diff --git a/_reference/analysis.qmd b/_reference/analysis.qmd
index bba30330..2ea79372 100644
--- a/_reference/analysis.qmd
+++ b/_reference/analysis.qmd
@@ -15,10 +15,10 @@ For command line usage, run `kimmdy-analysis -h`.
 | [get_analysis_dir](#kimmdy.analysis.get_analysis_dir) | Get analysis directory for a KIMMDY run. |
 | [plot_energy](#kimmdy.analysis.plot_energy) | Plot GROMACS energy for a KIMMDY run. |
 | [plot_rates](#kimmdy.analysis.plot_rates) | Plot rates of all possible reactions for each 'decide_recipe' step. |
-| [plot_runtime](#kimmdy.analysis.plot_runtime) | Plot runtime of all tasks. |
 | [radical_migration](#kimmdy.analysis.radical_migration) | Plot population of radicals for a KIMMDY run. |
 | [radical_population](#kimmdy.analysis.radical_population) | Plot population of radicals for a KIMMDY run. |
 | [reaction_participation](#kimmdy.analysis.reaction_participation) | Plot which atoms participate in reactions. |
+| [runtime_analysis](#kimmdy.analysis.runtime_analysis) | Plot which atoms participate in reactions. |
 
 ### concat_traj { #kimmdy.analysis.concat_traj }
 
@@ -101,21 +101,6 @@ Plot rates of all possible reactions for each 'decide_recipe' step.
 |--------|--------------|-------------------------|------------|
 | `dir`  | [str](`str`) | Directory of KIMMDY run | _required_ |
 
-### plot_runtime { #kimmdy.analysis.plot_runtime }
-
-`analysis.plot_runtime(dir, md_tasks, datefmt, open_plot=False)`
-
-Plot runtime of all tasks.
-
-#### Parameters
-
-| Name        | Type           | Description                         | Default    |
-|-------------|----------------|-------------------------------------|------------|
-| `dir`       | [str](`str`)   | Directory of KIMMDY run             | _required_ |
-| `md_tasks`  | [list](`list`) | Names of MD tasks to color          | _required_ |
-| `datefmt`   | [str](`str`)   | Date format in the KIMMDY logfile   | _required_ |
-| `open_plot` | [bool](`bool`) | Open plot in default system viewer. | `False`    |
-
 ### radical_migration { #kimmdy.analysis.radical_migration }
 
 `analysis.radical_migration(dirs, type='qualitative', cutoff=1)`
@@ -155,6 +140,19 @@ Plot which atoms participate in reactions.
 
 #### Parameters
 
+| Name        | Type           | Description                         | Default    |
+|-------------|----------------|-------------------------------------|------------|
+| `dir`       | [str](`str`)   | Directory of KIMMDY run             | _required_ |
+| `open_plot` | [bool](`bool`) | Open plot in default system viewer. | `False`    |
+
+### runtime_analysis { #kimmdy.analysis.runtime_analysis }
+
+`analysis.runtime_analysis(dir, open_plot=False)`
+
+Plot which atoms participate in reactions.
+
+#### Parameters
+
 | Name        | Type           | Description                         | Default    |
 |-------------|----------------|-------------------------------------|------------|
 | `dir`       | [str](`str`)   | Directory of KIMMDY run             | _required_ |
diff --git a/_reference/kmc.qmd b/_reference/kmc.qmd
index c7f1a0eb..ce53cb46 100644
--- a/_reference/kmc.qmd
+++ b/_reference/kmc.qmd
@@ -18,7 +18,7 @@ and because we have one reactant molecule
 
 ### KMCResult { #kimmdy.kmc.KMCResult }
 
-`kmc.KMCResult(self, recipe=lambda: Recipe([], [], [])(), reaction_probability=None, time_delta=None, time_start=None)`
+`kmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)`
 
 The result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.
 
diff --git a/_reference/recipe.qmd b/_reference/recipe.qmd
index a8c04b1e..69b34e2a 100644
--- a/_reference/recipe.qmd
+++ b/_reference/recipe.qmd
@@ -77,7 +77,7 @@ Change topology to break a bond
 
 ### CustomTopMod { #kimmdy.recipe.CustomTopMod }
 
-`recipe.CustomTopMod(self, f)`
+`recipe.CustomTopMod(f)`
 
 A custom recipe step that can be used to define a custom topology modification.
 
@@ -105,7 +105,7 @@ Either provide the index (ix_to_place) or the ID (id_to_place) of the atom to pl
 
 ### Recipe { #kimmdy.recipe.Recipe }
 
-`recipe.Recipe(self, recipe_steps, rates, timespans)`
+`recipe.Recipe(recipe_steps, rates, timespans)`
 
 A reaction path defined by one series of RecipeSteps.
 Defines everything necessart to build the
@@ -146,7 +146,7 @@ Combines this Recipe with another with the same RecipeSteps.
 
 ### RecipeCollection { #kimmdy.recipe.RecipeCollection }
 
-`recipe.RecipeCollection(self, recipes)`
+`recipe.RecipeCollection(recipes)`
 
 A RecipeCollection encompasses a number of reaction paths.
 They can originate from multiple reaction plugins, but do not need to.
@@ -234,7 +234,7 @@ id: 1-based, str
 
 ### Relax { #kimmdy.recipe.Relax }
 
-`recipe.Relax(self)`
+`recipe.Relax()`
 
 Start a relaxation MD.
 
diff --git a/docs/_reference/analysis.html b/docs/_reference/analysis.html
index d74d9717..6dd8d4ac 100644
--- a/docs/_reference/analysis.html
+++ b/docs/_reference/analysis.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
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   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
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+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
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             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/analysis.html">analysis</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -475,32 +488,33 @@ <h2 id="toc-title">On this page</h2>
   <ul class="collapse">
   <li><a href="#parameters-3" id="toc-parameters-3" class="nav-link" data-scroll-target="#parameters-3">Parameters</a></li>
   </ul></li>
-  <li><a href="#kimmdy.analysis.plot_runtime" id="toc-kimmdy.analysis.plot_runtime" class="nav-link" data-scroll-target="#kimmdy.analysis.plot_runtime">plot_runtime</a>
+  <li><a href="#kimmdy.analysis.radical_migration" id="toc-kimmdy.analysis.radical_migration" class="nav-link" data-scroll-target="#kimmdy.analysis.radical_migration">radical_migration</a>
   <ul class="collapse">
   <li><a href="#parameters-4" id="toc-parameters-4" class="nav-link" data-scroll-target="#parameters-4">Parameters</a></li>
   </ul></li>
-  <li><a href="#kimmdy.analysis.radical_migration" id="toc-kimmdy.analysis.radical_migration" class="nav-link" data-scroll-target="#kimmdy.analysis.radical_migration">radical_migration</a>
+  <li><a href="#kimmdy.analysis.radical_population" id="toc-kimmdy.analysis.radical_population" class="nav-link" data-scroll-target="#kimmdy.analysis.radical_population">radical_population</a>
   <ul class="collapse">
   <li><a href="#parameters-5" id="toc-parameters-5" class="nav-link" data-scroll-target="#parameters-5">Parameters</a></li>
   </ul></li>
-  <li><a href="#kimmdy.analysis.radical_population" id="toc-kimmdy.analysis.radical_population" class="nav-link" data-scroll-target="#kimmdy.analysis.radical_population">radical_population</a>
+  <li><a href="#kimmdy.analysis.reaction_participation" id="toc-kimmdy.analysis.reaction_participation" class="nav-link" data-scroll-target="#kimmdy.analysis.reaction_participation">reaction_participation</a>
   <ul class="collapse">
   <li><a href="#parameters-6" id="toc-parameters-6" class="nav-link" data-scroll-target="#parameters-6">Parameters</a></li>
   </ul></li>
-  <li><a href="#kimmdy.analysis.reaction_participation" id="toc-kimmdy.analysis.reaction_participation" class="nav-link" data-scroll-target="#kimmdy.analysis.reaction_participation">reaction_participation</a>
+  <li><a href="#kimmdy.analysis.runtime_analysis" id="toc-kimmdy.analysis.runtime_analysis" class="nav-link" data-scroll-target="#kimmdy.analysis.runtime_analysis">runtime_analysis</a>
   <ul class="collapse">
   <li><a href="#parameters-7" id="toc-parameters-7" class="nav-link" data-scroll-target="#parameters-7">Parameters</a></li>
   </ul></li>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/analysis.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/analysis.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.analysis" class="level1">
 <h1>analysis</h1>
 <p><code>analysis</code></p>
@@ -540,21 +554,21 @@ <h2 class="anchored" data-anchor-id="functions">Functions</h2>
 <td>Plot rates of all possible reactions for each ‘decide_recipe’ step.</td>
 </tr>
 <tr class="odd">
-<td><a href="#kimmdy.analysis.plot_runtime">plot_runtime</a></td>
-<td>Plot runtime of all tasks.</td>
-</tr>
-<tr class="even">
 <td><a href="#kimmdy.analysis.radical_migration">radical_migration</a></td>
 <td>Plot population of radicals for a KIMMDY run.</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td><a href="#kimmdy.analysis.radical_population">radical_population</a></td>
 <td>Plot population of radicals for a KIMMDY run.</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td><a href="#kimmdy.analysis.reaction_participation">reaction_participation</a></td>
 <td>Plot which atoms participate in reactions.</td>
 </tr>
+<tr class="even">
+<td><a href="#kimmdy.analysis.runtime_analysis">runtime_analysis</a></td>
+<td>Plot which atoms participate in reactions.</td>
+</tr>
 </tbody>
 </table>
 <section id="kimmdy.analysis.concat_traj" class="level3">
@@ -742,56 +756,12 @@ <h4 class="anchored" data-anchor-id="parameters-3">Parameters</h4>
 </table>
 </section>
 </section>
-<section id="kimmdy.analysis.plot_runtime" class="level3">
-<h3 class="anchored" data-anchor-id="kimmdy.analysis.plot_runtime">plot_runtime</h3>
-<p><code>analysis.plot_runtime(dir, md_tasks, datefmt, open_plot=False)</code></p>
-<p>Plot runtime of all tasks.</p>
-<section id="parameters-4" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-4">Parameters</h4>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>dir</code></td>
-<td><a href="https://docs.python.org/3.10/library/stdtypes.html#str">str</a></td>
-<td>Directory of KIMMDY run</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>md_tasks</code></td>
-<td><a href="https://docs.python.org/3.10/library/stdtypes.html#list">list</a></td>
-<td>Names of MD tasks to color</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>datefmt</code></td>
-<td><a href="https://docs.python.org/3.10/library/stdtypes.html#str">str</a></td>
-<td>Date format in the KIMMDY logfile</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>open_plot</code></td>
-<td><a href="https://docs.python.org/3.10/library/functions.html#bool">bool</a></td>
-<td>Open plot in default system viewer.</td>
-<td><code>False</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-</section>
 <section id="kimmdy.analysis.radical_migration" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.analysis.radical_migration">radical_migration</h3>
 <p><code>analysis.radical_migration(dirs, type='qualitative', cutoff=1)</code></p>
 <p>Plot population of radicals for a KIMMDY run.</p>
-<section id="parameters-5" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
+<section id="parameters-4" class="level4">
+<h4 class="anchored" data-anchor-id="parameters-4">Parameters</h4>
 <table class="table">
 <thead>
 <tr class="header">
@@ -828,8 +798,8 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
 <h3 class="anchored" data-anchor-id="kimmdy.analysis.radical_population">radical_population</h3>
 <p><code>analysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)</code></p>
 <p>Plot population of radicals for a KIMMDY run.</p>
-<section id="parameters-6" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
+<section id="parameters-5" class="level4">
+<h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
 <table class="table">
 <thead>
 <tr class="header">
@@ -884,6 +854,38 @@ <h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
 <h3 class="anchored" data-anchor-id="kimmdy.analysis.reaction_participation">reaction_participation</h3>
 <p><code>analysis.reaction_participation(dir, open_plot=False)</code></p>
 <p>Plot which atoms participate in reactions.</p>
+<section id="parameters-6" class="level4">
+<h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
+<table class="table">
+<thead>
+<tr class="header">
+<th>Name</th>
+<th>Type</th>
+<th>Description</th>
+<th>Default</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td><code>dir</code></td>
+<td><a href="https://docs.python.org/3.10/library/stdtypes.html#str">str</a></td>
+<td>Directory of KIMMDY run</td>
+<td><em>required</em></td>
+</tr>
+<tr class="even">
+<td><code>open_plot</code></td>
+<td><a href="https://docs.python.org/3.10/library/functions.html#bool">bool</a></td>
+<td>Open plot in default system viewer.</td>
+<td><code>False</code></td>
+</tr>
+</tbody>
+</table>
+</section>
+</section>
+<section id="kimmdy.analysis.runtime_analysis" class="level3">
+<h3 class="anchored" data-anchor-id="kimmdy.analysis.runtime_analysis">runtime_analysis</h3>
+<p><code>analysis.runtime_analysis(dir, open_plot=False)</code></p>
+<p>Plot which atoms participate in reactions.</p>
 <section id="parameters-7" class="level4">
 <h4 class="anchored" data-anchor-id="parameters-7">Parameters</h4>
 <table class="table">
@@ -1180,18 +1182,64 @@ <h4 class="anchored" data-anchor-id="parameters-7">Parameters</h4>
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+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -1201,27 +1249,56 @@ <h4 class="anchored" data-anchor-id="parameters-7">Parameters</h4>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1299,6 +1376,32 @@ <h4 class="anchored" data-anchor-id="parameters-7">Parameters</h4>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1360,12 +1463,12 @@ <h4 class="anchored" data-anchor-id="parameters-7">Parameters</h4>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/plugins.html" class="pagination-link">
+      <a href="../_reference/plugins.html" class="pagination-link  aria-label=" plugins"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">plugins</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/utils.html" class="pagination-link">
+      <a href="../_reference/utils.html" class="pagination-link" aria-label="utils">
         <span class="nav-page-text">utils</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/cmd.html b/docs/_reference/cmd.html
index ead9f5f1..b64e85a6 100644
--- a/docs/_reference/cmd.html
+++ b/docs/_reference/cmd.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">cmd</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -469,13 +482,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/cmd.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/cmd.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.cmd" class="level1">
 <h1>cmd</h1>
 <p><code>cmd</code></p>
@@ -881,18 +895,64 @@ <h4 class="anchored" data-anchor-id="parameters-1">Parameters</h4>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -902,27 +962,56 @@ <h4 class="anchored" data-anchor-id="parameters-1">Parameters</h4>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1000,6 +1089,32 @@ <h4 class="anchored" data-anchor-id="parameters-1">Parameters</h4>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1061,12 +1176,12 @@ <h4 class="anchored" data-anchor-id="parameters-1">Parameters</h4>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../guide/references/cmd_ref.html" class="pagination-link">
+      <a href="../guide/references/cmd_ref.html" class="pagination-link  aria-label=" cli="" arguments"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">CLI Arguments</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/topology.topology.html" class="pagination-link">
+      <a href="../_reference/topology.topology.html" class="pagination-link" aria-label="topology.topology">
         <span class="nav-page-text">topology.topology</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/config.html b/docs/_reference/config.html
index d9bf60ec..314b9a76 100644
--- a/docs/_reference/config.html
+++ b/docs/_reference/config.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/config.html">config</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -465,13 +478,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/config.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/config.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.config" class="level1">
 <h1>config</h1>
 <p><code>config</code></p>
@@ -835,18 +849,64 @@ <h5 class="anchored" data-anchor-id="kimmdy.config.Config.get_attributes">get_at
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -856,27 +916,56 @@ <h5 class="anchored" data-anchor-id="kimmdy.config.Config.get_attributes">get_at
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -954,6 +1043,32 @@ <h5 class="anchored" data-anchor-id="kimmdy.config.Config.get_attributes">get_at
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1015,12 +1130,12 @@ <h5 class="anchored" data-anchor-id="kimmdy.config.Config.get_attributes">get_at
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/coordinates.html" class="pagination-link">
+      <a href="../_reference/coordinates.html" class="pagination-link  aria-label=" coordinates"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">coordinates</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/kmc.html" class="pagination-link">
+      <a href="../_reference/kmc.html" class="pagination-link" aria-label="kmc">
         <span class="nav-page-text">kmc</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/constants.html b/docs/_reference/constants.html
index 676c92cd..8cfbe5d7 100644
--- a/docs/_reference/constants.html
+++ b/docs/_reference/constants.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">constants</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -454,13 +467,14 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#attributes" id="toc-attributes" class="nav-link" data-scroll-target="#attributes">Attributes</a></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/constants.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/constants.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.constants" class="level1">
 <h1>constants</h1>
 <p><code>constants</code></p>
@@ -753,18 +767,64 @@ <h2 class="anchored" data-anchor-id="attributes">Attributes</h2>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -774,27 +834,56 @@ <h2 class="anchored" data-anchor-id="attributes">Attributes</h2>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -872,6 +961,32 @@ <h2 class="anchored" data-anchor-id="attributes">Attributes</h2>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -933,12 +1048,12 @@ <h2 class="anchored" data-anchor-id="attributes">Attributes</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/dummyreaction.reaction.DummyReaction.html" class="pagination-link">
+      <a href="../_reference/dummyreaction.reaction.DummyReaction.html" class="pagination-link  aria-label=" dummyreaction.reaction.dummyreaction"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">dummyreaction.reaction.DummyReaction</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/coordinates.html" class="pagination-link">
+      <a href="../_reference/coordinates.html" class="pagination-link" aria-label="coordinates">
         <span class="nav-page-text">coordinates</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/coordinates.html b/docs/_reference/coordinates.html
index da7775f2..14995be7 100644
--- a/docs/_reference/coordinates.html
+++ b/docs/_reference/coordinates.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/coordinates.html">coordinates</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -467,13 +480,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/coordinates.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/coordinates.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.coordinates" class="level1">
 <h1>coordinates</h1>
 <p><code>coordinates</code></p>
@@ -858,18 +872,64 @@ <h3 class="anchored" data-anchor-id="kimmdy.coordinates.place_atom">place_atom</
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -879,27 +939,56 @@ <h3 class="anchored" data-anchor-id="kimmdy.coordinates.place_atom">place_atom</
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -977,6 +1066,32 @@ <h3 class="anchored" data-anchor-id="kimmdy.coordinates.place_atom">place_atom</
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1038,12 +1153,12 @@ <h3 class="anchored" data-anchor-id="kimmdy.coordinates.place_atom">place_atom</
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/constants.html" class="pagination-link">
+      <a href="../_reference/constants.html" class="pagination-link  aria-label=" constants"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">constants</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/config.html" class="pagination-link">
+      <a href="../_reference/config.html" class="pagination-link" aria-label="config">
         <span class="nav-page-text">config</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/dummyreaction.reaction.DummyReaction.html b/docs/_reference/dummyreaction.reaction.DummyReaction.html
index 144f2bd4..7908dbe6 100644
--- a/docs/_reference/dummyreaction.reaction.DummyReaction.html
+++ b/docs/_reference/dummyreaction.reaction.DummyReaction.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/homolysis.reaction.Homolysis.html">Reaction Plugins</a></li><li class="breadcrumb-item"><a href="../_reference/dummyreaction.reaction.DummyReaction.html">dummyreaction.reaction.DummyReaction</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -451,13 +464,14 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#dummyreaction.reaction.DummyReaction" id="toc-dummyreaction.reaction.DummyReaction" class="nav-link active" data-scroll-target="#dummyreaction.reaction.DummyReaction">dummyreaction.reaction.DummyReaction</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/dummyreaction.reaction.DummyReaction.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/dummyreaction.reaction.DummyReaction.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="dummyreaction.reaction.DummyReaction" class="level1">
 <h1>dummyreaction.reaction.DummyReaction</h1>
 <p><code>reaction.DummyReaction(self, name, runmng)</code></p>
@@ -729,18 +743,64 @@ <h1>dummyreaction.reaction.DummyReaction</h1>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -750,27 +810,56 @@ <h1>dummyreaction.reaction.DummyReaction</h1>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -848,6 +937,32 @@ <h1>dummyreaction.reaction.DummyReaction</h1>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -909,12 +1024,12 @@ <h1>dummyreaction.reaction.DummyReaction</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/hat_naive.reaction.NaiveHAT.html" class="pagination-link">
+      <a href="../_reference/hat_naive.reaction.NaiveHAT.html" class="pagination-link  aria-label=" hat_naive.reaction.naivehat"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">hat_naive.reaction.NaiveHAT</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/constants.html" class="pagination-link">
+      <a href="../_reference/constants.html" class="pagination-link" aria-label="constants">
         <span class="nav-page-text">constants</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/hat_naive.reaction.NaiveHAT.html b/docs/_reference/hat_naive.reaction.NaiveHAT.html
index a1300f98..63241882 100644
--- a/docs/_reference/hat_naive.reaction.NaiveHAT.html
+++ b/docs/_reference/hat_naive.reaction.NaiveHAT.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/homolysis.reaction.Homolysis.html">Reaction Plugins</a></li><li class="breadcrumb-item"><a href="../_reference/hat_naive.reaction.NaiveHAT.html">hat_naive.reaction.NaiveHAT</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -451,13 +464,14 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#hat_naive.reaction.NaiveHAT" id="toc-hat_naive.reaction.NaiveHAT" class="nav-link active" data-scroll-target="#hat_naive.reaction.NaiveHAT">hat_naive.reaction.NaiveHAT</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/hat_naive.reaction.NaiveHAT.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/hat_naive.reaction.NaiveHAT.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="hat_naive.reaction.NaiveHAT" class="level1">
 <h1>hat_naive.reaction.NaiveHAT</h1>
 <p><code>reaction.NaiveHAT(self, name, runmng)</code></p>
@@ -729,18 +743,64 @@ <h1>hat_naive.reaction.NaiveHAT</h1>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
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       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -750,27 +810,56 @@ <h1>hat_naive.reaction.NaiveHAT</h1>
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       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -848,6 +937,32 @@ <h1>hat_naive.reaction.NaiveHAT</h1>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -909,12 +1024,12 @@ <h1>hat_naive.reaction.NaiveHAT</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/homolysis.reaction.Homolysis.html" class="pagination-link">
+      <a href="../_reference/homolysis.reaction.Homolysis.html" class="pagination-link  aria-label=" homolysis.reaction.homolysis"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">homolysis.reaction.Homolysis</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/dummyreaction.reaction.DummyReaction.html" class="pagination-link">
+      <a href="../_reference/dummyreaction.reaction.DummyReaction.html" class="pagination-link" aria-label="dummyreaction.reaction.DummyReaction">
         <span class="nav-page-text">dummyreaction.reaction.DummyReaction</span> <i class="bi bi-arrow-right-short"></i>
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diff --git a/docs/_reference/homolysis.reaction.Homolysis.html b/docs/_reference/homolysis.reaction.Homolysis.html
index f4cc6ca1..a2eb78ac 100644
--- a/docs/_reference/homolysis.reaction.Homolysis.html
+++ b/docs/_reference/homolysis.reaction.Homolysis.html
@@ -2,7 +2,7 @@
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 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
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@@ -49,12 +49,13 @@
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-  "limit": 20,
+  "limit": 50,
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     "/",
     "s"
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+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
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       <div class="navbar-brand-container mx-auto">
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@@ -90,24 +91,24 @@
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-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
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@@ -138,11 +139,11 @@
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-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -451,13 +464,14 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#homolysis.reaction.Homolysis" id="toc-homolysis.reaction.Homolysis" class="nav-link active" data-scroll-target="#homolysis.reaction.Homolysis">homolysis.reaction.Homolysis</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/homolysis.reaction.Homolysis.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/homolysis.reaction.Homolysis.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="homolysis.reaction.Homolysis" class="level1">
 <h1>homolysis.reaction.Homolysis</h1>
 <p><code>reaction.Homolysis(self, name, runmng)</code></p>
@@ -729,18 +743,64 @@ <h1>homolysis.reaction.Homolysis</h1>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
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+    stripColumnClz(note)
+    const typesetMath = (el) => {
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+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
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+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
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       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
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+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
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+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
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@@ -750,27 +810,56 @@ <h1>homolysis.reaction.Homolysis</h1>
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       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -848,6 +937,32 @@ <h1>homolysis.reaction.Homolysis</h1>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -909,12 +1024,12 @@ <h1>homolysis.reaction.Homolysis</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/parsing.TopologyDict.html" class="pagination-link">
+      <a href="../_reference/parsing.TopologyDict.html" class="pagination-link  aria-label=" parsing.topologydict"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">parsing.TopologyDict</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/hat_naive.reaction.NaiveHAT.html" class="pagination-link">
+      <a href="../_reference/hat_naive.reaction.NaiveHAT.html" class="pagination-link" aria-label="hat_naive.reaction.NaiveHAT">
         <span class="nav-page-text">hat_naive.reaction.NaiveHAT</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/index.html b/docs/_reference/index.html
index f9abeffd..eff9f076 100644
--- a/docs/_reference/index.html
+++ b/docs/_reference/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -459,13 +472,14 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#reaction-plugins" id="toc-reaction-plugins" class="nav-link" data-scroll-target="#reaction-plugins">Reaction Plugins</a></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/index.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="references" class="level1 doc doc-index">
 <h1 class="doc doc-index">References</h1>
 <section id="input-file" class="level2">
@@ -867,18 +881,64 @@ <h2 class="anchored" data-anchor-id="reaction-plugins">Reaction Plugins</h2>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -888,27 +948,56 @@ <h2 class="anchored" data-anchor-id="reaction-plugins">Reaction Plugins</h2>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -986,6 +1075,32 @@ <h2 class="anchored" data-anchor-id="reaction-plugins">Reaction Plugins</h2>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1047,12 +1162,12 @@ <h2 class="anchored" data-anchor-id="reaction-plugins">Reaction Plugins</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../guide/explanation/topology.html" class="pagination-link">
+      <a href="../guide/explanation/topology.html" class="pagination-link  aria-label=" visualize="" topologies"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Visualize Topologies</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../guide/references/input.html" class="pagination-link">
+      <a href="../guide/references/input.html" class="pagination-link" aria-label="Input File">
         <span class="nav-page-text">Input File</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/kmc.html b/docs/_reference/kmc.html
index 3893a623..201c5226 100644
--- a/docs/_reference/kmc.html
+++ b/docs/_reference/kmc.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/kmc.html">kmc</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -481,13 +494,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/kmc.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/kmc.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.kmc" class="level1">
 <h1>kmc</h1>
 <p><code>kmc</code></p>
@@ -511,7 +525,7 @@ <h2 class="anchored" data-anchor-id="classes">Classes</h2>
 </table>
 <section id="kimmdy.kmc.KMCResult" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.kmc.KMCResult">KMCResult</h3>
-<p><code>kmc.KMCResult(self, recipe=lambda: Recipe([], [], [])(), reaction_probability=None, time_delta=None, time_start=None)</code></p>
+<p><code>kmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)</code></p>
 <p>The result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.</p>
 <section id="attributes" class="level4">
 <h4 class="anchored" data-anchor-id="attributes">Attributes</h4>
@@ -1030,18 +1044,64 @@ <h4 class="anchored" data-anchor-id="parameters-3">Parameters</h4>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -1051,27 +1111,56 @@ <h4 class="anchored" data-anchor-id="parameters-3">Parameters</h4>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1149,6 +1238,32 @@ <h4 class="anchored" data-anchor-id="parameters-3">Parameters</h4>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1210,12 +1325,12 @@ <h4 class="anchored" data-anchor-id="parameters-3">Parameters</h4>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/config.html" class="pagination-link">
+      <a href="../_reference/config.html" class="pagination-link  aria-label=" config"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">config</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/parsing.html" class="pagination-link">
+      <a href="../_reference/parsing.html" class="pagination-link" aria-label="parsing">
         <span class="nav-page-text">parsing</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/parsing.TopologyDict.html b/docs/_reference/parsing.TopologyDict.html
index 04a1c2f3..49e65f3d 100644
--- a/docs/_reference/parsing.TopologyDict.html
+++ b/docs/_reference/parsing.TopologyDict.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
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@@ -90,24 +91,24 @@
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-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
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 </ul>
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@@ -138,11 +139,11 @@
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+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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   </nav>
@@ -150,7 +151,7 @@
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 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -451,13 +464,14 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#kimmdy.parsing.TopologyDict" id="toc-kimmdy.parsing.TopologyDict" class="nav-link active" data-scroll-target="#kimmdy.parsing.TopologyDict">parsing.TopologyDict</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/parsing.TopologyDict.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/parsing.TopologyDict.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.parsing.TopologyDict" class="level1">
 <h1>parsing.TopologyDict</h1>
 <p><code>parsing.TopologyDict</code></p>
@@ -729,18 +743,64 @@ <h1>parsing.TopologyDict</h1>
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+        for (let i = 1; i < note.children.length; i++) {
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+      typesetMath(note);
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@@ -750,27 +810,56 @@ <h1>parsing.TopologyDict</h1>
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-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
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+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
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@@ -848,6 +937,32 @@ <h1>parsing.TopologyDict</h1>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -909,12 +1024,12 @@ <h1>parsing.TopologyDict</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/topology.atomic.html" class="pagination-link">
+      <a href="../_reference/topology.atomic.html" class="pagination-link  aria-label=" topology.atomic"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">topology.atomic</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/homolysis.reaction.Homolysis.html" class="pagination-link">
+      <a href="../_reference/homolysis.reaction.Homolysis.html" class="pagination-link" aria-label="homolysis.reaction.Homolysis">
         <span class="nav-page-text">homolysis.reaction.Homolysis</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/parsing.html b/docs/_reference/parsing.html
index cc759fda..c20fc3de 100644
--- a/docs/_reference/parsing.html
+++ b/docs/_reference/parsing.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -22,7 +22,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -83,12 +83,13 @@
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   "panel-placement": "end",
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-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
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     "/",
     "s"
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+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -110,7 +111,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -124,24 +125,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -172,11 +173,11 @@
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   <nav class="quarto-secondary-nav">
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-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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@@ -184,7 +185,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
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     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
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           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
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       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
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     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
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@@ -528,13 +541,14 @@ <h2 id="toc-title">On this page</h2>
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+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/parsing.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.parsing" class="level1">
 <h1>parsing</h1>
 <p><code>parsing</code></p>
@@ -1266,18 +1280,64 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
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+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -1287,27 +1347,56 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1385,6 +1474,32 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1446,12 +1561,12 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/kmc.html" class="pagination-link">
+      <a href="../_reference/kmc.html" class="pagination-link  aria-label=" kmc"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">kmc</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/runmanager.html" class="pagination-link">
+      <a href="../_reference/runmanager.html" class="pagination-link" aria-label="runmanager">
         <span class="nav-page-text">runmanager</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/plugins.html b/docs/_reference/plugins.html
index 14dd43e8..f5d3ecc5 100644
--- a/docs/_reference/plugins.html
+++ b/docs/_reference/plugins.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/plugins.html">plugins</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -471,13 +484,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/plugins.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/plugins.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.plugins" class="level1">
 <h1>plugins</h1>
 <p><code>plugins</code></p>
@@ -874,18 +888,64 @@ <h6 class="anchored" data-anchor-id="parameters-1">Parameters</h6>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -895,27 +955,56 @@ <h6 class="anchored" data-anchor-id="parameters-1">Parameters</h6>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -993,6 +1082,32 @@ <h6 class="anchored" data-anchor-id="parameters-1">Parameters</h6>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1054,12 +1169,12 @@ <h6 class="anchored" data-anchor-id="parameters-1">Parameters</h6>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/recipe.html" class="pagination-link">
+      <a href="../_reference/recipe.html" class="pagination-link  aria-label=" recipe"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">recipe</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/analysis.html" class="pagination-link">
+      <a href="../_reference/analysis.html" class="pagination-link" aria-label="analysis">
         <span class="nav-page-text">analysis</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/recipe.html b/docs/_reference/recipe.html
index 70d368e4..6dddd9d3 100644
--- a/docs/_reference/recipe.html
+++ b/docs/_reference/recipe.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/recipe.html">recipe</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -502,13 +515,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/recipe.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/recipe.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.recipe" class="level1">
 <h1>recipe</h1>
 <p><code>recipe</code></p>
@@ -717,7 +731,7 @@ <h4 class="anchored" data-anchor-id="parameters-2">Parameters</h4>
 </section>
 <section id="kimmdy.recipe.CustomTopMod" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.recipe.CustomTopMod">CustomTopMod</h3>
-<p><code>recipe.CustomTopMod(self, f)</code></p>
+<p><code>recipe.CustomTopMod(f)</code></p>
 <p>A custom recipe step that can be used to define a custom topology modification.</p>
 <section id="parameters-3" class="level4">
 <h4 class="anchored" data-anchor-id="parameters-3">Parameters</h4>
@@ -782,7 +796,7 @@ <h4 class="anchored" data-anchor-id="parameters-4">Parameters</h4>
 </section>
 <section id="kimmdy.recipe.Recipe" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.recipe.Recipe">Recipe</h3>
-<p><code>recipe.Recipe(self, recipe_steps, rates, timespans)</code></p>
+<p><code>recipe.Recipe(recipe_steps, rates, timespans)</code></p>
 <p>A reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.</p>
 <section id="parameters-5" class="level4">
 <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
@@ -872,7 +886,7 @@ <h6 class="anchored" data-anchor-id="parameters-6">Parameters</h6>
 </section>
 <section id="kimmdy.recipe.RecipeCollection" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.recipe.RecipeCollection">RecipeCollection</h3>
-<p><code>recipe.RecipeCollection(self, recipes)</code></p>
+<p><code>recipe.RecipeCollection(recipes)</code></p>
 <p>A RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.</p>
 <section id="returns" class="level4">
 <h4 class="anchored" data-anchor-id="returns">Returns</h4>
@@ -1032,7 +1046,7 @@ <h3 class="anchored" data-anchor-id="kimmdy.recipe.RecipeStep">RecipeStep</h3>
 </section>
 <section id="kimmdy.recipe.Relax" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.recipe.Relax">Relax</h3>
-<p><code>recipe.Relax(self)</code></p>
+<p><code>recipe.Relax()</code></p>
 <p>Start a relaxation MD.</p>
 <p>The molecular system coordinates are far out of equilibrium after most topology changes. A relaxtion MD simulation using for example the slow growth method helps to reach the new equilibrium.</p>
 
