deploy: 5a39e05

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 562afbd0e679804b822a56ca08cc3a5f
+config: db3f3add2635cbea62c521bf11e3ae71
 tags: 645f666f9bcd5a90fca523b33c5a78b7

PathSimAnalysis.html

@@ -90,6 +90,7 @@
 <li class="toctree-l2"><a class="reference internal" href="spyrmsdkit.html">spyrmsdkit</a></li>
 <li class="toctree-l2"><a class="reference internal" href="transport-analysis.html">transport-analysis</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="lipidorderkit.html">lipidorderkit</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="mdakit-sasa.html">mdakit-sasa</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mdahole2.html">mdahole2</a></li>

ProLIF.html

@@ -90,6 +90,7 @@
 <li class="toctree-l2"><a class="reference internal" href="spyrmsdkit.html">spyrmsdkit</a></li>
 <li class="toctree-l2"><a class="reference internal" href="transport-analysis.html">transport-analysis</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="lipidorderkit.html">lipidorderkit</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="mdakit-sasa.html">mdakit-sasa</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mdahole2.html">mdahole2</a></li>

_sources/lipidorderkit.rst.txt

@@ -0,0 +1,49 @@
+.. _lipidorderkit:
+
+************************************************
+lipidorderkit
+************************************************
+
+| 🖋️ **Authors**: `lipidorderkit authors`_
+| 🏠 **Project home:** https://github.com/ricard1997/lipidorderkit/
+| 📖 **Documentation:** https://lipidorderdocs.readthedocs.io/en/latest/
+| ⚖️ **License:** GPL-2.0-or-later
+| 🔑 **Keywords:** Lipids, Lipids order parameters, SCD, Lipid metrics, Lipid study
+| 🚀 **Development status:** Production/Stable
+| 📜 **Changelog:** https://github.com/ricard1997/lipidorderkit/blob/main/CHANGELOG.md
+| 📑 **Publications:**
+|    * https://doi.org/10.3389/fchem.2022.1088058
+| 🧪 **Tests (latest):** |lipidorderkit_latest| 
+| 🧪 **Tests (develop):** |lipidorderkit_develop| 
+| **Description:**
+| *This MDAKit allow for the calculation of lipid order parameters for all atom molecular dynamics simulations.*
+
+
+
+Installation instructions
+=========================
+
+The latest version of lipidorderkit can be installed using the following:
+
+.. code-block:: bash
+
+    pip install git+https://github.com/ricard1997/lipidorderkit@main
+
+The source code of lipidorderkit can be installed using the following:
+
+.. code-block:: bash
+
+    git clone https://github.com/ricard1997/lipidorderkit.git
+    cd lipidorderkit && pip install . && cd ..
+
+.. _`lipidorderkit authors`:
+   https://github.com/ricard1997/lipidorderkit/blob/main/AUTHORS.md
+
+.. |lipidorderkit_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
+   :alt: lipidorderkit develop CI status
+   :target: https://github.com/MDAnalysis/MDAKits/actions
+
+.. |lipidorderkit_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+   :alt: lipidorderkit develop CI status
+   :target: https://github.com/MDAnalysis/MDAKits/actions
+

_sources/mdakits.rst.txt

@@ -29,6 +29,10 @@ Each of the MDAKits in the following table links to a page with more details abo
       - pKa, protein
       - `propkatraj authors`_
       - |propkatraj_latest| |propkatraj_develop|
+    * - :ref:`lipidorderkit`
+      - Lipids, Lipids order parameters, SCD, Lipid metrics, Lipid study
+      - `lipidorderkit authors`_
+      - |lipidorderkit_latest| |lipidorderkit_develop|
     * - :ref:`openmm-mdanalysis-reporter`
       - OpenMM, Reporters
       - `openmm-mdanalysis-reporter authors`_
@@ -94,6 +98,7 @@ Each of the MDAKits in the following table links to a page with more details abo
    spyrmsdkit
    transport-analysis
    propkatraj
+   lipidorderkit
    openmm-mdanalysis-reporter
    mdakit-sasa
    mdahole2
@@ -143,6 +148,17 @@ Each of the MDAKits in the following table links to a page with more details abo
    :alt: propkatraj develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
+.. _`lipidorderkit authors`:
+   https://github.com/ricard1997/lipidorderkit/blob/main/AUTHORS.md
+
+.. |lipidorderkit_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
+   :alt: lipidorderkit develop CI status
+   :target: https://github.com/MDAnalysis/MDAKits/actions
+
+.. |lipidorderkit_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+   :alt: lipidorderkit 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
 

