:
-   https://github.com/Becksteinlab/propkatraj/blob/main/AUTHORS
-
-.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
-   :alt: propkatraj develop CI status
+.. |lipyds_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
+   :alt: lipyds develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. |propkatraj_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
-   :alt: propkatraj develop CI status
+.. |lipyds_develop| image:: https://img.shields.io/badge/develop-unavailable-inactive.svg
+   :alt: lipyds develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
 .. _`hole2-mdakit authors`:
@@ -97,12 +105,15 @@ Each of the MDAKits in the following table links to a page with more details abo
    :alt: hole2-mdakit develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. |mdachecker_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
-   :alt: mdachecker develop CI status
+.. _`propkatraj authors`:
+   https://github.com/Becksteinlab/propkatraj/blob/main/AUTHORS
+
+.. |propkatraj_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
+   :alt: propkatraj develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. |mdachecker_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
-   :alt: mdachecker develop CI status
+.. |propkatraj_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+   :alt: propkatraj develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
 .. _`mdacli authors`:
@@ -116,14 +127,3 @@ Each of the MDAKits in the following table links to a page with more details abo
    :alt: mdacli develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. _`openmm-mdanalysis-reporter authors`:
-   https://github.com/sef43/openmm-mdanalysis-reporter/blob/main/AUTHORS.md
-
-.. |openmm-mdanalysis-reporter_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
-   :alt: openmm-mdanalysis-reporter develop CI status
-   :target: https://github.com/MDAnalysis/MDAKits/actions
-
-.. |openmm-mdanalysis-reporter_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
-   :alt: openmm-mdanalysis-reporter develop CI status
-   :target: https://github.com/MDAnalysis/MDAKits/actions
-
diff --git a/about.html b/about.html
@@ -26,7 +26,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Making an MDAKit" href="makingakit.html" />
-    <link rel="prev" title="openmm-mdanalysis-reporter" href="openmm-mdanalysis-reporter.html" /> 
+    <link rel="prev" title="mdacli" href="mdacli.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -133,7 +133,7 @@ <h2>Read our SciPy proceedings paper!<a class="headerlink" href="#read-our-scipy
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="openmm-mdanalysis-reporter.html" class="btn btn-neutral float-left" title="openmm-mdanalysis-reporter" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="mdacli.html" class="btn btn-neutral float-left" title="mdacli" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="makingakit.html" class="btn btn-neutral float-right" title="Making an MDAKit" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

diff --git a/hole2-mdakit.html b/hole2-mdakit.html
@@ -25,8 +25,8 @@
     <link rel="author" title="About these documents" href="about.html" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="mdachecker" href="mdachecker.html" />
-    <link rel="prev" title="propkatraj" href="propkatraj.html" /> 
+    <link rel="next" title="propkatraj" href="propkatraj.html" />
+    <link rel="prev" title="lipyds" href="lipyds.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -52,16 +52,16 @@
               <p class="caption" role="heading"><span class="caption-text">Table of Contents</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="mdakits.html">Registry of MDAnalysis Toolkits (MDAKits)</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="lipyds.html">lipyds</a></li>
+<li class="toctree-l2"><a class="reference internal" href="openmm-mdanalysis-reporter.html">openmm-mdanalysis-reporter</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mdachecker.html">mdachecker</a></li>
 <li class="toctree-l2"><a class="reference internal" href="ProLIF.html">ProLIF</a></li>
-<li class="toctree-l2"><a class="reference internal" href="propkatraj.html">propkatraj</a></li>
+<li class="toctree-l2"><a class="reference internal" href="lipyds.html">lipyds</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">hole2-mdakit</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#installation-instructions">Installation instructions</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="mdachecker.html">mdachecker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="propkatraj.html">propkatraj</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mdacli.html">mdacli</a></li>
-<li class="toctree-l2"><a class="reference internal" href="openmm-mdanalysis-reporter.html">openmm-mdanalysis-reporter</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About MDAKits</a></li>
@@ -128,8 +128,8 @@ <h2>Installation instructions<a class="headerlink" href="#installation-instructi
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="propkatraj.html" class="btn btn-neutral float-left" title="propkatraj" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="mdachecker.html" class="btn btn-neutral float-right" title="mdachecker" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="lipyds.html" class="btn btn-neutral float-left" title="lipyds" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="propkatraj.html" class="btn btn-neutral float-right" title="propkatraj" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>

diff --git a/lipyds.html b/lipyds.html
@@ -25,8 +25,8 @@
     <link rel="author" title="About these documents" href="about.html" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="ProLIF" href="ProLIF.html" />
-    <link rel="prev" title="Registry of MDAnalysis Toolkits (MDAKits)" href="mdakits.html" /> 
+    <link rel="next" title="hole2-mdakit" href="hole2-mdakit.html" />
+    <link rel="prev" title="ProLIF" href="ProLIF.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -52,16 +52,16 @@
               <p class="caption" role="heading"><span class="caption-text">Table of Contents</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="mdakits.html">Registry of MDAnalysis Toolkits (MDAKits)</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="openmm-mdanalysis-reporter.html">openmm-mdanalysis-reporter</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mdachecker.html">mdachecker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ProLIF.html">ProLIF</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">lipyds</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#installation-instructions">Installation instructions</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="ProLIF.html">ProLIF</a></li>
-<li class="toctree-l2"><a class="reference internal" href="propkatraj.html">propkatraj</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hole2-mdakit.html">hole2-mdakit</a></li>
-<li class="toctree-l2"><a class="reference internal" href="mdachecker.html">mdachecker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="propkatraj.html">propkatraj</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mdacli.html">mdacli</a></li>
-<li class="toctree-l2"><a class="reference internal" href="openmm-mdanalysis-reporter.html">openmm-mdanalysis-reporter</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About MDAKits</a></li>
@@ -128,8 +128,8 @@ <h2>Installation instructions<a class="headerlink" href="#installation-instructi
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="mdakits.html" class="btn btn-neutral float-left" title="Registry of MDAnalysis Toolkits (MDAKits)" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="ProLIF.html" class="btn btn-neutral float-right" title="ProLIF" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="ProLIF.html" class="btn btn-neutral float-left" title="ProLIF" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="hole2-mdakit.html" class="btn btn-neutral float-right" title="hole2-mdakit" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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