@@ -1304,18 +1318,64 @@ <h3 class="anchored" data-anchor-id="kimmdy.recipe.Relax">Relax</h3>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -1325,27 +1385,56 @@ <h3 class="anchored" data-anchor-id="kimmdy.recipe.Relax">Relax</h3>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1423,6 +1512,32 @@ <h3 class="anchored" data-anchor-id="kimmdy.recipe.Relax">Relax</h3>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1484,12 +1599,12 @@ <h3 class="anchored" data-anchor-id="kimmdy.recipe.Relax">Relax</h3>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/tasks.html" class="pagination-link">
+      <a href="../_reference/tasks.html" class="pagination-link  aria-label=" tasks"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">tasks</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/plugins.html" class="pagination-link">
+      <a href="../_reference/plugins.html" class="pagination-link" aria-label="plugins">
         <span class="nav-page-text">plugins</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/runmanager.html b/docs/_reference/runmanager.html
index c976d5cd..7b890c41 100644
--- a/docs/_reference/runmanager.html
+++ b/docs/_reference/runmanager.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/runmanager.html">runmanager</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -469,13 +482,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/runmanager.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/runmanager.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.runmanager" class="level1">
 <h1>runmanager</h1>
 <p><code>runmanager</code></p>
@@ -899,18 +913,64 @@ <h3 class="anchored" data-anchor-id="kimmdy.runmanager.get_existing_files">get_e
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -920,27 +980,56 @@ <h3 class="anchored" data-anchor-id="kimmdy.runmanager.get_existing_files">get_e
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1018,6 +1107,32 @@ <h3 class="anchored" data-anchor-id="kimmdy.runmanager.get_existing_files">get_e
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1079,12 +1194,12 @@ <h3 class="anchored" data-anchor-id="kimmdy.runmanager.get_existing_files">get_e
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/parsing.html" class="pagination-link">
+      <a href="../_reference/parsing.html" class="pagination-link  aria-label=" parsing"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">parsing</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/tasks.html" class="pagination-link">
+      <a href="../_reference/tasks.html" class="pagination-link" aria-label="tasks">
         <span class="nav-page-text">tasks</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/schema.html b/docs/_reference/schema.html
index 107eff62..0d159e2d 100644
--- a/docs/_reference/schema.html
+++ b/docs/_reference/schema.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -47,12 +47,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -74,7 +75,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -88,24 +89,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -136,11 +137,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -148,7 +149,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -197,6 +198,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -238,6 +245,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -440,7 +453,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -472,13 +485,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/schema.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/schema.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.schema" class="level1">
 <h1>schema</h1>
 <p><code>schema</code></p>
@@ -913,18 +927,64 @@ <h3 class="anchored" data-anchor-id="kimmdy.schema.prune">prune</h3>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -934,27 +994,56 @@ <h3 class="anchored" data-anchor-id="kimmdy.schema.prune">prune</h3>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1032,6 +1121,32 @@ <h3 class="anchored" data-anchor-id="kimmdy.schema.prune">prune</h3>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
diff --git a/docs/_reference/tasks.html b/docs/_reference/tasks.html
index 607fa578..536bb206 100644
--- a/docs/_reference/tasks.html
+++ b/docs/_reference/tasks.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -22,7 +22,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -83,12 +83,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -110,7 +111,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -124,24 +125,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -172,11 +173,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/tasks.html">tasks</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -184,7 +185,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -233,6 +234,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -274,6 +281,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -476,7 +489,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -504,13 +517,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/tasks.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/tasks.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.tasks" class="level1">
 <h1>tasks</h1>
 <p><code>tasks</code></p>
@@ -591,7 +605,7 @@ <h4 class="anchored" data-anchor-id="parameters">Parameters</h4>
 </section>
 <section id="kimmdy.tasks.TaskFiles" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.tasks.TaskFiles">TaskFiles</h3>
-<p><code>tasks.TaskFiles(self, get_latest, input=dict(), output=dict(), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))</code></p>
+<p><code>tasks.TaskFiles(get_latest, input=field(default_factory=dict), output=field(default_factory=dict), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))</code></p>
 <p>Class for Task input and output files and directories.</p>
 <p>Hosts the input and output file paths belonging to a task. A function or method that wants to be callable as a Task has to return a TaskFiles object. The input defaultdict is populated on the fly using get_latest of the runmanager to find newest files. Files which can not be found by get_latest must be added manually.</p>
 <section id="attributes" class="level4">
@@ -936,18 +950,64 @@ <h3 class="anchored" data-anchor-id="kimmdy.tasks.create_task_directory">create_
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -957,27 +1017,56 @@ <h3 class="anchored" data-anchor-id="kimmdy.tasks.create_task_directory">create_
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1055,6 +1144,32 @@ <h3 class="anchored" data-anchor-id="kimmdy.tasks.create_task_directory">create_
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1116,12 +1231,12 @@ <h3 class="anchored" data-anchor-id="kimmdy.tasks.create_task_directory">create_
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/runmanager.html" class="pagination-link">
+      <a href="../_reference/runmanager.html" class="pagination-link  aria-label=" runmanager"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">runmanager</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/recipe.html" class="pagination-link">
+      <a href="../_reference/recipe.html" class="pagination-link" aria-label="recipe">
         <span class="nav-page-text">recipe</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/tools.html b/docs/_reference/tools.html
index 75b676c4..3a3b07c2 100644
--- a/docs/_reference/tools.html
+++ b/docs/_reference/tools.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -48,12 +48,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -75,7 +76,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -89,24 +90,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -137,11 +138,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/tools.html">tools</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -149,7 +150,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -198,6 +199,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -239,6 +246,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -441,7 +454,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -474,13 +487,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/tools.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/tools.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.tools" class="level1">
 <h1>tools</h1>
 <p><code>tools</code></p>
@@ -958,18 +972,64 @@ <h3 class="anchored" data-anchor-id="kimmdy.tools.write_top_as_dot">write_top_as
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -979,27 +1039,56 @@ <h3 class="anchored" data-anchor-id="kimmdy.tools.write_top_as_dot">write_top_as
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1077,6 +1166,32 @@ <h3 class="anchored" data-anchor-id="kimmdy.tools.write_top_as_dot">write_top_as
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1138,7 +1253,7 @@ <h3 class="anchored" data-anchor-id="kimmdy.tools.write_top_as_dot">write_top_as
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/utils.html" class="pagination-link">
+      <a href="../_reference/utils.html" class="pagination-link  aria-label=" utils"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">utils</span>
       </a>          
   </div>
diff --git a/docs/_reference/topology.atomic.html b/docs/_reference/topology.atomic.html
index 37085cff..78893ce7 100644
--- a/docs/_reference/topology.atomic.html
+++ b/docs/_reference/topology.atomic.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/topology.topology.html">Topology</a></li><li class="breadcrumb-item"><a href="../_reference/topology.atomic.html">topology.atomic</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -476,13 +489,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/topology.atomic.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/topology.atomic.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.topology.atomic" class="level1">
 <h1>topology.atomic</h1>
 <p><code>topology.atomic</code></p>
@@ -581,49 +595,49 @@ <h2 class="anchored" data-anchor-id="classes">Classes</h2>
 </table>
 <section id="kimmdy.topology.atomic.Angle" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Angle">Angle</h3>
-<p><code>topology.atomic.Angle(self, ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)</code></p>
+<p><code>topology.atomic.Angle(ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)</code></p>
 <p>Information about one angle</p>
 <p>A class containing angle information as in the angles section of the topology.</p>
 <p>From gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj &lt; ai &lt; ak</p>
 </section>
 <section id="kimmdy.topology.atomic.AngleType" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.AngleType">AngleType</h3>
-<p><code>topology.atomic.AngleType(self, i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)</code></p>
+<p><code>topology.atomic.AngleType(i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)</code></p>
 <p>Information about one angletype</p>
 <p>A class containing angle type information as in the angletypes section of the forcefield.</p>
 <p>From gromacs version of the amber* ff: ; i j k func th0 cth</p>
 </section>
 <section id="kimmdy.topology.atomic.Atom" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Atom">Atom</h3>
-<p><code>topology.atomic.Atom(self, nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=list(), is_radical=False)</code></p>
+<p><code>topology.atomic.Atom(nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=field(default_factory=list), is_radical=False)</code></p>
 <p>Information about one atom</p>
 <p>A class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.</p>
 <p>From gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB</p>
 </section>
 <section id="kimmdy.topology.atomic.AtomType" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.AtomType">AtomType</h3>
-<p><code>topology.atomic.AtomType(self, type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)</code></p>
+<p><code>topology.atomic.AtomType(type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)</code></p>
 <p>Information about one atom type</p>
 <p>A class containing atom type information as in the atomtypes section of the forcefield.</p>
 <p>From gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon</p>
 </section>
 <section id="kimmdy.topology.atomic.Bond" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Bond">Bond</h3>
-<p><code>topology.atomic.Bond(self, ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)</code></p>
+<p><code>topology.atomic.Bond(ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)</code></p>
 <p>Information about one bond</p>
 <p>A class containing bond information as in the bonds section of the topology.</p>
 <p>From gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai &lt; aj</p>
 </section>
 <section id="kimmdy.topology.atomic.BondType" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.BondType">BondType</h3>
-<p><code>topology.atomic.BondType(self, i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)</code></p>
+<p><code>topology.atomic.BondType(i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)</code></p>
 <p>Information about one bondtype</p>
 <p>A class containing bond information as in the bondtype section of the forcefield.</p>
 <p>From gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes</p>
 </section>
 <section id="kimmdy.topology.atomic.Dihedral" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Dihedral">Dihedral</h3>
-<p><code>topology.atomic.Dihedral(self, ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)</code></p>
+<p><code>topology.atomic.Dihedral(ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)</code></p>
 <p>Information about one proper or improper dihedral</p>
 <p>A class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.</p>
 <p>Note that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.</p>
@@ -631,14 +645,14 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Dihedral">Dihedral</
 </section>
 <section id="kimmdy.topology.atomic.DihedralRestraint" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.DihedralRestraint">DihedralRestraint</h3>
-<p><code>topology.atomic.DihedralRestraint(self, ai, aj, ak, al, type, phi, dphi, fc)</code></p>
+<p><code>topology.atomic.DihedralRestraint(ai, aj, ak, al, type, phi, dphi, fc)</code></p>
 <p>Information about one dihedral restraint.</p>
 <p>A class containing information as in the dihedral_restraints section of the topology.</p>
 <p>From gromacs topology: ; ai aj ak al type phi dphi fc</p>
 </section>
 <section id="kimmdy.topology.atomic.DihedralType" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.DihedralType">DihedralType</h3>
-<p><code>topology.atomic.DihedralType(self, i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)</code></p>
+<p><code>topology.atomic.DihedralType(i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)</code></p>
 <p>Information about one dihedraltype</p>
 <p>A class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.</p>
 <p>Note that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the <code>id</code>.</p>
@@ -646,67 +660,67 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.DihedralType">Dihedr
 </section>
 <section id="kimmdy.topology.atomic.Exclusion" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Exclusion">Exclusion</h3>
-<p><code>topology.atomic.Exclusion(self, ai, aj, ak=None, al=None)</code></p>
+<p><code>topology.atomic.Exclusion(ai, aj, ak=None, al=None)</code></p>
 <p>Information about one exclusion</p>
 <p>A class containing atom information as in the exclusions section of the topology.</p>
 <p>From gromacs topology: ; ai aj ak al</p>
 </section>
 <section id="kimmdy.topology.atomic.MultipleDihedralTypes" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.MultipleDihedralTypes">MultipleDihedralTypes</h3>
-<p><code>topology.atomic.MultipleDihedralTypes(self, ai, aj, ak, al, funct, dihedral_types)</code></p>
+<p><code>topology.atomic.MultipleDihedralTypes(ai, aj, ak, al, funct, dihedral_types)</code></p>
 <p>Multiple <code>DihedralTypes</code>s with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedral_types dict is the periodicity (c2).</p>
 </section>
 <section id="kimmdy.topology.atomic.MultipleDihedrals" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.MultipleDihedrals">MultipleDihedrals</h3>
-<p><code>topology.atomic.MultipleDihedrals(self, ai, aj, ak, al, funct, dihedrals)</code></p>
+<p><code>topology.atomic.MultipleDihedrals(ai, aj, ak, al, funct, dihedrals)</code></p>
 <p>Multiple <code>Dihedral</code>s with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedrals dict is the periodicity (c2).</p>
 </section>
 <section id="kimmdy.topology.atomic.Pair" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Pair">Pair</h3>
-<p><code>topology.atomic.Pair(self, ai, aj, funct, c0=None, c1=None, c2=None, c3=None)</code></p>
+<p><code>topology.atomic.Pair(ai, aj, funct, c0=None, c1=None, c2=None, c3=None)</code></p>
 <p>Information about one pair</p>
 <p>A class containing pair information as in the pair section of the topology.</p>
 <p>From gromacs topology: ; ai aj funct c0 c1 c2 c3</p>
 </section>
 <section id="kimmdy.topology.atomic.PositionRestraint" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.PositionRestraint">PositionRestraint</h3>
-<p><code>topology.atomic.PositionRestraint(self, ai, funct, fc, condition=None)</code></p>
+<p><code>topology.atomic.PositionRestraint(ai, funct, fc, condition=None)</code></p>
 <p>Information about one position restraint.</p>
 <p>A class containing information as in the position_restraints section of the topology.</p>
 <p>From gromacs topology: ; ai funct fc(x,y,z)</p>
 </section>
 <section id="kimmdy.topology.atomic.ResidueAtomSpec" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.ResidueAtomSpec">ResidueAtomSpec</h3>
-<p><code>topology.atomic.ResidueAtomSpec(self, name, type, charge, cgrp)</code></p>
+<p><code>topology.atomic.ResidueAtomSpec(name, type, charge, cgrp)</code></p>
 <p>Information about one atom in a residue</p>
 <p>; name type charge chargegroup</p>
 </section>
 <section id="kimmdy.topology.atomic.ResidueBondSpec" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.ResidueBondSpec">ResidueBondSpec</h3>
-<p><code>topology.atomic.ResidueBondSpec(self, atom1, atom2, b0=None, kb=None)</code></p>
+<p><code>topology.atomic.ResidueBondSpec(atom1, atom2, b0=None, kb=None)</code></p>
 <p>Information about one bond in a residue</p>
 <p>; atom1 atom2 b0 kb</p>
 </section>
 <section id="kimmdy.topology.atomic.ResidueImproperSpec" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.ResidueImproperSpec">ResidueImproperSpec</h3>
-<p><code>topology.atomic.ResidueImproperSpec(self, atom1, atom2, atom3, atom4, c0, c1, c2)</code></p>
+<p><code>topology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)</code></p>
 <p>Information about one improper dihedral in a residue</p>
 <p>; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)</p>
 </section>
 <section id="kimmdy.topology.atomic.ResidueProperSpec" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.ResidueProperSpec">ResidueProperSpec</h3>
-<p><code>topology.atomic.ResidueProperSpec(self, atom1, atom2, atom3, atom4, c0, c1, c2)</code></p>
+<p><code>topology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)</code></p>
 <p>Information about one proper dihedral in a residue</p>
 <p>; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2</p>
 </section>
 <section id="kimmdy.topology.atomic.ResidueType" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.ResidueType">ResidueType</h3>
-<p><code>topology.atomic.ResidueType(self, residue, atoms, bonds, proper_dihedrals, improper_dihedrals)</code></p>
+<p><code>topology.atomic.ResidueType(residue, atoms, bonds, proper_dihedrals, improper_dihedrals)</code></p>
 <p>Information about one residuetype from aminoacids.rtp</p>
 </section>
 <section id="kimmdy.topology.atomic.Settle" class="level3">
 <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Settle">Settle</h3>
-<p><code>topology.atomic.Settle(self, nr, funct, doh, dhh)</code></p>
+<p><code>topology.atomic.Settle(nr, funct, doh, dhh)</code></p>
 <p>Information about one settles</p>
 <p>A class containing atom information as in the settle section of the topology.</p>
 <p>From gromacs topology: ; nr funct doh dhh</p>
@@ -979,18 +993,64 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Settle">Settle</h3>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -1000,27 +1060,56 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Settle">Settle</h3>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1098,6 +1187,32 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Settle">Settle</h3>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1159,12 +1274,12 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Settle">Settle</h3>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/topology.utils.html" class="pagination-link">
+      <a href="../_reference/topology.utils.html" class="pagination-link  aria-label=" topology.utils"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">topology.utils</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/parsing.TopologyDict.html" class="pagination-link">
+      <a href="../_reference/parsing.TopologyDict.html" class="pagination-link" aria-label="parsing.TopologyDict">
         <span class="nav-page-text">parsing.TopologyDict</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/topology.ff.html b/docs/_reference/topology.ff.html
index d39d2668..f2013e8e 100644
--- a/docs/_reference/topology.ff.html
+++ b/docs/_reference/topology.ff.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/topology.topology.html">Topology</a></li><li class="breadcrumb-item"><a href="../_reference/topology.ff.html">topology.ff</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -457,13 +470,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/topology.ff.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/topology.ff.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.topology.ff" class="level1">
 <h1>topology.ff</h1>
 <p><code>topology.ff</code></p>
@@ -756,18 +770,64 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.ff.FF">FF</h3>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -777,27 +837,56 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.ff.FF">FF</h3>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -875,6 +964,32 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.ff.FF">FF</h3>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -936,12 +1051,12 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.ff.FF">FF</h3>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/topology.topology.html" class="pagination-link">
+      <a href="../_reference/topology.topology.html" class="pagination-link  aria-label=" topology.topology"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">topology.topology</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/topology.utils.html" class="pagination-link">
+      <a href="../_reference/topology.utils.html" class="pagination-link" aria-label="topology.utils">
         <span class="nav-page-text">topology.utils</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/topology.topology.html b/docs/_reference/topology.topology.html
index 18565824..35106cd7 100644
--- a/docs/_reference/topology.topology.html
+++ b/docs/_reference/topology.topology.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
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-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -478,13 +491,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/topology.topology.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/topology.topology.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.topology.topology" class="level1">
 <h1>topology.topology</h1>
 <p><code>topology.topology</code></p>
@@ -1066,18 +1080,64 @@ <h5 class="anchored" data-anchor-id="kimmdy.topology.topology.Topology.validate_
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -1087,27 +1147,56 @@ <h5 class="anchored" data-anchor-id="kimmdy.topology.topology.Topology.validate_
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1185,6 +1274,32 @@ <h5 class="anchored" data-anchor-id="kimmdy.topology.topology.Topology.validate_
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1246,12 +1361,12 @@ <h5 class="anchored" data-anchor-id="kimmdy.topology.topology.Topology.validate_
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/cmd.html" class="pagination-link">
+      <a href="../_reference/cmd.html" class="pagination-link  aria-label=" cmd"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">cmd</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/topology.ff.html" class="pagination-link">
+      <a href="../_reference/topology.ff.html" class="pagination-link" aria-label="topology.ff">
         <span class="nav-page-text">topology.ff</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/topology.utils.html b/docs/_reference/topology.utils.html
index 37743329..61f1e7fe 100644
--- a/docs/_reference/topology.utils.html
+++ b/docs/_reference/topology.utils.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/topology.topology.html">Topology</a></li><li class="breadcrumb-item"><a href="../_reference/topology.utils.html">topology.utils</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -472,13 +485,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/topology.utils.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/topology.utils.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.topology.utils" class="level1">
 <h1>topology.utils</h1>
 <p><code>topology.utils</code></p>
@@ -942,18 +956,64 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.utils.set_top_section">set_
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -963,27 +1023,56 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.utils.set_top_section">set_
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1061,6 +1150,32 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.utils.set_top_section">set_
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1122,12 +1237,12 @@ <h3 class="anchored" data-anchor-id="kimmdy.topology.utils.set_top_section">set_
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/topology.ff.html" class="pagination-link">
+      <a href="../_reference/topology.ff.html" class="pagination-link  aria-label=" topology.ff"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">topology.ff</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/topology.atomic.html" class="pagination-link">
+      <a href="../_reference/topology.atomic.html" class="pagination-link" aria-label="topology.atomic">
         <span class="nav-page-text">topology.atomic</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/_reference/utils.html b/docs/_reference/utils.html
index a0f9dbc7..8bbd7dd7 100644
--- a/docs/_reference/utils.html
+++ b/docs/_reference/utils.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/cmd.html">Python API</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Other Modules</a></li><li class="breadcrumb-item"><a href="../_reference/utils.html">utils</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -487,13 +500,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/utils.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/_reference/utils.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy.utils" class="level1">
 <h1>utils</h1>
 <p><code>utils</code></p>
@@ -1100,18 +1114,64 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -1121,27 +1181,56 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1219,6 +1308,32 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1280,12 +1395,12 @@ <h4 class="anchored" data-anchor-id="parameters-5">Parameters</h4>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../_reference/analysis.html" class="pagination-link">
+      <a href="../_reference/analysis.html" class="pagination-link  aria-label=" analysis"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">analysis</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../_reference/tools.html" class="pagination-link">
+      <a href="../_reference/tools.html" class="pagination-link" aria-label="tools">
         <span class="nav-page-text">tools</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/guide/explanation/components.html b/docs/guide/explanation/components.html
new file mode 100644
index 00000000..6ad9229e
--- /dev/null
+++ b/docs/guide/explanation/components.html
@@ -0,0 +1,1061 @@
+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
+
+<meta charset="utf-8">
+<meta name="generator" content="quarto-1.4.513">
+
+<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
+
+<meta name="author" content="Kai Riedmiller">
+
+<title>KIMMDY - Components of KIMMDY</title>
+<style>
+code{white-space: pre-wrap;}
+span.smallcaps{font-variant: small-caps;}
+div.columns{display: flex; gap: min(4vw, 1.5em);}
+div.column{flex: auto; overflow-x: auto;}
+div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+ul.task-list{list-style: none;}
+ul.task-list li input[type="checkbox"] {
+  width: 0.8em;
+  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
+  vertical-align: middle;
+}
+</style>
+
+
+<script src="../../site_libs/quarto-nav/quarto-nav.js"></script>
+<script src="../../site_libs/quarto-nav/headroom.min.js"></script>
+<script src="../../site_libs/clipboard/clipboard.min.js"></script>
+<script src="../../site_libs/quarto-search/autocomplete.umd.js"></script>
+<script src="../../site_libs/quarto-search/fuse.min.js"></script>
+<script src="../../site_libs/quarto-search/quarto-search.js"></script>
+<meta name="quarto:offset" content="../../">
+<link href="../../guide/explanation/topology.html" rel="next">
+<link href="../../guide/explanation/index.html" rel="prev">
+<script src="../../site_libs/quarto-html/quarto.js"></script>
+<script src="../../site_libs/quarto-html/popper.min.js"></script>
+<script src="../../site_libs/quarto-html/tippy.umd.min.js"></script>
+<script src="../../site_libs/quarto-html/anchor.min.js"></script>
+<link href="../../site_libs/quarto-html/tippy.css" rel="stylesheet">
+<link href="../../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
+<link href="../../site_libs/quarto-html/quarto-syntax-highlighting-dark.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
+<script src="../../site_libs/bootstrap/bootstrap.min.js"></script>
+<link href="../../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
+<link href="../../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
+<link href="../../site_libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
+<script id="quarto-search-options" type="application/json">{
+  "location": "navbar",
+  "copy-button": false,
+  "collapse-after": 3,
+  "panel-placement": "end",
+  "type": "overlay",
+  "limit": 50,
+  "keyboard-shortcut": [
+    "f",
+    "/",
+    "s"
+  ],
+  "show-item-context": false,
+  "language": {
+    "search-no-results-text": "No results",
+    "search-matching-documents-text": "matching documents",
+    "search-copy-link-title": "Copy link to search",
+    "search-hide-matches-text": "Hide additional matches",
+    "search-more-match-text": "more match in this document",
+    "search-more-matches-text": "more matches in this document",
+    "search-clear-button-title": "Clear",
+    "search-detached-cancel-button-title": "Cancel",
+    "search-submit-button-title": "Submit",
+    "search-label": "Search"
+  }
+}</script>
+
+
+</head>
+
+<body class="nav-sidebar floating nav-fixed">
+
+<div id="quarto-search-results"></div>
+  <header id="quarto-header" class="headroom fixed-top">
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+      <div class="navbar-container container-fluid">
+      <div class="navbar-brand-container mx-auto">
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+  <li class="nav-item">
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
+  </li>  
+  <li class="nav-item">
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
+  </li>  
+  <li class="nav-item">
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
+  </li>  
+  <li class="nav-item">
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
+  </li>  
+  <li class="nav-item">
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
+  </li>  
+</ul>
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+          <div class="quarto-navbar-tools tools-wide">
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+      <a href="" title="" id="quarto-navigation-tool-dropdown-0" class="quarto-navigation-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false" aria-label=""><i class="bi bi-github"></i></a>
+      <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="quarto-navigation-tool-dropdown-0">
+          <li>
+            <a class="dropdown-item quarto-navbar-tools-item" href="https://github.com/hits-mbm-dev/kimmdy">
+            Source Code
+            </a>
+          </li>
+          <li>
+            <a class="dropdown-item quarto-navbar-tools-item" href="https://github.com/hits-mbm-dev/kimmdy/issues/new">
+            Report a Bug
+            </a>
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+      </ul>
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+    <div class="container-fluid d-flex">
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+        <i class="bi bi-layout-text-sidebar-reverse"></i>
+      </button>
+        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../guide/explanation/index.html">Explanation</a></li><li class="breadcrumb-item"><a href="../../guide/explanation/components.html">Components of KIMMDY</a></li></ol></nav>
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        </a>
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+<!-- content -->
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+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">KIMMDY</span></a>
+  </div>
+</li>
+        <li class="sidebar-item sidebar-item-section">
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+            <a href="../../guide/tutorials/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Tutorials</span></a>
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+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 ">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/tutorials/colbuilder.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Run KIMMDY from Colbuilder fibril</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/tutorials/getting-started.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Get Started</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/tutorials/write-plugin.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Write a Reaction Plugin</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="../../guide/how-to/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">How-To</span></a>
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+      </div>
+      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Contribute</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/examples.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Examples</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/hcp.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">High Performance Computing</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/install-ml-plugins.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Install Machine Learning Plugins</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/reaction_only.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Reaction only</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="../../guide/explanation/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Explanation</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Visualize Topologies</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="../../_reference/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Reference</span></a>
+          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="false" aria-label="Toggle section">
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+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/references/input.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Input File</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../guide/references/cmd_ref.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">CLI Arguments</span></a>
+  </div>
+</li>
+          <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="false">
+ <span class="menu-text">Python API</span></a>
+          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="false" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth2 ">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/cmd.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">cmd</span></a>
+  </div>
+</li>
+          <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="false">
+ <span class="menu-text">Topology</span></a>
+          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="false" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth3 ">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/topology.topology.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">topology.topology</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/topology.ff.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">topology.ff</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/topology.utils.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">topology.utils</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/topology.atomic.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">topology.atomic</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/parsing.TopologyDict.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">parsing.TopologyDict</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+          <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="false">
+ <span class="menu-text">Reaction Plugins</span></a>
+          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="false" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth3 ">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/homolysis.reaction.Homolysis.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">homolysis.reaction.Homolysis</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/hat_naive.reaction.NaiveHAT.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">hat_naive.reaction.NaiveHAT</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/dummyreaction.reaction.DummyReaction.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">dummyreaction.reaction.DummyReaction</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+          <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="false">
+ <span class="menu-text">Other Modules</span></a>
+          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="false" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth3 ">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/constants.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">constants</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/coordinates.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">coordinates</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/config.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">config</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/kmc.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">kmc</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/parsing.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">parsing</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/runmanager.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">runmanager</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/tasks.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">tasks</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/recipe.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">recipe</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/plugins.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">plugins</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/analysis.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">analysis</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/utils.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">utils</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../_reference/tools.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">tools</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+      </ul>
+  </li>
+      </ul>
+  </li>
+    </ul>
+    </div>
+</nav>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
+<!-- margin-sidebar -->
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        
+    </div>
+<!-- main -->
+<main class="content" id="quarto-document-content">
+
+<header id="title-block-header" class="quarto-title-block default"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../guide/explanation/index.html">Explanation</a></li><li class="breadcrumb-item"><a href="../../guide/explanation/components.html">Components of KIMMDY</a></li></ol></nav>
+<div class="quarto-title">
+<h1 class="title">Components of KIMMDY</h1>
+</div>
+
+
+
+<div class="quarto-title-meta">
+
+    <div>
+    <div class="quarto-title-meta-heading">Author</div>
+    <div class="quarto-title-meta-contents">
+             <p>Kai Riedmiller </p>
+          </div>
+  </div>
+    
+  
+    
+  </div>
+  
+
+
+</header>
+
+
+<p>Here is an overview of the most important components of KIMMDY, and how they interact with each other:</p>
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+
+</div>
+<script type="text/javascript" src="https://viewer.diagrams.net/js/viewer-static.min.js"></script>
+<p>Attributes have a gray, the user-supplied input an orange backdrop.</p>
+<p>A KIMMDY run is orchestrated from a central class called <a href="../../_reference/runmanager.html"><code>RunManager</code></a>. After the user input from the command line interface is handled in the <a href="../../_reference/cmd.html"><code>cmd</code></a> module, a <a href="../../_reference/runmanager.html"><code>RunManager</code></a> is instantiated with a <a href="../../_reference/config.html"><code>config</code></a> built from the input yaml file. During the initialization, the <a href="../../_reference/topology.topology.html#kimmdy.topology.topology.Topology"><code>topology</code></a> is loaded, and the plugins for reactions and parametrizing are instantiated. The run then starts with a call to <a href="../../_reference/runmanager.html"><code>RunManager</code></a>.<code>run</code>. This triggers building of the initial task queue, which then gets processed. In addition to this main task queue, there is also a priority queue available, for tasks to submit other tasks to. These get executed as soon as the current task has finished, but before any eventual other tasks in the main queue. During the task queue building process, reactions are expanded into three tasks. The first one calls the plugin itself to obtain reaction recipes. Then, one recipe must be chosen from all possible ones in a kMC step. Finally, the recipe must be applied at the correct time of the last simulation.</p>
+
+
+
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+  }
+  // Switch to dark mode if need be
+  if (hasAlternateSentinel()) {
+    toggleColorMode(true);
+  } else {
+    toggleColorMode(false);
+  }
+  const icon = "";
+  const anchorJS = new window.AnchorJS();
+  anchorJS.options = {
+    placement: 'right',
+    icon: icon
+  };
+  anchorJS.add('.anchored');
+  const isCodeAnnotation = (el) => {
+    for (const clz of el.classList) {
+      if (clz.startsWith('code-annotation-')) {                     
+        return true;
+      }
+    }
+    return false;
+  }
+  const clipboard = new window.ClipboardJS('.code-copy-button', {
+    text: function(trigger) {
+      const codeEl = trigger.previousElementSibling.cloneNode(true);
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
+    }
+  });
+  clipboard.on('success', function(e) {
+    // button target
+    const button = e.trigger;
+    // don't keep focus
+    button.blur();
+    // flash "checked"
+    button.classList.add('code-copy-button-checked');
+    var currentTitle = button.getAttribute("title");
+    button.setAttribute("title", "Copied!");
+    let tooltip;
+    if (window.bootstrap) {
+      button.setAttribute("data-bs-toggle", "tooltip");
+      button.setAttribute("data-bs-placement", "left");
+      button.setAttribute("data-bs-title", "Copied!");
+      tooltip = new bootstrap.Tooltip(button, 
+        { trigger: "manual", 
+          customClass: "code-copy-button-tooltip",
+          offset: [0, -8]});
+      tooltip.show();    
+    }
+    setTimeout(function() {
+      if (tooltip) {
+        tooltip.hide();
+        button.removeAttribute("data-bs-title");
+        button.removeAttribute("data-bs-toggle");
+        button.removeAttribute("data-bs-placement");
+      }
+      button.setAttribute("title", currentTitle);
+      button.classList.remove('code-copy-button-checked');
+    }, 1000);
+    // clear code selection
+    e.clearSelection();
+  });
+  function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
+    const config = {
+      allowHTML: true,
+      maxWidth: 500,
+      delay: 100,
+      arrow: false,
+      appendTo: function(el) {
+          return el.parentElement;
+      },
+      interactive: true,
+      interactiveBorder: 10,
+      theme: 'quarto',
+      placement: 'bottom-start',
+    };
+    if (contentFn) {
+      config.content = contentFn;
+    }
+    if (onTriggerFn) {
+      config.onTrigger = onTriggerFn;
+    }
+    if (onUntriggerFn) {
+      config.onUntrigger = onUntriggerFn;
+    }
+    window.tippy(el, config); 
+  }
+  const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
+  for (var i=0; i<noterefs.length; i++) {
+    const ref = noterefs[i];
+    tippyHover(ref, function() {
+      // use id or data attribute instead here
+      let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
+      try { href = new URL(href).hash; } catch {}
+      const id = href.replace(/^#\/?/, "");
+      const note = window.document.getElementById(id);
+      return note.innerHTML;
+    });
+  }
+  const xrefs = window.document.querySelectorAll('a.quarto-xref');
+  const processXRef = (id, note) => {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
+      // Special case sections, only their first couple elements
+      const container = document.createElement("div");
+      if (note.children && note.children.length > 2) {
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
+        }
+        typesetMath(container);
+        return container.innerHTML
+      } else {
+        typesetMath(note);
+        return note.innerHTML;
+      }
+    } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
+      return note.innerHTML;
+    }
+  }
+  for (var i=0; i<xrefs.length; i++) {
+    const xref = xrefs[i];
+    tippyHover(xref, undefined, function(instance) {
+      instance.disable();
+      let url = xref.getAttribute('href');
+      let hash = undefined; 
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
+        }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
+          if (note !== null) {
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
+            instance.setContent(html);
+          } 
+        }).finally(() => {
+          instance.enable();
+          instance.show();
+        });
+      }
+    }, function(instance) {
+    });
+  }
+      let selectedAnnoteEl;
+      const selectorForAnnotation = ( cell, annotation) => {
+        let cellAttr = 'data-code-cell="' + cell + '"';
+        let lineAttr = 'data-code-annotation="' +  annotation + '"';
+        const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
+        return selector;
+      }
+      const selectCodeLines = (annoteEl) => {
+        const doc = window.document;
+        const targetCell = annoteEl.getAttribute("data-target-cell");
+        const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
+        const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
+        const lines = annoteSpan.getAttribute("data-code-lines").split(",");
+        const lineIds = lines.map((line) => {
+          return targetCell + "-" + line;
+        })
+        let top = null;
+        let height = null;
+        let parent = null;
+        if (lineIds.length > 0) {
+            //compute the position of the single el (top and bottom and make a div)
+            const el = window.document.getElementById(lineIds[0]);
+            top = el.offsetTop;
+            height = el.offsetHeight;
+            parent = el.parentElement.parentElement;
+          if (lineIds.length > 1) {
+            const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
+            const bottom = lastEl.offsetTop + lastEl.offsetHeight;
+            height = bottom - top;
+          }
+          if (top !== null && height !== null && parent !== null) {
+            // cook up a div (if necessary) and position it 
+            let div = window.document.getElementById("code-annotation-line-highlight");
+            if (div === null) {
+              div = window.document.createElement("div");
+              div.setAttribute("id", "code-annotation-line-highlight");
+              div.style.position = 'absolute';
+              parent.appendChild(div);
+            }
+            div.style.top = top - 2 + "px";
+            div.style.height = height + 4 + "px";
+            div.style.left = 0;
+            let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
+            if (gutterDiv === null) {
+              gutterDiv = window.document.createElement("div");
+              gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
+              gutterDiv.style.position = 'absolute';
+              const codeCell = window.document.getElementById(targetCell);
+              const gutter = codeCell.querySelector('.code-annotation-gutter');
+              gutter.appendChild(gutterDiv);
+            }
+            gutterDiv.style.top = top - 2 + "px";
+            gutterDiv.style.height = height + 4 + "px";
+          }
+          selectedAnnoteEl = annoteEl;
+        }
+      };
+      const unselectCodeLines = () => {
+        const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
+        elementsIds.forEach((elId) => {
+          const div = window.document.getElementById(elId);
+          if (div) {
+            div.remove();
+          }
+        });
+        selectedAnnoteEl = undefined;
+      };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
+      // Attach click handler to the DT
+      const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
+      for (const annoteDlNode of annoteDls) {
+        annoteDlNode.addEventListener('click', (event) => {
+          const clickedEl = event.target;
+          if (clickedEl !== selectedAnnoteEl) {
+            unselectCodeLines();
+            const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
+            if (activeEl) {
+              activeEl.classList.remove('code-annotation-active');
+            }
+            selectCodeLines(clickedEl);
+            clickedEl.classList.add('code-annotation-active');
+          } else {
+            // Unselect the line
+            unselectCodeLines();
+            clickedEl.classList.remove('code-annotation-active');
+          }
+        });
+      }
+  const findCites = (el) => {
+    const parentEl = el.parentElement;
+    if (parentEl) {
+      const cites = parentEl.dataset.cites;
+      if (cites) {
+        return {
+          el,
+          cites: cites.split(' ')
+        };
+      } else {
+        return findCites(el.parentElement)
+      }
+    } else {
+      return undefined;
+    }
+  };
+  var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
+  for (var i=0; i<bibliorefs.length; i++) {
+    const ref = bibliorefs[i];
+    const citeInfo = findCites(ref);
+    if (citeInfo) {
+      tippyHover(citeInfo.el, function() {
+        var popup = window.document.createElement('div');
+        citeInfo.cites.forEach(function(cite) {
+          var citeDiv = window.document.createElement('div');
+          citeDiv.classList.add('hanging-indent');
+          citeDiv.classList.add('csl-entry');
+          var biblioDiv = window.document.getElementById('ref-' + cite);
+          if (biblioDiv) {
+            citeDiv.innerHTML = biblioDiv.innerHTML;
+          }
+          popup.appendChild(citeDiv);
+        });
+        return popup.innerHTML;
+      });
+    }
+  }
+});
+</script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../../guide/explanation/index.html" class="pagination-link  aria-label=" explanation"="">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Explanation</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../../guide/explanation/topology.html" class="pagination-link" aria-label="Visualize Topologies">
+        <span class="nav-page-text">Visualize Topologies</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
+</div> <!-- /content -->
+
+
+
+
+<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/explanation/components.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div></div></footer></body></html>
\ No newline at end of file
diff --git a/docs/guide/explanation/index.html b/docs/guide/explanation/index.html
index a275d571..84ae6638 100644
--- a/docs/guide/explanation/index.html
+++ b/docs/guide/explanation/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -30,7 +30,7 @@
 <script src="../../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../../">
-<link href="../../guide/explanation/topology.html" rel="next">
+<link href="../../guide/explanation/components.html" rel="next">
 <link href="../../guide/how-to/reaction_only.html" rel="prev">
 <script src="../../site_libs/quarto-listing/list.min.js"></script>
 <script src="../../site_libs/quarto-listing/quarto-listing.js"></script>
@@ -51,12 +51,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -109,7 +110,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -123,24 +124,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -171,11 +172,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -183,7 +184,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -232,6 +233,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -273,6 +280,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -475,7 +488,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         
@@ -498,8 +511,10 @@ <h1 class="title">Explanations</h1>
   </div>
   
 
+
 </header>
 
+
 <p>Pages that help you understand the inner workings of KIMMDY</p>
 
 
@@ -537,7 +552,15 @@ <h1 class="title">Explanations</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1711385802333" data-listing-reading-time-sort="1" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
+<tr data-index="0" data-listing-file-modified-sort="1712934328000" data-listing-reading-time-sort="20" data-listing-word-count-sort="3838" data-listing-title-sort="Components of KIMMDY" data-listing-filename-sort="components.qmd">
+<td>
+<a href="../../guide/explanation/components.html" class="title listing-title">Components of KIMMDY</a>
+</td>
+<td>
+<span class="listing-author">Kai Riedmiller</span>
+</td>
+</tr>
+<tr data-index="1" data-listing-file-modified-sort="1701868360000" data-listing-reading-time-sort="1" data-listing-word-count-sort="188" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
 <td>
 <a href="../../guide/explanation/topology.html" class="title listing-title">Visualize Topologies</a>
 </td>
@@ -813,18 +836,64 @@ <h1 class="title">Explanations</h1>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
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     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
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@@ -834,27 +903,56 @@ <h1 class="title">Explanations</h1>
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       let hash = undefined; 
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-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -932,6 +1030,32 @@ <h1 class="title">Explanations</h1>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -993,13 +1117,13 @@ <h1 class="title">Explanations</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/how-to/reaction_only.html" class="pagination-link">
+      <a href="../../guide/how-to/reaction_only.html" class="pagination-link  aria-label=" reaction="" only"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Reaction only</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/explanation/topology.html" class="pagination-link">
-        <span class="nav-page-text">Visualize Topologies</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="../../guide/explanation/components.html" class="pagination-link" aria-label="Components of KIMMDY">
+        <span class="nav-page-text">Components of KIMMDY</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>
@@ -1008,4 +1132,4 @@ <h1 class="title">Explanations</h1>
 
 
 
-<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/explanation/index.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></div></div></footer></body></html>
\ No newline at end of file
+<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/explanation/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div></div></footer></body></html>
\ No newline at end of file
diff --git a/docs/guide/explanation/topology.html b/docs/guide/explanation/topology.html
index 4d9c93a4..84a33965 100644
--- a/docs/guide/explanation/topology.html
+++ b/docs/guide/explanation/topology.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -22,7 +22,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -65,7 +65,7 @@
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 <meta name="quarto:offset" content="../../">
 <link href="../../_reference/index.html" rel="next">
-<link href="../../guide/explanation/index.html" rel="prev">
+<link href="../../guide/explanation/components.html" rel="prev">
 <script src="../../site_libs/quarto-html/quarto.js"></script>
 <script src="../../site_libs/quarto-html/popper.min.js"></script>
 <script src="../../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -83,12 +83,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -110,7 +111,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -124,24 +125,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -172,11 +173,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
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   </nav>
@@ -184,7 +185,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -233,6 +234,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -274,6 +281,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link active">
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   </div>
@@ -476,7 +489,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -486,7 +499,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#capped-alanine-with-a-radical" id="toc-capped-alanine-with-a-radical" class="nav-link active" data-scroll-target="#capped-alanine-with-a-radical">Capped Alanine with a radical</a></li>
   <li><a href="#multiple-molecules" id="toc-multiple-molecules" class="nav-link" data-scroll-target="#multiple-molecules">Multiple molecules</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/explanation/topology.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/explanation/topology.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -506,8 +519,10 @@ <h1 class="title">Visualize Topologies</h1>
   </div>
   