_static/searchtools.js

@@ -178,7 +178,7 @@ const Search = {
 
   htmlToText: (htmlString, anchor) => {
     const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    for (const removalQuery of [".headerlinks", "script", "style"]) {
+    for (const removalQuery of [".headerlink", "script", "style"]) {
       htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
     }
     if (anchor) {
@@ -328,13 +328,14 @@ const Search = {
     for (const [title, foundTitles] of Object.entries(allTitles)) {
       if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
         for (const [file, id] of foundTitles) {
-          let score = Math.round(100 * queryLower.length / title.length)
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
           normalResults.push([
             docNames[file],
             titles[file] !== title ? `${titles[file]} > ${title}` : title,
             id !== null ? "#" + id : "",
             null,
-            score,
+            score + boost,
             filenames[file],
           ]);
         }

lipidorderkit.html

@@ -0,0 +1,237 @@
+
+
+
+
+
+
+
+
+
+
+<head>
+  <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/all.min.css" integrity="sha512-iBBXm8fW90+nuLcSKlbmrPcLa0OT92xO1BIsZ+ywDWZCvqsWgccV3gFoRBv0z+8dLJgyAHIhR35VZc2oM/gI1w==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+  <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/academicons/1.9.1/css/academicons.min.css" integrity="sha512-b1ASx0WHgVFL5ZQhTgiPWX+68KjS38Jk87jg7pe+qC7q9YkEtFq0z7xCglv7qGIs/68d3mAp+StfC8WKC5SSAg==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+  <link rel="shortcut icon" href="_static/mdakits-logo.ico">
+</head>
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="./">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>lipidorderkit &mdash; MDAKits Registry  documentation</title>
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/site.css" />
+      <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.13.6/css/jquery.dataTables.min.css" />
+
+
+    <link rel="shortcut icon" href="_static/mdakits-logo.ico"/>
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+        <script src="_static/main.js?v=71e46913"></script>
+        <script src="_static/js/versions.js"></script>
+    <script src="_static/js/theme.js"></script>
+    <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="openmm-mdanalysis-reporter" href="openmm-mdanalysis-reporter.html" />
+    <link rel="prev" title="propkatraj" href="propkatraj.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+
+
+
+
+
+
+<a href="index.html">
+
+    <img src="_static/mdakits-logo-1563x1563.png" class="logo" alt="Logo"/>
+</a>
+
+
+
+
+
+
+
+
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        </div>
+<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+
+        <p class="caption" role="heading"><span class="caption-text">MDAKit Registry</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="spyrmsdkit.html">spyrmsdkit</a></li>
+<li class="toctree-l2"><a class="reference internal" href="transport-analysis.html">transport-analysis</a></li>
+<li class="toctree-l2"><a class="reference internal" href="propkatraj.html">propkatraj</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">lipidorderkit</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="openmm-mdanalysis-reporter.html">openmm-mdanalysis-reporter</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mdakit-sasa.html">mdakit-sasa</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mdahole2.html">mdahole2</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mdaencore.html">mdaencore</a></li>
+<li class="toctree-l2"><a class="reference internal" href="mda-tui.html">mda-tui</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PathSimAnalysis.html">PathSimAnalysis</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="mdachecker.html">mdachecker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="membrane-curvature.html">membrane-curvature</a></li>
+<li class="toctree-l2"><a class="reference internal" href="waterdynamics.html">waterdynamics</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="maicos.html">maicos</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="solvation-analysis.html">solvation-analysis</a></li>
+</ul>
+</li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Resources</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="about.html">About MDAKits</a></li>
+<li class="toctree-l1"><a class="reference internal" href="makingakit.html">Making an MDAKit</a></li>
+<li class="toctree-l1"><a class="reference internal" href="add.html">Adding an MDAKit to the Registry</a></li>
+<li class="toctree-l1"><a class="reference internal" href="troubleshooting.html">Troubleshooting</a></li>
+<li class="toctree-l1"><a class="reference internal" href="reviewersguide.html">Guide for reviewers</a></li>
+</ul>
+
+</div>
+
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="index.html">MDAKits Registry</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="mdakits.html">Registry of MDAnalysis Toolkits (MDAKits)</a></li>
