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MDAnalysis · Sep 12, 2024 · e4fcff2 · e4fcff2
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diff --git a/.doctrees/domhmm.doctree b/.doctrees/domhmm.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/mda-tui.doctree b/.doctrees/mda-tui.doctree
diff --git a/.doctrees/mdakits.doctree b/.doctrees/mdakits.doctree
diff --git a/MDANCE.html b/MDANCE.html
@@ -102,6 +102,7 @@
 <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="mdakit-sasa.html">mdakit-sasa</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="domhmm.html">domhmm</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="mdachecker.html">mdachecker</a></li>
 <li class="toctree-l2"><a class="reference internal" href="spyrmsdkit.html">spyrmsdkit</a></li>

diff --git a/PathSimAnalysis.html b/PathSimAnalysis.html
@@ -44,7 +44,7 @@
     <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="lipidorderkit" href="lipidorderkit.html" /> 
+    <link rel="prev" title="domhmm" href="domhmm.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -99,6 +99,7 @@
 <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="mdakit-sasa.html">mdakit-sasa</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="domhmm.html">domhmm</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">PathSimAnalysis</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#installation-instructions">Installation instructions</a></li>
 </ul>
@@ -185,7 +186,7 @@ <h2>Installation instructions<a class="headerlink" href="#installation-instructi
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="lipidorderkit.html" class="btn btn-neutral float-left" title="lipidorderkit" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="domhmm.html" class="btn btn-neutral float-left" title="domhmm" 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>
     </div>
 

diff --git a/ProLIF.html b/ProLIF.html
@@ -102,6 +102,7 @@
 <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="mdakit-sasa.html">mdakit-sasa</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="domhmm.html">domhmm</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="mdachecker.html">mdachecker</a></li>
 <li class="toctree-l2"><a class="reference internal" href="spyrmsdkit.html">spyrmsdkit</a></li>

diff --git a/_sources/domhmm.rst.txt b/_sources/domhmm.rst.txt
@@ -0,0 +1,44 @@
+.. _domhmm:
+
+************************************************
+domhmm
+************************************************
+
+| 🖋️ **Authors**: `domhmm authors`_
+| 🏠 **Project home:** https://github.com/BioMemPhys-FAU/domhmm
+| 📖 **Documentation:** https://domhmm.readthedocs.io
+| ⚖️ **License:** GPL-2.0-or-later
+| 🔑 **Keywords:** membranes, molecular dynamics, nanodomains, microdomains, machine learning
+| 🚀 **Development status:** Production/Stable
+| 📜 **Changelog:** https://github.com/BioMemPhys-FAU/domhmm/blob/main/CHANGELOG.md
+| 📑 **Publications:**
+|    * https://doi.org/10.1016/bs.mie.2024.03.006
+| 🧪 **Tests (latest):** |domhmm_latest| 
+| 🧪 **Tests (develop):** |domhmm_develop| 
+| **Description:**
+| *TL;DR: DomHMM provides an automated workflow to identify liquid-ordered (Lo) domains from Molecular Dynamics simulations of bio-membranes. :-) Nano- and microdomains in lipid membranes are of great interest for understanding biological processes such as small molecule binding and signal transduction. Molecular Dynamics (MD) present a powerful tool for studying membranes with various lipid compositions at different levels of resolution. However, detecting these domains can be challenging, as most workflows are described in papers without available or maintained implementations. The MDAKit DomHMM faciliates the analysis of domains in your simulation trajectories by providing an automated workflow for the detection of lateral heterogeneities (i.e., liquid-ordered domains). It is a versatile tool to handle different use case scenarios, such as simulations of asymmetric membranes or membranes including small proteins. It utilizes therefore unsupervised machine learning algorithms, including Gaussian Mixture Models and Gaussian-based Hidden Markov Models, to detect ordered lipids based on their structural properties. Identified lipids are then clustered into domains using spatial autocorrelation analysis.
+*
+
+
+
+Installation instructions
+=========================
+
+
+The source code of domhmm can be installed using the following:
+
+.. code-block:: bash
+
+    pip install git+https://github.com/BioMemPhys-FAU/domhmm@main
+
+.. _`domhmm authors`:
+   https://github.com/BioMemPhys-FAU/domhmm/blob/main/AUTHORS.md
+
+.. |domhmm_latest| image:: https://img.shields.io/badge/latest-unavailable-inactive.svg
+   :alt: domhmm develop CI status
+   :target: https://github.com/MDAnalysis/MDAKits/actions
+
+.. |domhmm_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+   :alt: domhmm develop CI status
+   :target: https://github.com/MDAnalysis/MDAKits/actions
+
diff --git a/_sources/mda-tui.rst.txt b/_sources/mda-tui.rst.txt
@@ -36,11 +36,11 @@ The source code of mda-tui can be installed using the following:
 .. _`mda-tui authors`:
    https://github.com/p-j-smith/mda-tui/blob/main/AUTHORS.md
 