 
+
 </header>
 
+
 <section id="capped-alanine-with-a-radical" class="level2">
 <h2 class="anchored" data-anchor-id="capped-alanine-with-a-radical">Capped Alanine with a radical</h2>
 <div id="e416bbb7" class="cell" data-execution_count="1">
@@ -525,181 +540,246 @@ <h2 class="anchored" data-anchor-id="capped-alanine-with-a-radical">Capped Alani
 <div class="cell" data-file="ala-top.dot">
 <div class="cell-output-display">
 <div id="fig-ala" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure">
+<figure class="quarto-float quarto-float-fig figure">
+<div aria-describedby="fig-ala-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 <div>
 <svg width="672" height="480" viewbox="0.00 0.00 511.20 642.95" xmlns="http://www.w3.org/2000/svg" xlink="http://www.w3.org/1999/xlink" style="; max-width: none; max-height: none">
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-3 HC
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-1 CT–5 C
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-<path fill="none" stroke="black" d="M131.81,-136.01C136.98,-144.66 142.66,-154.17 147.59,-162.41"></path> </g> <!-- 6 O --> <g id="node6" class="node">
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-7 N
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-10 CT
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-9 CT–10 CT
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-14 C
-</title>
-<ellipse fill="none" stroke="black" cx="292.36" cy="-372.08" rx="29.6" ry="29.6"></ellipse> <text text-anchor="middle" x="292.36" y="-367.88" font-family="Times,serif" font-size="14.00">14 C</text> </g> <!-- 9 CT&#45;&#45;14 C --> <g id="edge10" class="edge">
-<title>
-9 CT–14 C
-</title>
-<path fill="none" stroke="black" d="M298.93,-314.68C297.9,-323.73 296.77,-333.6 295.74,-342.56"></path> </g> <!-- 11 HC --> <g id="node12" class="node">
-<title>
-11 HC
-</title>
-<ellipse fill="none" stroke="black" cx="459.93" cy="-291.61" rx="36.55" ry="36.55"></ellipse> <text text-anchor="middle" x="459.93" y="-287.41" font-family="Times,serif" font-size="14.00">11 HC</text> </g> <!-- 10 CT&#45;&#45;11 HC --> <g id="edge11" class="edge">
-<title>
-10 CT–11 HC
-</title>
-<path fill="none" stroke="black" d="M419.07,-268.33C421.95,-269.97 424.88,-271.64 427.77,-273.29"></path> </g> <!-- 12 HC --> <g id="node13" class="node">
-<title>
-12 HC
-</title>
-<ellipse fill="none" stroke="black" cx="416.85" cy="-173.76" rx="36.55" ry="36.55"></ellipse> <text text-anchor="middle" x="416.85" y="-169.56" font-family="Times,serif" font-size="14.00">12 HC</text> </g> <!-- 10 CT&#45;&#45;12 HC --> <g id="edge12" class="edge">
-<title>
-10 CT–12 HC
-</title>
-<path fill="none" stroke="black" d="M400.71,-217.22C401.8,-214.3 402.89,-211.34 403.98,-208.42"></path> </g> <!-- 13 HC --> <g id="node14" class="node">
-<title>
-13 HC
-</title>
-<ellipse fill="none" stroke="black" cx="466.67" cy="-223.07" rx="36.55" ry="36.55"></ellipse> <text text-anchor="middle" x="466.67" y="-218.87" font-family="Times,serif" font-size="14.00">13 HC</text> </g> <!-- 10 CT&#45;&#45;13 HC --> <g id="edge13" class="edge">
-<title>
-10 CT–13 HC
-</title>
-<path fill="none" stroke="black" d="M421.97,-238.87C425.29,-237.69 428.66,-236.5 431.99,-235.33"></path> </g> <!-- 15 O --> <g id="node15" class="node">
-<title>
-15 O
-</title>
-<ellipse fill="none" stroke="black" cx="367.38" cy="-397.21" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="367.38" y="-393.01" font-family="Times,serif" font-size="14.00">15 O</text> </g> <!-- 14 C&#45;&#45;15 O --> <g id="edge14" class="edge">
-<title>
-14 C–15 O
-</title>
-<path fill="none" stroke="black" d="M320.72,-381.58C326.61,-383.55 332.83,-385.63 338.73,-387.61"></path> </g> <!-- 16 N --> <g id="node16" class="node">
-<title>
-16 N
-</title>
-<ellipse fill="none" stroke="black" cx="274.14" cy="-456.71" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="274.14" y="-452.51" font-family="Times,serif" font-size="14.00">16 N</text> </g> <!-- 14 C&#45;&#45;16 N --> <g id="edge15" class="edge">
-<title>
-14 C–16 N
-</title>
-<path fill="none" stroke="black" d="M286.09,-401.2C284.28,-409.62 282.3,-418.81 280.48,-427.24"></path> </g> <!-- 17 H --> <g id="node17" class="node">
-<title>
-17 H
-</title>
-<ellipse fill="none" stroke="black" cx="346.34" cy="-502.76" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="346.34" y="-498.56" font-family="Times,serif" font-size="14.00">17 H</text> </g> <!-- 16 N&#45;&#45;17 H --> <g id="edge16" class="edge">
-<title>
-16 N–17 H
-</title>
-<path fill="none" stroke="black" d="M299.8,-473.07C306.61,-477.42 313.96,-482.11 320.76,-486.45"></path> </g> <!-- 18 CT --> <g id="node18" class="node">
-<title>
-18 CT
-</title>
-<ellipse fill="none" stroke="black" cx="229.9" cy="-528.77" rx="35.4" ry="35.4"></ellipse> <text text-anchor="middle" x="229.9" y="-524.57" font-family="Times,serif" font-size="14.00">18 CT</text> </g> <!-- 16 N&#45;&#45;18 CT --> <g id="edge17" class="edge">
-<title>
-16 N–18 CT
-</title>
-<path fill="none" stroke="black" d="M258.17,-482.72C255.1,-487.72 251.86,-493 248.71,-498.13"></path> </g> <!-- 19 H1 --> <g id="node19" class="node">
-<title>
-19 H1
-</title>
-<ellipse fill="none" stroke="black" cx="148.11" cy="-536.38" rx="34.82" ry="34.82"></ellipse> <text text-anchor="middle" x="148.11" y="-532.18" font-family="Times,serif" font-size="14.00">19 H1</text> </g> <!-- 18 CT&#45;&#45;19 H1 --> <g id="edge18" class="edge">
-<title>
-18 CT–19 H1
-</title>
-<path fill="none" stroke="black" d="M194.26,-532.08C190.56,-532.43 186.8,-532.78 183.11,-533.12"></path> </g> <!-- 20 H1 --> <g id="node20" class="node">
-<title>
-20 H1
-</title>
-<ellipse fill="none" stroke="black" cx="196.15" cy="-600.04" rx="34.82" ry="34.82"></ellipse> <text text-anchor="middle" x="196.15" y="-595.84" font-family="Times,serif" font-size="14.00">20 H1</text> </g> <!-- 18 CT&#45;&#45;20 H1 --> <g id="edge19" class="edge">
-<title>
-18 CT–20 H1
-</title>
-<path fill="none" stroke="black" d="M214.6,-561.07C213.49,-563.42 212.36,-565.8 211.25,-568.15"></path> </g> <!-- 21 H1 --> <g id="node21" class="node">
-<title>
-21 H1
-</title>
-<ellipse fill="none" stroke="black" cx="277.91" cy="-599.82" rx="34.82" ry="34.82"></ellipse> <text text-anchor="middle" x="277.91" y="-595.62" font-family="Times,serif" font-size="14.00">21 H1</text> </g> <!-- 18 CT&#45;&#45;21 H1 --> <g id="edge20" class="edge">
-<title>
-18 CT–21 H1
-</title>
-<path fill="none" stroke="black" d="M249.98,-558.49C252.66,-562.45 255.4,-566.5 258.06,-570.45"></path> </g> </g>
+<title>G</title>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-638.95 507.2,-638.95 507.2,4 -4,4"></polygon>
+<!-- 1 CT -->
+<g id="node1" class="node">
+<title>1 CT</title>
+<ellipse fill="none" stroke="black" cx="116.06" cy="-109.67" rx="30.74" ry="30.74"></ellipse>
+<text text-anchor="middle" x="116.06" y="-105.47" font-family="Times,serif" font-size="14.00">1 CT</text>
+</g>
+<!-- 2 HC -->
+<g id="node2" class="node">
+<title>2 HC</title>
+<ellipse fill="none" stroke="black" cx="147.34" cy="-31.69" rx="31.89" ry="31.89"></ellipse>
+<text text-anchor="middle" x="147.34" y="-27.49" font-family="Times,serif" font-size="14.00">2 HC</text>
+</g>
+<!-- 1 CT&#45;&#45;2 HC -->
+<g id="edge1" class="edge">
+<title>1 CT--2 HC</title>
+<path fill="none" stroke="black" d="M127.53,-81.08C130.11,-74.64 132.85,-67.8 135.45,-61.33"></path>
+</g>
+<!-- 3 HC -->
+<g id="node3" class="node">
+<title>3 HC</title>
+<ellipse fill="none" stroke="black" cx="68.12" cy="-47.43" rx="31.89" ry="31.89"></ellipse>
+<text text-anchor="middle" x="68.12" y="-43.23" font-family="Times,serif" font-size="14.00">3 HC</text>
+</g>
+<!-- 1 CT&#45;&#45;3 HC -->
+<g id="edge2" class="edge">
+<title>1 CT--3 HC</title>
+<path fill="none" stroke="black" d="M97.12,-85.07C93.98,-80.99 90.71,-76.76 87.56,-72.67"></path>
+</g>
+<!-- 4 HC -->
+<g id="node4" class="node">
+<title>4 HC</title>
+<ellipse fill="none" stroke="black" cx="31.69" cy="-120.73" rx="31.89" ry="31.89"></ellipse>
+<text text-anchor="middle" x="31.69" y="-116.53" font-family="Times,serif" font-size="14.00">4 HC</text>
+</g>
+<!-- 1 CT&#45;&#45;4 HC -->
+<g id="edge3" class="edge">
+<title>1 CT--4 HC</title>
+<path fill="none" stroke="black" d="M85.6,-113.66C78.33,-114.61 70.56,-115.63 63.24,-116.59"></path>
+</g>
+<!-- 5 C -->
+<g id="node5" class="node">
+<title>5 C</title>
+<ellipse fill="none" stroke="black" cx="160.37" cy="-183.79" rx="24.94" ry="24.94"></ellipse>
+<text text-anchor="middle" x="160.37" y="-179.59" font-family="Times,serif" font-size="14.00">5 C</text>
+</g>
+<!-- 1 CT&#45;&#45;5 C -->
+<g id="edge4" class="edge">
+<title>1 CT--5 C</title>
+<path fill="none" stroke="black" d="M131.81,-136.01C136.98,-144.66 142.66,-154.17 147.59,-162.41"></path>
+</g>
+<!-- 6 O -->
+<g id="node6" class="node">
+<title>6 O</title>
+<ellipse fill="none" stroke="black" cx="93.14" cy="-228.4" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="93.14" y="-224.2" font-family="Times,serif" font-size="14.00">6 O</text>
+</g>
+<!-- 5 C&#45;&#45;6 O -->
+<g id="edge5" class="edge">
+<title>5 C--6 O</title>
+<path fill="none" stroke="black" d="M139.46,-197.66C131.45,-202.98 122.3,-209.05 114.26,-214.38"></path>
+</g>
+<!-- 7 N -->
+<g id="node7" class="node">
+<title>7 N</title>
+<ellipse fill="none" stroke="black" cx="236.86" cy="-224.46" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="236.86" y="-220.26" font-family="Times,serif" font-size="14.00">7 N</text>
+</g>
+<!-- 5 C&#45;&#45;7 N -->
+<g id="edge6" class="edge">
+<title>5 C--7 N</title>
+<path fill="none" stroke="black" d="M182.49,-195.55C192.55,-200.9 204.44,-207.22 214.52,-212.58"></path>
+</g>
+<!-- 8 H -->
+<g id="node8" class="node">
+<title>8 H</title>
+<ellipse fill="none" stroke="black" cx="272.14" cy="-153.96" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="272.14" y="-149.76" font-family="Times,serif" font-size="14.00">8 H</text>
+</g>
+<!-- 7 N&#45;&#45;8 H -->
+<g id="edge7" class="edge">
+<title>7 N--8 H</title>
+<path fill="none" stroke="black" d="M248.22,-201.77C252.25,-193.72 256.78,-184.66 260.81,-176.61"></path>
+</g>
+<!-- 9 CT -->
+<g id="node9" class="node">
+<title>9 CT</title>
+<ellipse fill="none" stroke="red" cx="302.46" cy="-283.81" rx="30.74" ry="30.74"></ellipse>
+<text text-anchor="middle" x="302.46" y="-279.61" font-family="Times,serif" font-size="14.00">9 CT</text>
+</g>
+<!-- 7 N&#45;&#45;9 CT -->
+<g id="edge8" class="edge">
+<title>7 N--9 CT</title>
+<path fill="none" stroke="black" d="M255.84,-241.63C263.25,-248.34 271.83,-256.09 279.58,-263.11"></path>
+</g>
+<!-- 10 CT -->
+<g id="node10" class="node">
+<title>10 CT</title>
+<ellipse fill="none" stroke="black" cx="388.25" cy="-250.78" rx="35.4" ry="35.4"></ellipse>
+<text text-anchor="middle" x="388.25" y="-246.58" font-family="Times,serif" font-size="14.00">10 CT</text>
+</g>
+<!-- 9 CT&#45;&#45;10 CT -->
+<g id="edge9" class="edge">
+<title>9 CT--10 CT</title>
+<path fill="none" stroke="black" d="M331.51,-272.63C339.09,-269.71 347.32,-266.54 355.1,-263.54"></path>
+</g>
+<!-- 14 C -->
+<g id="node11" class="node">
+<title>14 C</title>
+<ellipse fill="none" stroke="black" cx="292.36" cy="-372.08" rx="29.6" ry="29.6"></ellipse>
+<text text-anchor="middle" x="292.36" y="-367.88" font-family="Times,serif" font-size="14.00">14 C</text>
+</g>
+<!-- 9 CT&#45;&#45;14 C -->
+<g id="edge10" class="edge">
+<title>9 CT--14 C</title>
+<path fill="none" stroke="black" d="M298.93,-314.68C297.9,-323.73 296.77,-333.6 295.74,-342.56"></path>
+</g>
+<!-- 11 HC -->
+<g id="node12" class="node">
+<title>11 HC</title>
+<ellipse fill="none" stroke="black" cx="459.93" cy="-291.61" rx="36.55" ry="36.55"></ellipse>
+<text text-anchor="middle" x="459.93" y="-287.41" font-family="Times,serif" font-size="14.00">11 HC</text>
+</g>
+<!-- 10 CT&#45;&#45;11 HC -->
+<g id="edge11" class="edge">
+<title>10 CT--11 HC</title>
+<path fill="none" stroke="black" d="M419.07,-268.33C421.95,-269.97 424.88,-271.64 427.77,-273.29"></path>
+</g>
+<!-- 12 HC -->
+<g id="node13" class="node">
+<title>12 HC</title>
+<ellipse fill="none" stroke="black" cx="416.85" cy="-173.76" rx="36.55" ry="36.55"></ellipse>
+<text text-anchor="middle" x="416.85" y="-169.56" font-family="Times,serif" font-size="14.00">12 HC</text>
+</g>
+<!-- 10 CT&#45;&#45;12 HC -->
+<g id="edge12" class="edge">
+<title>10 CT--12 HC</title>
+<path fill="none" stroke="black" d="M400.71,-217.22C401.8,-214.3 402.89,-211.34 403.98,-208.42"></path>
+</g>
+<!-- 13 HC -->
+<g id="node14" class="node">
+<title>13 HC</title>
+<ellipse fill="none" stroke="black" cx="466.67" cy="-223.07" rx="36.55" ry="36.55"></ellipse>
+<text text-anchor="middle" x="466.67" y="-218.87" font-family="Times,serif" font-size="14.00">13 HC</text>
+</g>
+<!-- 10 CT&#45;&#45;13 HC -->
+<g id="edge13" class="edge">
+<title>10 CT--13 HC</title>
+<path fill="none" stroke="black" d="M421.97,-238.87C425.29,-237.69 428.66,-236.5 431.99,-235.33"></path>
+</g>
+<!-- 15 O -->
+<g id="node15" class="node">
+<title>15 O</title>
+<ellipse fill="none" stroke="black" cx="367.38" cy="-397.21" rx="30.16" ry="30.16"></ellipse>
+<text text-anchor="middle" x="367.38" y="-393.01" font-family="Times,serif" font-size="14.00">15 O</text>
+</g>
+<!-- 14 C&#45;&#45;15 O -->
+<g id="edge14" class="edge">
+<title>14 C--15 O</title>
+<path fill="none" stroke="black" d="M320.72,-381.58C326.61,-383.55 332.83,-385.63 338.73,-387.61"></path>
+</g>
+<!-- 16 N -->
+<g id="node16" class="node">
+<title>16 N</title>
+<ellipse fill="none" stroke="black" cx="274.14" cy="-456.71" rx="30.16" ry="30.16"></ellipse>
+<text text-anchor="middle" x="274.14" y="-452.51" font-family="Times,serif" font-size="14.00">16 N</text>
+</g>
+<!-- 14 C&#45;&#45;16 N -->
+<g id="edge15" class="edge">
+<title>14 C--16 N</title>
+<path fill="none" stroke="black" d="M286.09,-401.2C284.28,-409.62 282.3,-418.81 280.48,-427.24"></path>
+</g>
+<!-- 17 H -->
+<g id="node17" class="node">
+<title>17 H</title>
+<ellipse fill="none" stroke="black" cx="346.34" cy="-502.76" rx="30.16" ry="30.16"></ellipse>
+<text text-anchor="middle" x="346.34" y="-498.56" font-family="Times,serif" font-size="14.00">17 H</text>
+</g>
+<!-- 16 N&#45;&#45;17 H -->
+<g id="edge16" class="edge">
+<title>16 N--17 H</title>
+<path fill="none" stroke="black" d="M299.8,-473.07C306.61,-477.42 313.96,-482.11 320.76,-486.45"></path>
+</g>
+<!-- 18 CT -->
+<g id="node18" class="node">
+<title>18 CT</title>
+<ellipse fill="none" stroke="black" cx="229.9" cy="-528.77" rx="35.4" ry="35.4"></ellipse>
+<text text-anchor="middle" x="229.9" y="-524.57" font-family="Times,serif" font-size="14.00">18 CT</text>
+</g>
+<!-- 16 N&#45;&#45;18 CT -->
+<g id="edge17" class="edge">
+<title>16 N--18 CT</title>
+<path fill="none" stroke="black" d="M258.17,-482.72C255.1,-487.72 251.86,-493 248.71,-498.13"></path>
+</g>
+<!-- 19 H1 -->
+<g id="node19" class="node">
+<title>19 H1</title>
+<ellipse fill="none" stroke="black" cx="148.11" cy="-536.38" rx="34.82" ry="34.82"></ellipse>
+<text text-anchor="middle" x="148.11" y="-532.18" font-family="Times,serif" font-size="14.00">19 H1</text>
+</g>
+<!-- 18 CT&#45;&#45;19 H1 -->
+<g id="edge18" class="edge">
+<title>18 CT--19 H1</title>
+<path fill="none" stroke="black" d="M194.26,-532.08C190.56,-532.43 186.8,-532.78 183.11,-533.12"></path>
+</g>
+<!-- 20 H1 -->
+<g id="node20" class="node">
+<title>20 H1</title>
+<ellipse fill="none" stroke="black" cx="196.15" cy="-600.04" rx="34.82" ry="34.82"></ellipse>
+<text text-anchor="middle" x="196.15" y="-595.84" font-family="Times,serif" font-size="14.00">20 H1</text>
+</g>
+<!-- 18 CT&#45;&#45;20 H1 -->
+<g id="edge19" class="edge">
+<title>18 CT--20 H1</title>
+<path fill="none" stroke="black" d="M214.6,-561.07C213.49,-563.42 212.36,-565.8 211.25,-568.15"></path>
+</g>
+<!-- 21 H1 -->
+<g id="node21" class="node">
+<title>21 H1</title>
+<ellipse fill="none" stroke="black" cx="277.91" cy="-599.82" rx="34.82" ry="34.82"></ellipse>
+<text text-anchor="middle" x="277.91" y="-595.62" font-family="Times,serif" font-size="14.00">21 H1</text>
+</g>
+<!-- 18 CT&#45;&#45;21 H1 -->
+<g id="edge20" class="edge">
+<title>18 CT--21 H1</title>
+<path fill="none" stroke="black" d="M249.98,-558.49C252.66,-562.45 255.4,-566.5 258.06,-570.45"></path>
+</g>
+</g>
 </svg>
 </div>
-<figcaption class="figure-caption">Figure&nbsp;1: A diagram of the Ala topology</figcaption>
+</div>
+<figcaption class="figure quarto-float-caption quarto-float-fig" id="fig-ala-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
+Figure&nbsp;1: A diagram of the Ala topology
+</figcaption>
 </figure>
 </div>
 </div>
@@ -715,77 +795,103 @@ <h2 class="anchored" data-anchor-id="multiple-molecules">Multiple molecules</h2>
 <div class="cell" data-file="urea-top.dot">
 <div class="cell-output-display">
 <div id="fig-ala" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure">
+<figure class="quarto-float quarto-float-fig figure">
+<div aria-describedby="fig-ala-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 <div>
 <svg width="672" height="480" viewbox="0.00 0.00 296.28 333.31" xmlns="http://www.w3.org/2000/svg" xlink="http://www.w3.org/1999/xlink" style="; max-width: none; max-height: none">
 <g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 329.31)">
-<title>
-G
-</title>
-<polygon fill="white" stroke="transparent" points="-4,4 -4,-329.31 292.28,-329.31 292.28,4 -4,4"></polygon> <!-- 1 C --> <g id="node1" class="node">
-<title>
-1 C
-</title>
-<ellipse fill="none" stroke="black" cx="171.49" cy="-150.97" rx="24.94" ry="24.94"></ellipse> <text text-anchor="middle" x="171.49" y="-146.77" font-family="Times,serif" font-size="14.00">1 C</text> </g> <!-- 2 O --> <g id="node2" class="node">
-<title>
-2 O
-</title>
-<ellipse fill="none" stroke="black" cx="238.59" cy="-104.78" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="238.59" y="-100.58" font-family="Times,serif" font-size="14.00">2 O</text> </g> <!-- 1 C&#45;&#45;2 O --> <g id="edge1" class="edge">
-<title>
-1 C–2 O
-</title>
-<path fill="none" stroke="black" d="M191.98,-136.86C200.16,-131.23 209.55,-124.76 217.75,-119.12"></path> </g> <!-- 3 N --> <g id="node3" class="node">
-<title>
-3 N
-</title>
-<ellipse fill="none" stroke="black" cx="190.42" cy="-230.8" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="190.42" y="-226.6" font-family="Times,serif" font-size="14.00">3 N</text> </g> <!-- 1 C&#45;&#45;3 N --> <g id="edge2" class="edge">
-<title>
-1 C–3 N
-</title>
-<path fill="none" stroke="black" d="M177.27,-175.35C179.58,-185.07 182.23,-196.25 184.54,-206.01"></path> </g> <!-- 6 N --> <g id="node4" class="node">
-<title>
-6 N
-</title>
-<ellipse fill="none" stroke="black" cx="103.68" cy="-104.8" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="103.68" y="-100.6" font-family="Times,serif" font-size="14.00">6 N</text> </g> <!-- 1 C&#45;&#45;6 N --> <g id="edge3" class="edge">
-<title>
-1 C–6 N
-</title>
-<path fill="none" stroke="black" d="M150.77,-136.86C142.52,-131.24 133.02,-124.78 124.73,-119.13"></path> </g> <!-- 4 H --> <g id="node5" class="node">
-<title>
-4 H
-</title>
-<ellipse fill="none" stroke="black" cx="263.03" cy="-263.51" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="263.03" y="-259.31" font-family="Times,serif" font-size="14.00">4 H</text> </g> <!-- 3 N&#45;&#45;4 H --> <g id="edge4" class="edge">
-<title>
-3 N–4 H
-</title>
-<path fill="none" stroke="black" d="M213.8,-241.33C222.09,-245.06 231.41,-249.26 239.7,-253"></path> </g> <!-- 5 H --> <g id="node6" class="node">
-<title>
-5 H
-</title>
-<ellipse fill="none" stroke="black" cx="152.07" cy="-300.06" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="152.07" y="-295.86" font-family="Times,serif" font-size="14.00">5 H</text> </g> <!-- 3 N&#45;&#45;5 H --> <g id="edge5" class="edge">
-<title>
-3 N–5 H
-</title>
-<path fill="none" stroke="black" d="M178.07,-253.09C173.69,-261 168.77,-269.9 164.39,-277.81"></path> </g> <!-- 7 H --> <g id="node7" class="node">
-<title>
-7 H
-</title>
-<ellipse fill="none" stroke="black" cx="25.25" cy="-115.69" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="25.25" y="-111.49" font-family="Times,serif" font-size="14.00">7 H</text> </g> <!-- 6 N&#45;&#45;7 H --> <g id="edge6" class="edge">
-<title>
-6 N–7 H
-</title>
-<path fill="none" stroke="black" d="M78.43,-108.3C69.48,-109.55 59.4,-110.95 50.45,-112.19"></path> </g> <!-- 8 H --> <g id="node8" class="node">
-<title>
-8 H
-</title>
-<ellipse fill="none" stroke="black" cx="99.21" cy="-25.25" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="99.21" y="-21.05" font-family="Times,serif" font-size="14.00">8 H</text> </g> <!-- 6 N&#45;&#45;8 H --> <g id="edge7" class="edge">
-<title>
-6 N–8 H
-</title>
-<path fill="none" stroke="black" d="M102.24,-79.19C101.72,-70.02 101.14,-59.69 100.63,-50.54"></path> </g> </g>
+<title>G</title>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-329.31 292.28,-329.31 292.28,4 -4,4"></polygon>
+<!-- 1 C -->
+<g id="node1" class="node">
+<title>1 C</title>
+<ellipse fill="none" stroke="black" cx="171.49" cy="-150.97" rx="24.94" ry="24.94"></ellipse>
+<text text-anchor="middle" x="171.49" y="-146.77" font-family="Times,serif" font-size="14.00">1 C</text>
+</g>
+<!-- 2 O -->
+<g id="node2" class="node">
+<title>2 O</title>
+<ellipse fill="none" stroke="black" cx="238.59" cy="-104.78" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="238.59" y="-100.58" font-family="Times,serif" font-size="14.00">2 O</text>
+</g>
+<!-- 1 C&#45;&#45;2 O -->
+<g id="edge1" class="edge">
+<title>1 C--2 O</title>
+<path fill="none" stroke="black" d="M191.98,-136.86C200.16,-131.23 209.55,-124.76 217.75,-119.12"></path>
+</g>
+<!-- 3 N -->
+<g id="node3" class="node">
+<title>3 N</title>
+<ellipse fill="none" stroke="black" cx="190.42" cy="-230.8" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="190.42" y="-226.6" font-family="Times,serif" font-size="14.00">3 N</text>
+</g>
+<!-- 1 C&#45;&#45;3 N -->
+<g id="edge2" class="edge">
+<title>1 C--3 N</title>
+<path fill="none" stroke="black" d="M177.27,-175.35C179.58,-185.07 182.23,-196.25 184.54,-206.01"></path>
+</g>
+<!-- 6 N -->
+<g id="node4" class="node">
+<title>6 N</title>
+<ellipse fill="none" stroke="black" cx="103.68" cy="-104.8" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="103.68" y="-100.6" font-family="Times,serif" font-size="14.00">6 N</text>
+</g>
+<!-- 1 C&#45;&#45;6 N -->
+<g id="edge3" class="edge">
+<title>1 C--6 N</title>
+<path fill="none" stroke="black" d="M150.77,-136.86C142.52,-131.24 133.02,-124.78 124.73,-119.13"></path>
+</g>
+<!-- 4 H -->
+<g id="node5" class="node">
+<title>4 H</title>
+<ellipse fill="none" stroke="black" cx="263.03" cy="-263.51" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="263.03" y="-259.31" font-family="Times,serif" font-size="14.00">4 H</text>
+</g>
+<!-- 3 N&#45;&#45;4 H -->
+<g id="edge4" class="edge">
+<title>3 N--4 H</title>
+<path fill="none" stroke="black" d="M213.8,-241.33C222.09,-245.06 231.41,-249.26 239.7,-253"></path>
+</g>
+<!-- 5 H -->
+<g id="node6" class="node">
+<title>5 H</title>
+<ellipse fill="none" stroke="black" cx="152.07" cy="-300.06" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="152.07" y="-295.86" font-family="Times,serif" font-size="14.00">5 H</text>
+</g>
+<!-- 3 N&#45;&#45;5 H -->
+<g id="edge5" class="edge">
+<title>3 N--5 H</title>
+<path fill="none" stroke="black" d="M178.07,-253.09C173.69,-261 168.77,-269.9 164.39,-277.81"></path>
+</g>
+<!-- 7 H -->
+<g id="node7" class="node">
+<title>7 H</title>
+<ellipse fill="none" stroke="black" cx="25.25" cy="-115.69" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="25.25" y="-111.49" font-family="Times,serif" font-size="14.00">7 H</text>
+</g>
+<!-- 6 N&#45;&#45;7 H -->
+<g id="edge6" class="edge">
+<title>6 N--7 H</title>
+<path fill="none" stroke="black" d="M78.43,-108.3C69.48,-109.55 59.4,-110.95 50.45,-112.19"></path>
+</g>
+<!-- 8 H -->
+<g id="node8" class="node">
+<title>8 H</title>
+<ellipse fill="none" stroke="black" cx="99.21" cy="-25.25" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="99.21" y="-21.05" font-family="Times,serif" font-size="14.00">8 H</text>
+</g>
+<!-- 6 N&#45;&#45;8 H -->
+<g id="edge7" class="edge">
+<title>6 N--8 H</title>
+<path fill="none" stroke="black" d="M102.24,-79.19C101.72,-70.02 101.14,-59.69 100.63,-50.54"></path>
+</g>
+</g>
 </svg>
 </div>
-<figcaption class="figure-caption">Figure&nbsp;2: Topology of one molecule of urea</figcaption>
+</div>
+<figcaption class="figure quarto-float-caption quarto-float-fig" id="fig-ala-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
+Figure&nbsp;2: Topology of one molecule of urea
+</figcaption>
 </figure>
 </div>
 </div>
@@ -808,137 +914,186 @@ <h2 class="anchored" data-anchor-id="multiple-molecules">Multiple molecules</h2>
 <div class="cell" data-file="urea-2-top.dot">
 <div class="cell-output-display">
 <div id="fig-ala" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure">
+<figure class="quarto-float quarto-float-fig figure">
+<div aria-describedby="fig-ala-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 <div>
 <svg width="672" height="480" viewbox="0.00 0.00 593.94 594.97" xmlns="http://www.w3.org/2000/svg" xlink="http://www.w3.org/1999/xlink" style="; max-width: none; max-height: none">
 <g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 590.97)">
-<title>
-G
-</title>
-<polygon fill="white" stroke="transparent" points="-4,4 -4,-590.97 589.94,-590.97 589.94,4 -4,4"></polygon> <!-- 1 C --> <g id="node1" class="node">
-<title>
-1 C
-</title>
-<ellipse fill="none" stroke="black" cx="171.49" cy="-150.97" rx="24.94" ry="24.94"></ellipse> <text text-anchor="middle" x="171.49" y="-146.77" font-family="Times,serif" font-size="14.00">1 C</text> </g> <!-- 2 O --> <g id="node2" class="node">
-<title>
-2 O
-</title>
-<ellipse fill="none" stroke="black" cx="238.59" cy="-104.78" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="238.59" y="-100.58" font-family="Times,serif" font-size="14.00">2 O</text> </g> <!-- 1 C&#45;&#45;2 O --> <g id="edge1" class="edge">
-<title>
-1 C–2 O
-</title>
-<path fill="none" stroke="black" d="M191.98,-136.86C200.16,-131.23 209.55,-124.76 217.75,-119.12"></path> </g> <!-- 3 N --> <g id="node3" class="node">
-<title>
-3 N
-</title>
-<ellipse fill="none" stroke="black" cx="190.42" cy="-230.8" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="190.42" y="-226.6" font-family="Times,serif" font-size="14.00">3 N</text> </g> <!-- 1 C&#45;&#45;3 N --> <g id="edge2" class="edge">
-<title>
-1 C–3 N
-</title>
-<path fill="none" stroke="black" d="M177.27,-175.35C179.58,-185.07 182.23,-196.25 184.54,-206.01"></path> </g> <!-- 6 N --> <g id="node4" class="node">
-<title>
-6 N
-</title>
-<ellipse fill="none" stroke="black" cx="103.68" cy="-104.8" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="103.68" y="-100.6" font-family="Times,serif" font-size="14.00">6 N</text> </g> <!-- 1 C&#45;&#45;6 N --> <g id="edge3" class="edge">
-<title>
-1 C–6 N
-</title>
-<path fill="none" stroke="black" d="M150.77,-136.86C142.52,-131.24 133.02,-124.78 124.73,-119.13"></path> </g> <!-- 4 H --> <g id="node5" class="node">
-<title>
-4 H
-</title>
-<ellipse fill="none" stroke="black" cx="263.03" cy="-263.51" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="263.03" y="-259.31" font-family="Times,serif" font-size="14.00">4 H</text> </g> <!-- 3 N&#45;&#45;4 H --> <g id="edge4" class="edge">
-<title>
-3 N–4 H
-</title>
-<path fill="none" stroke="black" d="M213.8,-241.33C222.09,-245.06 231.41,-249.26 239.7,-253"></path> </g> <!-- 5 H --> <g id="node6" class="node">
-<title>
-5 H
-</title>
-<ellipse fill="none" stroke="black" cx="152.07" cy="-300.06" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="152.07" y="-295.86" font-family="Times,serif" font-size="14.00">5 H</text> </g> <!-- 3 N&#45;&#45;5 H --> <g id="edge5" class="edge">
-<title>
-3 N–5 H
-</title>
-<path fill="none" stroke="black" d="M178.07,-253.09C173.69,-261 168.77,-269.9 164.39,-277.81"></path> </g> <!-- 7 H --> <g id="node7" class="node">
-<title>
-7 H
-</title>
-<ellipse fill="none" stroke="black" cx="25.25" cy="-115.69" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="25.25" y="-111.49" font-family="Times,serif" font-size="14.00">7 H</text> </g> <!-- 6 N&#45;&#45;7 H --> <g id="edge6" class="edge">
-<title>
-6 N–7 H
-</title>
-<path fill="none" stroke="black" d="M78.43,-108.3C69.48,-109.55 59.4,-110.95 50.45,-112.19"></path> </g> <!-- 8 H --> <g id="node8" class="node">
-<title>
-8 H
-</title>
-<ellipse fill="none" stroke="black" cx="99.21" cy="-25.25" rx="25.01" ry="25.01"></ellipse> <text text-anchor="middle" x="99.21" y="-21.05" font-family="Times,serif" font-size="14.00">8 H</text> </g> <!-- 6 N&#45;&#45;8 H --> <g id="edge7" class="edge">
-<title>
-6 N–8 H
-</title>
-<path fill="none" stroke="black" d="M102.24,-79.19C101.72,-70.02 101.14,-59.69 100.63,-50.54"></path> </g> <!-- 9 C --> <g id="node9" class="node">
-<title>
-9 C
-</title>
-<ellipse fill="none" stroke="black" cx="464.32" cy="-407.79" rx="24.94" ry="24.94"></ellipse> <text text-anchor="middle" x="464.32" y="-403.59" font-family="Times,serif" font-size="14.00">9 C</text> </g> <!-- 10 O --> <g id="node10" class="node">
-<title>
-10 O
-</title>
-<ellipse fill="none" stroke="black" cx="531.42" cy="-361.6" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="531.42" y="-357.4" font-family="Times,serif" font-size="14.00">10 O</text> </g> <!-- 9 C&#45;&#45;10 O --> <g id="edge8" class="edge">
-<title>
-9 C–10 O
-</title>
-<path fill="none" stroke="black" d="M484.81,-393.68C491.6,-389.02 499.22,-383.77 506.31,-378.89"></path> </g> <!-- 11 N --> <g id="node11" class="node">
-<title>
-11 N
-</title>
-<ellipse fill="none" stroke="black" cx="483.25" cy="-487.62" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="483.25" y="-483.42" font-family="Times,serif" font-size="14.00">11 N</text> </g> <!-- 9 C&#45;&#45;11 N --> <g id="edge9" class="edge">
-<title>
-9 C–11 N
-</title>
-<path fill="none" stroke="black" d="M470.1,-432.18C472.06,-440.43 474.26,-449.74 476.3,-458.33"></path> </g> <!-- 14 N --> <g id="node12" class="node">
-<title>
-14 N
-</title>
-<ellipse fill="none" stroke="black" cx="396.51" cy="-361.63" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="396.51" y="-357.43" font-family="Times,serif" font-size="14.00">14 N</text> </g> <!-- 9 C&#45;&#45;14 N --> <g id="edge10" class="edge">
-<title>
-9 C–14 N
-</title>
-<path fill="none" stroke="black" d="M443.6,-393.69C436.59,-388.92 428.69,-383.54 421.39,-378.57"></path> </g> <!-- 12 H --> <g id="node13" class="node">
-<title>
-12 H
-</title>
-<ellipse fill="none" stroke="black" cx="555.86" cy="-520.34" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="555.86" y="-516.14" font-family="Times,serif" font-size="14.00">12 H</text> </g> <!-- 11 N&#45;&#45;12 H --> <g id="edge11" class="edge">
-<title>
-11 N–12 H
-</title>
-<path fill="none" stroke="black" d="M510.7,-499.99C516.48,-502.6 522.59,-505.35 528.37,-507.95"></path> </g> <!-- 13 H --> <g id="node14" class="node">
-<title>
-13 H
-</title>
-<ellipse fill="none" stroke="black" cx="444.89" cy="-556.89" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="444.89" y="-552.69" font-family="Times,serif" font-size="14.00">13 H</text> </g> <!-- 11 N&#45;&#45;13 H --> <g id="edge12" class="edge">
-<title>
-11 N–13 H
-</title>
-<path fill="none" stroke="black" d="M468.53,-514.21C465.57,-519.55 462.47,-525.16 459.51,-530.49"></path> </g> <!-- 15 H --> <g id="node15" class="node">
-<title>
-15 H
-</title>
-<ellipse fill="none" stroke="black" cx="318.08" cy="-372.52" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="318.08" y="-368.32" font-family="Times,serif" font-size="14.00">15 H</text> </g> <!-- 14 N&#45;&#45;15 H --> <g id="edge13" class="edge">
-<title>
-14 N–15 H
-</title>
-<path fill="none" stroke="black" d="M366.41,-365.81C360.36,-366.65 354.01,-367.53 347.97,-368.37"></path> </g> <!-- 16 H --> <g id="node16" class="node">
-<title>
-16 H
-</title>
-<ellipse fill="none" stroke="black" cx="392.04" cy="-282.08" rx="30.16" ry="30.16"></ellipse> <text text-anchor="middle" x="392.04" y="-277.88" font-family="Times,serif" font-size="14.00">16 H</text> </g> <!-- 14 N&#45;&#45;16 H --> <g id="edge14" class="edge">
-<title>
-14 N–16 H
-</title>
-<path fill="none" stroke="black" d="M394.82,-331.55C394.46,-325.22 394.09,-318.53 393.73,-312.2"></path> </g> </g>
+<title>G</title>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-590.97 589.94,-590.97 589.94,4 -4,4"></polygon>
+<!-- 1 C -->
+<g id="node1" class="node">
+<title>1 C</title>
+<ellipse fill="none" stroke="black" cx="171.49" cy="-150.97" rx="24.94" ry="24.94"></ellipse>
+<text text-anchor="middle" x="171.49" y="-146.77" font-family="Times,serif" font-size="14.00">1 C</text>
+</g>
+<!-- 2 O -->
+<g id="node2" class="node">
+<title>2 O</title>
+<ellipse fill="none" stroke="black" cx="238.59" cy="-104.78" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="238.59" y="-100.58" font-family="Times,serif" font-size="14.00">2 O</text>
+</g>
+<!-- 1 C&#45;&#45;2 O -->
+<g id="edge1" class="edge">
+<title>1 C--2 O</title>
+<path fill="none" stroke="black" d="M191.98,-136.86C200.16,-131.23 209.55,-124.76 217.75,-119.12"></path>
+</g>
+<!-- 3 N -->
+<g id="node3" class="node">
+<title>3 N</title>
+<ellipse fill="none" stroke="black" cx="190.42" cy="-230.8" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="190.42" y="-226.6" font-family="Times,serif" font-size="14.00">3 N</text>
+</g>
+<!-- 1 C&#45;&#45;3 N -->
+<g id="edge2" class="edge">
+<title>1 C--3 N</title>
+<path fill="none" stroke="black" d="M177.27,-175.35C179.58,-185.07 182.23,-196.25 184.54,-206.01"></path>
+</g>
+<!-- 6 N -->
+<g id="node4" class="node">
+<title>6 N</title>
+<ellipse fill="none" stroke="black" cx="103.68" cy="-104.8" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="103.68" y="-100.6" font-family="Times,serif" font-size="14.00">6 N</text>
+</g>
+<!-- 1 C&#45;&#45;6 N -->
+<g id="edge3" class="edge">
+<title>1 C--6 N</title>
+<path fill="none" stroke="black" d="M150.77,-136.86C142.52,-131.24 133.02,-124.78 124.73,-119.13"></path>
+</g>
+<!-- 4 H -->
+<g id="node5" class="node">
+<title>4 H</title>
+<ellipse fill="none" stroke="black" cx="263.03" cy="-263.51" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="263.03" y="-259.31" font-family="Times,serif" font-size="14.00">4 H</text>
+</g>
+<!-- 3 N&#45;&#45;4 H -->
+<g id="edge4" class="edge">
+<title>3 N--4 H</title>
+<path fill="none" stroke="black" d="M213.8,-241.33C222.09,-245.06 231.41,-249.26 239.7,-253"></path>
+</g>
+<!-- 5 H -->
+<g id="node6" class="node">
+<title>5 H</title>
+<ellipse fill="none" stroke="black" cx="152.07" cy="-300.06" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="152.07" y="-295.86" font-family="Times,serif" font-size="14.00">5 H</text>
+</g>
+<!-- 3 N&#45;&#45;5 H -->
+<g id="edge5" class="edge">
+<title>3 N--5 H</title>
+<path fill="none" stroke="black" d="M178.07,-253.09C173.69,-261 168.77,-269.9 164.39,-277.81"></path>
+</g>
+<!-- 7 H -->
+<g id="node7" class="node">
+<title>7 H</title>
+<ellipse fill="none" stroke="black" cx="25.25" cy="-115.69" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="25.25" y="-111.49" font-family="Times,serif" font-size="14.00">7 H</text>
+</g>
+<!-- 6 N&#45;&#45;7 H -->
+<g id="edge6" class="edge">
+<title>6 N--7 H</title>
+<path fill="none" stroke="black" d="M78.43,-108.3C69.48,-109.55 59.4,-110.95 50.45,-112.19"></path>
+</g>
+<!-- 8 H -->
+<g id="node8" class="node">
+<title>8 H</title>
+<ellipse fill="none" stroke="black" cx="99.21" cy="-25.25" rx="25.01" ry="25.01"></ellipse>
+<text text-anchor="middle" x="99.21" y="-21.05" font-family="Times,serif" font-size="14.00">8 H</text>
+</g>
+<!-- 6 N&#45;&#45;8 H -->
+<g id="edge7" class="edge">
+<title>6 N--8 H</title>
+<path fill="none" stroke="black" d="M102.24,-79.19C101.72,-70.02 101.14,-59.69 100.63,-50.54"></path>
+</g>
+<!-- 9 C -->
+<g id="node9" class="node">
+<title>9 C</title>
+<ellipse fill="none" stroke="black" cx="464.32" cy="-407.79" rx="24.94" ry="24.94"></ellipse>
+<text text-anchor="middle" x="464.32" y="-403.59" font-family="Times,serif" font-size="14.00">9 C</text>
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-<figcaption class="figure-caption">Figure&nbsp;3: A diagram of the two urea molecules topology</figcaption>
+</div>
+<figcaption class="figure quarto-float-caption quarto-float-fig" id="fig-ala-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
+Figure&nbsp;3: A diagram of the two urea molecules topology
+</figcaption>
 </figure>
 </div>
 </div>
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+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
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+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
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+            throttle = true;
+        } else { // all the others get throttled
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+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
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+        }
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-      <a href="../../guide/explanation/index.html" class="pagination-link">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Explanation</span>
+      <a href="../../guide/explanation/components.html" class="pagination-link  aria-label=" components="" of="" kimmdy"="">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Components of KIMMDY</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../_reference/index.html" class="pagination-link">
+      <a href="../../_reference/index.html" class="pagination-link" aria-label="Reference">
         <span class="nav-page-text">Reference</span> <i class="bi bi-arrow-right-short"></i>
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+  <li><a href="#radical-migrations" id="toc-radical-migrations" class="nav-link" data-scroll-target="#radical-migrations">Radical Migrations</a></li>
+  <li><a href="#reaction-rates" id="toc-reaction-rates" class="nav-link" data-scroll-target="#reaction-rates">Reaction Rates</a></li>
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+<header id="title-block-header" class="quarto-title-block default"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../guide/how-to/index.html">How-To</a></li><li class="breadcrumb-item"><a href="../../guide/how-to/analyze.html">Analyze a KIMMDY run</a></li></ol></nav>
+<div class="quarto-title">
+<h1 class="title">Analyze a KIMMDY run</h1>
+</div>
+
+
+
+<div class="quarto-title-meta">
+
+    <div>
+    <div class="quarto-title-meta-heading">Author</div>
+    <div class="quarto-title-meta-contents">
+             <p>Kai Riedmiller </p>
+          </div>
+  </div>
+    
+  
+    
+  </div>
+  
+
+
+</header>
+
+
+<p>Through <a href="../../guide/references/cmd_ref.html#analysis"><code>kimmdy-analysis</code></a>, several tools are provided to analyze various aspects of KIMMDY runs.</p>
+<section id="energy" class="level2">
+<h2 class="anchored" data-anchor-id="energy">Energy</h2>
+<p><code>kimmdy-analysis energy</code> sets the usual energy analysis by gmx energy into the context of KIMMDY, by showing the KIMMDY MD steps next to the energy plot. An example KIMMDY run of three HAT reactions is shown below.</p>
+<p>All energy terms supported in the GROMACS tool <code>gmx energy</code> can be plotted. The lowest plot shows which KIMMDY MD run is running at a given time. Here, three HAT reactions are performed, each in between two equilibrium MD simulations.</p>
+<p><a href="../../guide/how-to/analysis_figures/ala_3hat_energy.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1"><img src="../../guide/how-to/analysis_figures/ala_3hat_energy.png" class="img-fluid" style="width:60.0%"></a></p>
+</section>
+<section id="radical-occupancy" class="level2">
+<h2 class="anchored" data-anchor-id="radical-occupancy">Radical Occupancy</h2>
+<p><code>kimmdy-analysis radical_population</code> analyzes where, and for how long radi- cals are in the system. The resulting statistic can be visualized in two ways. First, as values on a three-dimensional snapshot of the system, as shown in below. For this, a pdb file of the structure is generated, containing the calculated radical occupancy as its beta value for visualization with established software, like vmd. And second, as a bar plot of the fractional radical occupancy per atom. Depending on the number of involved atoms, the structure, or the bar plot might be more useful.</p>
+<div>
+
+</div>
+<div class="quarto-layout-panel" data-layout-ncol="2">
+<div class="quarto-layout-row quarto-layout-valign-top">
+<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: center;">
+<p><a href="../../guide/how-to/analysis_figures/hat_ch_pep_occ.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2"><img src="../../guide/how-to/analysis_figures/hat_ch_pep_occ.png" class="img-fluid"></a></p>
+</div>
+<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: center;">
+<p><a href="../../guide/how-to/analysis_figures/hat_radical_population_fingerprint.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3"><img src="../../guide/how-to/analysis_figures/hat_radical_population_fingerprint.png" class="img-fluid"></a></p>
+</div>
+</div>
+</div>
+</section>
+<section id="radical-migrations" class="level2">
+<h2 class="anchored" data-anchor-id="radical-migrations">Radical Migrations</h2>
+<p>The <code>kimmdy-analysis radical_migration</code> tool can generate visualizations. Depicting between which atoms HAT reactions occur. The arrows can be colored according to the number of HAT reactions, or the maximum rate for the respective transition.</p>
+<p><a href="../../guide/how-to/analysis_figures/hat_ch_pep_arr.png" class="lightbox" data-gallery="quarto-lightbox-gallery-4"><img src="../../guide/how-to/analysis_figures/hat_ch_pep_arr.png" class="img-fluid" style="width:60.0%"></a></p>
+</section>
+<section id="reaction-rates" class="level2">
+<h2 class="anchored" data-anchor-id="reaction-rates">Reaction Rates</h2>
+<p><code>kimmdy-analysis rates</code> can generate plots of all available rates entering a kMC step. By default, KIMMDY generates in the kMC step of every reaction a plot, showing calculated rates over the course of the latest simulation. This can be turned off in the input yaml. If in the kMC step a reaction is chosen, the corresponding rates are highlighted bold and dashed. Each reaction recipe has a string representation, consisting of the involved atom numbers and symbols for the actions. Bonds breaking are depicted as bolt. A new bond, and a movement are both represented with an arrow.</p>
+<p><a href="../../guide/how-to/analysis_figures/reaction_rates.svg" class="lightbox" data-gallery="quarto-lightbox-gallery-5"><img src="../../guide/how-to/analysis_figures/reaction_rates.svg" class="img-fluid" style="width:60.0%"></a></p>
+</section>
+<section id="runtimes" class="level2">
+<h2 class="anchored" data-anchor-id="runtimes">Runtimes</h2>
+<p><code>kimmdy-analysis runtime</code> analyzes the runtime of kimmdy. Besides showing the runtime of all tasks performed it can group tasks, and types of tasks together. The example analyzes the runtime of KIMMDY performing 20 consecutive HAT reactions after an initial homolysis reaction. As the simulated system is quite small (the charged_peptide example is used), the MD simulations are comparatively fast. For bigger systems, the MD runtime will increase, while the time required for HAT reaction barrier predictions will not, as it only atoms close to a radical are taken into account. Therefore, the computational overhead of KIMMDY should be negligible in most use cases.</p>
+<div>
+
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+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
+        }
+        typesetMath(container);
+        return container.innerHTML
+      } else {
+        typesetMath(note);
+        return note.innerHTML;
+      }
+    } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
+      return note.innerHTML;
+    }
+  }
+  for (var i=0; i<xrefs.length; i++) {
+    const xref = xrefs[i];
+    tippyHover(xref, undefined, function(instance) {
+      instance.disable();
+      let url = xref.getAttribute('href');
+      let hash = undefined; 
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
+        }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
+          if (note !== null) {
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
+            instance.setContent(html);
+          } 
+        }).finally(() => {
+          instance.enable();
+          instance.show();
+        });
+      }
+    }, function(instance) {
+    });
+  }
+      let selectedAnnoteEl;
+      const selectorForAnnotation = ( cell, annotation) => {
+        let cellAttr = 'data-code-cell="' + cell + '"';
+        let lineAttr = 'data-code-annotation="' +  annotation + '"';
+        const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
+        return selector;
+      }
+      const selectCodeLines = (annoteEl) => {
+        const doc = window.document;
+        const targetCell = annoteEl.getAttribute("data-target-cell");
+        const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
+        const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
+        const lines = annoteSpan.getAttribute("data-code-lines").split(",");
+        const lineIds = lines.map((line) => {
+          return targetCell + "-" + line;
+        })
+        let top = null;
+        let height = null;
+        let parent = null;
+        if (lineIds.length > 0) {
+            //compute the position of the single el (top and bottom and make a div)
+            const el = window.document.getElementById(lineIds[0]);
+            top = el.offsetTop;
+            height = el.offsetHeight;
+            parent = el.parentElement.parentElement;
+          if (lineIds.length > 1) {
+            const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
+            const bottom = lastEl.offsetTop + lastEl.offsetHeight;
+            height = bottom - top;
+          }
+          if (top !== null && height !== null && parent !== null) {
+            // cook up a div (if necessary) and position it 
+            let div = window.document.getElementById("code-annotation-line-highlight");
+            if (div === null) {
+              div = window.document.createElement("div");
+              div.setAttribute("id", "code-annotation-line-highlight");
+              div.style.position = 'absolute';
+              parent.appendChild(div);
+            }
+            div.style.top = top - 2 + "px";
+            div.style.height = height + 4 + "px";
+            div.style.left = 0;
+            let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
+            if (gutterDiv === null) {
+              gutterDiv = window.document.createElement("div");
+              gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
+              gutterDiv.style.position = 'absolute';
+              const codeCell = window.document.getElementById(targetCell);
+              const gutter = codeCell.querySelector('.code-annotation-gutter');
+              gutter.appendChild(gutterDiv);
+            }
+            gutterDiv.style.top = top - 2 + "px";
+            gutterDiv.style.height = height + 4 + "px";
+          }
+          selectedAnnoteEl = annoteEl;
+        }
+      };
+      const unselectCodeLines = () => {
+        const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
+        elementsIds.forEach((elId) => {
+          const div = window.document.getElementById(elId);
+          if (div) {
+            div.remove();
+          }
+        });
+        selectedAnnoteEl = undefined;
+      };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
+      // Attach click handler to the DT
+      const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
+      for (const annoteDlNode of annoteDls) {
+        annoteDlNode.addEventListener('click', (event) => {
+          const clickedEl = event.target;
+          if (clickedEl !== selectedAnnoteEl) {
+            unselectCodeLines();
+            const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
+            if (activeEl) {
+              activeEl.classList.remove('code-annotation-active');
+            }
+            selectCodeLines(clickedEl);
+            clickedEl.classList.add('code-annotation-active');
+          } else {
+            // Unselect the line
+            unselectCodeLines();
+            clickedEl.classList.remove('code-annotation-active');
+          }
+        });
+      }
+  const findCites = (el) => {
+    const parentEl = el.parentElement;
+    if (parentEl) {
+      const cites = parentEl.dataset.cites;
+      if (cites) {
+        return {
+          el,
+          cites: cites.split(' ')
+        };
+      } else {
+        return findCites(el.parentElement)
+      }
+    } else {
+      return undefined;
+    }
+  };
+  var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
+  for (var i=0; i<bibliorefs.length; i++) {
+    const ref = bibliorefs[i];
+    const citeInfo = findCites(ref);
+    if (citeInfo) {
+      tippyHover(citeInfo.el, function() {
+        var popup = window.document.createElement('div');
+        citeInfo.cites.forEach(function(cite) {
+          var citeDiv = window.document.createElement('div');
+          citeDiv.classList.add('hanging-indent');
+          citeDiv.classList.add('csl-entry');
+          var biblioDiv = window.document.getElementById('ref-' + cite);
+          if (biblioDiv) {
+            citeDiv.innerHTML = biblioDiv.innerHTML;
+          }
+          popup.appendChild(citeDiv);
+        });
+        return popup.innerHTML;
+      });
+    }
+  }
+});
+</script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+      <a href="../../guide/how-to/index.html" class="pagination-link  aria-label=" how-to"="">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">How-To</span>
+      </a>          
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="../../guide/how-to/contribute.html" class="pagination-link" aria-label="Contribute">
+        <span class="nav-page-text">Contribute</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
+</div> <!-- /content -->
+<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","selector":".lightbox","loop":false,"descPosition":"bottom","openEffect":"zoom"});</script>
+
+
+
+
+</body></html>
\ No newline at end of file
diff --git a/docs/guide/how-to/contribute.html b/docs/guide/how-to/contribute.html
index 0fcec579..f3609bfc 100644
--- a/docs/guide/how-to/contribute.html
+++ b/docs/guide/how-to/contribute.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -31,7 +31,7 @@
 <script src="../../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../../">
 <link href="../../guide/how-to/examples.html" rel="next">
-<link href="../../guide/how-to/index.html" rel="prev">
+<link href="../../guide/how-to/analyze.html" rel="prev">
 <script src="../../site_libs/quarto-html/quarto.js"></script>
 <script src="../../site_libs/quarto-html/popper.min.js"></script>
 <script src="../../site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -49,12 +49,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -76,7 +77,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -90,24 +91,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -138,11 +139,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../guide/how-to/index.html">How-To</a></li><li class="breadcrumb-item"><a href="../../guide/how-to/contribute.html">Contribute</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -150,7 +151,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -199,6 +200,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -240,6 +247,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -442,7 +455,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -451,7 +464,7 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#local-testing" id="toc-local-testing" class="nav-link active" data-scroll-target="#local-testing">Local testing</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/contribute.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/contribute.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -472,8 +485,10 @@ <h1 class="title">Contribute</h1>
   </div>
   