+      <li class="breadcrumb-item active">lipidorderkit</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="_sources/lipidorderkit.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <section id="lipidorderkit">
+<span id="id1"></span><h1>lipidorderkit<a class="headerlink" href="#lipidorderkit" title="Link to this heading"></a></h1>
+<div class="line-block">
+<div class="line">🖋️ <strong>Authors</strong>: <a class="reference external" href="https://github.com/ricard1997/lipidorderkit/blob/main/AUTHORS.md">lipidorderkit authors</a></div>
+<div class="line">🏠 <strong>Project home:</strong> <a class="reference external" href="https://github.com/ricard1997/lipidorderkit/">https://github.com/ricard1997/lipidorderkit/</a></div>
+<div class="line">📖 <strong>Documentation:</strong> <a class="reference external" href="https://lipidorderdocs.readthedocs.io/en/latest/">https://lipidorderdocs.readthedocs.io/en/latest/</a></div>
+<div class="line">⚖️ <strong>License:</strong> GPL-2.0-or-later</div>
+<div class="line">🔑 <strong>Keywords:</strong> Lipids, Lipids order parameters, SCD, Lipid metrics, Lipid study</div>
+<div class="line">🚀 <strong>Development status:</strong> Production/Stable</div>
+<div class="line">📜 <strong>Changelog:</strong> <a class="reference external" href="https://github.com/ricard1997/lipidorderkit/blob/main/CHANGELOG.md">https://github.com/ricard1997/lipidorderkit/blob/main/CHANGELOG.md</a></div>
+<div class="line">📑 <strong>Publications:</strong></div>
+<div class="line-block">
+<div class="line">* <a class="reference external" href="https://doi.org/10.3389/fchem.2022.1088058">https://doi.org/10.3389/fchem.2022.1088058</a></div>
+</div>
+<div class="line">🧪 <strong>Tests (latest):</strong> <a class="reference external" href="https://github.com/MDAnalysis/MDAKits/actions"><img alt="lipidorderkit 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="lipidorderkit develop CI status" src="https://img.shields.io/badge/develop-passed-green.svg" /></a></div>
+<div class="line"><strong>Description:</strong></div>
+<div class="line"><em>This MDAKit allow for the calculation of lipid order parameters for all atom molecular dynamics simulations.</em></div>
+</div>
+<section id="installation-instructions">
+<h2>Installation instructions<a class="headerlink" href="#installation-instructions" title="Link to this heading"></a></h2>
+<p>The latest version of lipidorderkit can be installed using the following:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>git+https://github.com/ricard1997/lipidorderkit@main
+</pre></div>
+</div>
+<p>The source code of lipidorderkit can be installed using the following:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/ricard1997/lipidorderkit.git
+<span class="nb">cd</span><span class="w"> </span>lipidorderkit<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>.<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>..
+</pre></div>
+</div>
+</section>
+</section>
+
+
+           </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="openmm-mdanalysis-reporter.html" class="btn btn-neutral float-right" title="openmm-mdanalysis-reporter" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+    </div>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2022-2024, .</p>
+  </div>
+
+
+
+<div class="footer"><p>Please see
+    our <a href="https://www.mdanalysis.org/pages/privacy/">Privacy Policy</a>
+    to learn how <a href="https://www.mdanalysis.org">MDAnalysis</a> collects data.</p>
+    <script data-goatcounter="https://mdanalysis.goatcounter.com/count"
+        async src="//gc.zgo.at/count.js"></script>
+</div>
+
+
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+    var versions_json_url = ''
+</script>
+
+<div class="rst-versions" data-toggle="rst-versions" role="note"
+     aria-label="versions">
+    <span class="rst-current-version" data-toggle="rst-current-version">
+      <span class="fa fa-book"></span>
+
+      <span class="fa fa-caret-down"></span>
+    </span>
+
+    <div class="rst-other-versions">
+        <dl id="versionselector">
+            <dt>Other Versions</dt>
+        </dl>
+
+    </div>
+</div><script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>

lipyds.html

@@ -90,6 +90,7 @@
 <li class="toctree-l2"><a class="reference internal" href="spyrmsdkit.html">spyrmsdkit</a></li>
 <li class="toctree-l2"><a class="reference internal" href="transport-analysis.html">transport-analysis</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="lipidorderkit.html">lipidorderkit</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="mdakit-sasa.html">mdakit-sasa</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mdahole2.html">mdahole2</a></li>

maicos.html

@@ -90,6 +90,7 @@
 <li class="toctree-l2"><a class="reference internal" href="spyrmsdkit.html">spyrmsdkit</a></li>
 <li class="toctree-l2"><a class="reference internal" href="transport-analysis.html">transport-analysis</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="lipidorderkit.html">lipidorderkit</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="mdakit-sasa.html">mdakit-sasa</a></li>
 <li class="toctree-l2"><a class="reference internal" href="mdahole2.html">mdahole2</a></li>