-.. |mda-tui_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
+.. |mda-tui_latest| image:: https://img.shields.io/badge/latest-failed-red.svg
    :alt: mda-tui develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. |mda-tui_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+.. |mda-tui_develop| image:: https://img.shields.io/badge/develop-failed-red.svg
    :alt: mda-tui develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
diff --git a/_sources/mdakits.rst.txt b/_sources/mdakits.rst.txt
@@ -65,6 +65,10 @@ Each of the MDAKits in the following table links to a page with more details abo
       - Lipids, Lipids order parameters, SCD, Lipid metrics, Lipid study
       - `lipidorderkit authors`_
       - |lipidorderkit_latest| |lipidorderkit_develop|
+    * - :ref:`domhmm`
+      - membranes, molecular dynamics, nanodomains, microdomains, machine learning
+      - `domhmm authors`_
+      - |domhmm_latest| |domhmm_develop|
     * - :ref:`PathSimAnalysis`
       - similarity, paths, metrics
       - `PathSimAnalysis authors`_
@@ -119,6 +123,7 @@ Each of the MDAKits in the following table links to a page with more details abo
    transport-analysis
    mdakit-sasa
    lipidorderkit
+   domhmm
    PathSimAnalysis
    mdachecker
    spyrmsdkit
@@ -144,11 +149,11 @@ Each of the MDAKits in the following table links to a page with more details abo
 .. _`mda-tui authors`:
    https://github.com/p-j-smith/mda-tui/blob/main/AUTHORS.md
 
-.. |mda-tui_latest| image:: https://img.shields.io/badge/latest-passed-green.svg
+.. |mda-tui_latest| image:: https://img.shields.io/badge/latest-failed-red.svg
    :alt: mda-tui develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
-.. |mda-tui_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+.. |mda-tui_develop| image:: https://img.shields.io/badge/develop-failed-red.svg
    :alt: mda-tui develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
@@ -256,6 +261,17 @@ Each of the MDAKits in the following table links to a page with more details abo
    :alt: lipidorderkit develop CI status
    :target: https://github.com/MDAnalysis/MDAKits/actions
 
+.. _`domhmm authors`:
+   https://github.com/BioMemPhys-FAU/domhmm/blob/main/AUTHORS.md
+
+.. |domhmm_latest| image:: https://img.shields.io/badge/latest-unavailable-inactive.svg
+   :alt: domhmm develop CI status
+   :target: https://github.com/MDAnalysis/MDAKits/actions
+
+.. |domhmm_develop| image:: https://img.shields.io/badge/develop-passed-green.svg
+   :alt: domhmm develop CI status
+   :target: https://github.com/MDAnalysis/MDAKits/actions
+
 .. _`PathSimAnalysis authors`:
    https://github.com/MDAnalysis/PathSimAnalysis/blob/main/AUTHORS.md