 
+
 </header>
 
+
 <p>KIMMDY uses conventional commits and semantic versioning, automated via <a href="https://github.com/googleapis/release-please">release please</a>.</p>
 <p>If a PR adds multiple commits, we use the <code>squash and merge</code> option to keep the commit history clean. If a PR unavoidably contains changes the message can be edited before merging to ensure release please picks up all changes.</p>
 <p>The following example message (first line is the title in the GitHub UI, the rest is the body in the window below):</p>
@@ -802,18 +817,64 @@ <h2 class="anchored" data-anchor-id="local-testing">Local testing</h2>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -823,27 +884,56 @@ <h2 class="anchored" data-anchor-id="local-testing">Local testing</h2>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -921,6 +1011,32 @@ <h2 class="anchored" data-anchor-id="local-testing">Local testing</h2>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -982,12 +1098,12 @@ <h2 class="anchored" data-anchor-id="local-testing">Local testing</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/how-to/index.html" class="pagination-link">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">How-To</span>
+      <a href="../../guide/how-to/analyze.html" class="pagination-link  aria-label=" analyze="" a="" kimmdy="" run"="">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Analyze a KIMMDY run</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/how-to/examples.html" class="pagination-link">
+      <a href="../../guide/how-to/examples.html" class="pagination-link" aria-label="Examples">
         <span class="nav-page-text">Examples</span> <i class="bi bi-arrow-right-short"></i>
       </a>
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diff --git a/docs/guide/how-to/examples.html b/docs/guide/how-to/examples.html
index 6271f4dd..269957db 100644
--- a/docs/guide/how-to/examples.html
+++ b/docs/guide/how-to/examples.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -22,7 +22,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -83,12 +83,13 @@
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   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
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     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -110,7 +111,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
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       <div class="navbar-brand-container mx-auto">
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@@ -124,24 +125,24 @@
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-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
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@@ -172,11 +173,11 @@
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+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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   </nav>
@@ -184,7 +185,7 @@
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-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
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     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -233,6 +234,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
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@@ -274,6 +281,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -476,7 +489,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -492,7 +505,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#charged_peptide_homolysis_hat_naive" id="toc-charged_peptide_homolysis_hat_naive" class="nav-link" data-scroll-target="#charged_peptide_homolysis_hat_naive">charged_peptide_homolysis_hat_naive</a></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/examples.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/examples.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -513,8 +526,10 @@ <h1 class="title">Examples</h1>
   </div>
   
 
+
 </header>
 
+
 <section id="further-examples" class="level2">
 <h2 class="anchored" data-anchor-id="further-examples">Further Examples</h2>
 <p>KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.</p>
@@ -966,18 +981,64 @@ <h3 class="anchored" data-anchor-id="charged_peptide_homolysis_hat_naive">charge
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
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+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
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+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -987,27 +1048,56 @@ <h3 class="anchored" data-anchor-id="charged_peptide_homolysis_hat_naive">charge
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       let url = xref.getAttribute('href');
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-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1085,6 +1175,32 @@ <h3 class="anchored" data-anchor-id="charged_peptide_homolysis_hat_naive">charge
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1146,12 +1262,12 @@ <h3 class="anchored" data-anchor-id="charged_peptide_homolysis_hat_naive">charge
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/how-to/contribute.html" class="pagination-link">
+      <a href="../../guide/how-to/contribute.html" class="pagination-link  aria-label=" contribute"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Contribute</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/how-to/hcp.html" class="pagination-link">
+      <a href="../../guide/how-to/hcp.html" class="pagination-link" aria-label="High Performance Computing">
         <span class="nav-page-text">High Performance Computing</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/guide/how-to/hcp.html b/docs/guide/how-to/hcp.html
index 33cbddb5..9af631ca 100644
--- a/docs/guide/how-to/hcp.html
+++ b/docs/guide/how-to/hcp.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -22,7 +22,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -83,12 +83,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -110,7 +111,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -124,24 +125,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -172,11 +173,11 @@
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   <nav class="quarto-secondary-nav">
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-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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@@ -184,7 +185,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -233,6 +234,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -274,6 +281,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -476,7 +489,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -485,7 +498,7 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#setup" id="toc-setup" class="nav-link active" data-scroll-target="#setup">Setup</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/hcp.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/hcp.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -506,8 +519,10 @@ <h1 class="title">High Performance Computing</h1>
   </div>
   
 
+
 </header>
 
+
 <section id="setup" class="level2">
 <h2 class="anchored" data-anchor-id="setup">Setup</h2>
 <p>You need an installation of python (<code>&gt;= 3.10</code>) and (possibly PLUMED patched) GROMACS in your HPC environment.</p>
@@ -789,18 +804,64 @@ <h2 class="anchored" data-anchor-id="setup">Setup</h2>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
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+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
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+    if (id === null || id.startsWith('sec-')) {
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-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
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+        for (let i = 1; i < note.children.length; i++) {
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+          if (child.tagName === "P" && child.innerText === "") {
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+        typesetMath(container);
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+        typesetMath(note);
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+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
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@@ -810,27 +871,56 @@ <h2 class="anchored" data-anchor-id="setup">Setup</h2>
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-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
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-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -908,6 +998,32 @@ <h2 class="anchored" data-anchor-id="setup">Setup</h2>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -969,12 +1085,12 @@ <h2 class="anchored" data-anchor-id="setup">Setup</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/how-to/examples.html" class="pagination-link">
+      <a href="../../guide/how-to/examples.html" class="pagination-link  aria-label=" examples"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Examples</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/how-to/install-ml-plugins.html" class="pagination-link">
+      <a href="../../guide/how-to/install-ml-plugins.html" class="pagination-link" aria-label="Install Machine Learning Plugins">
         <span class="nav-page-text">Install Machine Learning Plugins</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/guide/how-to/index.html b/docs/guide/how-to/index.html
index b5711791..4703eb56 100644
--- a/docs/guide/how-to/index.html
+++ b/docs/guide/how-to/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -30,7 +30,7 @@
 <script src="../../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../../">
-<link href="../../guide/how-to/contribute.html" rel="next">
+<link href="../../guide/how-to/analyze.html" rel="next">
 <link href="../../guide/tutorials/write-plugin.html" rel="prev">
 <script src="../../site_libs/quarto-listing/list.min.js"></script>
 <script src="../../site_libs/quarto-listing/quarto-listing.js"></script>
@@ -51,12 +51,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -109,7 +110,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -123,24 +124,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -171,11 +172,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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   </nav>
@@ -183,7 +184,7 @@
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 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
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         <li class="sidebar-item">
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       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -273,6 +280,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -475,7 +488,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         
@@ -498,8 +511,10 @@ <h1 class="title">How-To</h1>
   </div>
   
 
+
 </header>
 
+
 <p>How-To Guides</p>
 
 
@@ -537,7 +552,15 @@ <h1 class="title">How-To</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1711385802333" data-listing-reading-time-sort="2" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
+<tr data-index="0" data-listing-file-modified-sort="1712934328000" data-listing-reading-time-sort="2" data-listing-word-count-sort="390" data-listing-title-sort="Analyze a KIMMDY run" data-listing-filename-sort="analyze.qmd">
+<td>
+<a href="../../guide/how-to/analyze.html" class="title listing-title">Analyze a KIMMDY run</a>
+</td>
+<td>
+<span class="listing-author">Kai Riedmiller</span>
+</td>
+</tr>
+<tr data-index="1" data-listing-file-modified-sort="1701868360000" data-listing-reading-time-sort="2" data-listing-word-count-sort="266" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
 <td>
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@@ -545,7 +568,7 @@ <h1 class="title">How-To</h1>
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-<tr data-index="1" data-listing-file-modified-sort="1711385802333" data-listing-reading-time-sort="1" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
+<tr data-index="2" data-listing-file-modified-sort="1701868360000" data-listing-reading-time-sort="1" data-listing-word-count-sort="105" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
 <td>
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@@ -553,7 +576,7 @@ <h1 class="title">How-To</h1>
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+<tr data-index="3" data-listing-file-modified-sort="1701868360000" data-listing-reading-time-sort="1" data-listing-word-count-sort="87" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
 <td>
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 </td>
@@ -561,7 +584,7 @@ <h1 class="title">How-To</h1>
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+<tr data-index="4" data-listing-file-modified-sort="1702029759000" data-listing-reading-time-sort="1" data-listing-word-count-sort="152" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
 <td>
 <a href="../../guide/how-to/install-ml-plugins.html" class="title listing-title">Install Machine Learning Plugins</a>
 </td>
@@ -569,7 +592,7 @@ <h1 class="title">How-To</h1>
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 </td>
 </tr>
-<tr data-index="4" data-listing-file-modified-sort="1711385802333" data-listing-reading-time-sort="1" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
+<tr data-index="5" data-listing-file-modified-sort="1708597294000" data-listing-reading-time-sort="1" data-listing-word-count-sort="165" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
 <td>
 <a href="../../guide/how-to/reaction_only.html" class="title listing-title">Reaction only</a>
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@@ -845,18 +868,64 @@ <h1 class="title">How-To</h1>
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   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
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+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
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+    stripColumnClz(note)
+    const typesetMath = (el) => {
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+        // MathJax Typeset
+        window.MathJax.typeset([el]);
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+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
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+              throwOnError: false,
+              macros: macros,
+              fleqn: false
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-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
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+          if (child.tagName === "P" && child.innerText === "") {
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@@ -866,27 +935,56 @@ <h1 class="title">How-To</h1>
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-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
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-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -964,6 +1062,32 @@ <h1 class="title">How-To</h1>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1025,13 +1149,13 @@ <h1 class="title">How-To</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/tutorials/write-plugin.html" class="pagination-link">
+      <a href="../../guide/tutorials/write-plugin.html" class="pagination-link  aria-label=" write="" a="" reaction="" plugin"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Write a Reaction Plugin</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/how-to/contribute.html" class="pagination-link">
-        <span class="nav-page-text">Contribute</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="../../guide/how-to/analyze.html" class="pagination-link" aria-label="Analyze a KIMMDY run">
+        <span class="nav-page-text">Analyze a KIMMDY run</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>
@@ -1040,4 +1164,4 @@ <h1 class="title">How-To</h1>
 
 
 
-<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/index.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></div></div></footer></body></html>
\ No newline at end of file
+<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div></div></footer></body></html>
\ No newline at end of file
diff --git a/docs/guide/how-to/install-ml-plugins.html b/docs/guide/how-to/install-ml-plugins.html
index 2767f2e5..c568be08 100644
--- a/docs/guide/how-to/install-ml-plugins.html
+++ b/docs/guide/how-to/install-ml-plugins.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -22,7 +22,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -83,12 +83,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -110,7 +111,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -124,24 +125,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -172,11 +173,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../guide/how-to/index.html">How-To</a></li><li class="breadcrumb-item"><a href="../../guide/how-to/install-ml-plugins.html">Install Machine Learning Plugins</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -184,7 +185,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -233,6 +234,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -274,6 +281,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -476,7 +489,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -488,7 +501,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#potential-problems-when-running" id="toc-potential-problems-when-running" class="nav-link" data-scroll-target="#potential-problems-when-running">Potential problems when running</a></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/install-ml-plugins.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/install-ml-plugins.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -509,8 +522,10 @@ <h1 class="title">Install Machine Learning Plugins</h1>
   </div>
   
 
+
 </header>
 
+
 <div class="callout callout-style-default callout-warning callout-titled">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
@@ -832,18 +847,64 @@ <h3 class="anchored" data-anchor-id="potential-problems-when-running">Potential
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -853,27 +914,56 @@ <h3 class="anchored" data-anchor-id="potential-problems-when-running">Potential
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -951,6 +1041,32 @@ <h3 class="anchored" data-anchor-id="potential-problems-when-running">Potential
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1012,12 +1128,12 @@ <h3 class="anchored" data-anchor-id="potential-problems-when-running">Potential
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/how-to/hcp.html" class="pagination-link">
+      <a href="../../guide/how-to/hcp.html" class="pagination-link  aria-label=" high="" performance="" computing"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">High Performance Computing</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/how-to/reaction_only.html" class="pagination-link">
+      <a href="../../guide/how-to/reaction_only.html" class="pagination-link" aria-label="Reaction only">
         <span class="nav-page-text">Reaction only</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/guide/how-to/reaction_only.html b/docs/guide/how-to/reaction_only.html
index 2d38607a..f0b51a24 100644
--- a/docs/guide/how-to/reaction_only.html
+++ b/docs/guide/how-to/reaction_only.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -50,12 +50,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -77,7 +78,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -91,24 +92,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -139,11 +140,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -151,7 +152,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -200,6 +201,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -241,6 +248,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -443,7 +456,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -453,7 +466,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#kimmdy-yaml" id="toc-kimmdy-yaml" class="nav-link active" data-scroll-target="#kimmdy-yaml">KIMMDY yaml</a></li>
   <li><a href="#pre-averaged-plumed-input" id="toc-pre-averaged-plumed-input" class="nav-link" data-scroll-target="#pre-averaged-plumed-input">Pre-averaged plumed input</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/reaction_only.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/how-to/reaction_only.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -480,8 +493,10 @@ <h1 class="title">Reaction only</h1>
   </div>
   
 
+
 </header>
 
+
 <p>You might want to apply a KIMMDY reaction to an already existing simulation. Here are some important points for doing so.</p>
 <section id="kimmdy-yaml" class="level2">
 <h2 class="anchored" data-anchor-id="kimmdy-yaml">KIMMDY yaml</h2>
@@ -761,18 +776,64 @@ <h2 class="anchored" data-anchor-id="pre-averaged-plumed-input">Pre-averaged plu
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
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+      }
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+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
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+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
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@@ -782,27 +843,56 @@ <h2 class="anchored" data-anchor-id="pre-averaged-plumed-input">Pre-averaged plu
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       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -880,6 +970,32 @@ <h2 class="anchored" data-anchor-id="pre-averaged-plumed-input">Pre-averaged plu
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -941,12 +1057,12 @@ <h2 class="anchored" data-anchor-id="pre-averaged-plumed-input">Pre-averaged plu
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/how-to/install-ml-plugins.html" class="pagination-link">
+      <a href="../../guide/how-to/install-ml-plugins.html" class="pagination-link  aria-label=" install="" machine="" learning="" plugins"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Install Machine Learning Plugins</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/explanation/index.html" class="pagination-link">
+      <a href="../../guide/explanation/index.html" class="pagination-link" aria-label="Explanation">
         <span class="nav-page-text">Explanation</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/guide/references/cmd_ref.html b/docs/guide/references/cmd_ref.html
index 7bf7b74f..c83fa6e6 100644
--- a/docs/guide/references/cmd_ref.html
+++ b/docs/guide/references/cmd_ref.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -22,7 +22,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -83,12 +83,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -110,7 +111,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -124,24 +125,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -172,11 +173,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
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-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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   </nav>
@@ -184,7 +185,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -233,6 +234,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -274,6 +281,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -476,7 +489,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -488,7 +501,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#remove-hydrogen" id="toc-remove-hydrogen" class="nav-link" data-scroll-target="#remove-hydrogen">Remove Hydrogen</a></li>
   <li><a href="#examples" id="toc-examples" class="nav-link" data-scroll-target="#examples">Examples</a></li>
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-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/references/cmd_ref.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/references/cmd_ref.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -508,8 +521,10 @@ <h1 class="title">CLI Arguments</h1>
   </div>
   
 
+
 </header>
 
+
 <p>The prefered method of starting a KIMMDY run is via the command line, though <a href="../../_reference/cmd.html">Python entry points</a> are supported as well.</p>
 <section id="kimmdy" class="level2">
 <h2 class="anchored" data-anchor-id="kimmdy">KIMMDY</h2>
@@ -892,18 +907,64 @@ <h2 class="anchored" data-anchor-id="examples">Examples</h2>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
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+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
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+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
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+    if (id === null || id.startsWith('sec-')) {
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-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
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+        typesetMath(container);
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@@ -913,27 +974,56 @@ <h2 class="anchored" data-anchor-id="examples">Examples</h2>
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       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1011,6 +1101,32 @@ <h2 class="anchored" data-anchor-id="examples">Examples</h2>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1072,12 +1188,12 @@ <h2 class="anchored" data-anchor-id="examples">Examples</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/references/input.html" class="pagination-link">
+      <a href="../../guide/references/input.html" class="pagination-link  aria-label=" input="" file"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Input File</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../_reference/cmd.html" class="pagination-link">
+      <a href="../../_reference/cmd.html" class="pagination-link" aria-label="cmd">
         <span class="nav-page-text">cmd</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/guide/references/input.html b/docs/guide/references/input.html
index 55b1d552..64a82d34 100644
--- a/docs/guide/references/input.html
+++ b/docs/guide/references/input.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -22,7 +22,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -83,12 +83,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -110,7 +111,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -124,24 +125,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -172,11 +173,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../../guide/references/input.html">Input File</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -184,7 +185,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -233,6 +234,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -274,6 +281,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -476,7 +489,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -487,7 +500,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#all-options" id="toc-all-options" class="nav-link" data-scroll-target="#all-options">All Options</a></li>
   <li><a href="#example-kimmdy.yml-files" id="toc-example-kimmdy.yml-files" class="nav-link" data-scroll-target="#example-kimmdy.yml-files">Example <code>kimmdy.yml</code> Files</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/references/input.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/references/input.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -507,33 +520,36 @@ <h1 class="title">Input File</h1>
   </div>
   
 
+
 </header>
 
+
 <section id="autocompletion" class="level2">
 <h2 class="anchored" data-anchor-id="autocompletion">Autocompletion</h2>
 <p>KIMMDY comes with autocompletion and tooltips insight your editor for its configuration file <code>kimmdy.yml</code>.</p>
 <p>All you need to do is activate a <a href="https://github.com/redhat-developer/yaml-language-server">yaml-language-server</a> in your editor (e.g.&nbsp;<a href="https://code.visualstudio.com/">VS Code</a> via the <a href="https://marketplace.visualstudio.com/items?itemName=redhat.vscode-yaml">YAML extension</a> or <a href="https://neovim.io/">Neovim</a> via <a href="https://github.com/neovim/nvim-lspconfig">lspconfig</a>).</p>
 <p>Activating this is very much recommended, as it prevents many typos and missaligned braces.</p>
-<div class="callout callout-style-simple callout-tip callout-titled">
-<div class="callout-header d-flex align-content-center">
+<div class="callout callout-style-simple callout-tip">
+<div class="callout-body d-flex">
 <div class="callout-icon-container">
 <i class="callout-icon"></i>
 </div>
-<div class="callout-title-container flex-fill">
-
-</div>
-</div>
-<div class="callout-body-container callout-body">
+<div class="callout-body-container">
 <p>This only works, if your config file is called <code>kimmdy.yml</code> and the Scheme Store hasn’t been disabled in your editor settings (e.g.&nbsp;<code>Yaml &gt; Schema Store: Enable</code>.</p>
 </div>
 </div>
+</div>
 </section>
 <section id="all-options" class="level2">
 <h2 class="anchored" data-anchor-id="all-options">All Options</h2>
 <p>The following is a list of the options that can be set in the <code>kimmdy.yml</code> file. It includes reactions currently available in KIMMDY as plugins. Nested options are separated by a <code>.</code>. <code>*</code> denotes an arbitrary name for a section. The key for a section is <strong>bold</strong>.</p>
-<div id="tbl-options" class="anchored">
+<div id="tbl-options" class="striped hover anchored">
+<figure class="quarto-float quarto-float-tbl figure">
+<figcaption class="table quarto-float-caption quarto-float-tbl" id="tbl-options-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
+Table&nbsp;1: KIMMDY options
+</figcaption>
+<div aria-describedby="tbl-options-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 <table class="table-striped table-hover table">
-<caption>Table&nbsp;1: KIMMDY options</caption>
 <colgroup>
 <col style="width: 21%">
 <col style="width: 42%">
@@ -785,6 +801,8 @@ <h2 class="anchored" data-anchor-id="all-options">All Options</h2>
 </tbody>
 </table>
 </div>
+</figure>
+</div>
 </section>
 <section id="example-kimmdy.yml-files" class="level2">
 <h2 class="anchored" data-anchor-id="example-kimmdy.yml-files">Example <code>kimmdy.yml</code> Files</h2>
@@ -792,7 +810,7 @@ <h2 class="anchored" data-anchor-id="example-kimmdy.yml-files">Example <code>kim
 <div class="code-with-filename-file">
 <pre><strong>kimmdy.yml</strong></pre>
 </div>
-<div class="sourceCode" id="cb1"><pre class="sourceCode yaml code-with-copy"><code class="sourceCode yaml"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dryrun</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
+<div class="sourceCode" id="cb1" data-filename="kimmdy.yml"><pre class="sourceCode yaml code-with-copy"><code class="sourceCode yaml"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dryrun</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">max_tasks</span><span class="kw">:</span><span class="at"> </span><span class="dv">100</span></span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">name</span><span class="kw">:</span><span class="at"> </span><span class="st">'hat_tf_000'</span></span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">gromacs_alias</span><span class="kw">:</span><span class="at"> </span><span class="st">'gmx'</span></span>
@@ -1087,18 +1105,64 @@ <h2 class="anchored" data-anchor-id="example-kimmdy.yml-files">Example <code>kim
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -1108,27 +1172,56 @@ <h2 class="anchored" data-anchor-id="example-kimmdy.yml-files">Example <code>kim
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1206,6 +1299,32 @@ <h2 class="anchored" data-anchor-id="example-kimmdy.yml-files">Example <code>kim
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1267,12 +1386,12 @@ <h2 class="anchored" data-anchor-id="example-kimmdy.yml-files">Example <code>kim
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../_reference/index.html" class="pagination-link">
+      <a href="../../_reference/index.html" class="pagination-link  aria-label=" reference"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Reference</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/references/cmd_ref.html" class="pagination-link">
+      <a href="../../guide/references/cmd_ref.html" class="pagination-link" aria-label="CLI Arguments">
         <span class="nav-page-text">CLI Arguments</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/guide/tutorials/colbuilder.html b/docs/guide/tutorials/colbuilder.html
index 889ced0a..865ef179 100644
--- a/docs/guide/tutorials/colbuilder.html
+++ b/docs/guide/tutorials/colbuilder.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -23,7 +23,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -84,12 +84,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -111,7 +112,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -125,24 +126,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -173,11 +174,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../guide/tutorials/index.html">Tutorials</a></li><li class="breadcrumb-item"><a href="../../guide/tutorials/colbuilder.html">Run KIMMDY from Colbuilder fibril</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -185,7 +186,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -234,6 +235,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -275,6 +282,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -477,7 +490,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -496,7 +509,7 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   <li><a href="#analysis" id="toc-analysis" class="nav-link" data-scroll-target="#analysis">Analysis</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/tutorials/colbuilder.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/tutorials/colbuilder.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -525,8 +538,10 @@ <h1 class="title">Run KIMMDY from Colbuilder fibril</h1>
   </div>
   
 
+
 </header>
 
+
 <p>In this tutorial we will download a collagen fibril from <a href="https://colbuilder.h-its.org/">colbuilder</a> and run a KIMMDY simulation on it.</p>
 <section id="preparation" class="level2">
 <h2 class="anchored" data-anchor-id="preparation">Preparation</h2>
@@ -617,7 +632,7 @@ <h4 class="anchored" data-anchor-id="configuration-file-template">Configuration
 <div class="code-with-filename-file">
 <pre><strong>kimmdy.yml</strong></pre>
 </div>
-<div class="sourceCode" id="cb4"><pre class="sourceCode yml code-with-copy"><code class="sourceCode yaml"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dryrun</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
+<div class="sourceCode" id="cb4" data-filename="kimmdy.yml"><pre class="sourceCode yml code-with-copy"><code class="sourceCode yaml"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dryrun</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
 <span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="fu">name</span><span class="kw">:</span><span class="at"> </span><span class="st">'hexalanine_homolysis_000'</span></span>
 <span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="fu">max_tasks</span><span class="kw">:</span><span class="at"> </span><span class="dv">100</span></span>
 <span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="fu">gromacs_alias</span><span class="kw">:</span><span class="at"> </span><span class="st">'gmx'</span></span>
@@ -688,7 +703,7 @@ <h4 class="anchored" data-anchor-id="kimmdy-run-sequence-mdp-files">KIMMDY Run S
 <div class="code-with-filename-file">
 <pre><strong>kimmdy.yml</strong></pre>
 </div>
-<div class="sourceCode" id="cb8"><pre class="sourceCode yml code-with-copy"><code class="sourceCode yaml"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># yaml-language-server: $schema=../../src/kimmdy/kimmdy-yaml-schema.json</span></span>
+<div class="sourceCode" id="cb8" data-filename="kimmdy.yml"><pre class="sourceCode yml code-with-copy"><code class="sourceCode yaml"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># yaml-language-server: $schema=../../src/kimmdy/kimmdy-yaml-schema.json</span></span>
 <span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="fu">dryrun</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
 <span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a><span class="fu">name</span><span class="kw">:</span><span class="at"> </span><span class="st">'fibril_000'</span></span>
@@ -999,18 +1014,64 @@ <h2 class="anchored" data-anchor-id="analysis">Analysis</h2>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -1020,27 +1081,56 @@ <h2 class="anchored" data-anchor-id="analysis">Analysis</h2>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1118,6 +1208,32 @@ <h2 class="anchored" data-anchor-id="analysis">Analysis</h2>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1179,12 +1295,12 @@ <h2 class="anchored" data-anchor-id="analysis">Analysis</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/tutorials/index.html" class="pagination-link">
+      <a href="../../guide/tutorials/index.html" class="pagination-link  aria-label=" tutorials"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Tutorials</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/tutorials/getting-started.html" class="pagination-link">
+      <a href="../../guide/tutorials/getting-started.html" class="pagination-link" aria-label="Get Started">
         <span class="nav-page-text">Get Started</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/guide/tutorials/getting-started.html b/docs/guide/tutorials/getting-started.html
index 53c82656..43d75e08 100644
--- a/docs/guide/tutorials/getting-started.html
+++ b/docs/guide/tutorials/getting-started.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -23,7 +23,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -87,12 +87,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -114,7 +115,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -128,24 +129,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -176,11 +177,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../guide/tutorials/index.html">Tutorials</a></li><li class="breadcrumb-item"><a href="../../guide/tutorials/getting-started.html">Get Started</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -188,7 +189,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -237,6 +238,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -278,6 +285,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -480,7 +493,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -496,7 +509,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#analyse-the-simulation" id="toc-analyse-the-simulation" class="nav-link" data-scroll-target="#analyse-the-simulation">Analyse the Simulation</a></li>
   <li><a href="#next-steps" id="toc-next-steps" class="nav-link" data-scroll-target="#next-steps">Next steps</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/tutorials/getting-started.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/tutorials/getting-started.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -525,8 +538,10 @@ <h1 class="title">Get Started</h1>
   </div>
   
 
+
 </header>
 
+
 <p>In this tutorial we will be simulating hydrogen atom transfer in a simple ACE/NME-capped Alanine molecule in a box of water.</p>
 <section id="installation" class="level2">
 <h2 class="anchored" data-anchor-id="installation">Installation</h2>
@@ -540,19 +555,16 @@ <h3 class="anchored" data-anchor-id="prerequisites">Prerequisites</h3>
 <ul>
 <li><code>plumed</code>-patched version of <code>gromacs</code> (for the homolysis reaction).</li>
 </ul>
-<div class="callout callout-style-simple callout-tip callout-titled">
-<div class="callout-header d-flex align-content-center">
+<div class="callout callout-style-simple callout-tip">
+<div class="callout-body d-flex">
 <div class="callout-icon-container">
 <i class="callout-icon"></i>
 </div>
-<div class="callout-title-container flex-fill">
-
-</div>
-</div>
-<div class="callout-body-container callout-body">
+<div class="callout-body-container">
 <p>If you plan to use our machine-learning plugins, take a look at the <a href="../../guide/how-to/install-ml-plugins.html">full installation instruction</a></p>
 </div>
 </div>
+</div>
 <p>Let’s first create a directory and a virtual environment for <code>kimmdy</code>:</p>
 <div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> kimmdy-tutorial</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> kimmdy-tutorial</span>
@@ -572,7 +584,7 @@ <h2 class="anchored" data-anchor-id="setup-the-simulation">Setup the Simulation<
 <div class="code-with-filename-file">
 <pre><strong>kimmdy.yml</strong></pre>
 </div>
-<div class="sourceCode" id="cb4"><pre class="sourceCode yaml code-with-copy"><code class="sourceCode yaml"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dryrun</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
+<div class="sourceCode" id="cb4" data-filename="kimmdy.yml"><pre class="sourceCode yaml code-with-copy"><code class="sourceCode yaml"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dryrun</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
 <span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="fu">max_tasks</span><span class="kw">:</span><span class="at"> </span><span class="dv">100</span></span>
 <span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="fu">name</span><span class="kw">:</span><span class="at"> </span><span class="st">'hat_tf_000'</span></span>
 <span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="fu">gromacs_alias</span><span class="kw">:</span><span class="at"> </span><span class="st">'gmx'</span></span>
@@ -603,7 +615,7 @@ <h2 class="anchored" data-anchor-id="setup-the-simulation">Setup the Simulation<
 <p>Our starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin <code>hat_reaction</code> to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.</p>
     <div id="app-./getting-started-files/vis-ala.molj" class="molstar-app"></div>
     <script type="text/javascript">
-    molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutShowSequence":false,"layoutShowLog":false,"viewportShowSelectionMode":false,"emdbProvider":"rcsb","layoutIsExpanded":false,"pdbProvider":"rcsb","viewportShowAnimation":true,"layoutShowControls":false,"layoutShowLeftPanel":true,"layoutShowRemoteState":false,"viewportShowExpand":true}).then(viewer => {
+    molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutShowLeftPanel":true,"viewportShowExpand":true,"pdbProvider":"rcsb","layoutIsExpanded":false,"layoutShowLog":false,"emdbProvider":"rcsb","viewportShowAnimation":true,"viewportShowSelectionMode":false,"layoutShowRemoteState":false,"layoutShowSequence":false,"layoutShowControls":false}).then(viewer => {
     viewer.loadSnapshotFromUrl(url="./getting-started-files/vis-ala.molj", "molj");    });
     </script>
     
@@ -638,7 +650,7 @@ <h2 class="anchored" data-anchor-id="analyse-the-simulation">Analyse the Simulat
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
 <p><img src="./img/getting-started-energy.png" class="img-fluid figure-img"></p>
-<figcaption class="figure-caption">Energy plot</figcaption>
+<figcaption>Energy plot</figcaption>
 </figure>
 </div>
 <p>Visualize where the radicals end up:</p>
@@ -647,13 +659,13 @@ <h2 class="anchored" data-anchor-id="analyse-the-simulation">Analyse the Simulat
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
 <p><img src="./img/getting-started-vmd-radicals.png" class="img-fluid figure-img"></p>
-<figcaption class="figure-caption">VMD representation settings</figcaption>
+<figcaption>VMD representation settings</figcaption>
 </figure>
 </div>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
 <p><img src="./img/getting-started-radicals.png" class="img-fluid figure-img"></p>
-<figcaption class="figure-caption">Radical population plot</figcaption>
+<figcaption>Radical population plot</figcaption>
 </figure>
 </div>
 <p>Plot the reaction rates:</p>
@@ -662,7 +674,7 @@ <h2 class="anchored" data-anchor-id="analyse-the-simulation">Analyse the Simulat
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
 <p><img src="./img/getting-started-rates.svg" class="img-fluid figure-img"></p>
-<figcaption class="figure-caption">Reaction rates plot</figcaption>
+<figcaption>Reaction rates plot</figcaption>
 </figure>
 </div>
 <p>Or do all of the above directly from python:</p>
@@ -948,18 +960,64 @@ <h2 class="anchored" data-anchor-id="next-steps">Next steps</h2>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -969,27 +1027,56 @@ <h2 class="anchored" data-anchor-id="next-steps">Next steps</h2>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1067,6 +1154,32 @@ <h2 class="anchored" data-anchor-id="next-steps">Next steps</h2>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1128,12 +1241,12 @@ <h2 class="anchored" data-anchor-id="next-steps">Next steps</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/tutorials/colbuilder.html" class="pagination-link">
+      <a href="../../guide/tutorials/colbuilder.html" class="pagination-link  aria-label=" run="" kimmdy="" from="" colbuilder="" fibril"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Run KIMMDY from Colbuilder fibril</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/tutorials/write-plugin.html" class="pagination-link">
+      <a href="../../guide/tutorials/write-plugin.html" class="pagination-link" aria-label="Write a Reaction Plugin">
         <span class="nav-page-text">Write a Reaction Plugin</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/guide/tutorials/index.html b/docs/guide/tutorials/index.html
index c093a6b6..5e4e14be 100644
--- a/docs/guide/tutorials/index.html
+++ b/docs/guide/tutorials/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -51,12 +51,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -109,7 +110,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -123,24 +124,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -171,11 +172,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../guide/tutorials/index.html">Tutorials</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -183,7 +184,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -232,6 +233,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -273,6 +280,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -475,7 +488,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         
@@ -498,8 +511,10 @@ <h1 class="title">Tutorials</h1>
   </div>
   
 
+
 </header>
 
+
 <p>Tutorials to help you get familiar with KIMMDY.</p>
 
 
@@ -507,96 +522,90 @@ <h1 class="title">Tutorials</h1>
 
 <div class="quarto-listing quarto-listing-container-default" id="listing-listing">
 <div class="list quarto-listing-default">
-<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1711385802337" data-listing-reading-time-sort="3">
+<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1712908469000" data-listing-reading-time-sort="3" data-listing-word-count-sort="507">
 <div class="thumbnail">
-<p><a href="../../guide/tutorials/getting-started.html"> <img src="../../guide/tutorials/img/getting-started-vmd-radicals.png" class="thumbnail-image"> </a></p>
+<p><a href="../../guide/tutorials/getting-started.html" class="no-external"></a></p><a href="../../guide/tutorials/getting-started.html" class="no-external">
+<p><img src="../../guide/tutorials/img/getting-started-vmd-radicals.png" class="thumbnail-image"></p>
+</a><p><a href="../../guide/tutorials/getting-started.html" class="no-external"></a></p>
 </div>
 <div class="body">
-<a href="../../guide/tutorials/getting-started.html">
 <h3 class="no-anchor listing-title">
-Get Started
+<a href="../../guide/tutorials/getting-started.html" class="no-external">Get Started</a>
 </h3>
 <div class="listing-subtitle">
-
+<a href="../../guide/tutorials/getting-started.html" class="no-external"></a>
 </div>
-</a>
 <div class="listing-categories">
 <div class="listing-category" onclick="window.quartoListingCategory('user'); return false;">
 user
 </div>
 </div>
-<a href="../../guide/tutorials/getting-started.html">
 <div class="listing-description">
-In this tutorial we will be simulating hydrogen atom transfer in a simple ACE/NME-capped Alanine molecule in a box of water.
+<a href="../../guide/tutorials/getting-started.html" class="no-external">In this tutorial we will be simulating hydrogen atom transfer in a simple ACE/NME-capped Alanine molecule in a box of water.</a>
 </div>
-</a>
 </div>
 <div class="metadata">
-<a href="../../guide/tutorials/getting-started.html">
+<p><a href="../../guide/tutorials/getting-started.html" class="no-external"></a></p><a href="../../guide/tutorials/getting-started.html" class="no-external">
 <div class="listing-author">
 Jannik Buhr
 </div>
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1711385802333" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1712908428000" data-listing-reading-time-sort="6" data-listing-word-count-sort="1188">
 <div class="thumbnail">
-<p><a href="../../guide/tutorials/colbuilder.html"> <img src="../../guide/tutorials/img/colbuilder.png" class="thumbnail-image"> </a></p>
+<p><a href="../../guide/tutorials/colbuilder.html" class="no-external"></a></p><a href="../../guide/tutorials/colbuilder.html" class="no-external">
+<p><img src="../../guide/tutorials/img/colbuilder.png" class="thumbnail-image"></p>
+</a><p><a href="../../guide/tutorials/colbuilder.html" class="no-external"></a></p>
 </div>
 <div class="body">
-<a href="../../guide/tutorials/colbuilder.html">
 <h3 class="no-anchor listing-title">
-Run KIMMDY from Colbuilder fibril
+<a href="../../guide/tutorials/colbuilder.html" class="no-external">Run KIMMDY from Colbuilder fibril</a>
 </h3>
 <div class="listing-subtitle">
-
+<a href="../../guide/tutorials/colbuilder.html" class="no-external"></a>
 </div>
-</a>
 <div class="listing-categories">
 <div class="listing-category" onclick="window.quartoListingCategory('user'); return false;">
 user
 </div>
 </div>
-<a href="../../guide/tutorials/colbuilder.html">
 <div class="listing-description">
-In this tutorial we will download a collagen fibril from colbuilder and run a KIMMDY simulation on it.
+<a href="../../guide/tutorials/colbuilder.html" class="no-external">In this tutorial we will download a collagen fibril from colbuilder and run a KIMMDY simulation on it.</a>
 </div>
-</a>
 </div>
 <div class="metadata">
-<a href="../../guide/tutorials/colbuilder.html">
+<p><a href="../../guide/tutorials/colbuilder.html" class="no-external"></a></p><a href="../../guide/tutorials/colbuilder.html" class="no-external">
 <div class="listing-author">
 Eric Hartmann
 </div>
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1711385802341" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1701868360000" data-listing-reading-time-sort="6" data-listing-word-count-sort="1112">
 <div class="thumbnail">
-<p><a href="../../guide/tutorials/write-plugin.html"> <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div> </a></p>
+<p><a href="../../guide/tutorials/write-plugin.html" class="no-external"></a></p><a href="../../guide/tutorials/write-plugin.html" class="no-external">
+<div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>
+</a><p><a href="../../guide/tutorials/write-plugin.html" class="no-external"></a></p>
 </div>
 <div class="body">
-<a href="../../guide/tutorials/write-plugin.html">
 <h3 class="no-anchor listing-title">
-Write a Reaction Plugin
+<a href="../../guide/tutorials/write-plugin.html" class="no-external">Write a Reaction Plugin</a>
 </h3>
 <div class="listing-subtitle">
-
+<a href="../../guide/tutorials/write-plugin.html" class="no-external"></a>
 </div>
-</a>
 <div class="listing-categories">
 <div class="listing-category" onclick="window.quartoListingCategory('developer'); return false;">
 developer
 </div>
 </div>
-<a href="../../guide/tutorials/write-plugin.html">
 <div class="listing-description">
-<p>In this tutorial, you will learn how to create your own reaction plugin in a GitHub repository.</p>
+<a href="../../guide/tutorials/write-plugin.html" class="no-external">In this tutorial, you will learn how to create your own reaction plugin in a GitHub repository.</a>
 </div>
-</a>
 </div>
 <div class="metadata">
-<a href="../../guide/tutorials/write-plugin.html">
+<p><a href="../../guide/tutorials/write-plugin.html" class="no-external"></a></p><a href="../../guide/tutorials/write-plugin.html" class="no-external">
 <div class="listing-author">
 Eric Hartmann
 </div>
@@ -870,18 +879,64 @@ <h3 class="no-anchor listing-title">
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -891,27 +946,56 @@ <h3 class="no-anchor listing-title">
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -989,6 +1073,32 @@ <h3 class="no-anchor listing-title">
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1050,12 +1160,12 @@ <h3 class="no-anchor listing-title">
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../index.html" class="pagination-link">
+      <a href="../../index.html" class="pagination-link  aria-label=" kimmdy"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">KIMMDY</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/tutorials/colbuilder.html" class="pagination-link">
+      <a href="../../guide/tutorials/colbuilder.html" class="pagination-link" aria-label="Run KIMMDY from Colbuilder fibril">
         <span class="nav-page-text">Run KIMMDY from Colbuilder fibril</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
@@ -1065,4 +1175,4 @@ <h3 class="no-anchor listing-title">
 
 
 
-<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/tutorials/index.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></div></div></footer></body></html>
\ No newline at end of file
+<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/tutorials/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div></div></footer></body></html>
\ No newline at end of file
diff --git a/docs/guide/tutorials/write-plugin.html b/docs/guide/tutorials/write-plugin.html
index 9d5f8fcb..b5c31805 100644
--- a/docs/guide/tutorials/write-plugin.html
+++ b/docs/guide/tutorials/write-plugin.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -24,7 +24,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -85,12 +85,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -112,7 +113,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="../../index.html">
@@ -126,24 +127,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="../../guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="../../guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="../../guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="../../guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../../_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="../../_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -174,11 +175,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../../guide/tutorials/index.html">Tutorials</a></li><li class="breadcrumb-item"><a href="../../guide/tutorials/write-plugin.html">Write a Reaction Plugin</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -186,7 +187,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -235,6 +236,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -276,6 +283,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../../guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../../guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -478,7 +491,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -494,7 +507,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#making-a-python-package" id="toc-making-a-python-package" class="nav-link" data-scroll-target="#making-a-python-package">Making a python package</a></li>
   <li><a href="#improving-code-quality-and-reproducibility" id="toc-improving-code-quality-and-reproducibility" class="nav-link" data-scroll-target="#improving-code-quality-and-reproducibility">Improving code quality and reproducibility</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/tutorials/write-plugin.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/guide/tutorials/write-plugin.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -528,8 +541,10 @@ <h1 class="title">Write a Reaction Plugin</h1>
   </div>
   
 
+
 </header>
 
+
 <section id="creating-a-github-repository" class="level2">
 <h2 class="anchored" data-anchor-id="creating-a-github-repository">Creating a GitHub repository</h2>
 <p>By creating a GitHub repository, you have version control for your plugin and can share it with others. To set it up, follow <a href="https://docs.github.com/en/get-started/quickstart/create-a-repo">these instructions</a>.</p>
@@ -541,7 +556,7 @@ <h3 class="anchored" data-anchor-id="main-code">Main code</h3>
 <p>A reaction plugin has to be a derived class from the <code>ReactionPlugin</code> base class. Such a class has the attributes <code>name</code>, <code>runmng</code> and <code>config</code> and the method <code>get_recipe_collection</code>, which takes a <code>TaskFiles</code> object as argument and returns a <code>RecipeCollection</code>.</p>
 <p>The <code>name</code> is a simple string and may be useful for logging. <code>runmng</code> is the central <code>RunManager</code> of a kimmdy run and has plenty of useful attributes for your plugin, especially the system <code>Topology</code>, which can be accessed via <code>self.runmg.top</code>. <code>config</code> contains the reaction plugin configuration as specified in the kimmdy configuration file (typically named kimmdy.yml). A <code>RecipeCollection</code> contains <code>Recipe</code>s with predefined <code>RecipeStep</code>s that can be used to define the modification to the system for the reaction. A <code>Recipe</code> also contains the <code>rates</code> of the specified reaction and the <code>timespans</code> during which the corresponding rates are valid. An example plugin can be seen below.</p>
 <div id="2641ff7c" class="cell" data-execution_count="1">
-<details>
+<details class="code-fold">
 <summary>Plugin main code (reaction.py)</summary>
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> kimmdy.recipe <span class="im">import</span> (</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>    Bind,</span>
@@ -608,7 +623,7 @@ <h3 class="anchored" data-anchor-id="configuration-file-schema">Configuration fi
 <div class="code-with-filename-file">
 <pre><strong>kimmdy-yaml-schema.json</strong></pre>
 </div>
-<div class="sourceCode" id="cb2"><pre class="sourceCode json code-with-copy"><code class="sourceCode json"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">{</span></span>
+<div class="sourceCode" id="cb2" data-filename="kimmdy-yaml-schema.json"><pre class="sourceCode json code-with-copy"><code class="sourceCode json"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">{</span></span>
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>  <span class="dt">"$schema"</span><span class="fu">:</span> <span class="st">"https://json-schema.org/draft/2020-12/schema"</span><span class="fu">,</span></span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>  <span class="dt">"type"</span><span class="fu">:</span> <span class="st">"object"</span><span class="fu">,</span></span>
 <span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>  <span class="dt">"$id"</span><span class="fu">:</span> <span class="st">"bind-config"</span><span class="fu">,</span></span>
@@ -638,7 +653,7 @@ <h3 class="anchored" data-anchor-id="configuration-file-schema">Configuration fi
 <h2 class="anchored" data-anchor-id="making-a-python-package">Making a python package</h2>
 <p>It is necessary to make the plugin a python package to interface with Kimmdy. For this, package setup configuration files are necessary, for example <code>setup.py</code> and <code>setup.cfg</code>. In <code>setup.cfg</code> dependencies can be specified, which will be installed alongside the plugin. The interface with kimmdy is specified in the <code>[options.entry_points]</code> section. This section needs to refer to the class we created in the plugin main code and assign it to <code>kimmdy.reaction_plugins</code>, i.e.&nbsp;<code>kimmdy.reaction_plugins = bind = &lt;path&gt;.&lt;to&gt;.&lt;main file&gt;:&lt;ClassName&gt;</code>. Also, the directory containing the source code (typically <code>src</code>) is defined in <code>[options.packages.find]</code>. An example for <code>setup.py</code> and <code>setup.cfg</code> can be found below.</p>
 <div id="e96ba74b" class="cell" data-execution_count="2">
-<details>
+<details class="code-fold">
 <summary>setup.py</summary>
 <div class="sourceCode cell-code" id="cb3"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> setuptools <span class="im">import</span> setup</span>
 <span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a></span>
@@ -653,7 +668,7 @@ <h2 class="anchored" data-anchor-id="making-a-python-package">Making a python pa
 <div class="code-with-filename-file">
 <pre><strong>setup.cfg</strong></pre>
 </div>
-<div class="sourceCode" id="cb4"><pre class="sourceCode ini code-with-copy"><code class="sourceCode ini"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="kw">[metadata]</span></span>
+<div class="sourceCode" id="cb4" data-filename="setup.cfg"><pre class="sourceCode ini code-with-copy"><code class="sourceCode ini"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="kw">[metadata]</span></span>
 <span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="dt">name </span><span class="ot">=</span><span class="st"> kimmdy-reactions</span></span>
 <span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="dt">version </span><span class="ot">=</span><span class="st"> </span><span class="fl">0.1</span></span>
 <span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="dt">license </span><span class="ot">=</span><span class="st"> GPL-3.0 </span></span>
@@ -969,18 +984,64 @@ <h2 class="anchored" data-anchor-id="improving-code-quality-and-reproducibility"
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -990,27 +1051,56 @@ <h2 class="anchored" data-anchor-id="improving-code-quality-and-reproducibility"
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -1088,6 +1178,32 @@ <h2 class="anchored" data-anchor-id="improving-code-quality-and-reproducibility"
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1149,12 +1265,12 @@ <h2 class="anchored" data-anchor-id="improving-code-quality-and-reproducibility"
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../../guide/tutorials/getting-started.html" class="pagination-link">
+      <a href="../../guide/tutorials/getting-started.html" class="pagination-link  aria-label=" get="" started"="">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Get Started</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../../guide/how-to/index.html" class="pagination-link">
+      <a href="../../guide/how-to/index.html" class="pagination-link" aria-label="How-To">
         <span class="nav-page-text">How-To</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/index.html b/docs/index.html
index cdecb470..800c40cc 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.176">
+<meta name="generator" content="quarto-1.4.513">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -22,7 +22,7 @@
 }
 /* CSS for syntax highlighting */
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -82,12 +82,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
     "s"
   ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -109,7 +110,7 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="./index.html">
@@ -123,24 +124,24 @@
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link active" href="./guide/tutorials/getting-started.html" rel="" target="" aria-current="page">
- <span class="menu-text">Getting Started</span></a>
+    <a class="nav-link active" href="./guide/tutorials/getting-started.html" aria-current="page"> 
+<span class="menu-text">Getting Started</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="./guide/how-to/index.html" rel="" target="">
- <span class="menu-text">How-To</span></a>
+    <a class="nav-link" href="./guide/how-to/index.html"> 
+<span class="menu-text">How-To</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="./guide/tutorials/index.html" rel="" target="">
- <span class="menu-text">Tutorials</span></a>
+    <a class="nav-link" href="./guide/tutorials/index.html"> 
+<span class="menu-text">Tutorials</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="./guide/explanation/index.html" rel="" target="">
- <span class="menu-text">Explanations</span></a>
+    <a class="nav-link" href="./guide/explanation/index.html"> 
+<span class="menu-text">Explanations</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="./_reference/index.html" rel="" target="">
- <span class="menu-text">Reference</span></a>
+    <a class="nav-link" href="./_reference/index.html"> 
+<span class="menu-text">Reference</span></a>
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
@@ -171,11 +172,11 @@
     </nav>
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html">KIMMDY</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
   </nav>
@@ -183,7 +184,7 @@
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -232,6 +233,12 @@
       <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="./guide/how-to/analyze.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Analyze a KIMMDY run</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="./guide/how-to/contribute.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Contribute</span></a>
   </div>
@@ -273,6 +280,12 @@
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 ">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="./guide/explanation/components.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Components of KIMMDY</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="./guide/explanation/topology.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Visualize Topologies</span></a>
   </div>
@@ -475,7 +488,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active" data-toc-expanded="99">
@@ -494,13 +507,14 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/index.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><ul><li><a href="https://github.com/hits-mbm-dev/kimmdy/edit/main/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/hits-mbm-dev/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 
 
+
 <section id="kimmdy" class="level1">
 <h1>KIMMDY</h1>
 <div class="quarto-figure quarto-figure-center">
@@ -827,18 +841,64 @@ <h3 class="anchored" data-anchor-id="local-testing">Local testing</h3>
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
   const processXRef = (id, note) => {
-    if (id.startsWith('sec-')) {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
-        for (let i = 0; i < 2; i++) {
-          container.appendChild(note.children[i].cloneNode(true));
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -848,27 +908,56 @@ <h3 class="anchored" data-anchor-id="local-testing">Local testing</h3>
       instance.disable();
       let url = xref.getAttribute('href');
       let hash = undefined; 
-      try { hash = new URL(url).hash; } catch {}
-      const id = hash.replace(/^#\/?/, "");
-      const note = window.document.getElementById(id);
-      if (note !== null) {
-        try {
-          const html = processXRef(id, note);
-          instance.setContent(html);
-        } finally {
-          instance.enable();
-          instance.show();
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
         }
       } else {
-        // See if we can fetch this
-        fetch(url.split('#')[0])
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
         .then(res => res.text())
         .then(html => {
           const parser = new DOMParser();
           const htmlDoc = parser.parseFromString(html, "text/html");
-          const note = htmlDoc.getElementById(id);
+          const note = htmlDoc.querySelector('main.content');
           if (note !== null) {
-            const html = processXRef(id, note);
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
             instance.setContent(html);
           } 
         }).finally(() => {
@@ -946,6 +1035,32 @@ <h3 class="anchored" data-anchor-id="local-testing">Local testing</h3>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -1009,7 +1124,7 @@ <h3 class="anchored" data-anchor-id="local-testing">Local testing</h3>
   <div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./guide/tutorials/index.html" class="pagination-link">
+      <a href="./guide/tutorials/index.html" class="pagination-link" aria-label="Tutorials">
         <span class="nav-page-text">Tutorials</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
diff --git a/docs/listings.json b/docs/listings.json
index 92ab3a37..11d34398 100644
--- a/docs/listings.json
+++ b/docs/listings.json
@@ -1,13 +1,16 @@
 [
   {
-    "listing": "/guide/explanation/index.html",
+    "listing": "/guide/tutorials/index.html",
     "items": [
-      "/guide/explanation/topology.html"
+      "/guide/tutorials/getting-started.html",
+      "/guide/tutorials/colbuilder.html",
+      "/guide/tutorials/write-plugin.html"
     ]
   },
   {
     "listing": "/guide/how-to/index.html",
     "items": [
+      "/guide/how-to/analyze.html",
       "/guide/how-to/contribute.html",
       "/guide/how-to/examples.html",
       "/guide/how-to/hcp.html",
@@ -16,11 +19,10 @@
     ]
   },
   {
-    "listing": "/guide/tutorials/index.html",
+    "listing": "/guide/explanation/index.html",
     "items": [
-      "/guide/tutorials/getting-started.html",
-      "/guide/tutorials/colbuilder.html",
-      "/guide/tutorials/write-plugin.html"
+      "/guide/explanation/components.html",
+      "/guide/explanation/topology.html"
     ]
   }
 ]
\ No newline at end of file
diff --git a/docs/search.json b/docs/search.json
index 07131534..d3aa11c8 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1,709 +1,1249 @@
 [
   {
-    "objectID": "guide/explanation/index.html",
-    "href": "guide/explanation/index.html",
-    "title": "Explanations",
+    "objectID": "guide/explanation/components.html",
+    "href": "guide/explanation/components.html",
+    "title": "Components of KIMMDY",
     "section": "",
-    "text": "Pages that help you understand the inner workings of KIMMDY\n\n\n\n\n\n\n   \n     \n     \n       Order By\n       Default\n         \n          Title\n        \n         \n          Author\n        \n     \n  \n    \n      \n      \n    \n\n\n\n\n\nTitle\n\n\nAuthor\n\n\n\n\n\n\nVisualize Topologies\n\n\n \n\n\n\n\n\nNo matching items\n\n Back to top"
+    "text": "Here is an overview of the most important components of KIMMDY, and how they interact with each other:\n\n\n\n\nAttributes have a gray, the user-supplied input an orange backdrop.\nA KIMMDY run is orchestrated from a central class called RunManager. After the user input from the command line interface is handled in the cmd module, a RunManager is instantiated with a config built from the input yaml file. During the initialization, the topology is loaded, and the plugins for reactions and parametrizing are instantiated. The run then starts with a call to RunManager.run. This triggers building of the initial task queue, which then gets processed. In addition to this main task queue, there is also a priority queue available, for tasks to submit other tasks to. These get executed as soon as the current task has finished, but before any eventual other tasks in the main queue. During the task queue building process, reactions are expanded into three tasks. The first one calls the plugin itself to obtain reaction recipes. Then, one recipe must be chosen from all possible ones in a kMC step. Finally, the recipe must be applied at the correct time of the last simulation.\n\n\n\n Back to top",
+    "crumbs": [
+      "Explanation",
+      "Components of KIMMDY"
+    ]
   },
   {
-    "objectID": "guide/how-to/index.html",
-    "href": "guide/how-to/index.html",
-    "title": "How-To",
+    "objectID": "guide/explanation/topology.html",
+    "href": "guide/explanation/topology.html",
+    "title": "Visualize Topologies",
+    "section": "",
+    "text": "from kimmdy.parsing import read_top\nfrom kimmdy.topology.topology import Topology\nfrom pathlib import Path\nfrom kimmdy.tools import write_top_as_dot\n\n\nala_top = read_top(Path('../../tests/test_files/test_topology/Ala_R_prm.top'), use_gmx_dir=False)\ntop = Topology(ala_top)\n\nwrite_top_as_dot(top, \"ala-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n\n\n1 CT\n\n1 CT\n\n\n\n2 HC\n\n2 HC\n\n\n\n1 CT--2 HC\n\n\n\n\n3 HC\n\n3 HC\n\n\n\n1 CT--3 HC\n\n\n\n\n4 HC\n\n4 HC\n\n\n\n1 CT--4 HC\n\n\n\n\n5 C\n\n5 C\n\n\n\n1 CT--5 C\n\n\n\n\n6 O\n\n6 O\n\n\n\n5 C--6 O\n\n\n\n\n7 N\n\n7 N\n\n\n\n5 C--7 N\n\n\n\n\n8 H\n\n8 H\n\n\n\n7 N--8 H\n\n\n\n\n9 CT\n\n9 CT\n\n\n\n7 N--9 CT\n\n\n\n\n10 CT\n\n10 CT\n\n\n\n9 CT--10 CT\n\n\n\n\n14 C\n\n14 C\n\n\n\n9 CT--14 C\n\n\n\n\n11 HC\n\n11 HC\n\n\n\n10 CT--11 HC\n\n\n\n\n12 HC\n\n12 HC\n\n\n\n10 CT--12 HC\n\n\n\n\n13 HC\n\n13 HC\n\n\n\n10 CT--13 HC\n\n\n\n\n15 O\n\n15 O\n\n\n\n14 C--15 O\n\n\n\n\n16 N\n\n16 N\n\n\n\n14 C--16 N\n\n\n\n\n17 H\n\n17 H\n\n\n\n16 N--17 H\n\n\n\n\n18 CT\n\n18 CT\n\n\n\n16 N--18 CT\n\n\n\n\n19 H1\n\n19 H1\n\n\n\n18 CT--19 H1\n\n\n\n\n20 H1\n\n20 H1\n\n\n\n18 CT--20 H1\n\n\n\n\n21 H1\n\n21 H1\n\n\n\n18 CT--21 H1\n\n\n\n\n\n\n\nFigure 1: A diagram of the Ala topology",
+    "crumbs": [
+      "Explanation",
+      "Visualize Topologies"
+    ]
+  },
+  {
+    "objectID": "guide/explanation/topology.html#capped-alanine-with-a-radical",
+    "href": "guide/explanation/topology.html#capped-alanine-with-a-radical",
+    "title": "Visualize Topologies",
     "section": "",
-    "text": "How-To Guides\n\n\n\n\n\n\n   \n     \n     \n       Order By\n       Default\n         \n          Title\n        \n         \n          Author\n        \n     \n  \n    \n      \n      \n    \n\n\n\n\n\nTitle\n\n\nAuthor\n\n\n\n\n\n\nContribute\n\n\n \n\n\n\n\nExamples\n\n\n \n\n\n\n\nHigh Performance Computing\n\n\n \n\n\n\n\nInstall Machine Learning Plugins\n\n\n \n\n\n\n\nReaction only\n\n\nKai Riedmiller\n\n\n\n\n\nNo matching items\n\n Back to top"
+    "text": "from kimmdy.parsing import read_top\nfrom kimmdy.topology.topology import Topology\nfrom pathlib import Path\nfrom kimmdy.tools import write_top_as_dot\n\n\nala_top = read_top(Path('../../tests/test_files/test_topology/Ala_R_prm.top'), use_gmx_dir=False)\ntop = Topology(ala_top)\n\nwrite_top_as_dot(top, \"ala-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n\n\n1 CT\n\n1 CT\n\n\n\n2 HC\n\n2 HC\n\n\n\n1 CT--2 HC\n\n\n\n\n3 HC\n\n3 HC\n\n\n\n1 CT--3 HC\n\n\n\n\n4 HC\n\n4 HC\n\n\n\n1 CT--4 HC\n\n\n\n\n5 C\n\n5 C\n\n\n\n1 CT--5 C\n\n\n\n\n6 O\n\n6 O\n\n\n\n5 C--6 O\n\n\n\n\n7 N\n\n7 N\n\n\n\n5 C--7 N\n\n\n\n\n8 H\n\n8 H\n\n\n\n7 N--8 H\n\n\n\n\n9 CT\n\n9 CT\n\n\n\n7 N--9 CT\n\n\n\n\n10 CT\n\n10 CT\n\n\n\n9 CT--10 CT\n\n\n\n\n14 C\n\n14 C\n\n\n\n9 CT--14 C\n\n\n\n\n11 HC\n\n11 HC\n\n\n\n10 CT--11 HC\n\n\n\n\n12 HC\n\n12 HC\n\n\n\n10 CT--12 HC\n\n\n\n\n13 HC\n\n13 HC\n\n\n\n10 CT--13 HC\n\n\n\n\n15 O\n\n15 O\n\n\n\n14 C--15 O\n\n\n\n\n16 N\n\n16 N\n\n\n\n14 C--16 N\n\n\n\n\n17 H\n\n17 H\n\n\n\n16 N--17 H\n\n\n\n\n18 CT\n\n18 CT\n\n\n\n16 N--18 CT\n\n\n\n\n19 H1\n\n19 H1\n\n\n\n18 CT--19 H1\n\n\n\n\n20 H1\n\n20 H1\n\n\n\n18 CT--20 H1\n\n\n\n\n21 H1\n\n21 H1\n\n\n\n18 CT--21 H1\n\n\n\n\n\n\n\nFigure 1: A diagram of the Ala topology",
+    "crumbs": [
+      "Explanation",
+      "Visualize Topologies"
+    ]
+  },
+  {
+    "objectID": "guide/explanation/topology.html#multiple-molecules",
+    "href": "guide/explanation/topology.html#multiple-molecules",
+    "title": "Visualize Topologies",
+    "section": "Multiple molecules",
+    "text": "Multiple molecules\n\nurea_dict = read_top(Path('../../tests/test_files/test_topology/urea.top'), use_gmx_dir=False)\nurea = Topology(urea_dict)\nwrite_top_as_dot(urea, \"urea-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n\n\n1 C\n\n1 C\n\n\n\n2 O\n\n2 O\n\n\n\n1 C--2 O\n\n\n\n\n3 N\n\n3 N\n\n\n\n1 C--3 N\n\n\n\n\n6 N\n\n6 N\n\n\n\n1 C--6 N\n\n\n\n\n4 H\n\n4 H\n\n\n\n3 N--4 H\n\n\n\n\n5 H\n\n5 H\n\n\n\n3 N--5 H\n\n\n\n\n7 H\n\n7 H\n\n\n\n6 N--7 H\n\n\n\n\n8 H\n\n8 H\n\n\n\n6 N--8 H\n\n\n\n\n\n\n\nFigure 2: Topology of one molecule of urea\n\n\n\n\n\nWhen we want to run reactions within molecules that are either separate moleculetypes or multiples of the same moleculetype, KIMMDY can combine those into a single moleculetype and make multiples explicit.\ni.e. if we have a topology with two molecules of urea defined as:\n[ system ]\nUrea in Water\n\n[ molecules ]\n;molecule name   nr.\nUrea             2\nSOL              1000\n\nurea_dict = read_top(Path('../../tests/test_files/test_topology/urea-times-2.top'), use_gmx_dir=False)\nurea = Topology(urea_dict)\nwrite_top_as_dot(urea, \"urea-2-top.dot\")\n\nWe end up with\n\n\n\n\n\n\n\n\nG\n\n\n\n1 C\n\n1 C\n\n\n\n2 O\n\n2 O\n\n\n\n1 C--2 O\n\n\n\n\n3 N\n\n3 N\n\n\n\n1 C--3 N\n\n\n\n\n6 N\n\n6 N\n\n\n\n1 C--6 N\n\n\n\n\n4 H\n\n4 H\n\n\n\n3 N--4 H\n\n\n\n\n5 H\n\n5 H\n\n\n\n3 N--5 H\n\n\n\n\n7 H\n\n7 H\n\n\n\n6 N--7 H\n\n\n\n\n8 H\n\n8 H\n\n\n\n6 N--8 H\n\n\n\n\n9 C\n\n9 C\n\n\n\n10 O\n\n10 O\n\n\n\n9 C--10 O\n\n\n\n\n11 N\n\n11 N\n\n\n\n9 C--11 N\n\n\n\n\n14 N\n\n14 N\n\n\n\n9 C--14 N\n\n\n\n\n12 H\n\n12 H\n\n\n\n11 N--12 H\n\n\n\n\n13 H\n\n13 H\n\n\n\n11 N--13 H\n\n\n\n\n15 H\n\n15 H\n\n\n\n14 N--15 H\n\n\n\n\n16 H\n\n16 H\n\n\n\n14 N--16 H\n\n\n\n\n\n\n\nFigure 3: A diagram of the two urea molecules topology\n\n\n\n\n\nThis way, explicit atom numbers match up with the atom numbers in the coordinate file (or rather, line numbers - 2, since the numbers in the actual atomnr column can overflow due to the fixed-width file format).",
+    "crumbs": [
+      "Explanation",
+      "Visualize Topologies"
+    ]
   },
   {
     "objectID": "guide/how-to/examples.html",
     "href": "guide/how-to/examples.html",
     "title": "Examples",
     "section": "",
-    "text": "KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.\nThe examples are located in the examples directory of the KIMMDY source code here.\nHere are their kimmdy.yml files at a glance:\n\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'\n    slow_growth: True\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - pull  \n  - reactions\n  - equilibrium\n  - pull\n\n\n\ndryrun: false\nname: 'alanine_hat_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'  \n    slow_growth: True\n  topology:\n    parameterization: 'basic'\nreactions:\n  hat_naive:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n  tasks:\n  - equilibrium\n  - reactions\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 10\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'topol.top'\ngro: 'npt.gro'\nndx: 'index_backbone.ndx'\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'pullf1500_equil.mdp'\n  prod:\n    mdp: 'pullf1500.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'pullf1500.mdp'\nchanger:\n  coordinates:\n    md: 'relax'     \n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - mult: 1\n    tasks:\n      - prod\n      - reactions\n\n\n\n\ndryrun: false\nname: 'single_reaction_000'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\ntrr: 'pull.trr'\nchanger:\n  coordinates: {}\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\n  dummyreaction: {}\nsequence:\n  - homolysis\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\ntop: 'IMREE.top'\ngro: 'IMREE_npt.gro'\nndx: 'index.ndx'\nkmc: rfkmc\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'    \n    slow_growth: True\n  topology:\n    parameterization: 'grappa' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\n  hat_naive:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\nplot_rates: true\nsave_recipes: true\nsequence:\n  - equilibrium\n  - pull\n  - homolysis\n  -\n    mult: 2\n    tasks:\n      - equilibrium\n      - pull\n      - reactions"
+    "text": "KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.\nThe examples are located in the examples directory of the KIMMDY source code here.\nHere are their kimmdy.yml files at a glance:\n\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'\n    slow_growth: True\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - pull  \n  - reactions\n  - equilibrium\n  - pull\n\n\n\ndryrun: false\nname: 'alanine_hat_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'  \n    slow_growth: True\n  topology:\n    parameterization: 'basic'\nreactions:\n  hat_naive:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n  tasks:\n  - equilibrium\n  - reactions\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 10\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'topol.top'\ngro: 'npt.gro'\nndx: 'index_backbone.ndx'\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'pullf1500_equil.mdp'\n  prod:\n    mdp: 'pullf1500.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'pullf1500.mdp'\nchanger:\n  coordinates:\n    md: 'relax'     \n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - mult: 1\n    tasks:\n      - prod\n      - reactions\n\n\n\n\ndryrun: false\nname: 'single_reaction_000'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\ntrr: 'pull.trr'\nchanger:\n  coordinates: {}\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\n  dummyreaction: {}\nsequence:\n  - homolysis\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\ntop: 'IMREE.top'\ngro: 'IMREE_npt.gro'\nndx: 'index.ndx'\nkmc: rfkmc\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'    \n    slow_growth: True\n  topology:\n    parameterization: 'grappa' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\n  hat_naive:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\nplot_rates: true\nsave_recipes: true\nsequence:\n  - equilibrium\n  - pull\n  - homolysis\n  -\n    mult: 2\n    tasks:\n      - equilibrium\n      - pull\n      - reactions",
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-    "text": "KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.\nThe examples are located in the examples directory of the KIMMDY source code here.\nHere are their kimmdy.yml files at a glance:\n\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'\n    slow_growth: True\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - pull  \n  - reactions\n  - equilibrium\n  - pull\n\n\n\ndryrun: false\nname: 'alanine_hat_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'  \n    slow_growth: True\n  topology:\n    parameterization: 'basic'\nreactions:\n  hat_naive:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n  tasks:\n  - equilibrium\n  - reactions\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 10\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'topol.top'\ngro: 'npt.gro'\nndx: 'index_backbone.ndx'\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'pullf1500_equil.mdp'\n  prod:\n    mdp: 'pullf1500.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'pullf1500.mdp'\nchanger:\n  coordinates:\n    md: 'relax'     \n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - mult: 1\n    tasks:\n      - prod\n      - reactions\n\n\n\n\ndryrun: false\nname: 'single_reaction_000'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\ntrr: 'pull.trr'\nchanger:\n  coordinates: {}\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\n  dummyreaction: {}\nsequence:\n  - homolysis\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\ntop: 'IMREE.top'\ngro: 'IMREE_npt.gro'\nndx: 'index.ndx'\nkmc: rfkmc\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'    \n    slow_growth: True\n  topology:\n    parameterization: 'grappa' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\n  hat_naive:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\nplot_rates: true\nsave_recipes: true\nsequence:\n  - equilibrium\n  - pull\n  - homolysis\n  -\n    mult: 2\n    tasks:\n      - equilibrium\n      - pull\n      - reactions"
+    "text": "KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.\nThe examples are located in the examples directory of the KIMMDY source code here.\nHere are their kimmdy.yml files at a glance:\n\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'\n    slow_growth: True\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - pull  \n  - reactions\n  - equilibrium\n  - pull\n\n\n\ndryrun: false\nname: 'alanine_hat_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'  \n    slow_growth: True\n  topology:\n    parameterization: 'basic'\nreactions:\n  hat_naive:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n  tasks:\n  - equilibrium\n  - reactions\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 10\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default \ntop: 'topol.top'\ngro: 'npt.gro'\nndx: 'index_backbone.ndx'\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'pullf1500_equil.mdp'\n  prod:\n    mdp: 'pullf1500.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'pullf1500.mdp'\nchanger:\n  coordinates:\n    md: 'relax'     \n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - mult: 1\n    tasks:\n      - prod\n      - reactions\n\n\n\n\ndryrun: false\nname: 'single_reaction_000'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\ntrr: 'pull.trr'\nchanger:\n  coordinates: {}\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\n  dummyreaction: {}\nsequence:\n  - homolysis\n\n\n\nname: 'kimmdy_001'\ndryrun: false\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\ntop: 'IMREE.top'\ngro: 'IMREE_npt.gro'\nndx: 'index.ndx'\nkmc: rfkmc\nplumed: 'plumed.dat'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'    \n    slow_growth: True\n  topology:\n    parameterization: 'grappa' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\n  hat_naive:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\nplot_rates: true\nsave_recipes: true\nsequence:\n  - equilibrium\n  - pull\n  - homolysis\n  -\n    mult: 2\n    tasks:\n      - equilibrium\n      - pull\n      - reactions",
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-    "text": "You need an installation of python (&gt;= 3.10) and (possibly PLUMED patched) GROMACS in your HPC environment.\nExample setup:\nsrun -t 1400:00 --mem=16000 -n20 --pty /bin/bash\nml EasyBuild\neb ./assets/Python-3.10.8.eb\nPrepare a bash script _modules.sh that loads the required modules and activates the python environment in which KIMMDY is installed.\nRun\nkimmdy --generate-jobscript\nto generate a file jobscript.sh that can be submitted to the HPC cluster.\nThis commands generates a kimmdy checkpoint and prepares the output folder. KIMMDY can then be started and re-started from the checkpoint via the jobscript, which uses\n# -c = continue, same  as --from-latest-checkpoint\nkimmdy -c"
+    "text": "You might want to apply a KIMMDY reaction to an already existing simulation. Here are some important points for doing so.",
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+    "section": "KIMMDY yaml",
+    "text": "KIMMDY yaml\nIf you want to start your sequence of tasks with a reaction, you have to give KIMMDY a trajectory. This, you do with the trr key in the kimmdy.yml file.",
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+    "section": "Pre-averaged plumed input",
+    "text": "Pre-averaged plumed input\nSometimes it is handy to pre-compute the averages of the distances plumed recordes. Usually, the plumed output (distances.dat) contains one line per timestep, each line starting with the time.\nIf you calculate the averages yourself, you end up having only one line, but need to tell KIMMDY how long the timeframe was, which was averaged. To do this, make sure to write the duration of your averaged simulation in the time field like this for a 10ps simulation:\n#! FIELDS time d0 d1 d2 d3 d4\n10.000000 0.142401 0.151588 0.143725 0.156734 0.152581\nYou still need the plumed config file, even if KIMMDY does not execute plumed in the current example, as KIMMDY reads the filename of the plumed output from the plumed config.",
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     "section": "",
-    "text": "You need an installation of python (&gt;= 3.10) and (possibly PLUMED patched) GROMACS in your HPC environment.\nExample setup:\nsrun -t 1400:00 --mem=16000 -n20 --pty /bin/bash\nml EasyBuild\neb ./assets/Python-3.10.8.eb\nPrepare a bash script _modules.sh that loads the required modules and activates the python environment in which KIMMDY is installed.\nRun\nkimmdy --generate-jobscript\nto generate a file jobscript.sh that can be submitted to the HPC cluster.\nThis commands generates a kimmdy checkpoint and prepares the output folder. KIMMDY can then be started and re-started from the checkpoint via the jobscript, which uses\n# -c = continue, same  as --from-latest-checkpoint\nkimmdy -c"
+    "text": "KIMMDY uses conventional commits and semantic versioning, automated via release please.\nIf a PR adds multiple commits, we use the squash and merge option to keep the commit history clean. If a PR unavoidably contains changes the message can be edited before merging to ensure release please picks up all changes.\nThe following example message (first line is the title in the GitHub UI, the rest is the body in the window below):\nGenerates the following changelog:",
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+    "title": "Contribute",
+    "section": "Local testing",
+    "text": "Local testing\nFor developoment, we provide a docker image containing gromacs and multiple python versions to test against.\nTo run the test locally, you must:\n\ninstall docker\ninstall act, easiest option is with github cli\n\ninstall github cli (gh)\ngh extension install https://github.com/nektos/gh-act\n\nrun tests with gh extension exec act -j test --artifact-server-path ./artifacts\n\ncustomize which python versions to test in tox.ini\nhtml coverage report is exported into artifacts",
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-    "text": "KIMMDY comes with autocompletion and tooltips insight your editor for its configuration file kimmdy.yml.\nAll you need to do is activate a yaml-language-server in your editor (e.g. VS Code via the YAML extension or Neovim via lspconfig).\nActivating this is very much recommended, as it prevents many typos and missaligned braces.\n\n\n\n\n\n\n\n\n\n\nThis only works, if your config file is called kimmdy.yml and the Scheme Store hasn’t been disabled in your editor settings (e.g. Yaml &gt; Schema Store: Enable."
+    "text": "KIMMDY comes with autocompletion and tooltips insight your editor for its configuration file kimmdy.yml.\nAll you need to do is activate a yaml-language-server in your editor (e.g. VS Code via the YAML extension or Neovim via lspconfig).\nActivating this is very much recommended, as it prevents many typos and missaligned braces.\n\n\n\n\n\n\nThis only works, if your config file is called kimmdy.yml and the Scheme Store hasn’t been disabled in your editor settings (e.g. Yaml &gt; Schema Store: Enable.",
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-    "text": "KIMMDY comes with autocompletion and tooltips insight your editor for its configuration file kimmdy.yml.\nAll you need to do is activate a yaml-language-server in your editor (e.g. VS Code via the YAML extension or Neovim via lspconfig).\nActivating this is very much recommended, as it prevents many typos and missaligned braces.\n\n\n\n\n\n\n\n\n\n\nThis only works, if your config file is called kimmdy.yml and the Scheme Store hasn’t been disabled in your editor settings (e.g. Yaml &gt; Schema Store: Enable."
+    "text": "KIMMDY comes with autocompletion and tooltips insight your editor for its configuration file kimmdy.yml.\nAll you need to do is activate a yaml-language-server in your editor (e.g. VS Code via the YAML extension or Neovim via lspconfig).\nActivating this is very much recommended, as it prevents many typos and missaligned braces.\n\n\n\n\n\n\nThis only works, if your config file is called kimmdy.yml and the Scheme Store hasn’t been disabled in your editor settings (e.g. Yaml &gt; Schema Store: Enable.",
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-    "text": "All Options\nThe following is a list of the options that can be set in the kimmdy.yml file. It includes reactions currently available in KIMMDY as plugins. Nested options are separated by a .. * denotes an arbitrary name for a section. The key for a section is bold.\n\n\nTable 1: KIMMDY options\n\n\n\n\n\n\n\n\n\nOption\nDescription\nType\nDefault\n\n\n\n\n\ndryrun\nDon’t run the actual simulations, just print the tasks\nbool\nFalse\n\n\n\nwrite_checkpoint\nWrite checkpoints to continue a KIMMDY run from. Default True\nbool\nTrue\n\n\n\ncwd\nWorking directory. Default is current working directory\nPath\n\n\n\n\nname\nUsed for output folder if out is not specified\nstr\nkimmdy\n\n\n\nout\nOutput folder\nPath\n\n\n\n\nlog\nSettings for logging\n\n\n\n\n\nmax_tasks\nMaximum number of tasks to run. This is useful when a task in the sequence can dymanically add more tasks. 0 means no limit.\nint\n0\n\n\n\nmax_hours\nStop KIMMDY after max_hours hours. Set this lower than the limit of your HPC cluster for use with a re-submit jobscript. 0 Means no limit.\nint\n0\n\n\n\nkmc\nKMC algorithm overwrite. Should be set by the reactions, but can be changed here.\nstr\n\n\n\n\ntau_scale\nScaling parameter for tau in the extrande kmc algorithm.\nfloat\n1.0\n\n\n\ntop\nTopology file\nPath\ntopol.top\n\n\n\ntopology\nSettings for handling the topology file.\n\n\n\n\n\ntopology.reactive.include\nExplicitly include a moleculetype or list of moleculetypes as a space-separated string.\nstr\n\n\n\n\ntopology.reactive.exclude\nExplicitly exclude a moleculetype or a list as a space-separated string. For example the lipid moleculetype in a bilayer simulation e.g. DPPC POPC'\nstr\n\n\n\n\ngro\nCoordinate file\nPath\nconf.gro\n\n\n\nndx\nGromaxs index file\nPath\nindex.ndx\n\n\n\ngromacs_alias\nGromacs alias. e.g. gmx or mpirun gmx_mpi\nstr\ngmx\n\n\n\ngmx_mdrun_flags\nFlags passed to gmx mdrun. Default -maxh 24 -dlb yes\nstr\n-maxh 24 -dlb yes\n\n\n\nff\nForce field directory (looks for .ff in cwd if not set)\nPath\n*.ff\n\n\n\nplumed\n.dat file containing plumed config\nPath\n\n\n\n\ntpr\n.tpr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\ntrr\n.trr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\nmds\nSettings for MD steps, e.g. mdp files, plumed files, etc.\n\n\n\n\n\nmds.*.mdp\nMDP file for the MD step\nPath\n\n\n\n\nmds.*.use_plumed\nWhether plumed should be used for this run or not\nbool\nFalse\n\n\n\nchanger\nSettings for applying a reaction recipe\n\n\n\n\n\nchanger.coordinates.md\nMD step from the ‘mds’ section that is used for relaxation MDs\nstr\n\n\n\n\nchanger.coordinates.slow_growth\nWhether the chosen MD step is a slow growth/free-energy simulation\nbool\nFalse\n\n\n\nchanger.topology.parameterization\nParameterization scheme that is used on the topology file after changes to it\nstr\nbasic\n\n\n\nsequence\nList of tasks. Each task can be a string (the name of the task) or an object with the task name and a multiplicity mult: &lt;int&gt;\nSequence\n\n\n\n\nreactions\nSettings for reactions\n\n\n\n\n\nplot_rates\nPlot the reaction rates during the reactions step\nbool\nTrue\n\n\n\nsave_recipes\nSave recipes as csv during the reactions step\nbool\nTrue"
+    "text": "All Options\nThe following is a list of the options that can be set in the kimmdy.yml file. It includes reactions currently available in KIMMDY as plugins. Nested options are separated by a .. * denotes an arbitrary name for a section. The key for a section is bold.\n\n\n\nTable 1: KIMMDY options\n\n\n\n\n\n\n\n\n\n\n\n\nOption\nDescription\nType\nDefault\n\n\n\n\n\ndryrun\nDon’t run the actual simulations, just print the tasks\nbool\nFalse\n\n\n\nwrite_checkpoint\nWrite checkpoints to continue a KIMMDY run from. Default True\nbool\nTrue\n\n\n\ncwd\nWorking directory. Default is current working directory\nPath\n\n\n\n\nname\nUsed for output folder if out is not specified\nstr\nkimmdy\n\n\n\nout\nOutput folder\nPath\n\n\n\n\nlog\nSettings for logging\n\n\n\n\n\nmax_tasks\nMaximum number of tasks to run. This is useful when a task in the sequence can dymanically add more tasks. 0 means no limit.\nint\n0\n\n\n\nmax_hours\nStop KIMMDY after max_hours hours. Set this lower than the limit of your HPC cluster for use with a re-submit jobscript. 0 Means no limit.\nint\n0\n\n\n\nkmc\nKMC algorithm overwrite. Should be set by the reactions, but can be changed here.\nstr\n\n\n\n\ntau_scale\nScaling parameter for tau in the extrande kmc algorithm.\nfloat\n1.0\n\n\n\ntop\nTopology file\nPath\ntopol.top\n\n\n\ntopology\nSettings for handling the topology file.\n\n\n\n\n\ntopology.reactive.include\nExplicitly include a moleculetype or list of moleculetypes as a space-separated string.\nstr\n\n\n\n\ntopology.reactive.exclude\nExplicitly exclude a moleculetype or a list as a space-separated string. For example the lipid moleculetype in a bilayer simulation e.g. DPPC POPC'\nstr\n\n\n\n\ngro\nCoordinate file\nPath\nconf.gro\n\n\n\nndx\nGromaxs index file\nPath\nindex.ndx\n\n\n\ngromacs_alias\nGromacs alias. e.g. gmx or mpirun gmx_mpi\nstr\ngmx\n\n\n\ngmx_mdrun_flags\nFlags passed to gmx mdrun. Default -maxh 24 -dlb yes\nstr\n-maxh 24 -dlb yes\n\n\n\nff\nForce field directory (looks for .ff in cwd if not set)\nPath\n*.ff\n\n\n\nplumed\n.dat file containing plumed config\nPath\n\n\n\n\ntpr\n.tpr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\ntrr\n.trr file of a finished simulation for starting directly with a reaction\nPath\n\n\n\n\nmds\nSettings for MD steps, e.g. mdp files, plumed files, etc.\n\n\n\n\n\nmds.*.mdp\nMDP file for the MD step\nPath\n\n\n\n\nmds.*.use_plumed\nWhether plumed should be used for this run or not\nbool\nFalse\n\n\n\nchanger\nSettings for applying a reaction recipe\n\n\n\n\n\nchanger.coordinates.md\nMD step from the ‘mds’ section that is used for relaxation MDs\nstr\n\n\n\n\nchanger.coordinates.slow_growth\nWhether the chosen MD step is a slow growth/free-energy simulation\nbool\nFalse\n\n\n\nchanger.topology.parameterization\nParameterization scheme that is used on the topology file after changes to it\nstr\nbasic\n\n\n\nsequence\nList of tasks. Each task can be a string (the name of the task) or an object with the task name and a multiplicity mult: &lt;int&gt;\nSequence\n\n\n\n\nreactions\nSettings for reactions\n\n\n\n\n\nplot_rates\nPlot the reaction rates during the reactions step\nbool\nTrue\n\n\n\nsave_recipes\nSave recipes as csv during the reactions step\nbool\nTrue",
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-    "text": "Example kimmdy.yml Files\n\n\nkimmdy.yml\n\ndryrun: false\nmax_tasks: 100\nname: 'hat_tf_000'\ngromacs_alias: 'gmx'\ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  relax:\n    mdp: 'md_slow.mdp'\nchanger:\n  coordinates:\n    md: 'relax'      \nreactions:\n  hat_reaction:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n  tasks:\n  - equilibrium\n  - reactions"
+    "text": "Example kimmdy.yml Files\n\n\nkimmdy.yml\n\ndryrun: false\nmax_tasks: 100\nname: 'hat_tf_000'\ngromacs_alias: 'gmx'\ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  relax:\n    mdp: 'md_slow.mdp'\nchanger:\n  coordinates:\n    md: 'relax'      \nreactions:\n  hat_reaction:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n  tasks:\n  - equilibrium\n  - reactions",
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-    "text": "In this tutorial we will be simulating hydrogen atom transfer in a simple ACE/NME-capped Alanine molecule in a box of water."
+    "text": "In this tutorial we will be simulating hydrogen atom transfer in a simple ACE/NME-capped Alanine molecule in a box of water.",
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-    "text": "Installation\n\nPrerequisites\n\npython3.9 or higher\ngromacs (tested with version 2021.4, gmx should be available in the PATH)\n\nOptional:\n\nplumed-patched version of gromacs (for the homolysis reaction).\n\n\n\n\n\n\n\n\n\n\n\nIf you plan to use our machine-learning plugins, take a look at the full installation instruction\n\n\nLet’s first create a directory and a virtual environment for kimmdy:\nmkdir kimmdy-tutorial\ncd kimmdy-tutorial\npython -m venv .venv\nsource .venv/bin/activate\nTo install KIMMDY, the builtin reaction plugins and the analysis tools use\npip install kimmdy[reactions,analysis]"
+    "text": "Installation\n\nPrerequisites\n\npython3.9 or higher\ngromacs (tested with version 2021.4, gmx should be available in the PATH)\n\nOptional:\n\nplumed-patched version of gromacs (for the homolysis reaction).\n\n\n\n\n\n\n\nIf you plan to use our machine-learning plugins, take a look at the full installation instruction\n\n\n\nLet’s first create a directory and a virtual environment for kimmdy:\nmkdir kimmdy-tutorial\ncd kimmdy-tutorial\npython -m venv .venv\nsource .venv/bin/activate\nTo install KIMMDY, the builtin reaction plugins and the analysis tools use\npip install kimmdy[reactions,analysis]",
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-    "text": "Setup the Simulation\nDownload and unzip the input files to this directory.\nwget https://hits-mbm-dev.github.io/kimmdy/guide/tutorials/getting-started-files/setup.zip\nunzip setup.zip\nThe kimmdy.yml file should look like this:\n\n\nkimmdy.yml\n\ndryrun: false\nmax_tasks: 100\nname: 'hat_tf_000'\ngromacs_alias: 'gmx'\ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  relax:\n    mdp: 'md_slow.mdp'\nchanger:\n  coordinates:\n    md: 'relax'      \nreactions:\n  hat_reaction:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n  tasks:\n  - equilibrium\n  - reactions\n\nOur starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin hat_reaction to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.\n    \n    \n    \nStart the KIMMDY run with the kimmdy command:"
+    "text": "Setup the Simulation\nDownload and unzip the input files to this directory.\nwget https://hits-mbm-dev.github.io/kimmdy/guide/tutorials/getting-started-files/setup.zip\nunzip setup.zip\nThe kimmdy.yml file should look like this:\n\n\nkimmdy.yml\n\ndryrun: false\nmax_tasks: 100\nname: 'hat_tf_000'\ngromacs_alias: 'gmx'\ntop: 'Ala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nmds:\n  equilibrium:\n    mdp: 'md.mdp'\n  relax:\n    mdp: 'md_slow.mdp'\nchanger:\n  coordinates:\n    md: 'relax'      \nreactions:\n  hat_reaction:\n    frequency_factor: 100000000\n    h_cutoff: 3\n    polling_rate: 1\n\nsequence:\n- equilibrium\n- mult: 2\n  tasks:\n  - equilibrium\n  - reactions\n\nOur starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin hat_reaction to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.\n    \n    \n    \nStart the KIMMDY run with the kimmdy command:",
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-    "text": "Run the Simulation\nkimmdy\nYou can also run kimmdy directly from python with\nfrom kimmdy.cmd import kimmdy_run\nkimmdy_run()\n\n\n\n\n\n\nTip\n\n\n\nKIMMDY parses your topology to generate its internal representation and writes out a new topology to be used in future steps. This topology includes everything gromacs needs to run the simulation, including forcefield parameters. KIMMDY combines all moleculetypes that are meant to take part in reactions into one moleculetype named “Reactive”. It also makes multiples explicit (e.g. 10 molecules of a peptide), such that each reactive atom has a unique representation. You can always find this topology in the output directory for the kimmdy setup task, e.g. alanine_hat_000/0_setup/&lt;name-of-your-top.top. By default, everything that is not a solvent or ion is considered reactive. To exclude or include certain moleculetypes from this (e.g. in a lipid bilayer simulation), check out the topology.reactive options in the input file documentation. You can find another example of merging topologies in the topology explanation."
+    "text": "Run the Simulation\nkimmdy\nYou can also run kimmdy directly from python with\nfrom kimmdy.cmd import kimmdy_run\nkimmdy_run()\n\n\n\n\n\n\nTip\n\n\n\nKIMMDY parses your topology to generate its internal representation and writes out a new topology to be used in future steps. This topology includes everything gromacs needs to run the simulation, including forcefield parameters. KIMMDY combines all moleculetypes that are meant to take part in reactions into one moleculetype named “Reactive”. It also makes multiples explicit (e.g. 10 molecules of a peptide), such that each reactive atom has a unique representation. You can always find this topology in the output directory for the kimmdy setup task, e.g. alanine_hat_000/0_setup/&lt;name-of-your-top.top. By default, everything that is not a solvent or ion is considered reactive. To exclude or include certain moleculetypes from this (e.g. in a lipid bilayer simulation), check out the topology.reactive options in the input file documentation. You can find another example of merging topologies in the topology explanation.",
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-    "text": "Analyse the Simulation\nConcatenate the trajectories from the individual steps into one for viewing:\nkimmdy-analysis trjcat alanine_hat_000 --open-vmd\nCheck the energy of the system:\nkimmdy-analysis energy alanine_hat_000 --open-plot --terms Potential Kinetic\n\n\n\nEnergy plot\n\n\nVisualize where the radicals end up:\nkimmdy-analysis radical_population alanine_hat_000 --open-plot --open-vmd\nIn VMD, color the atoms by beta factor to show the radical occupancy.\n\n\n\nVMD representation settings\n\n\n\n\n\nRadical population plot\n\n\nPlot the reaction rates:\nkimmdy-analysis rates alanine_hat_000\nIn the alanine_hat_000/analysis directory you will then find a plot of rates for each possible reaction at every step they were queried, e.g.\n\n\n\nReaction rates plot\n\n\nOr do all of the above directly from python:\nfrom kimmdy.analysis import concat_trj, plot_energy, radical_population, plot_rates\nconcat_trj('alanine_hat_000', open_vmd=True)\nplot_energy('alanine_hat_000', terms=['Potential', 'Kinetic'], open_plot=True)\nradical_population('alanine_hat_000', open_plot=True, open_vmd=True)\nplot_rates('alanine_hat_000')\nCongratulations, you have successfully run your first KIMMDY simulation!"
+    "text": "Analyse the Simulation\nConcatenate the trajectories from the individual steps into one for viewing:\nkimmdy-analysis trjcat alanine_hat_000 --open-vmd\nCheck the energy of the system:\nkimmdy-analysis energy alanine_hat_000 --open-plot --terms Potential Kinetic\n\n\n\nEnergy plot\n\n\nVisualize where the radicals end up:\nkimmdy-analysis radical_population alanine_hat_000 --open-plot --open-vmd\nIn VMD, color the atoms by beta factor to show the radical occupancy.\n\n\n\nVMD representation settings\n\n\n\n\n\nRadical population plot\n\n\nPlot the reaction rates:\nkimmdy-analysis rates alanine_hat_000\nIn the alanine_hat_000/analysis directory you will then find a plot of rates for each possible reaction at every step they were queried, e.g.\n\n\n\nReaction rates plot\n\n\nOr do all of the above directly from python:\nfrom kimmdy.analysis import concat_trj, plot_energy, radical_population, plot_rates\nconcat_trj('alanine_hat_000', open_vmd=True)\nplot_energy('alanine_hat_000', terms=['Potential', 'Kinetic'], open_plot=True)\nradical_population('alanine_hat_000', open_plot=True, open_vmd=True)\nplot_rates('alanine_hat_000')\nCongratulations, you have successfully run your first KIMMDY simulation!",
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-    "text": "Next steps\n\nLearn more about the kimmdy.yml input file\nRun KIMMDY with a collagen fibril from Colbuilder\nWrite your own reaction plugin\nDiscover more plugins by looking for the kimmdy tag on GitHub"
+    "text": "Next steps\n\nLearn more about the kimmdy.yml input file\nRun KIMMDY with a collagen fibril from Colbuilder\nWrite your own reaction plugin\nDiscover more plugins by looking for the kimmdy tag on GitHub",
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-    "text": "In this tutorial we will download a collagen fibril from colbuilder and run a KIMMDY simulation on it."
+    "text": "In this tutorial we will download a collagen fibril from colbuilder and run a KIMMDY simulation on it.",
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-    "text": "Preparation\n\nDownload the desired model and the ff parameters for gromacs from colbuilder\nClean the force field files by moving amber99sb-star-ildnp.ff up to the working directory, adding residuetypes.dat and specbond.dat to the working directory, removing temporary files ._* and deleting the rest of collagen.ff\nConvert the pdb file to .gro format and create a unified topology file\n\n\n\n\n\n\n\nCaution\n\n\n\nDue to some issues in GROMACS, pdb2gmx may take a while (~16 hours). The majority of the time is actually spend on checks that happen just before the final lines are written to the file. It is possible to stop the process early and add the final lines manually.\n\n\ngmx pdb2gmx -f Homo_sapiens_aln_N_HLKNL_12_C_PYD_2_fibril.pdb -o fibril2.gro -ignh -water tip3p -merge all &lt;&lt;&lt;1"
+    "text": "Preparation\n\nDownload the desired model and the ff parameters for gromacs from colbuilder\nClean the force field files by moving amber99sb-star-ildnp.ff up to the working directory, adding residuetypes.dat and specbond.dat to the working directory, removing temporary files ._* and deleting the rest of collagen.ff\nConvert the pdb file to .gro format and create a unified topology file\n\n\n\n\n\n\n\nCaution\n\n\n\nDue to some issues in GROMACS, pdb2gmx may take a while (~16 hours). The majority of the time is actually spend on checks that happen just before the final lines are written to the file. It is possible to stop the process early and add the final lines manually.\n\n\ngmx pdb2gmx -f Homo_sapiens_aln_N_HLKNL_12_C_PYD_2_fibril.pdb -o fibril2.gro -ignh -water tip3p -merge all &lt;&lt;&lt;1",
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-    "text": "Equilibration\nmdp files for the following steps are located in &lt;kimmdy root&gt;/www/colbuilder_files.\ngmx editconf -f fibril.gro -o fibril_x.gro -c -princ  &lt;&lt;&lt;1\n\ngmx editconf -f fibril_x.gro -o fibril_z.gro -rotate 0 270 0 -c\n\ngmx editconf -f fibril_z.gro -o fibril_box.gro -c -box 16.3 17.7 95.0 -bt triclinic\n\ngmx solvate -cp fibril_box.gro -p topol.top -o fibril_solv.gro\n\ntouch ions.mdp\n\ngmx grompp -f ions.mdp -c fibril_solv.gro -p topol.top -o fibril_genion.tpr\n\ngmx genion -s fibril_genion.tpr -p topol.top -o fibril_ion.gro -conc 0.15 -neutral &lt; SOL\n\ngmx grompp -f minim.mdp -c fibril_ion.gro -p topol.top -o fibril_min.tpr\n\ngmx mdrun -deffnm fibril_min -v\n\n\n\n\n\n\nCaution\n\n\n\nHeavy computational load from here on.\n\n\ngmx grompp -f nvt.mdp -c fibril_min.gro -r fibril_min.gro -p topol.top -o fibril_nvt.tpr\n\ngmx mdrun -deffnm fibril_nvt -v -dlb yes -ntomp 4 -ntmpi 10  -pme gpu -bonded gpu -npme 1\n\ngmx grompp -f npt.mdp -c fibril_nvt.gro -r fibril_nvt.gro -p topol.top -o fibril_npt.tpr\n\ngmx mdrun -deffnm fibril_npt -v -dlb yes -ntomp 4 -ntmpi 10  -pme gpu -bonded gpu -npme 1\n\n\n\n\n\n\nTip\n\n\n\nThe equilibration process can take up to 4 days. An equilibrated system will be provided in the release assets."
+    "text": "Equilibration\nmdp files for the following steps are located in &lt;kimmdy root&gt;/www/colbuilder_files.\ngmx editconf -f fibril.gro -o fibril_x.gro -c -princ  &lt;&lt;&lt;1\n\ngmx editconf -f fibril_x.gro -o fibril_z.gro -rotate 0 270 0 -c\n\ngmx editconf -f fibril_z.gro -o fibril_box.gro -c -box 16.3 17.7 95.0 -bt triclinic\n\ngmx solvate -cp fibril_box.gro -p topol.top -o fibril_solv.gro\n\ntouch ions.mdp\n\ngmx grompp -f ions.mdp -c fibril_solv.gro -p topol.top -o fibril_genion.tpr\n\ngmx genion -s fibril_genion.tpr -p topol.top -o fibril_ion.gro -conc 0.15 -neutral &lt; SOL\n\ngmx grompp -f minim.mdp -c fibril_ion.gro -p topol.top -o fibril_min.tpr\n\ngmx mdrun -deffnm fibril_min -v\n\n\n\n\n\n\nCaution\n\n\n\nHeavy computational load from here on.\n\n\ngmx grompp -f nvt.mdp -c fibril_min.gro -r fibril_min.gro -p topol.top -o fibril_nvt.tpr\n\ngmx mdrun -deffnm fibril_nvt -v -dlb yes -ntomp 4 -ntmpi 10  -pme gpu -bonded gpu -npme 1\n\ngmx grompp -f npt.mdp -c fibril_nvt.gro -r fibril_nvt.gro -p topol.top -o fibril_npt.tpr\n\ngmx mdrun -deffnm fibril_npt -v -dlb yes -ntomp 4 -ntmpi 10  -pme gpu -bonded gpu -npme 1\n\n\n\n\n\n\nTip\n\n\n\nThe equilibration process can take up to 4 days. An equilibrated system will be provided in the release assets.",
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     "section": "KIMMDY Run Preparation and Simulation",
-    "text": "KIMMDY Run Preparation and Simulation\n\nConfiguration File Template\nFor a KIMMDY run, some additional setup is required. A suitable KIMMDY config file for homolysis can be found in the hexalanine_homolysis example:\n\n\nKIMMDY config file (kimmdy.yml)\n\n\n\nkimmdy.yml\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n  pull:\n    mdp: 'pull_fibril.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'\n    slow_growth: True\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - pull  \n  - reactions\n  - equilibrium\n  - pull\n\n\n\n\nGromacs index file v1\nThe config file mentions three important gromacs file for your system: top, gro, idx. We have the top and gro file from the equilibration and can update the file names in the config file. A basic index file can be generated with\necho 'q' | gmx make_ndx -f fibril_npt.gro -o index.ndx\n\n\nPlumed.dat and index file v2\nThe next entry in the config file is plumed and references a plumed configuration file (plumed.dat) which we don’t yet have. This file is needed for the homolysis reaction plugin.\nFor homolysis, the plumed.dat file should contain instructions to sample distances between bonds. Homolysis can then occur for the bonds mentioned in this file. A script to create a plumed.dat file (create_plumed_config.py) can be found in the tutorial files. Check out the script to understand its input and output!\nWe want to sample homolysis in the backbone and in crosslinks. By providing a gromacs index file with all backbone and crosslink atoms, the script generates the necessary plumed.dat file. Our initial index file does not contain those sections, so we have to create them ourselves. Such a index file can be generated with\necho -ne \"\\\"Backbone\\\"| r LY2 LY3 L4Y L5Y LYX\\nq\\n\"| gmx make_ndx -f fibril_npt.gro -o index.ndx\nNow run the python script to generate a plumed.dat file and check its contents.\n\n\nHomolysis Plugin Files: edissoc.dat and ffbonded.itp\nIn the reactions section, other files which are necessary for the homolysis reaction can also be seen: edissoc.dat and ffbonded.itp. The ffbonded.itp file is specific to the force field and can be copied from the force field directory. Edissoc.dat contains a table of bond dissociation energies by atom name and can be taken from the hexalanine_homolysis example if only standard amino acids and the HLKNL and PYD crosslinks are part of the system. The file should be separated into sections with bracketed headings.\nFor other crosslinks, the bond dissociation energy has to be provided by the user.\n\n\nKIMMDY Run Sequence: mdp files\nNow let’s look at the sequence. It mentions the reactions, which we have taken care of, and the names of different md runs. A good first Kimmdy run would include a first pulling simulation to stretch the fibril followed by a pulling simulation with distance sampling for the subsequent reaction and a final pulling simulation. For both types of pulling simulation the same mdp file can be used from the tutorial files. The pulling simulations also need torque restraints to prevent unphysiological unwinding of the fibrils. The torque restraints can be set in the mdp file and are applied to the capping groups of a tripelhelix.\nRunning the script prepare_enforced_rotation.py creates mdp and index files that only have to be appended to the current file of the respective type to use torque restraints. However, you will get an error saying that some index group is missing. Use gmx make_ndx to add these groups to your file and then run the script.\nBond distance sampling can be turned on for a md run by the tag use_plumed. You want to use this option for the MD run before checking for homolysis reactions. Another md run, in this case called relax, is mentioned under changer.coordinates.md. It is used after the homolysis reaction to interpolate between new and old parameters. An example mdp file is included in the tutorial files.\nIn a mdp file you would also define temperature coupling groups. To separate between protein and solvent, you might have to create new index groups to include the crosslinks in the protein group:\necho -ne \"r ACE & a CH3\\nr NME & a CH3\\n\\\"Protein\\\"|\\\"Other\\\"\\n\\\"Backbone\\\"| r LY2 LY3 L4Y L5Y LYX\\nq\\n\"| gmx make_ndx -f fibril_npt.gro -o index.ndx\nFinally, the KIMMDY run name and gmx_mdrun_flags can be adjusted. For large systems, writing checkpoints takes considerable time. This is why the write_checkpoint setting is on False for our tutorial run. A final KIMMDY config file could look like this:\n\n\nKIMMDY config file (kimmdy.yml)\n\n\n\nkimmdy.yml\n\n# yaml-language-server: $schema=../../src/kimmdy/kimmdy-yaml-schema.json\n\ndryrun: false\nname: 'fibril_000'\nmax_tasks: 100\nwrite_checkpoint: False\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -ntomp 4 -ntmpi 10  -pme gpu -bonded gpu -npme 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'topol.top'\ngro: 'fibril_npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n  pull:\n    mdp: 'pull_fibril.mdp'\n  sample:\n    mdp: 'pull_fibril.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'pull_fibril_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'\n    slow_growth: True\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - pull\n  - sample  \n  - reactions\n  - pull\n\n\nThe run can be started by typing kimmdy in the command line. The output files are located in fibril_000"
+    "text": "KIMMDY Run Preparation and Simulation\n\nConfiguration File Template\nFor a KIMMDY run, some additional setup is required. A suitable KIMMDY config file for homolysis can be found in the hexalanine_homolysis example:\n\n\nKIMMDY config file (kimmdy.yml)\n\n\n\nkimmdy.yml\n\ndryrun: false\nname: 'hexalanine_homolysis_000'\nmax_tasks: 100\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -nt 8\nff: 'amber99sb-star-ildnp.ff'\ntop: 'hexala_out.top'\ngro: 'npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n  pull:\n    mdp: 'pull_fibril.mdp'\n  pull:\n    mdp: 'md.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'md_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'\n    slow_growth: True\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - equilibrium\n  - pull  \n  - reactions\n  - equilibrium\n  - pull\n\n\n\n\nGromacs index file v1\nThe config file mentions three important gromacs file for your system: top, gro, idx. We have the top and gro file from the equilibration and can update the file names in the config file. A basic index file can be generated with\necho 'q' | gmx make_ndx -f fibril_npt.gro -o index.ndx\n\n\nPlumed.dat and index file v2\nThe next entry in the config file is plumed and references a plumed configuration file (plumed.dat) which we don’t yet have. This file is needed for the homolysis reaction plugin.\nFor homolysis, the plumed.dat file should contain instructions to sample distances between bonds. Homolysis can then occur for the bonds mentioned in this file. A script to create a plumed.dat file (create_plumed_config.py) can be found in the tutorial files. Check out the script to understand its input and output!\nWe want to sample homolysis in the backbone and in crosslinks. By providing a gromacs index file with all backbone and crosslink atoms, the script generates the necessary plumed.dat file. Our initial index file does not contain those sections, so we have to create them ourselves. Such a index file can be generated with\necho -ne \"\\\"Backbone\\\"| r LY2 LY3 L4Y L5Y LYX\\nq\\n\"| gmx make_ndx -f fibril_npt.gro -o index.ndx\nNow run the python script to generate a plumed.dat file and check its contents.\n\n\nHomolysis Plugin Files: edissoc.dat and ffbonded.itp\nIn the reactions section, other files which are necessary for the homolysis reaction can also be seen: edissoc.dat and ffbonded.itp. The ffbonded.itp file is specific to the force field and can be copied from the force field directory. Edissoc.dat contains a table of bond dissociation energies by atom name and can be taken from the hexalanine_homolysis example if only standard amino acids and the HLKNL and PYD crosslinks are part of the system. The file should be separated into sections with bracketed headings.\nFor other crosslinks, the bond dissociation energy has to be provided by the user.\n\n\nKIMMDY Run Sequence: mdp files\nNow let’s look at the sequence. It mentions the reactions, which we have taken care of, and the names of different md runs. A good first Kimmdy run would include a first pulling simulation to stretch the fibril followed by a pulling simulation with distance sampling for the subsequent reaction and a final pulling simulation. For both types of pulling simulation the same mdp file can be used from the tutorial files. The pulling simulations also need torque restraints to prevent unphysiological unwinding of the fibrils. The torque restraints can be set in the mdp file and are applied to the capping groups of a tripelhelix.\nRunning the script prepare_enforced_rotation.py creates mdp and index files that only have to be appended to the current file of the respective type to use torque restraints. However, you will get an error saying that some index group is missing. Use gmx make_ndx to add these groups to your file and then run the script.\nBond distance sampling can be turned on for a md run by the tag use_plumed. You want to use this option for the MD run before checking for homolysis reactions. Another md run, in this case called relax, is mentioned under changer.coordinates.md. It is used after the homolysis reaction to interpolate between new and old parameters. An example mdp file is included in the tutorial files.\nIn a mdp file you would also define temperature coupling groups. To separate between protein and solvent, you might have to create new index groups to include the crosslinks in the protein group:\necho -ne \"r ACE & a CH3\\nr NME & a CH3\\n\\\"Protein\\\"|\\\"Other\\\"\\n\\\"Backbone\\\"| r LY2 LY3 L4Y L5Y LYX\\nq\\n\"| gmx make_ndx -f fibril_npt.gro -o index.ndx\nFinally, the KIMMDY run name and gmx_mdrun_flags can be adjusted. For large systems, writing checkpoints takes considerable time. This is why the write_checkpoint setting is on False for our tutorial run. A final KIMMDY config file could look like this:\n\n\nKIMMDY config file (kimmdy.yml)\n\n\n\nkimmdy.yml\n\n# yaml-language-server: $schema=../../src/kimmdy/kimmdy-yaml-schema.json\n\ndryrun: false\nname: 'fibril_000'\nmax_tasks: 100\nwrite_checkpoint: False\ngromacs_alias: 'gmx'\ngmx_mdrun_flags: -maxh 24 -dlb yes -ntomp 4 -ntmpi 10  -pme gpu -bonded gpu -npme 1\nff: 'amber99sb-star-ildnp.ff'\ntop: 'topol.top'\ngro: 'fibril_npt.gro'\nndx: 'index.ndx'\nplumed: 'plumed.dat'\nmds:\n  pull:\n    mdp: 'pull_fibril.mdp'\n  sample:\n    mdp: 'pull_fibril.mdp'\n    use_plumed: true\n  relax:\n    mdp: 'pull_fibril_slow_growth.mdp'\nchanger:\n  coordinates:\n    md: 'relax'\n    slow_growth: True\n  topology:\n    parameterization: 'basic' \nreactions:\n  homolysis:\n    edis: 'edissoc.dat'\n    itp: 'ffbonded.itp'\nsequence:\n  - pull\n  - sample  \n  - reactions\n  - pull\n\n\nThe run can be started by typing kimmdy in the command line. The output files are located in fibril_000",
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-    "text": "Analysis\nTry the options in kimmdy-analysis to visualize your kimmdy run."
+    "text": "Analysis\nTry the options in kimmdy-analysis to visualize your kimmdy run.",
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-    "text": "parsing.TopologyDict\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n Back to top"
+    "text": "recipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\n\n\n\nName\nDescription\n\n\n\n\nBind\nChange topology to form a bond\n\n\nBondOperation\nHandle a bond operation on the recipe step.\n\n\nBreak\nChange topology to break a bond\n\n\nCustomTopMod\nA custom recipe step that can be used to define a custom topology modification.\n\n\nPlace\nChange topology and/or coordinates to place an atom.\n\n\nRecipe\nA reaction path defined by one series of RecipeSteps.\n\n\nRecipeCollection\nA RecipeCollection encompasses a number of reaction paths.\n\n\nRecipeStep\nBase class for all RecipeSteps.\n\n\nRelax\nStart a relaxation MD.\n\n\n\n\n\nrecipe.Bind(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to form a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.BondOperation(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nHandle a bond operation on the recipe step.\nThis class takes in either zero-based indices or one-base IDs for two atoms.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf neither an index nor an ID is provided for any of the atoms.\n\n\n\n\n\n\nInternally, this class stores the atom indices and converts IDs to indices as needed.\n\n\n\n\nrecipe.Break(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to break a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.CustomTopMod(f)\nA custom recipe step that can be used to define a custom topology modification.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nf\nCallable[[Topology], Topology]\nA function that takes a Topology object and modifies it in place.\nrequired\n\n\n\n\n\n\n\nrecipe.Place(self, new_coords, ix_to_place=None, id_to_place=None)\nChange topology and/or coordinates to place an atom.\nEither provide the index (ix_to_place) or the ID (id_to_place) of the atom to place.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nnew_coords\ntuple[float, float, float]\nNew xyz coordinates for atom to place to. Valid for the end point of the recipe timespan.\nrequired\n\n\nix_to_place\nint\nIndex of atom to place. 0-based.\nNone\n\n\nid_to_place\nstr\nIndex of atom to place. 1-based\nNone\n\n\n\n\n\n\n\nrecipe.Recipe(recipe_steps, rates, timespans)\nA reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_steps\nlist[RecipeStep]\nSingle sequence of RecipeSteps to build product\nrequired\n\n\nrates\nlist[float]\nReaction rates corresponding 1:1 to timespans.\nrequired\n\n\ntimespans\nlist[list[float, float]]\nList of half-open timespans (t1, t2] in ps, at which this rate is valid. Recipe steps which change the coordinates only need to be applicable at the first time in the interval. Must have same number of timespans as rates. t1 can equal t2 for the last frame.\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_consistency\nRun consistency checks for correct size of variables\n\n\ncombine_with\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nrecipe.Recipe.check_consistency()\nRun consistency checks for correct size of variables\n\n\n\nrecipe.Recipe.combine_with(other)\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nother\nRecipe\n\nrequired\n\n\n\n\n\n\n\n\n\nrecipe.RecipeCollection(recipes)\nA RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nunique_recipes_ixs\nList of lists binning the old recipe indices and maps to the new recipes list.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\naggregate_reactions\nCombines reactions having the same sequence of RecipeSteps.\n\n\ncalc_cumprob\nCalculate cumulative probability of all contained recipe steps.\n\n\ncalc_ratesum\nCalculate the sum of rates over all timesteps\n\n\nfrom_csv\nCreate a RecipeCollection object from a CSV file\n\n\nplot\nPlot reaction rates over time\n\n\nto_csv\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeCollection.aggregate_reactions()\nCombines reactions having the same sequence of RecipeSteps.\n\n\n\nrecipe.RecipeCollection.calc_cumprob()\nCalculate cumulative probability of all contained recipe steps. Sums up to 1 over all recipes. Assumes constant rate for given timespan and rate zero otherwise.\n\n\n\nrecipe.RecipeCollection.calc_ratesum()\nCalculate the sum of rates over all timesteps\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nboarders\nflat list containing times of rate changes marking the boarders of the windows\n\n\nrate_windows\nflat list containing all rates in between the boarders. Each window is orderd as in recipe_windows\n\n\nrecipe_windows\nflat list containing the recipes of the corresponding window. Each window is orderd as in rate_windows\n\n\n\n\n\n\n\nrecipe.RecipeCollection.from_csv(path)\nCreate a RecipeCollection object from a CSV file Returns the recipe collection and a single recipe that was picked, otherwise None\n\n\n\nrecipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)\nPlot reaction rates over time\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\noutfile\nPath\nWhere to save the plot, must have compatible suffix.\nrequired\n\n\nhighlight_r\nRecipe\nRecipe to highlight, by default None\nNone\n\n\nhighlight_t\nfloat\nTime at which the reactions starts\nNone\n\n\n\n\n\n\n\nrecipe.RecipeCollection.to_csv(path, picked_recipe=None)\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeStep()\nBase class for all RecipeSteps. Indices can be accessed as 0-based or 1-based. ix: 0-based, int id: 1-based, str\n\n\n\nrecipe.Relax()\nStart a relaxation MD.\nThe molecular system coordinates are far out of equilibrium after most topology changes. A relaxtion MD simulation using for example the slow growth method helps to reach the new equilibrium.",
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-    "text": "topology.ff\n\n\n\n\n\nName\nDescription\n\n\n\n\nFF\nContainer for parsed forcefield data.\n\n\n\n\n\ntopology.ff.FF(self, top, residuetypes_path=None)\nContainer for parsed forcefield data."
+    "text": "Name\nDescription\n\n\n\n\nBind\nChange topology to form a bond\n\n\nBondOperation\nHandle a bond operation on the recipe step.\n\n\nBreak\nChange topology to break a bond\n\n\nCustomTopMod\nA custom recipe step that can be used to define a custom topology modification.\n\n\nPlace\nChange topology and/or coordinates to place an atom.\n\n\nRecipe\nA reaction path defined by one series of RecipeSteps.\n\n\nRecipeCollection\nA RecipeCollection encompasses a number of reaction paths.\n\n\nRecipeStep\nBase class for all RecipeSteps.\n\n\nRelax\nStart a relaxation MD.\n\n\n\n\n\nrecipe.Bind(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to form a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.BondOperation(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nHandle a bond operation on the recipe step.\nThis class takes in either zero-based indices or one-base IDs for two atoms.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf neither an index nor an ID is provided for any of the atoms.\n\n\n\n\n\n\nInternally, this class stores the atom indices and converts IDs to indices as needed.\n\n\n\n\nrecipe.Break(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to break a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.CustomTopMod(f)\nA custom recipe step that can be used to define a custom topology modification.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nf\nCallable[[Topology], Topology]\nA function that takes a Topology object and modifies it in place.\nrequired\n\n\n\n\n\n\n\nrecipe.Place(self, new_coords, ix_to_place=None, id_to_place=None)\nChange topology and/or coordinates to place an atom.\nEither provide the index (ix_to_place) or the ID (id_to_place) of the atom to place.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nnew_coords\ntuple[float, float, float]\nNew xyz coordinates for atom to place to. Valid for the end point of the recipe timespan.\nrequired\n\n\nix_to_place\nint\nIndex of atom to place. 0-based.\nNone\n\n\nid_to_place\nstr\nIndex of atom to place. 1-based\nNone\n\n\n\n\n\n\n\nrecipe.Recipe(recipe_steps, rates, timespans)\nA reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_steps\nlist[RecipeStep]\nSingle sequence of RecipeSteps to build product\nrequired\n\n\nrates\nlist[float]\nReaction rates corresponding 1:1 to timespans.\nrequired\n\n\ntimespans\nlist[list[float, float]]\nList of half-open timespans (t1, t2] in ps, at which this rate is valid. Recipe steps which change the coordinates only need to be applicable at the first time in the interval. Must have same number of timespans as rates. t1 can equal t2 for the last frame.\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_consistency\nRun consistency checks for correct size of variables\n\n\ncombine_with\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nrecipe.Recipe.check_consistency()\nRun consistency checks for correct size of variables\n\n\n\nrecipe.Recipe.combine_with(other)\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nother\nRecipe\n\nrequired\n\n\n\n\n\n\n\n\n\nrecipe.RecipeCollection(recipes)\nA RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nunique_recipes_ixs\nList of lists binning the old recipe indices and maps to the new recipes list.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\naggregate_reactions\nCombines reactions having the same sequence of RecipeSteps.\n\n\ncalc_cumprob\nCalculate cumulative probability of all contained recipe steps.\n\n\ncalc_ratesum\nCalculate the sum of rates over all timesteps\n\n\nfrom_csv\nCreate a RecipeCollection object from a CSV file\n\n\nplot\nPlot reaction rates over time\n\n\nto_csv\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeCollection.aggregate_reactions()\nCombines reactions having the same sequence of RecipeSteps.\n\n\n\nrecipe.RecipeCollection.calc_cumprob()\nCalculate cumulative probability of all contained recipe steps. Sums up to 1 over all recipes. Assumes constant rate for given timespan and rate zero otherwise.\n\n\n\nrecipe.RecipeCollection.calc_ratesum()\nCalculate the sum of rates over all timesteps\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nboarders\nflat list containing times of rate changes marking the boarders of the windows\n\n\nrate_windows\nflat list containing all rates in between the boarders. Each window is orderd as in recipe_windows\n\n\nrecipe_windows\nflat list containing the recipes of the corresponding window. Each window is orderd as in rate_windows\n\n\n\n\n\n\n\nrecipe.RecipeCollection.from_csv(path)\nCreate a RecipeCollection object from a CSV file Returns the recipe collection and a single recipe that was picked, otherwise None\n\n\n\nrecipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)\nPlot reaction rates over time\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\noutfile\nPath\nWhere to save the plot, must have compatible suffix.\nrequired\n\n\nhighlight_r\nRecipe\nRecipe to highlight, by default None\nNone\n\n\nhighlight_t\nfloat\nTime at which the reactions starts\nNone\n\n\n\n\n\n\n\nrecipe.RecipeCollection.to_csv(path, picked_recipe=None)\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeStep()\nBase class for all RecipeSteps. Indices can be accessed as 0-based or 1-based. ix: 0-based, int id: 1-based, str\n\n\n\nrecipe.Relax()\nStart a relaxation MD.\nThe molecular system coordinates are far out of equilibrium after most topology changes. A relaxtion MD simulation using for example the slow growth method helps to reach the new equilibrium.",
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-    "text": "Name\nDescription\n\n\n\n\nFF\nContainer for parsed forcefield data.\n\n\n\n\n\ntopology.ff.FF(self, top, residuetypes_path=None)\nContainer for parsed forcefield data."
+    "text": "tasks\nThe tasks module holds the TaskFiles class which organizes input and output paths and the Task class for steps in the runmanager.\n\n\n\n\n\nName\nDescription\n\n\n\n\nAutoFillDict\nDictionary that gets populated by calling get_missing.\n\n\nTask\nA task to be performed as as a step in the RunManager.\n\n\nTaskFiles\nClass for Task input and output files and directories.\n\n\n\n\n\ntasks.AutoFillDict(self, get_missing)\nDictionary that gets populated by calling get_missing.\n\n\n\ntasks.Task(self, runmng, f, kwargs=None, out=None)\nA task to be performed as as a step in the RunManager.\nA task consists of a function and its keyword arguments. Calling a taks calls the stored function. The function must return a TaskFiles object.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrunmng\n\nRunmanager instance from which the task is called\nrequired\n\n\nf\nCallable[…, Optional[TaskFiles]]\nFunction that will be called when the task is called\nrequired\n\n\nkwargs\nOptional[dict[str, Any]]\nkwargs to be passed to f\nNone\n\n\nout\nOptional[str]\nIf not None, an output dir will be created with this name\nNone\n\n\n\n\n\n\n\ntasks.TaskFiles(get_latest, input=field(default_factory=dict), output=field(default_factory=dict), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))\nClass for Task input and output files and directories.\nHosts the input and output file paths belonging to a task. A function or method that wants to be callable as a Task has to return a TaskFiles object. The input defaultdict is populated on the fly using get_latest of the runmanager to find newest files. Files which can not be found by get_latest must be added manually.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nget_latest\nCallable\nRunmanager.get_latest function that returns paths to the latest file of given type.\n\n\ninput\ndict[str, Path]\nInput file paths for a Task. Is populated by get_latest or manually.\n\n\noutput\ndict[str, Path]\nOutput file paths for a Task. Is populated by runmanager._discover_output_files or manually.\n\n\noutputdir\nPath\nOutput directory for a Task. Typically populated by create_task_directory called by Task.\n\n\nlogger\nlogging.Logger\nLogger for a Task. Initialized in create_task_directory.\n\n\n\n\n\n\n&gt;&gt;&gt; class run():\n&gt;&gt;&gt;     def get_latest(self, s):\n&gt;&gt;&gt;         return f\"latest {s}\"\n&gt;&gt;&gt; runmng = run()\n&gt;&gt;&gt; files = TaskFiles(runmng)\n&gt;&gt;&gt; files.input\n&gt;&gt;&gt; files.input[\"top\"]\n{'top': 'latest top'}\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncreate_task_directory\nCreates TaskFiles object, output directory, logger and symlinks ff.\n\n\n\n\n\ntasks.create_task_directory(runmng, postfix)\nCreates TaskFiles object, output directory, logger and symlinks ff.\nGets called when a Task is called (from the runmanager.tasks queue).",
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-    "text": "Options of the main KIMMDY input file\n\n\n\nArguments of all KIMMDY parts.\n\n\n\nStart KIMMDY from a python script or the command line\n\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\n\n\n\n\nTopology modules\n\n\n\ntopology.topology\n\n\n\ntopology.ff\n\n\n\ntopology.utils\n\n\n\ntopology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc.\n\n\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n\n\nModules\n\n\n\nanalysis\nAnalysis tools for KIMMDY runs.\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\nconfig\nRead and validate kimmdy.yml configuration files\n\n\nconstants\nComstants used throughout KIMMDY\n\n\ncoordinates\ncoordinate, topology and plumed modification functions\n\n\nkmc\nKinetic Monte Carlo (KMC) classes and functions.\n\n\nparsing\nAll read_&lt;…&gt; and write_&lt;…&gt; functions.\n\n\nplugins\nPlugin base classes and basic instances thereof.\n\n\nrecipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\nrunmanager\nThe Runmanager is the main entry point of the program.\n\n\nschema\nHandle the schema for the config file.\n\n\ntasks\nThe tasks module holds the TaskFiles class which organizes input and\n\n\ntools\nStandalone tools that are complementary to KIMMDY.\n\n\nutils\nUtilities for building plugins, shell convenience functions and GROMACS related functions\n\n\n\n\n\n\nReaction plugins bundled with KIMMDY and the protocol to add a new reaction plugin to KIMMDY\n\n\n\nhomolysis.reaction.Homolysis\nHomolytic bond breaking leading to 2 radicals.\n\n\nhat_naive.reaction.NaiveHAT\nNaive HAT reaction, selects hydrogens at random\n\n\ndummyreaction.reaction.DummyReaction\nDummy reaction, returns empty RecipeCollection"
+    "text": "Name\nDescription\n\n\n\n\nAutoFillDict\nDictionary that gets populated by calling get_missing.\n\n\nTask\nA task to be performed as as a step in the RunManager.\n\n\nTaskFiles\nClass for Task input and output files and directories.\n\n\n\n\n\ntasks.AutoFillDict(self, get_missing)\nDictionary that gets populated by calling get_missing.\n\n\n\ntasks.Task(self, runmng, f, kwargs=None, out=None)\nA task to be performed as as a step in the RunManager.\nA task consists of a function and its keyword arguments. Calling a taks calls the stored function. The function must return a TaskFiles object.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrunmng\n\nRunmanager instance from which the task is called\nrequired\n\n\nf\nCallable[…, Optional[TaskFiles]]\nFunction that will be called when the task is called\nrequired\n\n\nkwargs\nOptional[dict[str, Any]]\nkwargs to be passed to f\nNone\n\n\nout\nOptional[str]\nIf not None, an output dir will be created with this name\nNone\n\n\n\n\n\n\n\ntasks.TaskFiles(get_latest, input=field(default_factory=dict), output=field(default_factory=dict), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))\nClass for Task input and output files and directories.\nHosts the input and output file paths belonging to a task. A function or method that wants to be callable as a Task has to return a TaskFiles object. The input defaultdict is populated on the fly using get_latest of the runmanager to find newest files. Files which can not be found by get_latest must be added manually.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nget_latest\nCallable\nRunmanager.get_latest function that returns paths to the latest file of given type.\n\n\ninput\ndict[str, Path]\nInput file paths for a Task. Is populated by get_latest or manually.\n\n\noutput\ndict[str, Path]\nOutput file paths for a Task. Is populated by runmanager._discover_output_files or manually.\n\n\noutputdir\nPath\nOutput directory for a Task. Typically populated by create_task_directory called by Task.\n\n\nlogger\nlogging.Logger\nLogger for a Task. Initialized in create_task_directory.\n\n\n\n\n\n\n&gt;&gt;&gt; class run():\n&gt;&gt;&gt;     def get_latest(self, s):\n&gt;&gt;&gt;         return f\"latest {s}\"\n&gt;&gt;&gt; runmng = run()\n&gt;&gt;&gt; files = TaskFiles(runmng)\n&gt;&gt;&gt; files.input\n&gt;&gt;&gt; files.input[\"top\"]\n{'top': 'latest top'}",
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+    "text": "Name\nDescription\n\n\n\n\ncreate_task_directory\nCreates TaskFiles object, output directory, logger and symlinks ff.\n\n\n\n\n\ntasks.create_task_directory(runmng, postfix)\nCreates TaskFiles object, output directory, logger and symlinks ff.\nGets called when a Task is called (from the runmanager.tasks queue).",
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+    "text": "plugins\nPlugin base classes and basic instances thereof.\nAlso discovers and loads KIMMDY plugins.\n\n\n\n\n\nName\nDescription\n\n\n\n\nBasicParameterizer\nreconstruct base force field state\n\n\nReactionPlugin\nReaction base class\n\n\n\n\n\nplugins.BasicParameterizer()\nreconstruct base force field state\n\n\n\n\n\nName\nDescription\n\n\n\n\nparameterize_topology\nDo nothing,\n\n\n\n\n\nplugins.BasicParameterizer.parameterize_topology(current_topology, focus_nrs=None)\nDo nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology\n\n\n\n\n\nplugins.ReactionPlugin(self, name, runmng)\nReaction base class\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nName of the reaction\nrequired\n\n\nrunmng\nRunmanager\nRunManager instance\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_recipe_collection\nGet a RecipeCollection as a result of the reaction.\n\n\n\n\n\nplugins.ReactionPlugin.get_recipe_collection(files)\nGet a RecipeCollection as a result of the reaction.\nThis is run as a Task in the RunManager. How the RecipeCollection is built is up to the reaction. It has access to the current state of the system via the runmanager self.runmng and the files.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\nTaskFiles instance\nrequired",
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-    "text": "Start KIMMDY from a python script or the command line\n\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line."
+    "text": "Name\nDescription\n\n\n\n\nBasicParameterizer\nreconstruct base force field state\n\n\nReactionPlugin\nReaction base class\n\n\n\n\n\nplugins.BasicParameterizer()\nreconstruct base force field state\n\n\n\n\n\nName\nDescription\n\n\n\n\nparameterize_topology\nDo nothing,\n\n\n\n\n\nplugins.BasicParameterizer.parameterize_topology(current_topology, focus_nrs=None)\nDo nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology\n\n\n\n\n\nplugins.ReactionPlugin(self, name, runmng)\nReaction base class\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nName of the reaction\nrequired\n\n\nrunmng\nRunmanager\nRunManager instance\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_recipe_collection\nGet a RecipeCollection as a result of the reaction.\n\n\n\n\n\nplugins.ReactionPlugin.get_recipe_collection(files)\nGet a RecipeCollection as a result of the reaction.\nThis is run as a Task in the RunManager. How the RecipeCollection is built is up to the reaction. It has access to the current state of the system via the runmanager self.runmng and the files.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\nTaskFiles instance\nrequired",
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-    "text": "Topology modules\n\n\n\ntopology.topology\n\n\n\ntopology.ff\n\n\n\ntopology.utils\n\n\n\ntopology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc.\n\n\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top."
+    "text": "kmc\nKinetic Monte Carlo (KMC) classes and functions.\nIn our system, the reaction rate r = (deterministic) reaction constant k = stochastic reaction constant c (from gillespie 1977) = propensity a (from Anderson 2007) because of the fundamental premise of chemical kinetics and because we have one reactant molecule\n\n\n\n\n\nName\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()",
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-    "text": "Modules\n\n\n\nanalysis\nAnalysis tools for KIMMDY runs.\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\nconfig\nRead and validate kimmdy.yml configuration files\n\n\nconstants\nComstants used throughout KIMMDY\n\n\ncoordinates\ncoordinate, topology and plumed modification functions\n\n\nkmc\nKinetic Monte Carlo (KMC) classes and functions.\n\n\nparsing\nAll read_&lt;…&gt; and write_&lt;…&gt; functions.\n\n\nplugins\nPlugin base classes and basic instances thereof.\n\n\nrecipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\nrunmanager\nThe Runmanager is the main entry point of the program.\n\n\nschema\nHandle the schema for the config file.\n\n\ntasks\nThe tasks module holds the TaskFiles class which organizes input and\n\n\ntools\nStandalone tools that are complementary to KIMMDY.\n\n\nutils\nUtilities for building plugins, shell convenience functions and GROMACS related functions"
+    "text": "Name\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]",
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-    "text": "Reaction plugins bundled with KIMMDY and the protocol to add a new reaction plugin to KIMMDY\n\n\n\nhomolysis.reaction.Homolysis\nHomolytic bond breaking leading to 2 radicals.\n\n\nhat_naive.reaction.NaiveHAT\nNaive HAT reaction, selects hydrogens at random\n\n\ndummyreaction.reaction.DummyReaction\nDummy reaction, returns empty RecipeCollection"
+    "text": "Name\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()",
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-    "text": "config\nRead and validate kimmdy.yml configuration files and package into a parsed format for internal use.\n\n\n\n\n\nName\nDescription\n\n\n\n\nConfig\nInternal representation of the configuration generated\n\n\n\n\n\nconfig.Config(self, input_file=None, recursive_dict=None, scheme=None, section='config', logfile=None, loglevel=None)\nInternal representation of the configuration generated from the input file, which enables validation before running and computationally expensive operations.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput_file\nPath | None\nPath to the config yaml file.\nNone\n\n\nrecursive_dict\ndict | None\nFor internal use only, used in reading settings in recursively.\nNone\n\n\nscheme\ndict | None\ndict containing types and defaults for casting and validating settings.\nNone\n\n\nsection\nstr\ncurrent section e.g. to determine the level of recursion in nested configs e.g. “config”, “config.mds” or “config.reactions.homolysis”\n'config'\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nattr\nGet the value of a specific attribute.\n\n\nget_attributes\nGet a list of all attributes without hidden ones (_&lt;…&gt;).\n\n\n\n\n\nconfig.Config.attr(attribute)\nGet the value of a specific attribute. Alias for self.__getattribute__\n\n\n\nconfig.Config.get_attributes()\nGet a list of all attributes without hidden ones (_&lt;…&gt;)."
+    "text": "topology.utils\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_is_reactive_predicate_f\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\nget_moleculetype_atomics\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nget_moleculetype_header\nGet content of the header of a moleculetype from a topology dict.\n\n\nget_protein_section\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nget_reactive_section\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\nget_residue_fragments\nSplits a residue into fragments after a bond has been broken.\n\n\nget_top_section\nGet content of a section from a topology dict.\n\n\nis_not_solvent_or_ion\nReturns whether a moleculetype name is not solvent or ion.\n\n\nset_moleculetype_atomics\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nset_protein_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_reactive_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_top_section\nSet content of a section from a topology dict.\n\n\n\n\n\ntopology.utils.get_is_reactive_predicate_f(cfg)\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\n\ntopology.utils.get_moleculetype_atomics(top, moleculetype)\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_moleculetype_header(top, moleculetype)\nGet content of the header of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_protein_section(top, name)\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.get_reactive_section(top, name)\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\n\ntopology.utils.get_residue_fragments(top, residue, start1, start2, iterations=20)\nSplits a residue into fragments after a bond has been broken.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopology\nTopology\nrequired\n\n\nresidue\nlist[Atom]\nAll atoms of current residue. Ok, when it contains more atoms as long as those are not connected to broken bond.\nrequired\n\n\nstart1\nAtom\nFirst atom with broken bond\nrequired\n\n\nstart2\nAtom\nSecond atom with broken bond\nrequired\n\n\niterations\nint\nMax number of bonds from start atoms to be included when building fragmets, by default 20\n20\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nTwo fragments, or one fragment and empty set in case the\nresidue did not change its size.\n\n\n\n\n\n\n\ntopology.utils.get_top_section(top, name, moleculetype=None)\nGet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.is_not_solvent_or_ion(name)\nReturns whether a moleculetype name is not solvent or ion.\n\n\n\ntopology.utils.set_moleculetype_atomics(top, name, atomics, create=False)\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\nIf create is True, a new section is created if it does not exist.\n\n\n\ntopology.utils.set_protein_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_reactive_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_top_section(top, name, value, moleculetype=None)\nSet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.",
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+    "text": "Name\nDescription\n\n\n\n\nget_is_reactive_predicate_f\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\nget_moleculetype_atomics\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nget_moleculetype_header\nGet content of the header of a moleculetype from a topology dict.\n\n\nget_protein_section\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nget_reactive_section\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\nget_residue_fragments\nSplits a residue into fragments after a bond has been broken.\n\n\nget_top_section\nGet content of a section from a topology dict.\n\n\nis_not_solvent_or_ion\nReturns whether a moleculetype name is not solvent or ion.\n\n\nset_moleculetype_atomics\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nset_protein_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_reactive_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_top_section\nSet content of a section from a topology dict.\n\n\n\n\n\ntopology.utils.get_is_reactive_predicate_f(cfg)\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\n\ntopology.utils.get_moleculetype_atomics(top, moleculetype)\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_moleculetype_header(top, moleculetype)\nGet content of the header of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_protein_section(top, name)\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.get_reactive_section(top, name)\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\n\ntopology.utils.get_residue_fragments(top, residue, start1, start2, iterations=20)\nSplits a residue into fragments after a bond has been broken.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopology\nTopology\nrequired\n\n\nresidue\nlist[Atom]\nAll atoms of current residue. Ok, when it contains more atoms as long as those are not connected to broken bond.\nrequired\n\n\nstart1\nAtom\nFirst atom with broken bond\nrequired\n\n\nstart2\nAtom\nSecond atom with broken bond\nrequired\n\n\niterations\nint\nMax number of bonds from start atoms to be included when building fragmets, by default 20\n20\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nTwo fragments, or one fragment and empty set in case the\nresidue did not change its size.\n\n\n\n\n\n\n\ntopology.utils.get_top_section(top, name, moleculetype=None)\nGet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.is_not_solvent_or_ion(name)\nReturns whether a moleculetype name is not solvent or ion.\n\n\n\ntopology.utils.set_moleculetype_atomics(top, name, atomics, create=False)\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\nIf create is True, a new section is created if it does not exist.\n\n\n\ntopology.utils.set_protein_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_reactive_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_top_section(top, name, value, moleculetype=None)\nSet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.",
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-    "text": "kmc\nKinetic Monte Carlo (KMC) classes and functions.\nIn our system, the reaction rate r = (deterministic) reaction constant k = stochastic reaction constant c (from gillespie 1977) = propensity a (from Anderson 2007) because of the fundamental premise of chemical kinetics and because we have one reactant molecule\n\n\n\n\n\nName\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(self, recipe=lambda: Recipe([], [], [])(), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()"
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-    "text": "Name\nDescription\n\n\n\n\nKMCResult\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nkmc.KMCResult(self, recipe=lambda: Recipe([], [], [])(), reaction_probability=None, time_delta=None, time_start=None)\nThe result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nrecipe\nRecipe\nSingle sequence of RecipeSteps to build product\n\n\nreaction_probability\nOptional[list[float]]\nIntegral of reaction propensity with respect to time\n\n\ntime_delta\nOptional[float]\nMC time jump during which the reaction occurs [ps]\n\n\ntime_start\nOptional[float]\nTime, from which the reaction starts. The reaction changes the geometry/topology of this timestep and continues from there. [ps]"
+    "text": "Name\nDescription\n\n\n\n\nFF\nContainer for parsed forcefield data.\n\n\n\n\n\ntopology.ff.FF(self, top, residuetypes_path=None)\nContainer for parsed forcefield data.",
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-    "text": "Name\nDescription\n\n\n\n\nextrande\nExtrande KMC\n\n\nextrande_mod\nModified Extrande KMC\n\n\nfrm\nFirst Reaction Method variant of Kinetic Monte Carlo.\n\n\nrf_kmc\nRejection-Free Monte Carlo.\n\n\n\n\n\nkmc.extrande(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nExtrande KMC\nImplemented as in Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.extrande_mod(recipe_collection, tau_scale, logger=logging.getLogger(__name__), rng=default_rng())\nModified Extrande KMC\nImproved implementation of Stochastic Simulation of Biomolecular Networks in Dynamic Environments 10.1371/journal.pcbi.1004923 Changes: The considered time window is chosen to be a window containing constant rates. This prevents very small tau caused by a spike in the rate at a later point. As a side effect, the upper rate bound b and current rate a0 are the same, and the ‘extra’ side channel can not be triggered anymore.\nThis should be more efficient given a limited number of time windows containing constant rates.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()\n\n\ntau_scale\nfloat\nScaling factor for tau, by default 1.0\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nKMCResult\ntime delta set to 0\n\n\n\n\n\n\n\nkmc.frm(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng(), MD_time=None)\nFirst Reaction Method variant of Kinetic Monte Carlo. takes RecipeCollection and choses a recipe based on which reaction would occur.\nCompare e.g. Wikipedia KMC - time dependent\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nto generate random numbers in the KMC step\ndefault_rng()\n\n\nMD_time\nOptional[float]\ntime [ps] to compare conformational events with reaction events in the time domain\nNone\n\n\n\n\n\n\n\nkmc.rf_kmc(recipe_collection, logger=logging.getLogger(__name__), rng=default_rng())\nRejection-Free Monte Carlo. Takes RecipeCollection and choses a recipe based on the relative propensity of the events. The ‘start’ time of the reaction is the time of the highest rate of the accepted reaction.\nCompare e.g. Wikipedia KMC - rejection free\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_collection\nRecipeCollection\nfrom which one will be choosen\nrequired\n\n\nrng\nnp.random.Generator\nfunction to generate random numbers in the KMC step\ndefault_rng()"
+    "text": "runmanager\nThe Runmanager is the main entry point of the program.\nIt manages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nDescription\n\n\n\n\nRunManager\nThe Runmanager is the main entry point of the program.\n\n\nState\nState of the system.\n\n\n\n\n\nrunmanager.RunManager(self, config)\nThe Runmanager is the main entry point of the program.\nManages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nconfig\nConfig\nThe configuration object.\n\n\ntasks\nqueue.Queue[Task]\nTasks from config.\n\n\ncrr_tasks\nqueue.Queue[Task]\nCurrent tasks.\n\n\niteration\nint\nCurrent iteration.\n\n\nstate\nState\nCurrent state of the system.\n\n\nrecipe_collection\nRecipeCollection\nCollection of recipes.\n\n\nlatest_files\ndict[str, Path]\nDictionary of latest files.\n\n\nhistfile\nPath\nPath to history file.\n\n\ntop\n\nTopology object.\n\n\nfilehist\nlist[dict[str, TaskFiles]]\nList of dictionaries of TaskFiles.\n\n\ntask_mapping\n\nMapping of task names to runmanager methods.\n\n\nreaction_plugins\nlist[ReactionPlugin]\nList of initialized reaction plugins used in the sequence.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_latest\nReturns path to latest file of given type.\n\n\n\n\n\nrunmanager.RunManager.get_latest(suffix)\nReturns path to latest file of given type.\nFor .dat files (in general ambiguous extensions) use full file name. Errors if file is not found.\n\n\n\n\n\nrunmanager.State()\nState of the system. one of IDLE, MD, REACTION, SETUP, DONE.\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_existing_files\nInitialize latest_files with every existing file defined in config\n\n\n\n\n\nrunmanager.get_existing_files(config)\nInitialize latest_files with every existing file defined in config",
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-    "text": "topology.topology\n\n\n\n\n\nName\nDescription\n\n\n\n\nMoleculeType\nOne moleculetype in the topology\n\n\nTopology\nSmart container for parsed topology data.\n\n\n\n\n\ntopology.topology.MoleculeType(self, header, atomics, radicals=None)\nOne moleculetype in the topology\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\natoms\ndict[str, Atom]\n\n\n\nbonds\ndict[tuple[str, str], Bond]\n\n\n\npairs\ndict[tuple[str, str], Pair]\n\n\n\nangles\ndict[tuple[str, str, str], Angle]\n\n\n\nproper_dihedrals\ndict[tuple[str, str, str, str], MultipleDihedrals]\n\n\n\nimproper_dihedrals\ndict[tuple[str, str, str, str], Dihedral]\n\n\n\nposition_restraints\ndict[str, PositionRestraint]\n\n\n\ndihedral_restraints\ndict[tuple[str, str, str, str], DihedralRestraint]\n\n\n\nradicals\ndict[str, Atom]\ndict mapping atom indices to atom objects for storing all radical atoms\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nfind_radicals\nFind atoms that are radicals and update self.radicals.\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\n\n\n\ntopology.topology.MoleculeType.find_radicals()\nFind atoms that are radicals and update self.radicals.\nIterate over all atoms and designate them as radicals if they have fewer bounds than their natural bond order.\n\n\n\ntopology.topology.MoleculeType.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict, mapping of old atom number strings to new ones\n\n\n\n\n\ntopology.topology.Topology(self, top, parametrizer=BasicParameterizer(), is_reactive_predicate_f=is_not_solvent_or_ion, radicals=None, residuetypes_path=None)\nSmart container for parsed topology data.\nA topology keeps track of connections when bonds are broken or formed. Reparametrization is triggerd automatically if to_dict is called after bonds have changed.\nAssumptions:\n\nthe topology of interest (the Reactive moleculetype) consists of the first moleculetypes (non-solvent).\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nA dictionary containing the parsed topology data, produced by kimmdy.parsing.read_top\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nbind_bond\nAdd a bond in topology.\n\n\nbreak_bond\nBreak bonds in topology homolytically.\n\n\ndel_atom\nDeletes atom\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\nupdate_partial_charges\nUpdate the topology atom partial charges.\n\n\nvalidate_bond\nValidates bond consistency between both atoms and top\n\n\n\n\n\ntopology.topology.Topology.bind_bond(atompair_addresses)\nAdd a bond in topology.\nModifies the topology dictionary in place. It keeps track of affected terms in the topology via a graph representation of the topology and applies the necessary changes to bonds, angles and dihedrals (proper and improper). Furthermore, it modifies to function types in the topology to account for radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nAtoms to bind together.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.break_bond(atompair_addresses)\nBreak bonds in topology homolytically.\nRemoves bond, angles and dihedrals where atompair was involved. Modifies the topology dictionary in place. Atom pairs become radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nBetween which atoms to break the bond.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.del_atom(atom_nr, parameterize=True)\nDeletes atom\nDeletes atom and all attached bonds. Reindexes the top and updates the parameters if requested. Also moves charges to first bound_nrs atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_nr\nUnion[list[str], str]\n1-based atom number as string to delete\nrequired\n\n\nparameterize\nbool\nIf true and bonds are removed triggers reparameterization, by default True\nTrue\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nupdate_map\nDict, mapping of old atom number strings to new ones.\n\n\n\n\n\n\n\ntopology.topology.Topology.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict of all moleculetypes to their update maps (old -&gt; new).\n\n\n\ntopology.topology.Topology.update_partial_charges(recipe_steps)\nUpdate the topology atom partial charges.\nThis function must be called after the recipe_steps are applied. Changes are based on the recipe_steps. Update rules follow a simple assignment scheme that works well with grappa. If fragments are created, their partial charges are kept integers. If previously broken bonds are formed again, the original partial charges are restored.\n\n\n\ntopology.topology.Topology.validate_bond(atm1, atm2)\nValidates bond consistency between both atoms and top Returns True if bond exists, False if not. Raises RuntimeError if bond is not consistent."
+    "text": "Name\nDescription\n\n\n\n\nRunManager\nThe Runmanager is the main entry point of the program.\n\n\nState\nState of the system.\n\n\n\n\n\nrunmanager.RunManager(self, config)\nThe Runmanager is the main entry point of the program.\nManages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nconfig\nConfig\nThe configuration object.\n\n\ntasks\nqueue.Queue[Task]\nTasks from config.\n\n\ncrr_tasks\nqueue.Queue[Task]\nCurrent tasks.\n\n\niteration\nint\nCurrent iteration.\n\n\nstate\nState\nCurrent state of the system.\n\n\nrecipe_collection\nRecipeCollection\nCollection of recipes.\n\n\nlatest_files\ndict[str, Path]\nDictionary of latest files.\n\n\nhistfile\nPath\nPath to history file.\n\n\ntop\n\nTopology object.\n\n\nfilehist\nlist[dict[str, TaskFiles]]\nList of dictionaries of TaskFiles.\n\n\ntask_mapping\n\nMapping of task names to runmanager methods.\n\n\nreaction_plugins\nlist[ReactionPlugin]\nList of initialized reaction plugins used in the sequence.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_latest\nReturns path to latest file of given type.\n\n\n\n\n\nrunmanager.RunManager.get_latest(suffix)\nReturns path to latest file of given type.\nFor .dat files (in general ambiguous extensions) use full file name. Errors if file is not found.\n\n\n\n\n\nrunmanager.State()\nState of the system. one of IDLE, MD, REACTION, SETUP, DONE.",
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-    "text": "Name\nDescription\n\n\n\n\nMoleculeType\nOne moleculetype in the topology\n\n\nTopology\nSmart container for parsed topology data.\n\n\n\n\n\ntopology.topology.MoleculeType(self, header, atomics, radicals=None)\nOne moleculetype in the topology\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\natoms\ndict[str, Atom]\n\n\n\nbonds\ndict[tuple[str, str], Bond]\n\n\n\npairs\ndict[tuple[str, str], Pair]\n\n\n\nangles\ndict[tuple[str, str, str], Angle]\n\n\n\nproper_dihedrals\ndict[tuple[str, str, str, str], MultipleDihedrals]\n\n\n\nimproper_dihedrals\ndict[tuple[str, str, str, str], Dihedral]\n\n\n\nposition_restraints\ndict[str, PositionRestraint]\n\n\n\ndihedral_restraints\ndict[tuple[str, str, str, str], DihedralRestraint]\n\n\n\nradicals\ndict[str, Atom]\ndict mapping atom indices to atom objects for storing all radical atoms\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nfind_radicals\nFind atoms that are radicals and update self.radicals.\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\n\n\n\ntopology.topology.MoleculeType.find_radicals()\nFind atoms that are radicals and update self.radicals.\nIterate over all atoms and designate them as radicals if they have fewer bounds than their natural bond order.\n\n\n\ntopology.topology.MoleculeType.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict, mapping of old atom number strings to new ones\n\n\n\n\n\ntopology.topology.Topology(self, top, parametrizer=BasicParameterizer(), is_reactive_predicate_f=is_not_solvent_or_ion, radicals=None, residuetypes_path=None)\nSmart container for parsed topology data.\nA topology keeps track of connections when bonds are broken or formed. Reparametrization is triggerd automatically if to_dict is called after bonds have changed.\nAssumptions:\n\nthe topology of interest (the Reactive moleculetype) consists of the first moleculetypes (non-solvent).\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nA dictionary containing the parsed topology data, produced by kimmdy.parsing.read_top\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nbind_bond\nAdd a bond in topology.\n\n\nbreak_bond\nBreak bonds in topology homolytically.\n\n\ndel_atom\nDeletes atom\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\nupdate_partial_charges\nUpdate the topology atom partial charges.\n\n\nvalidate_bond\nValidates bond consistency between both atoms and top\n\n\n\n\n\ntopology.topology.Topology.bind_bond(atompair_addresses)\nAdd a bond in topology.\nModifies the topology dictionary in place. It keeps track of affected terms in the topology via a graph representation of the topology and applies the necessary changes to bonds, angles and dihedrals (proper and improper). Furthermore, it modifies to function types in the topology to account for radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nAtoms to bind together.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.break_bond(atompair_addresses)\nBreak bonds in topology homolytically.\nRemoves bond, angles and dihedrals where atompair was involved. Modifies the topology dictionary in place. Atom pairs become radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nBetween which atoms to break the bond.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.del_atom(atom_nr, parameterize=True)\nDeletes atom\nDeletes atom and all attached bonds. Reindexes the top and updates the parameters if requested. Also moves charges to first bound_nrs atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_nr\nUnion[list[str], str]\n1-based atom number as string to delete\nrequired\n\n\nparameterize\nbool\nIf true and bonds are removed triggers reparameterization, by default True\nTrue\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nupdate_map\nDict, mapping of old atom number strings to new ones.\n\n\n\n\n\n\n\ntopology.topology.Topology.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict of all moleculetypes to their update maps (old -&gt; new).\n\n\n\ntopology.topology.Topology.update_partial_charges(recipe_steps)\nUpdate the topology atom partial charges.\nThis function must be called after the recipe_steps are applied. Changes are based on the recipe_steps. 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-    "text": "schema\nHandle the schema for the config file. To be used by the config module to validate the config file and set defaults for the Config object.\nReserved keywords: - pytype - default - description - type - required\n\n\n\n\n\nName\nDescription\n\n\n\n\nSequence\nA sequence of tasks.\n\n\n\n\n\nschema.Sequence(self, tasks)\nA sequence of tasks.\nTasks can be grouped together by using a dictionary with the following keys: - mult: number of times to repeat the tasks - tasks: list of tasks to repeat\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\ntasks\n\nlist of tasks\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nconvert_schema_to_dict\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\nflatten_scheme\nRecursively get properties and their desicripions from the scheme\n\n\ngenerate_markdown_table\nGenerate markdown table from scheme\n\n\nget_combined_scheme\nReturn the schema for the config file.\n\n\nload_kimmdy_schema\nReturn the schema for the config file\n\n\nload_plugin_schemas\nReturn the schemas for the reaction plugins known to kimmdy\n\n\nprune\nRemove empty dicts from a nested dict\n\n\n\n\n\nschema.convert_schema_to_dict(dictionary)\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndictionary\ndict\ndictionary from a raw json schema\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nnested dictionary where each leaf entry is a dictionary with the\n“pytype”, “default” and “description” keys.\n\n\n\n\n\n\n\nschema.flatten_scheme(scheme, section='')\nRecursively get properties and their desicripions from the scheme\n\n\n\nschema.generate_markdown_table(scheme, append=False)\nGenerate markdown table from scheme\nUsed in documentation generation.\n\n\n\nschema.get_combined_scheme()\nReturn the schema for the config file.\nNested scheme where each leaf entry is a dictionary with the “pytype”, “default” and “description”. Contains the schema for the main kimmdy config file and all the plugins known at runtime.\n\n\n\nschema.load_kimmdy_schema()\nReturn the schema for the config file\n\n\n\nschema.load_plugin_schemas()\nReturn the schemas for the reaction plugins known to kimmdy\n\n\n\nschema.prune(d)\nRemove empty dicts from a nested dict"
+    "text": "homolysis.reaction.Homolysis\nreaction.Homolysis(self, name, runmng)\nHomolytic bond breaking leading to 2 radicals. Implementation for time-varying rates\n\n\n\n\n Back to top",
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-    "text": "Name\nDescription\n\n\n\n\nSequence\nA sequence of tasks.\n\n\n\n\n\nschema.Sequence(self, tasks)\nA sequence of tasks.\nTasks can be grouped together by using a dictionary with the following keys: - mult: number of times to repeat the tasks - tasks: list of tasks to repeat\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\ntasks\n\nlist of tasks"
+    "text": "utils\nUtilities for building plugins, shell convenience functions and GROMACS related functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyAtomAddress\nAddress to an atom in the topology.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nget_task_directories\ncreate list of subdirectories that match the tasks.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.get_task_directories(dir, tasks='all')\ncreate list of subdirectories that match the tasks. If tasks is “all”, all subdirectories are returned.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory to search for subdirectories\nrequired\n\n\ntasks\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\n'all'\n\n\n\n\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nfrequency_factor\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\ntemperature\nfloat\nTemperature for the Arrhenius equation in GROMACS units.\n300\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired",
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-    "text": "Name\nDescription\n\n\n\n\nconvert_schema_to_dict\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\nflatten_scheme\nRecursively get properties and their desicripions from the scheme\n\n\ngenerate_markdown_table\nGenerate markdown table from scheme\n\n\nget_combined_scheme\nReturn the schema for the config file.\n\n\nload_kimmdy_schema\nReturn the schema for the config file\n\n\nload_plugin_schemas\nReturn the schemas for the reaction plugins known to kimmdy\n\n\nprune\nRemove empty dicts from a nested dict\n\n\n\n\n\nschema.convert_schema_to_dict(dictionary)\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndictionary\ndict\ndictionary from a raw json schema\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nnested dictionary where each leaf entry is a dictionary with the\n“pytype”, “default” and “description” keys.\n\n\n\n\n\n\n\nschema.flatten_scheme(scheme, section='')\nRecursively get properties and their desicripions from the scheme\n\n\n\nschema.generate_markdown_table(scheme, append=False)\nGenerate markdown table from scheme\nUsed in documentation generation.\n\n\n\nschema.get_combined_scheme()\nReturn the schema for the config file.\nNested scheme where each leaf entry is a dictionary with the “pytype”, “default” and “description”. Contains the schema for the main kimmdy config file and all the plugins known at runtime.\n\n\n\nschema.load_kimmdy_schema()\nReturn the schema for the config file\n\n\n\nschema.load_plugin_schemas()\nReturn the schemas for the reaction plugins known to kimmdy\n\n\n\nschema.prune(d)\nRemove empty dicts from a nested dict"
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-    "text": "homolysis.reaction.Homolysis\nreaction.Homolysis(self, name, runmng)\nHomolytic bond breaking leading to 2 radicals. Implementation for time-varying rates\n\n\n\n\n Back to top"
+    "text": "Name\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nget_task_directories\ncreate list of subdirectories that match the tasks.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.get_task_directories(dir, tasks='all')\ncreate list of subdirectories that match the tasks. If tasks is “all”, all subdirectories are returned.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory to search for subdirectories\nrequired\n\n\ntasks\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\n'all'\n\n\n\n\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nfrequency_factor\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\ntemperature\nfloat\nTemperature for the Arrhenius equation in GROMACS units.\n300\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired",
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-    "text": "recipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\n\n\n\nName\nDescription\n\n\n\n\nBind\nChange topology to form a bond\n\n\nBondOperation\nHandle a bond operation on the recipe step.\n\n\nBreak\nChange topology to break a bond\n\n\nCustomTopMod\nA custom recipe step that can be used to define a custom topology modification.\n\n\nPlace\nChange topology and/or coordinates to place an atom.\n\n\nRecipe\nA reaction path defined by one series of RecipeSteps.\n\n\nRecipeCollection\nA RecipeCollection encompasses a number of reaction paths.\n\n\nRecipeStep\nBase class for all RecipeSteps.\n\n\nRelax\nStart a relaxation MD.\n\n\n\n\n\nrecipe.Bind(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to form a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.BondOperation(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nHandle a bond operation on the recipe step.\nThis class takes in either zero-based indices or one-base IDs for two atoms.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf neither an index nor an ID is provided for any of the atoms.\n\n\n\n\n\n\nInternally, this class stores the atom indices and converts IDs to indices as needed.\n\n\n\n\nrecipe.Break(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to break a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.CustomTopMod(self, f)\nA custom recipe step that can be used to define a custom topology modification.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nf\nCallable[[Topology], Topology]\nA function that takes a Topology object and modifies it in place.\nrequired\n\n\n\n\n\n\n\nrecipe.Place(self, new_coords, ix_to_place=None, id_to_place=None)\nChange topology and/or coordinates to place an atom.\nEither provide the index (ix_to_place) or the ID (id_to_place) of the atom to place.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nnew_coords\ntuple[float, float, float]\nNew xyz coordinates for atom to place to. Valid for the end point of the recipe timespan.\nrequired\n\n\nix_to_place\nint\nIndex of atom to place. 0-based.\nNone\n\n\nid_to_place\nstr\nIndex of atom to place. 1-based\nNone\n\n\n\n\n\n\n\nrecipe.Recipe(self, recipe_steps, rates, timespans)\nA reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_steps\nlist[RecipeStep]\nSingle sequence of RecipeSteps to build product\nrequired\n\n\nrates\nlist[float]\nReaction rates corresponding 1:1 to timespans.\nrequired\n\n\ntimespans\nlist[list[float, float]]\nList of half-open timespans (t1, t2] in ps, at which this rate is valid. Recipe steps which change the coordinates only need to be applicable at the first time in the interval. Must have same number of timespans as rates. t1 can equal t2 for the last frame.\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_consistency\nRun consistency checks for correct size of variables\n\n\ncombine_with\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nrecipe.Recipe.check_consistency()\nRun consistency checks for correct size of variables\n\n\n\nrecipe.Recipe.combine_with(other)\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nother\nRecipe\n\nrequired\n\n\n\n\n\n\n\n\n\nrecipe.RecipeCollection(self, recipes)\nA RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nunique_recipes_ixs\nList of lists binning the old recipe indices and maps to the new recipes list.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\naggregate_reactions\nCombines reactions having the same sequence of RecipeSteps.\n\n\ncalc_cumprob\nCalculate cumulative probability of all contained recipe steps.\n\n\ncalc_ratesum\nCalculate the sum of rates over all timesteps\n\n\nfrom_csv\nCreate a RecipeCollection object from a CSV file\n\n\nplot\nPlot reaction rates over time\n\n\nto_csv\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeCollection.aggregate_reactions()\nCombines reactions having the same sequence of RecipeSteps.\n\n\n\nrecipe.RecipeCollection.calc_cumprob()\nCalculate cumulative probability of all contained recipe steps. Sums up to 1 over all recipes. Assumes constant rate for given timespan and rate zero otherwise.\n\n\n\nrecipe.RecipeCollection.calc_ratesum()\nCalculate the sum of rates over all timesteps\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nboarders\nflat list containing times of rate changes marking the boarders of the windows\n\n\nrate_windows\nflat list containing all rates in between the boarders. Each window is orderd as in recipe_windows\n\n\nrecipe_windows\nflat list containing the recipes of the corresponding window. Each window is orderd as in rate_windows\n\n\n\n\n\n\n\nrecipe.RecipeCollection.from_csv(path)\nCreate a RecipeCollection object from a CSV file Returns the recipe collection and a single recipe that was picked, otherwise None\n\n\n\nrecipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)\nPlot reaction rates over time\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\noutfile\nPath\nWhere to save the plot, must have compatible suffix.\nrequired\n\n\nhighlight_r\nRecipe\nRecipe to highlight, by default None\nNone\n\n\nhighlight_t\nfloat\nTime at which the reactions starts\nNone\n\n\n\n\n\n\n\nrecipe.RecipeCollection.to_csv(path, picked_recipe=None)\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeStep()\nBase class for all RecipeSteps. Indices can be accessed as 0-based or 1-based. ix: 0-based, int id: 1-based, str\n\n\n\nrecipe.Relax(self)\nStart a relaxation MD.\nThe molecular system coordinates are far out of equilibrium after most topology changes. A relaxtion MD simulation using for example the slow growth method helps to reach the new equilibrium."
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-    "text": "Name\nDescription\n\n\n\n\nBind\nChange topology to form a bond\n\n\nBondOperation\nHandle a bond operation on the recipe step.\n\n\nBreak\nChange topology to break a bond\n\n\nCustomTopMod\nA custom recipe step that can be used to define a custom topology modification.\n\n\nPlace\nChange topology and/or coordinates to place an atom.\n\n\nRecipe\nA reaction path defined by one series of RecipeSteps.\n\n\nRecipeCollection\nA RecipeCollection encompasses a number of reaction paths.\n\n\nRecipeStep\nBase class for all RecipeSteps.\n\n\nRelax\nStart a relaxation MD.\n\n\n\n\n\nrecipe.Bind(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to form a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.BondOperation(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nHandle a bond operation on the recipe step.\nThis class takes in either zero-based indices or one-base IDs for two atoms.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf neither an index nor an ID is provided for any of the atoms.\n\n\n\n\n\n\nInternally, this class stores the atom indices and converts IDs to indices as needed.\n\n\n\n\nrecipe.Break(self, atom_ix_1=None, atom_ix_2=None, atom_id_1=None, atom_id_2=None)\nChange topology to break a bond\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_ix_1\nint\nThe index of the first atom. zero-based, by default None\nNone\n\n\natom_ix_2\nint\nThe index of the second atom. zero-based, by default None\nNone\n\n\natom_id_1\nstr\nThe ID of the first atom. one-based, by default None\nNone\n\n\natom_id_2\nstr\nThe ID of the second atom. one-based, by default None\nNone\n\n\n\n\n\n\n\nrecipe.CustomTopMod(self, f)\nA custom recipe step that can be used to define a custom topology modification.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nf\nCallable[[Topology], Topology]\nA function that takes a Topology object and modifies it in place.\nrequired\n\n\n\n\n\n\n\nrecipe.Place(self, new_coords, ix_to_place=None, id_to_place=None)\nChange topology and/or coordinates to place an atom.\nEither provide the index (ix_to_place) or the ID (id_to_place) of the atom to place.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nnew_coords\ntuple[float, float, float]\nNew xyz coordinates for atom to place to. Valid for the end point of the recipe timespan.\nrequired\n\n\nix_to_place\nint\nIndex of atom to place. 0-based.\nNone\n\n\nid_to_place\nstr\nIndex of atom to place. 1-based\nNone\n\n\n\n\n\n\n\nrecipe.Recipe(self, recipe_steps, rates, timespans)\nA reaction path defined by one series of RecipeSteps. Defines everything necessart to build the product state from the educt state.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrecipe_steps\nlist[RecipeStep]\nSingle sequence of RecipeSteps to build product\nrequired\n\n\nrates\nlist[float]\nReaction rates corresponding 1:1 to timespans.\nrequired\n\n\ntimespans\nlist[list[float, float]]\nList of half-open timespans (t1, t2] in ps, at which this rate is valid. Recipe steps which change the coordinates only need to be applicable at the first time in the interval. Must have same number of timespans as rates. t1 can equal t2 for the last frame.\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_consistency\nRun consistency checks for correct size of variables\n\n\ncombine_with\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nrecipe.Recipe.check_consistency()\nRun consistency checks for correct size of variables\n\n\n\nrecipe.Recipe.combine_with(other)\nCombines this Recipe with another with the same RecipeSteps.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nother\nRecipe\n\nrequired\n\n\n\n\n\n\n\n\n\nrecipe.RecipeCollection(self, recipes)\nA RecipeCollection encompasses a number of reaction paths. They can originate from multiple reaction plugins, but do not need to.\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nunique_recipes_ixs\nList of lists binning the old recipe indices and maps to the new recipes list.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\naggregate_reactions\nCombines reactions having the same sequence of RecipeSteps.\n\n\ncalc_cumprob\nCalculate cumulative probability of all contained recipe steps.\n\n\ncalc_ratesum\nCalculate the sum of rates over all timesteps\n\n\nfrom_csv\nCreate a RecipeCollection object from a CSV file\n\n\nplot\nPlot reaction rates over time\n\n\nto_csv\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeCollection.aggregate_reactions()\nCombines reactions having the same sequence of RecipeSteps.\n\n\n\nrecipe.RecipeCollection.calc_cumprob()\nCalculate cumulative probability of all contained recipe steps. Sums up to 1 over all recipes. Assumes constant rate for given timespan and rate zero otherwise.\n\n\n\nrecipe.RecipeCollection.calc_ratesum()\nCalculate the sum of rates over all timesteps\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nboarders\nflat list containing times of rate changes marking the boarders of the windows\n\n\nrate_windows\nflat list containing all rates in between the boarders. Each window is orderd as in recipe_windows\n\n\nrecipe_windows\nflat list containing the recipes of the corresponding window. Each window is orderd as in rate_windows\n\n\n\n\n\n\n\nrecipe.RecipeCollection.from_csv(path)\nCreate a RecipeCollection object from a CSV file Returns the recipe collection and a single recipe that was picked, otherwise None\n\n\n\nrecipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)\nPlot reaction rates over time\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\noutfile\nPath\nWhere to save the plot, must have compatible suffix.\nrequired\n\n\nhighlight_r\nRecipe\nRecipe to highlight, by default None\nNone\n\n\nhighlight_t\nfloat\nTime at which the reactions starts\nNone\n\n\n\n\n\n\n\nrecipe.RecipeCollection.to_csv(path, picked_recipe=None)\nWrite a ReactionResult as defined in the reaction module to a csv file\n\n\n\n\n\nrecipe.RecipeStep()\nBase class for all RecipeSteps. 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-    "text": "analysis\nAnalysis tools for KIMMDY runs. For command line usage, run kimmdy-analysis -h.\n\n\n\n\n\nName\nDescription\n\n\n\n\nconcat_traj\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.\n\n\nentry_point_analysis\nAnalyse existing KIMMDY runs.\n\n\nget_analysis_cmdline_args\nParse command line arguments.\n\n\nget_analysis_dir\nGet analysis directory for a KIMMDY run.\n\n\nplot_energy\nPlot GROMACS energy for a KIMMDY run.\n\n\nplot_rates\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\nplot_runtime\nPlot runtime of all tasks.\n\n\nradical_migration\nPlot population of radicals for a KIMMDY run.\n\n\nradical_population\nPlot population of radicals for a KIMMDY run.\n\n\nreaction_participation\nPlot which atoms participate in reactions.\n\n\n\n\n\nanalysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\nrequired\n\n\nopen_vmd\nbool\nOpen concatenated trajectory in VMD\nFalse\n\n\noutput_group\nOptional[str]\nindex group for output. Default is “Protein” for xtc and “System” for trr.\nNone\n\n\n\n\n\n\n\nanalysis.entry_point_analysis()\nAnalyse existing KIMMDY runs.\n\n\n\nanalysis.get_analysis_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\nanalysis.get_analysis_dir(dir)\nGet analysis directory for a KIMMDY run.\nCreates the directory if it does not exist.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPath to analysis directory\n\n\n\n\n\n\n\n\nanalysis.plot_energy(dir, steps, terms, open_plot=False)\nPlot GROMACS energy for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\nrequired\n\n\nterms\nlist[str]\nTerms from gmx energy that will be plotted. Uses ‘Potential’ by default.\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.plot_rates(dir)\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\nanalysis.plot_runtime(dir, md_tasks, datefmt, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nmd_tasks\nlist\nNames of MD tasks to color\nrequired\n\n\ndatefmt\nstr\nDate format in the KIMMDY logfile\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.radical_migration(dirs, type='qualitative', cutoff=1)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndirs\nlist[str]\nKIMMDY run directories to be analysed.\nrequired\n\n\ntype\nstr\nHow to analyse radical migration. Available are ‘qualitative’,‘occurence’ and ‘min_rate’“,\n'qualitative'\n\n\ncutoff\nint\nIgnore migration between two atoms if it happened less often than the specified value.\n1\n\n\n\n\n\n\n\nanalysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nKIMMDY run directory to be analysed.\nrequired\n\n\npopulation_type\nstr\nHow to calculate the fractional radical occupancy. Available are ‘frequency’ and ‘time’\n'frequency'\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\n'all'\n\n\nselect_atoms\nstr\nAtoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax)\n'protein'\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\nopen_vmd\nbool\nOpen a pdb in VMD with the radical occupation as B-factors.\nFalse\n\n\n\n\n\n\n\nanalysis.reaction_participation(dir, open_plot=False)\nPlot which atoms participate in reactions.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse"
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-    "text": "Name\nDescription\n\n\n\n\nconcat_traj\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.\n\n\nentry_point_analysis\nAnalyse existing KIMMDY runs.\n\n\nget_analysis_cmdline_args\nParse command line arguments.\n\n\nget_analysis_dir\nGet analysis directory for a KIMMDY run.\n\n\nplot_energy\nPlot GROMACS energy for a KIMMDY run.\n\n\nplot_rates\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\nplot_runtime\nPlot runtime of all tasks.\n\n\nradical_migration\nPlot population of radicals for a KIMMDY run.\n\n\nradical_population\nPlot population of radicals for a KIMMDY run.\n\n\nreaction_participation\nPlot which atoms participate in reactions.\n\n\n\n\n\nanalysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\nrequired\n\n\nopen_vmd\nbool\nOpen concatenated trajectory in VMD\nFalse\n\n\noutput_group\nOptional[str]\nindex group for output. Default is “Protein” for xtc and “System” for trr.\nNone\n\n\n\n\n\n\n\nanalysis.entry_point_analysis()\nAnalyse existing KIMMDY runs.\n\n\n\nanalysis.get_analysis_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\nanalysis.get_analysis_dir(dir)\nGet analysis directory for a KIMMDY run.\nCreates the directory if it does not exist.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPath to analysis directory\n\n\n\n\n\n\n\n\nanalysis.plot_energy(dir, steps, terms, open_plot=False)\nPlot GROMACS energy for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\nrequired\n\n\nterms\nlist[str]\nTerms from gmx energy that will be plotted. Uses ‘Potential’ by default.\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.plot_rates(dir)\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\nanalysis.plot_runtime(dir, md_tasks, datefmt, open_plot=False)\nPlot runtime of all tasks.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nmd_tasks\nlist\nNames of MD tasks to color\nrequired\n\n\ndatefmt\nstr\nDate format in the KIMMDY logfile\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.radical_migration(dirs, type='qualitative', cutoff=1)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndirs\nlist[str]\nKIMMDY run directories to be analysed.\nrequired\n\n\ntype\nstr\nHow to analyse radical migration. Available are ‘qualitative’,‘occurence’ and ‘min_rate’“,\n'qualitative'\n\n\ncutoff\nint\nIgnore migration between two atoms if it happened less often than the specified value.\n1\n\n\n\n\n\n\n\nanalysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nKIMMDY run directory to be analysed.\nrequired\n\n\npopulation_type\nstr\nHow to calculate the fractional radical occupancy. Available are ‘frequency’ and ‘time’\n'frequency'\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\n'all'\n\n\nselect_atoms\nstr\nAtoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax)\n'protein'\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\nopen_vmd\nbool\nOpen a pdb in VMD with the radical occupation as B-factors.\nFalse\n\n\n\n\n\n\n\nanalysis.reaction_participation(dir, open_plot=False)\nPlot which atoms participate in reactions.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse"
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-    "text": "hat_naive.reaction.NaiveHAT\nreaction.NaiveHAT(self, name, runmng)\nNaive HAT reaction, selects hydrogens at random\n\n\n\n\n Back to top"
+    "text": "Topology modules\n\n\n\ntopology.topology\n\n\n\ntopology.ff\n\n\n\ntopology.utils\n\n\n\ntopology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc.\n\n\nparsing.TopologyDict\nA raw representation of a topology file returned by read_top.",
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-    "text": "topology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc. The order of the fields comes from the gromacs topology file format. See gromacs manual\n\n\n\n\n\nName\nDescription\n\n\n\n\nAngle\nInformation about one angle\n\n\nAngleType\nInformation about one angletype\n\n\nAtom\nInformation about one atom\n\n\nAtomType\nInformation about one atom type\n\n\nBond\nInformation about one bond\n\n\nBondType\nInformation about one bondtype\n\n\nDihedral\nInformation about one proper or improper dihedral\n\n\nDihedralRestraint\nInformation about one dihedral restraint.\n\n\nDihedralType\nInformation about one dihedraltype\n\n\nExclusion\nInformation about one exclusion\n\n\nMultipleDihedralTypes\nMultiple DihedralTypess with the same ai, aj, ak, al\n\n\nMultipleDihedrals\nMultiple Dihedrals with the same ai, aj, ak, al\n\n\nPair\nInformation about one pair\n\n\nPositionRestraint\nInformation about one position restraint.\n\n\nResidueAtomSpec\nInformation about one atom in a residue\n\n\nResidueBondSpec\nInformation about one bond in a residue\n\n\nResidueImproperSpec\nInformation about one improper dihedral in a residue\n\n\nResidueProperSpec\nInformation about one proper dihedral in a residue\n\n\nResidueType\nInformation about one residuetype from aminoacids.rtp\n\n\nSettle\nInformation about one settles\n\n\n\n\n\ntopology.atomic.Angle(self, ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angle\nA class containing angle information as in the angles section of the topology.\nFrom gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj &lt; ai &lt; ak\n\n\n\ntopology.atomic.AngleType(self, i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angletype\nA class containing angle type information as in the angletypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j k func th0 cth\n\n\n\ntopology.atomic.Atom(self, nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=list(), is_radical=False)\nInformation about one atom\nA class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.\nFrom gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n\n\n\ntopology.atomic.AtomType(self, type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)\nInformation about one atom type\nA class containing atom type information as in the atomtypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon\n\n\n\ntopology.atomic.Bond(self, ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)\nInformation about one bond\nA class containing bond information as in the bonds section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai &lt; aj\n\n\n\ntopology.atomic.BondType(self, i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one bondtype\nA class containing bond information as in the bondtype section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes\n\n\n\ntopology.atomic.Dihedral(self, ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)\nInformation about one proper or improper dihedral\nA class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.\nFrom gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj &lt; ak\n\n\n\ntopology.atomic.DihedralRestraint(self, ai, aj, ak, al, type, phi, dphi, fc)\nInformation about one dihedral restraint.\nA class containing information as in the dihedral_restraints section of the topology.\nFrom gromacs topology: ; ai aj ak al type phi dphi fc\n\n\n\ntopology.atomic.DihedralType(self, i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)\nInformation about one dihedraltype\nA class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.\nFrom gromacs version of the amber* ff: ; i j k l func phase kd pn\n\n\n\ntopology.atomic.Exclusion(self, ai, aj, ak=None, al=None)\nInformation about one exclusion\nA class containing atom information as in the exclusions section of the topology.\nFrom gromacs topology: ; ai aj ak al\n\n\n\ntopology.atomic.MultipleDihedralTypes(self, ai, aj, ak, al, funct, dihedral_types)\nMultiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedral_types dict is the periodicity (c2).\n\n\n\ntopology.atomic.MultipleDihedrals(self, ai, aj, ak, al, funct, dihedrals)\nMultiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedrals dict is the periodicity (c2).\n\n\n\ntopology.atomic.Pair(self, ai, aj, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one pair\nA class containing pair information as in the pair section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3\n\n\n\ntopology.atomic.PositionRestraint(self, ai, funct, fc, condition=None)\nInformation about one position restraint.\nA class containing information as in the position_restraints section of the topology.\nFrom gromacs topology: ; ai funct fc(x,y,z)\n\n\n\ntopology.atomic.ResidueAtomSpec(self, name, type, charge, cgrp)\nInformation about one atom in a residue\n; name type charge chargegroup\n\n\n\ntopology.atomic.ResidueBondSpec(self, atom1, atom2, b0=None, kb=None)\nInformation about one bond in a residue\n; atom1 atom2 b0 kb\n\n\n\ntopology.atomic.ResidueImproperSpec(self, atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one improper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)\n\n\n\ntopology.atomic.ResidueProperSpec(self, atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one proper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2\n\n\n\ntopology.atomic.ResidueType(self, residue, atoms, bonds, proper_dihedrals, improper_dihedrals)\nInformation about one residuetype from aminoacids.rtp\n\n\n\ntopology.atomic.Settle(self, nr, funct, doh, dhh)\nInformation about one settles\nA class containing atom information as in the settle section of the topology.\nFrom gromacs topology: ; nr funct doh dhh"
+    "text": "Modules\n\n\n\nanalysis\nAnalysis tools for KIMMDY runs.\n\n\ncmd\nFunctions for starting KIMMDY either from python or the command line.\n\n\nconfig\nRead and validate kimmdy.yml configuration files\n\n\nconstants\nComstants used throughout KIMMDY\n\n\ncoordinates\ncoordinate, topology and plumed modification functions\n\n\nkmc\nKinetic Monte Carlo (KMC) classes and functions.\n\n\nparsing\nAll read_&lt;…&gt; and write_&lt;…&gt; functions.\n\n\nplugins\nPlugin base classes and basic instances thereof.\n\n\nrecipe\nContains the Reaction Recipe, RecipeStep and RecipeCollection.\n\n\nrunmanager\nThe Runmanager is the main entry point of the program.\n\n\nschema\nHandle the schema for the config file.\n\n\ntasks\nThe tasks module holds the TaskFiles class which organizes input and\n\n\ntools\nStandalone tools that are complementary to KIMMDY.\n\n\nutils\nUtilities for building plugins, shell convenience functions and GROMACS related functions",
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+    "text": "Reaction plugins bundled with KIMMDY and the protocol to add a new reaction plugin to KIMMDY\n\n\n\nhomolysis.reaction.Homolysis\nHomolytic bond breaking leading to 2 radicals.\n\n\nhat_naive.reaction.NaiveHAT\nNaive HAT reaction, selects hydrogens at random\n\n\ndummyreaction.reaction.DummyReaction\nDummy reaction, returns empty RecipeCollection",
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-    "text": "Name\nDescription\n\n\n\n\nAngle\nInformation about one angle\n\n\nAngleType\nInformation about one angletype\n\n\nAtom\nInformation about one atom\n\n\nAtomType\nInformation about one atom type\n\n\nBond\nInformation about one bond\n\n\nBondType\nInformation about one bondtype\n\n\nDihedral\nInformation about one proper or improper dihedral\n\n\nDihedralRestraint\nInformation about one dihedral restraint.\n\n\nDihedralType\nInformation about one dihedraltype\n\n\nExclusion\nInformation about one exclusion\n\n\nMultipleDihedralTypes\nMultiple DihedralTypess with the same ai, aj, ak, al\n\n\nMultipleDihedrals\nMultiple Dihedrals with the same ai, aj, ak, al\n\n\nPair\nInformation about one pair\n\n\nPositionRestraint\nInformation about one position restraint.\n\n\nResidueAtomSpec\nInformation about one atom in a residue\n\n\nResidueBondSpec\nInformation about one bond in a residue\n\n\nResidueImproperSpec\nInformation about one improper dihedral in a residue\n\n\nResidueProperSpec\nInformation about one proper dihedral in a residue\n\n\nResidueType\nInformation about one residuetype from aminoacids.rtp\n\n\nSettle\nInformation about one settles\n\n\n\n\n\ntopology.atomic.Angle(self, ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angle\nA class containing angle information as in the angles section of the topology.\nFrom gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj &lt; ai &lt; ak\n\n\n\ntopology.atomic.AngleType(self, i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angletype\nA class containing angle type information as in the angletypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j k func th0 cth\n\n\n\ntopology.atomic.Atom(self, nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=list(), is_radical=False)\nInformation about one atom\nA class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.\nFrom gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n\n\n\ntopology.atomic.AtomType(self, type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)\nInformation about one atom type\nA class containing atom type information as in the atomtypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon\n\n\n\ntopology.atomic.Bond(self, ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)\nInformation about one bond\nA class containing bond information as in the bonds section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai &lt; aj\n\n\n\ntopology.atomic.BondType(self, i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one bondtype\nA class containing bond information as in the bondtype section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes\n\n\n\ntopology.atomic.Dihedral(self, ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)\nInformation about one proper or improper dihedral\nA class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.\nFrom gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj &lt; ak\n\n\n\ntopology.atomic.DihedralRestraint(self, ai, aj, ak, al, type, phi, dphi, fc)\nInformation about one dihedral restraint.\nA class containing information as in the dihedral_restraints section of the topology.\nFrom gromacs topology: ; ai aj ak al type phi dphi fc\n\n\n\ntopology.atomic.DihedralType(self, i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)\nInformation about one dihedraltype\nA class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.\nFrom gromacs version of the amber* ff: ; i j k l func phase kd pn\n\n\n\ntopology.atomic.Exclusion(self, ai, aj, ak=None, al=None)\nInformation about one exclusion\nA class containing atom information as in the exclusions section of the topology.\nFrom gromacs topology: ; ai aj ak al\n\n\n\ntopology.atomic.MultipleDihedralTypes(self, ai, aj, ak, al, funct, dihedral_types)\nMultiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedral_types dict is the periodicity (c2).\n\n\n\ntopology.atomic.MultipleDihedrals(self, ai, aj, ak, al, funct, dihedrals)\nMultiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedrals dict is the periodicity (c2).\n\n\n\ntopology.atomic.Pair(self, ai, aj, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one pair\nA class containing pair information as in the pair section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3\n\n\n\ntopology.atomic.PositionRestraint(self, ai, funct, fc, condition=None)\nInformation about one position restraint.\nA class containing information as in the position_restraints section of the topology.\nFrom gromacs topology: ; ai funct fc(x,y,z)\n\n\n\ntopology.atomic.ResidueAtomSpec(self, name, type, charge, cgrp)\nInformation about one atom in a residue\n; name type charge chargegroup\n\n\n\ntopology.atomic.ResidueBondSpec(self, atom1, atom2, b0=None, kb=None)\nInformation about one bond in a residue\n; atom1 atom2 b0 kb\n\n\n\ntopology.atomic.ResidueImproperSpec(self, atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one improper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)\n\n\n\ntopology.atomic.ResidueProperSpec(self, atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one proper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2\n\n\n\ntopology.atomic.ResidueType(self, residue, atoms, bonds, proper_dihedrals, improper_dihedrals)\nInformation about one residuetype from aminoacids.rtp\n\n\n\ntopology.atomic.Settle(self, nr, funct, doh, dhh)\nInformation about one settles\nA class containing atom information as in the settle section of the topology.\nFrom gromacs topology: ; nr funct doh dhh"
+    "text": "cmd\nFunctions for starting KIMMDY either from python or the command line. Other entry points such as kimmdy-analysis also live here.\n\n\n\n\n\nName\nDescription\n\n\n\n\nconfigure_logger\nConfigure logging.\n\n\nentry_point_kimmdy\nRun KIMMDY from the command line.\n\n\nget_cmdline_args\nParse command line arguments.\n\n\nkimmdy_run\nRun KIMMDY from python.\n\n\n\n\n\ncmd.configure_logger(config)\nConfigure logging.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nconfig\nConfig\nconfiguration that contains log.level and log.file\nrequired\n\n\n\n\n\n\n\ncmd.entry_point_kimmdy()\nRun KIMMDY from the command line.\nThe configuration is gathered from the input file, which is kimmdy.yml by default. See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\ncmd.get_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\ncmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, show_plugins=False, generate_jobscript=False, debug=False, callgraph=False)\nRun KIMMDY from python.\nAlso see See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput\nPath\nkimmdy input yml file.\nPath('kimmdy.yml')\n\n\nloglevel\nOptional[str]\nLoglevel. One of [“INFO”, “WARNING”, “MESSAGE”, “DEBUG”]\nNone\n\n\nlogfile\nOptional[Path]\nFile path of the logfile.\nNone\n\n\nshow_plugins\nbool\nShow available plugins and exit.\nFalse\n\n\ngenerate_jobscript\nbool\nInstead of running KIMMDY directly, generate at jobscript.sh for slurm HPC clusters\nFalse",
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+    "text": "Name\nDescription\n\n\n\n\nconfigure_logger\nConfigure logging.\n\n\nentry_point_kimmdy\nRun KIMMDY from the command line.\n\n\nget_cmdline_args\nParse command line arguments.\n\n\nkimmdy_run\nRun KIMMDY from python.\n\n\n\n\n\ncmd.configure_logger(config)\nConfigure logging.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nconfig\nConfig\nconfiguration that contains log.level and log.file\nrequired\n\n\n\n\n\n\n\ncmd.entry_point_kimmdy()\nRun KIMMDY from the command line.\nThe configuration is gathered from the input file, which is kimmdy.yml by default. See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\ncmd.get_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\ncmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, show_plugins=False, generate_jobscript=False, debug=False, callgraph=False)\nRun KIMMDY from python.\nAlso see See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput\nPath\nkimmdy input yml file.\nPath('kimmdy.yml')\n\n\nloglevel\nOptional[str]\nLoglevel. One of [“INFO”, “WARNING”, “MESSAGE”, “DEBUG”]\nNone\n\n\nlogfile\nOptional[Path]\nFile path of the logfile.\nNone\n\n\nshow_plugins\nbool\nShow available plugins and exit.\nFalse\n\n\ngenerate_jobscript\nbool\nInstead of running KIMMDY directly, generate at jobscript.sh for slurm HPC clusters\nFalse",
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+    "text": "topology.topology\n\n\n\n\n\nName\nDescription\n\n\n\n\nMoleculeType\nOne moleculetype in the topology\n\n\nTopology\nSmart container for parsed topology data.\n\n\n\n\n\ntopology.topology.MoleculeType(self, header, atomics, radicals=None)\nOne moleculetype in the topology\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\natoms\ndict[str, Atom]\n\n\n\nbonds\ndict[tuple[str, str], Bond]\n\n\n\npairs\ndict[tuple[str, str], Pair]\n\n\n\nangles\ndict[tuple[str, str, str], Angle]\n\n\n\nproper_dihedrals\ndict[tuple[str, str, str, str], MultipleDihedrals]\n\n\n\nimproper_dihedrals\ndict[tuple[str, str, str, str], Dihedral]\n\n\n\nposition_restraints\ndict[str, PositionRestraint]\n\n\n\ndihedral_restraints\ndict[tuple[str, str, str, str], DihedralRestraint]\n\n\n\nradicals\ndict[str, Atom]\ndict mapping atom indices to atom objects for storing all radical atoms\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nfind_radicals\nFind atoms that are radicals and update self.radicals.\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\n\n\n\ntopology.topology.MoleculeType.find_radicals()\nFind atoms that are radicals and update self.radicals.\nIterate over all atoms and designate them as radicals if they have fewer bounds than their natural bond order.\n\n\n\ntopology.topology.MoleculeType.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict, mapping of old atom number strings to new ones\n\n\n\n\n\ntopology.topology.Topology(self, top, parametrizer=BasicParameterizer(), is_reactive_predicate_f=is_not_solvent_or_ion, radicals=None, residuetypes_path=None)\nSmart container for parsed topology data.\nA topology keeps track of connections when bonds are broken or formed. Reparametrization is triggerd automatically if to_dict is called after bonds have changed.\nAssumptions:\n\nthe topology of interest (the Reactive moleculetype) consists of the first moleculetypes (non-solvent).\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nA dictionary containing the parsed topology data, produced by kimmdy.parsing.read_top\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nbind_bond\nAdd a bond in topology.\n\n\nbreak_bond\nBreak bonds in topology homolytically.\n\n\ndel_atom\nDeletes atom\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\nupdate_partial_charges\nUpdate the topology atom partial charges.\n\n\nvalidate_bond\nValidates bond consistency between both atoms and top\n\n\n\n\n\ntopology.topology.Topology.bind_bond(atompair_addresses)\nAdd a bond in topology.\nModifies the topology dictionary in place. It keeps track of affected terms in the topology via a graph representation of the topology and applies the necessary changes to bonds, angles and dihedrals (proper and improper). Furthermore, it modifies to function types in the topology to account for radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nAtoms to bind together.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.break_bond(atompair_addresses)\nBreak bonds in topology homolytically.\nRemoves bond, angles and dihedrals where atompair was involved. Modifies the topology dictionary in place. Atom pairs become radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nBetween which atoms to break the bond.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.del_atom(atom_nr, parameterize=True)\nDeletes atom\nDeletes atom and all attached bonds. Reindexes the top and updates the parameters if requested. Also moves charges to first bound_nrs atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_nr\nUnion[list[str], str]\n1-based atom number as string to delete\nrequired\n\n\nparameterize\nbool\nIf true and bonds are removed triggers reparameterization, by default True\nTrue\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nupdate_map\nDict, mapping of old atom number strings to new ones.\n\n\n\n\n\n\n\ntopology.topology.Topology.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict of all moleculetypes to their update maps (old -&gt; new).\n\n\n\ntopology.topology.Topology.update_partial_charges(recipe_steps)\nUpdate the topology atom partial charges.\nThis function must be called after the recipe_steps are applied. Changes are based on the recipe_steps. Update rules follow a simple assignment scheme that works well with grappa. If fragments are created, their partial charges are kept integers. If previously broken bonds are formed again, the original partial charges are restored.\n\n\n\ntopology.topology.Topology.validate_bond(atm1, atm2)\nValidates bond consistency between both atoms and top Returns True if bond exists, False if not. Raises RuntimeError if bond is not consistent.",
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+    "text": "Name\nDescription\n\n\n\n\nMoleculeType\nOne moleculetype in the topology\n\n\nTopology\nSmart container for parsed topology data.\n\n\n\n\n\ntopology.topology.MoleculeType(self, header, atomics, radicals=None)\nOne moleculetype in the topology\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\natoms\ndict[str, Atom]\n\n\n\nbonds\ndict[tuple[str, str], Bond]\n\n\n\npairs\ndict[tuple[str, str], Pair]\n\n\n\nangles\ndict[tuple[str, str, str], Angle]\n\n\n\nproper_dihedrals\ndict[tuple[str, str, str, str], MultipleDihedrals]\n\n\n\nimproper_dihedrals\ndict[tuple[str, str, str, str], Dihedral]\n\n\n\nposition_restraints\ndict[str, PositionRestraint]\n\n\n\ndihedral_restraints\ndict[tuple[str, str, str, str], DihedralRestraint]\n\n\n\nradicals\ndict[str, Atom]\ndict mapping atom indices to atom objects for storing all radical atoms\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nfind_radicals\nFind atoms that are radicals and update self.radicals.\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\n\n\n\ntopology.topology.MoleculeType.find_radicals()\nFind atoms that are radicals and update self.radicals.\nIterate over all atoms and designate them as radicals if they have fewer bounds than their natural bond order.\n\n\n\ntopology.topology.MoleculeType.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict, mapping of old atom number strings to new ones\n\n\n\n\n\ntopology.topology.Topology(self, top, parametrizer=BasicParameterizer(), is_reactive_predicate_f=is_not_solvent_or_ion, radicals=None, residuetypes_path=None)\nSmart container for parsed topology data.\nA topology keeps track of connections when bonds are broken or formed. Reparametrization is triggerd automatically if to_dict is called after bonds have changed.\nAssumptions:\n\nthe topology of interest (the Reactive moleculetype) consists of the first moleculetypes (non-solvent).\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nA dictionary containing the parsed topology data, produced by kimmdy.parsing.read_top\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nbind_bond\nAdd a bond in topology.\n\n\nbreak_bond\nBreak bonds in topology homolytically.\n\n\ndel_atom\nDeletes atom\n\n\nreindex_atomnrs\nReindex atom numbers in topology.\n\n\nupdate_partial_charges\nUpdate the topology atom partial charges.\n\n\nvalidate_bond\nValidates bond consistency between both atoms and top\n\n\n\n\n\ntopology.topology.Topology.bind_bond(atompair_addresses)\nAdd a bond in topology.\nModifies the topology dictionary in place. It keeps track of affected terms in the topology via a graph representation of the topology and applies the necessary changes to bonds, angles and dihedrals (proper and improper). Furthermore, it modifies to function types in the topology to account for radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nAtoms to bind together.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.break_bond(atompair_addresses)\nBreak bonds in topology homolytically.\nRemoves bond, angles and dihedrals where atompair was involved. Modifies the topology dictionary in place. Atom pairs become radicals.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natompair_addresses\ntuple[TopologyAtomAddress, TopologyAtomAddress]\nBetween which atoms to break the bond.\nrequired\n\n\n\n\n\n\n\ntopology.topology.Topology.del_atom(atom_nr, parameterize=True)\nDeletes atom\nDeletes atom and all attached bonds. Reindexes the top and updates the parameters if requested. Also moves charges to first bound_nrs atom.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natom_nr\nUnion[list[str], str]\n1-based atom number as string to delete\nrequired\n\n\nparameterize\nbool\nIf true and bonds are removed triggers reparameterization, by default True\nTrue\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nupdate_map\nDict, mapping of old atom number strings to new ones.\n\n\n\n\n\n\n\ntopology.topology.Topology.reindex_atomnrs()\nReindex atom numbers in topology.\nStarts at index 1. This also updates the numbers for bonds, angles, dihedrals and pairs. Returns a dict of all moleculetypes to their update maps (old -&gt; new).\n\n\n\ntopology.topology.Topology.update_partial_charges(recipe_steps)\nUpdate the topology atom partial charges.\nThis function must be called after the recipe_steps are applied. Changes are based on the recipe_steps. 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-    "text": "Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)\n\n\nNote: KIMMDY requires GROMACS to be installed. Some reactions need a GROMACS version patched with PLUMED. The gromacs version name should then contain MODIFIED or plumed.\npip install kimmdy\nThis installation includes only the most basic functionality as no plugins and analysis tools are installed.\nTo install the builtin reaction plugins, use\npip install kimmdy[reactions]\nTo install the builtin reactions and analysis tools use\npip install kimmdy[reactions,analysis]\nHowever, this is only half the fun!\nKIMMDY has two exciting plugins in the making, which properly parameterize your molecules for radicals using GrAPPa (Graph Attentional Protein Parametrization) and predict Hydrogen Atom Transfer (HAT) rates. Full installation instructions are available here\n\n\n\nThe documentation is available here.\n\n\n\nHead over to the getting started tutorial.\n\n\n\n\n\nClone kimmdy and the default reaction and parameterization plugins and install requirements and kimmdy as editable via\ngit clone git@github.com:hits-mbm-dev/kimmdy.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-reactions.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-grappa.git\ncd kimmdy\npython -m venv .venv\nsource ./venv/bin/activate\npip install -r requirements.txt\nConventions:\n\ncode style: black\ndocstrings: numpy\nConventional commit messages when possible for pretty release notes.\n\n\n\n\nFor developoment, we provide a docker image containing gromacs and multiple python versions to test against.\nTo run the test locally, you must:\n\ninstall docker\ninstall act, the easiest option is with github cli via gh extension install https://github.com/nektos/gh-act\nrun tests with gh extension exec act -j test --artifact-server-path ./artifacts\nhtml coverage report is exported into artifacts"
+    "text": "Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)\n\n\nNote: KIMMDY requires GROMACS to be installed. Some reactions need a GROMACS version patched with PLUMED. The gromacs version name should then contain MODIFIED or plumed.\npip install kimmdy\nThis installation includes only the most basic functionality as no plugins and analysis tools are installed.\nTo install the builtin reaction plugins, use\npip install kimmdy[reactions]\nTo install the builtin reactions and analysis tools use\npip install kimmdy[reactions,analysis]\nHowever, this is only half the fun!\nKIMMDY has two exciting plugins in the making, which properly parameterize your molecules for radicals using GrAPPa (Graph Attentional Protein Parametrization) and predict Hydrogen Atom Transfer (HAT) rates. Full installation instructions are available here\n\n\n\nThe documentation is available here.\n\n\n\nHead over to the getting started tutorial.\n\n\n\n\n\nClone kimmdy and the default reaction and parameterization plugins and install requirements and kimmdy as editable via\ngit clone git@github.com:hits-mbm-dev/kimmdy.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-reactions.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-grappa.git\ncd kimmdy\npython -m venv .venv\nsource ./venv/bin/activate\npip install -r requirements.txt\nConventions:\n\ncode style: black\ndocstrings: numpy\nConventional commit messages when possible for pretty release notes.\n\n\n\n\nFor developoment, we provide a docker image containing gromacs and multiple python versions to test against.\nTo run the test locally, you must:\n\ninstall docker\ninstall act, the easiest option is with github cli via gh extension install https://github.com/nektos/gh-act\nrun tests with gh extension exec act -j test --artifact-server-path ./artifacts\nhtml coverage report is exported into artifacts",
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-    "text": "Note: KIMMDY requires GROMACS to be installed. Some reactions need a GROMACS version patched with PLUMED. The gromacs version name should then contain MODIFIED or plumed.\npip install kimmdy\nThis installation includes only the most basic functionality as no plugins and analysis tools are installed.\nTo install the builtin reaction plugins, use\npip install kimmdy[reactions]\nTo install the builtin reactions and analysis tools use\npip install kimmdy[reactions,analysis]\nHowever, this is only half the fun!\nKIMMDY has two exciting plugins in the making, which properly parameterize your molecules for radicals using GrAPPa (Graph Attentional Protein Parametrization) and predict Hydrogen Atom Transfer (HAT) rates. Full installation instructions are available here"
+    "text": "Note: KIMMDY requires GROMACS to be installed. Some reactions need a GROMACS version patched with PLUMED. The gromacs version name should then contain MODIFIED or plumed.\npip install kimmdy\nThis installation includes only the most basic functionality as no plugins and analysis tools are installed.\nTo install the builtin reaction plugins, use\npip install kimmdy[reactions]\nTo install the builtin reactions and analysis tools use\npip install kimmdy[reactions,analysis]\nHowever, this is only half the fun!\nKIMMDY has two exciting plugins in the making, which properly parameterize your molecules for radicals using GrAPPa (Graph Attentional Protein Parametrization) and predict Hydrogen Atom Transfer (HAT) rates. Full installation instructions are available here",
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-    "text": "Head over to the getting started tutorial."
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-    "text": "Clone kimmdy and the default reaction and parameterization plugins and install requirements and kimmdy as editable via\ngit clone git@github.com:hits-mbm-dev/kimmdy.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-reactions.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-grappa.git\ncd kimmdy\npython -m venv .venv\nsource ./venv/bin/activate\npip install -r requirements.txt\nConventions:\n\ncode style: black\ndocstrings: numpy\nConventional commit messages when possible for pretty release notes.\n\n\n\n\nFor developoment, we provide a docker image containing gromacs and multiple python versions to test against.\nTo run the test locally, you must:\n\ninstall docker\ninstall act, the easiest option is with github cli via gh extension install https://github.com/nektos/gh-act\nrun tests with gh extension exec act -j test --artifact-server-path ./artifacts\nhtml coverage report is exported into artifacts"
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-    "text": "dummyreaction.reaction.DummyReaction\nreaction.DummyReaction(self, name, runmng)\nDummy reaction, returns empty RecipeCollection\n\n\n\n\n Back to top"
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-    "text": "constants\nComstants used throughout KIMMDY\n\n\n\n\n\nName\nDescription\n\n\n\n\nATOMTYPE_BONDORDER\nTo determin if an atom is a radical.\n\n\nATOMTYPE_BONDORDER_FLAT\nTo determin if an atom is a radical."
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-    "text": "Name\nDescription\n\n\n\n\nATOMTYPE_BONDORDER\nTo determin if an atom is a radical.\n\n\nATOMTYPE_BONDORDER_FLAT\nTo determin if an atom is a radical."
+    "text": "Clone kimmdy and the default reaction and parameterization plugins and install requirements and kimmdy as editable via\ngit clone git@github.com:hits-mbm-dev/kimmdy.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-reactions.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-grappa.git\ncd kimmdy\npython -m venv .venv\nsource ./venv/bin/activate\npip install -r requirements.txt\nConventions:\n\ncode style: black\ndocstrings: numpy\nConventional commit messages when possible for pretty release notes.\n\n\n\n\nFor developoment, we provide a docker image containing gromacs and multiple python versions to test against.\nTo run the test locally, you must:\n\ninstall docker\ninstall act, the easiest option is with github cli via gh extension install https://github.com/nektos/gh-act\nrun tests with gh extension exec act -j test --artifact-server-path ./artifacts\nhtml coverage report is exported into artifacts",
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-    "text": "tasks\nThe tasks module holds the TaskFiles class which organizes input and output paths and the Task class for steps in the runmanager.\n\n\n\n\n\nName\nDescription\n\n\n\n\nAutoFillDict\nDictionary that gets populated by calling get_missing.\n\n\nTask\nA task to be performed as as a step in the RunManager.\n\n\nTaskFiles\nClass for Task input and output files and directories.\n\n\n\n\n\ntasks.AutoFillDict(self, get_missing)\nDictionary that gets populated by calling get_missing.\n\n\n\ntasks.Task(self, runmng, f, kwargs=None, out=None)\nA task to be performed as as a step in the RunManager.\nA task consists of a function and its keyword arguments. Calling a taks calls the stored function. The function must return a TaskFiles object.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrunmng\n\nRunmanager instance from which the task is called\nrequired\n\n\nf\nCallable[…, Optional[TaskFiles]]\nFunction that will be called when the task is called\nrequired\n\n\nkwargs\nOptional[dict[str, Any]]\nkwargs to be passed to f\nNone\n\n\nout\nOptional[str]\nIf not None, an output dir will be created with this name\nNone\n\n\n\n\n\n\n\ntasks.TaskFiles(self, get_latest, input=dict(), output=dict(), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))\nClass for Task input and output files and directories.\nHosts the input and output file paths belonging to a task. A function or method that wants to be callable as a Task has to return a TaskFiles object. The input defaultdict is populated on the fly using get_latest of the runmanager to find newest files. Files which can not be found by get_latest must be added manually.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nget_latest\nCallable\nRunmanager.get_latest function that returns paths to the latest file of given type.\n\n\ninput\ndict[str, Path]\nInput file paths for a Task. Is populated by get_latest or manually.\n\n\noutput\ndict[str, Path]\nOutput file paths for a Task. Is populated by runmanager._discover_output_files or manually.\n\n\noutputdir\nPath\nOutput directory for a Task. Typically populated by create_task_directory called by Task.\n\n\nlogger\nlogging.Logger\nLogger for a Task. Initialized in create_task_directory.\n\n\n\n\n\n\n&gt;&gt;&gt; class run():\n&gt;&gt;&gt;     def get_latest(self, s):\n&gt;&gt;&gt;         return f\"latest {s}\"\n&gt;&gt;&gt; runmng = run()\n&gt;&gt;&gt; files = TaskFiles(runmng)\n&gt;&gt;&gt; files.input\n&gt;&gt;&gt; files.input[\"top\"]\n{'top': 'latest top'}\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncreate_task_directory\nCreates TaskFiles object, output directory, logger and symlinks ff.\n\n\n\n\n\ntasks.create_task_directory(runmng, postfix)\nCreates TaskFiles object, output directory, logger and symlinks ff.\nGets called when a Task is called (from the runmanager.tasks queue)."
+    "text": "tools\nStandalone tools that are complementary to KIMMDY.\n\n\n\n\n\nName\nDescription\n\n\n\n\nbuild_examples\nBuild example directories for KIMMDY from integration tests.\n\n\nedgelist_to_dot_graph\nConvert a list of edges to a dot graph.\n\n\nentry_point_build_examples\nBuild examples from the command line.\n\n\nentry_point_modify_top\nModify topology file in various ways\n\n\nget_build_example_cmdline_args\nParse command line arguments.\n\n\nget_modify_top_cmdline_args\nparse cmdline args for modify_top\n\n\nmodify_top\nModify topology in various ways.\n\n\ntop_to_graph\nConvert a topology to a dot graph.\n\n\ntopology_to_edgelist\nConvert a topology to a list of edges for a dot graph.\n\n\nwrite_top_as_dot\nWrite a topology as a dot graph to a file.\n\n\n\n\n\ntools.build_examples(restore)\nBuild example directories for KIMMDY from integration tests.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrestore\nstr\nIf True, overwrite input files in existing example directories. If “hard”, also delete output files.\nrequired\n\n\n\n\n\n\n\ntools.edgelist_to_dot_graph(ls, overlap='true')\nConvert a list of edges to a dot graph.\n\n\n\ntools.entry_point_build_examples()\nBuild examples from the command line.\n\n\n\ntools.entry_point_modify_top()\nModify topology file in various ways\n\n\n\ntools.get_build_example_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nNamespace\nparsed command line arguments\n\n\n\n\n\n\n\ntools.get_modify_top_cmdline_args()\nparse cmdline args for modify_top\n\n\n\ntools.modify_top(topology, out, parameterize=False, removeH=None, gro=None, residuetypes=None, radicals=None, search_amber_rad=True)\nModify topology in various ways.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntopology\nstr\nPath to GROMACS top file\nrequired\n\n\nout\nstr\nOutput topology file path, stem also used for gro. Can be relative to cwd.\nrequired\n\n\nparameterize\nbool\nParameterize topology with grappa after removing hydrogen\nFalse\n\n\nremoveH\nOptional[list[int]]\nRemove one or more hydrogens by atom nrs in the top file. One based.\nNone\n\n\ngro\nOptional[str]\nGROMACS gro input file. Updates structure when deleting H. Output named like top output.\nNone\n\n\nresiduetypes\nOptional[str]\nGROMACS style residuetypes file. Necessary for parameterization with non-amber atom types.\nNone\n\n\nradicals\nOptional[list[int]]\nRadicals in the system PRIOR to removing hydrogens with the removeH option. One based. Can be detected automatically in amber topologies.\nNone\n\n\nsearch_amber_rad\nbool\nAutomatic radical search only implemented for amber. If you do use another ff, set this to false, and provide a list of radicals manually, if necessary.\nTrue\n\n\n\n\n\n\n\ntools.top_to_graph(top, overlap='true')\nConvert a topology to a dot graph.\nCan be used in notebooks to write a dot file and render with quarto.\n\n\n\ntools.topology_to_edgelist(top)\nConvert a topology to a list of edges for a dot graph.\n\n\n\ntools.write_top_as_dot(top, path, overlap='true')\nWrite a topology as a dot graph to a file.\nCan be used in notebooks to write a dot file and render with quarto.",
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-    "text": "Name\nDescription\n\n\n\n\nAutoFillDict\nDictionary that gets populated by calling get_missing.\n\n\nTask\nA task to be performed as as a step in the RunManager.\n\n\nTaskFiles\nClass for Task input and output files and directories.\n\n\n\n\n\ntasks.AutoFillDict(self, get_missing)\nDictionary that gets populated by calling get_missing.\n\n\n\ntasks.Task(self, runmng, f, kwargs=None, out=None)\nA task to be performed as as a step in the RunManager.\nA task consists of a function and its keyword arguments. Calling a taks calls the stored function. The function must return a TaskFiles object.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrunmng\n\nRunmanager instance from which the task is called\nrequired\n\n\nf\nCallable[…, Optional[TaskFiles]]\nFunction that will be called when the task is called\nrequired\n\n\nkwargs\nOptional[dict[str, Any]]\nkwargs to be passed to f\nNone\n\n\nout\nOptional[str]\nIf not None, an output dir will be created with this name\nNone\n\n\n\n\n\n\n\ntasks.TaskFiles(self, get_latest, input=dict(), output=dict(), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))\nClass for Task input and output files and directories.\nHosts the input and output file paths belonging to a task. A function or method that wants to be callable as a Task has to return a TaskFiles object. The input defaultdict is populated on the fly using get_latest of the runmanager to find newest files. Files which can not be found by get_latest must be added manually.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nget_latest\nCallable\nRunmanager.get_latest function that returns paths to the latest file of given type.\n\n\ninput\ndict[str, Path]\nInput file paths for a Task. Is populated by get_latest or manually.\n\n\noutput\ndict[str, Path]\nOutput file paths for a Task. Is populated by runmanager._discover_output_files or manually.\n\n\noutputdir\nPath\nOutput directory for a Task. Typically populated by create_task_directory called by Task.\n\n\nlogger\nlogging.Logger\nLogger for a Task. Initialized in create_task_directory.\n\n\n\n\n\n\n&gt;&gt;&gt; class run():\n&gt;&gt;&gt;     def get_latest(self, s):\n&gt;&gt;&gt;         return f\"latest {s}\"\n&gt;&gt;&gt; runmng = run()\n&gt;&gt;&gt; files = TaskFiles(runmng)\n&gt;&gt;&gt; files.input\n&gt;&gt;&gt; files.input[\"top\"]\n{'top': 'latest top'}"
+    "text": "Name\nDescription\n\n\n\n\nbuild_examples\nBuild example directories for KIMMDY from integration tests.\n\n\nedgelist_to_dot_graph\nConvert a list of edges to a dot graph.\n\n\nentry_point_build_examples\nBuild examples from the command line.\n\n\nentry_point_modify_top\nModify topology file in various ways\n\n\nget_build_example_cmdline_args\nParse command line arguments.\n\n\nget_modify_top_cmdline_args\nparse cmdline args for modify_top\n\n\nmodify_top\nModify topology in various ways.\n\n\ntop_to_graph\nConvert a topology to a dot graph.\n\n\ntopology_to_edgelist\nConvert a topology to a list of edges for a dot graph.\n\n\nwrite_top_as_dot\nWrite a topology as a dot graph to a file.\n\n\n\n\n\ntools.build_examples(restore)\nBuild example directories for KIMMDY from integration tests.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrestore\nstr\nIf True, overwrite input files in existing example directories. If “hard”, also delete output files.\nrequired\n\n\n\n\n\n\n\ntools.edgelist_to_dot_graph(ls, overlap='true')\nConvert a list of edges to a dot graph.\n\n\n\ntools.entry_point_build_examples()\nBuild examples from the command line.\n\n\n\ntools.entry_point_modify_top()\nModify topology file in various ways\n\n\n\ntools.get_build_example_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nNamespace\nparsed command line arguments\n\n\n\n\n\n\n\ntools.get_modify_top_cmdline_args()\nparse cmdline args for modify_top\n\n\n\ntools.modify_top(topology, out, parameterize=False, removeH=None, gro=None, residuetypes=None, radicals=None, search_amber_rad=True)\nModify topology in various ways.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntopology\nstr\nPath to GROMACS top file\nrequired\n\n\nout\nstr\nOutput topology file path, stem also used for gro. Can be relative to cwd.\nrequired\n\n\nparameterize\nbool\nParameterize topology with grappa after removing hydrogen\nFalse\n\n\nremoveH\nOptional[list[int]]\nRemove one or more hydrogens by atom nrs in the top file. One based.\nNone\n\n\ngro\nOptional[str]\nGROMACS gro input file. Updates structure when deleting H. Output named like top output.\nNone\n\n\nresiduetypes\nOptional[str]\nGROMACS style residuetypes file. Necessary for parameterization with non-amber atom types.\nNone\n\n\nradicals\nOptional[list[int]]\nRadicals in the system PRIOR to removing hydrogens with the removeH option. One based. Can be detected automatically in amber topologies.\nNone\n\n\nsearch_amber_rad\nbool\nAutomatic radical search only implemented for amber. If you do use another ff, set this to false, and provide a list of radicals manually, if necessary.\nTrue\n\n\n\n\n\n\n\ntools.top_to_graph(top, overlap='true')\nConvert a topology to a dot graph.\nCan be used in notebooks to write a dot file and render with quarto.\n\n\n\ntools.topology_to_edgelist(top)\nConvert a topology to a list of edges for a dot graph.\n\n\n\ntools.write_top_as_dot(top, path, overlap='true')\nWrite a topology as a dot graph to a file.\nCan be used in notebooks to write a dot file and render with quarto.",
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-    "text": "Name\nDescription\n\n\n\n\ncreate_task_directory\nCreates TaskFiles object, output directory, logger and symlinks ff.\n\n\n\n\n\ntasks.create_task_directory(runmng, postfix)\nCreates TaskFiles object, output directory, logger and symlinks ff.\nGets called when a Task is called (from the runmanager.tasks queue)."
+    "text": "analysis\nAnalysis tools for KIMMDY runs. For command line usage, run kimmdy-analysis -h.\n\n\n\n\n\nName\nDescription\n\n\n\n\nconcat_traj\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.\n\n\nentry_point_analysis\nAnalyse existing KIMMDY runs.\n\n\nget_analysis_cmdline_args\nParse command line arguments.\n\n\nget_analysis_dir\nGet analysis directory for a KIMMDY run.\n\n\nplot_energy\nPlot GROMACS energy for a KIMMDY run.\n\n\nplot_rates\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\nradical_migration\nPlot population of radicals for a KIMMDY run.\n\n\nradical_population\nPlot population of radicals for a KIMMDY run.\n\n\nreaction_participation\nPlot which atoms participate in reactions.\n\n\nruntime_analysis\nPlot which atoms participate in reactions.\n\n\n\n\n\nanalysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\nrequired\n\n\nopen_vmd\nbool\nOpen concatenated trajectory in VMD\nFalse\n\n\noutput_group\nOptional[str]\nindex group for output. Default is “Protein” for xtc and “System” for trr.\nNone\n\n\n\n\n\n\n\nanalysis.entry_point_analysis()\nAnalyse existing KIMMDY runs.\n\n\n\nanalysis.get_analysis_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\nanalysis.get_analysis_dir(dir)\nGet analysis directory for a KIMMDY run.\nCreates the directory if it does not exist.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPath to analysis directory\n\n\n\n\n\n\n\n\nanalysis.plot_energy(dir, steps, terms, open_plot=False)\nPlot GROMACS energy for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\nrequired\n\n\nterms\nlist[str]\nTerms from gmx energy that will be plotted. Uses ‘Potential’ by default.\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.plot_rates(dir)\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\nanalysis.radical_migration(dirs, type='qualitative', cutoff=1)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndirs\nlist[str]\nKIMMDY run directories to be analysed.\nrequired\n\n\ntype\nstr\nHow to analyse radical migration. Available are ‘qualitative’,‘occurence’ and ‘min_rate’“,\n'qualitative'\n\n\ncutoff\nint\nIgnore migration between two atoms if it happened less often than the specified value.\n1\n\n\n\n\n\n\n\nanalysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nKIMMDY run directory to be analysed.\nrequired\n\n\npopulation_type\nstr\nHow to calculate the fractional radical occupancy. Available are ‘frequency’ and ‘time’\n'frequency'\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\n'all'\n\n\nselect_atoms\nstr\nAtoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax)\n'protein'\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\nopen_vmd\nbool\nOpen a pdb in VMD with the radical occupation as B-factors.\nFalse\n\n\n\n\n\n\n\nanalysis.reaction_participation(dir, open_plot=False)\nPlot which atoms participate in reactions.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.runtime_analysis(dir, open_plot=False)\nPlot which atoms participate in reactions.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse",
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-    "text": "plugins\nPlugin base classes and basic instances thereof.\nAlso discovers and loads KIMMDY plugins.\n\n\n\n\n\nName\nDescription\n\n\n\n\nBasicParameterizer\nreconstruct base force field state\n\n\nReactionPlugin\nReaction base class\n\n\n\n\n\nplugins.BasicParameterizer()\nreconstruct base force field state\n\n\n\n\n\nName\nDescription\n\n\n\n\nparameterize_topology\nDo nothing,\n\n\n\n\n\nplugins.BasicParameterizer.parameterize_topology(current_topology, focus_nrs=None)\nDo nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology\n\n\n\n\n\nplugins.ReactionPlugin(self, name, runmng)\nReaction base class\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nName of the reaction\nrequired\n\n\nrunmng\nRunmanager\nRunManager instance\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_recipe_collection\nGet a RecipeCollection as a result of the reaction.\n\n\n\n\n\nplugins.ReactionPlugin.get_recipe_collection(files)\nGet a RecipeCollection as a result of the reaction.\nThis is run as a Task in the RunManager. How the RecipeCollection is built is up to the reaction. It has access to the current state of the system via the runmanager self.runmng and the files.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\nTaskFiles instance\nrequired"
+    "text": "Name\nDescription\n\n\n\n\nconcat_traj\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory.\n\n\nentry_point_analysis\nAnalyse existing KIMMDY runs.\n\n\nget_analysis_cmdline_args\nParse command line arguments.\n\n\nget_analysis_dir\nGet analysis directory for a KIMMDY run.\n\n\nplot_energy\nPlot GROMACS energy for a KIMMDY run.\n\n\nplot_rates\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\nradical_migration\nPlot population of radicals for a KIMMDY run.\n\n\nradical_population\nPlot population of radicals for a KIMMDY run.\n\n\nreaction_participation\nPlot which atoms participate in reactions.\n\n\nruntime_analysis\nPlot which atoms participate in reactions.\n\n\n\n\n\nanalysis.concat_traj(dir, filetype, steps, open_vmd=False, output_group=None)\nFind and concatenate trajectories (.xtc files) from a KIMMDY run into one trajectory. The concatenated trajectory is centered and pbc corrected.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\nrequired\n\n\nopen_vmd\nbool\nOpen concatenated trajectory in VMD\nFalse\n\n\noutput_group\nOptional[str]\nindex group for output. Default is “Protein” for xtc and “System” for trr.\nNone\n\n\n\n\n\n\n\nanalysis.entry_point_analysis()\nAnalyse existing KIMMDY runs.\n\n\n\nanalysis.get_analysis_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\nanalysis.get_analysis_dir(dir)\nGet analysis directory for a KIMMDY run.\nCreates the directory if it does not exist.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPath to analysis directory\n\n\n\n\n\n\n\n\nanalysis.plot_energy(dir, steps, terms, open_plot=False)\nPlot GROMACS energy for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory to search for subdirectories\nrequired\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\nrequired\n\n\nterms\nlist[str]\nTerms from gmx energy that will be plotted. Uses ‘Potential’ by default.\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.plot_rates(dir)\nPlot rates of all possible reactions for each ‘decide_recipe’ step.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\n\n\n\n\n\nanalysis.radical_migration(dirs, type='qualitative', cutoff=1)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndirs\nlist[str]\nKIMMDY run directories to be analysed.\nrequired\n\n\ntype\nstr\nHow to analyse radical migration. Available are ‘qualitative’,‘occurence’ and ‘min_rate’“,\n'qualitative'\n\n\ncutoff\nint\nIgnore migration between two atoms if it happened less often than the specified value.\n1\n\n\n\n\n\n\n\nanalysis.radical_population(dir, population_type='frequency', steps='all', select_atoms='protein', open_plot=False, open_vmd=False)\nPlot population of radicals for a KIMMDY run.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nKIMMDY run directory to be analysed.\nrequired\n\n\npopulation_type\nstr\nHow to calculate the fractional radical occupancy. Available are ‘frequency’ and ‘time’\n'frequency'\n\n\nsteps\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories. Default is “all”.\n'all'\n\n\nselect_atoms\nstr\nAtoms chosen for radical population analysis, default is protein (uses MDAnalysis selection syntax)\n'protein'\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\nopen_vmd\nbool\nOpen a pdb in VMD with the radical occupation as B-factors.\nFalse\n\n\n\n\n\n\n\nanalysis.reaction_participation(dir, open_plot=False)\nPlot which atoms participate in reactions.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse\n\n\n\n\n\n\n\nanalysis.runtime_analysis(dir, open_plot=False)\nPlot which atoms participate in reactions.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nstr\nDirectory of KIMMDY run\nrequired\n\n\nopen_plot\nbool\nOpen plot in default system viewer.\nFalse",
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-    "text": "Name\nDescription\n\n\n\n\nBasicParameterizer\nreconstruct base force field state\n\n\nReactionPlugin\nReaction base class\n\n\n\n\n\nplugins.BasicParameterizer()\nreconstruct base force field state\n\n\n\n\n\nName\nDescription\n\n\n\n\nparameterize_topology\nDo nothing,\n\n\n\n\n\nplugins.BasicParameterizer.parameterize_topology(current_topology, focus_nrs=None)\nDo nothing, all necessary actions should already have happened in bind_bond and break_bond of Topology\n\n\n\n\n\nplugins.ReactionPlugin(self, name, runmng)\nReaction base class\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nName of the reaction\nrequired\n\n\nrunmng\nRunmanager\nRunManager instance\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_recipe_collection\nGet a RecipeCollection as a result of the reaction.\n\n\n\n\n\nplugins.ReactionPlugin.get_recipe_collection(files)\nGet a RecipeCollection as a result of the reaction.\nThis is run as a Task in the RunManager. How the RecipeCollection is built is up to the reaction. It has access to the current state of the system via the runmanager self.runmng and the files.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\nTaskFiles instance\nrequired"
+    "text": "hat_naive.reaction.NaiveHAT\nreaction.NaiveHAT(self, name, runmng)\nNaive HAT reaction, selects hydrogens at random\n\n\n\n\n Back to top",
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-    "text": "tools\nStandalone tools that are complementary to KIMMDY.\n\n\n\n\n\nName\nDescription\n\n\n\n\nbuild_examples\nBuild example directories for KIMMDY from integration tests.\n\n\nedgelist_to_dot_graph\nConvert a list of edges to a dot graph.\n\n\nentry_point_build_examples\nBuild examples from the command line.\n\n\nentry_point_modify_top\nModify topology file in various ways\n\n\nget_build_example_cmdline_args\nParse command line arguments.\n\n\nget_modify_top_cmdline_args\nparse cmdline args for modify_top\n\n\nmodify_top\nModify topology in various ways.\n\n\ntop_to_graph\nConvert a topology to a dot graph.\n\n\ntopology_to_edgelist\nConvert a topology to a list of edges for a dot graph.\n\n\nwrite_top_as_dot\nWrite a topology as a dot graph to a file.\n\n\n\n\n\ntools.build_examples(restore)\nBuild example directories for KIMMDY from integration tests.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrestore\nstr\nIf True, overwrite input files in existing example directories. If “hard”, also delete output files.\nrequired\n\n\n\n\n\n\n\ntools.edgelist_to_dot_graph(ls, overlap='true')\nConvert a list of edges to a dot graph.\n\n\n\ntools.entry_point_build_examples()\nBuild examples from the command line.\n\n\n\ntools.entry_point_modify_top()\nModify topology file in various ways\n\n\n\ntools.get_build_example_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nNamespace\nparsed command line arguments\n\n\n\n\n\n\n\ntools.get_modify_top_cmdline_args()\nparse cmdline args for modify_top\n\n\n\ntools.modify_top(topology, out, parameterize=False, removeH=None, gro=None, residuetypes=None, radicals=None, search_amber_rad=True)\nModify topology in various ways.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntopology\nstr\nPath to GROMACS top file\nrequired\n\n\nout\nstr\nOutput topology file path, stem also used for gro. Can be relative to cwd.\nrequired\n\n\nparameterize\nbool\nParameterize topology with grappa after removing hydrogen\nFalse\n\n\nremoveH\nOptional[list[int]]\nRemove one or more hydrogens by atom nrs in the top file. One based.\nNone\n\n\ngro\nOptional[str]\nGROMACS gro input file. Updates structure when deleting H. Output named like top output.\nNone\n\n\nresiduetypes\nOptional[str]\nGROMACS style residuetypes file. Necessary for parameterization with non-amber atom types.\nNone\n\n\nradicals\nOptional[list[int]]\nRadicals in the system PRIOR to removing hydrogens with the removeH option. One based. Can be detected automatically in amber topologies.\nNone\n\n\nsearch_amber_rad\nbool\nAutomatic radical search only implemented for amber. If you do use another ff, set this to false, and provide a list of radicals manually, if necessary.\nTrue\n\n\n\n\n\n\n\ntools.top_to_graph(top, overlap='true')\nConvert a topology to a dot graph.\nCan be used in notebooks to write a dot file and render with quarto.\n\n\n\ntools.topology_to_edgelist(top)\nConvert a topology to a list of edges for a dot graph.\n\n\n\ntools.write_top_as_dot(top, path, overlap='true')\nWrite a topology as a dot graph to a file.\nCan be used in notebooks to write a dot file and render with quarto."
+    "text": "parsing\nAll read_&lt;…&gt; and write_&lt;…&gt; functions.\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nJSONEncoder\nEncoder that enables writing JSONs with numpy types.\n\n\nPlumed_dict\nDict representation of a plumed.dat file.\n\n\n\n\n\nparsing.JSONEncoder()\nEncoder that enables writing JSONs with numpy types.\n\n\n\nparsing.Plumed_dict()\nDict representation of a plumed.dat file.\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nis_not_comment\nReturns whether a string is not a comment.\n\n\nread_distances_dat\nRead a distances.dat plumed output file.\n\n\nread_edissoc\nReads a edissoc file and turns it into a dict.\n\n\nread_json\nReturn JSON file content as dict.\n\n\nread_plumed\nRead a plumed.dat configuration file.\n\n\nread_top\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\n\n\nresolve_includes\nResolve #include statements in a (top/itp) file.\n\n\nwrite_json\nWrite dict to file according to JSON format.\n\n\nwrite_plumed\nWrite a plumed.dat configuration file.\n\n\nwrite_top\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nparsing.is_not_comment(c)\nReturns whether a string is not a comment.\nUsed for topology like files that use ‘;’ for comments.\n\n\n\nparsing.read_distances_dat(distances_dat)\nRead a distances.dat plumed output file.\n\n\n\nparsing.read_edissoc(path)\nReads a edissoc file and turns it into a dict.\nThe dissociation energy is assigned per pair of atom names. Atom names are unique to a residue, and the dict is nested by residues. The set of bond atoms make up the key, the dissociation energy E_dissoc [kJ mol-1] is the value.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. Path(“edissoc.dat”)\nrequired\n\n\n\n\n\n\n\nparsing.read_json(path)\nReturn JSON file content as dict.\n\n\n\nparsing.read_plumed(path)\nRead a plumed.dat configuration file.\nFollows the plumed naming scheme of label, keyword, action.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPlumed_dict\ndict with keys: ‘distances’ and ‘prints’ Each is a dict/list of dicts containing plumed keywords\n\n\n\n\n\n\n\nparsing.read_top(path, ffdir=None, use_gmx_dir=True)\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\nAssumptions and limitation:\n\n#include statements will be resolved\ncomments will be removed\nall lines are stripped of leading and trailing whitespace\n#undef is not supported\na section within ifdef may be a subsection of a section that was started outside of the ifdef\n#if..#endif statements only surround a full section or subsection, not individual lines within a section and a section may either be contained within if … else or it may not be, but it can not be duplicated with one part inside and one outside.\nif .. else can’t be nested\n#include s that don’t resolve to a valid file path are silently dropped\nsections that can have subsections can also exist multiple, separate times e.g. moleculetype will appear multiple times and they should not be merged\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the topology file.\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nEvery section, apart from ffdir and define,\n\n\n\ncomes with a condition that can be checked against the\n\n\n\ndefines by the helper functions to determine if the content\n\n\n\n(a list of lists) should come from content or else_content.\n\n\n\nSome sections such as moleculetype also come with subsections.\n\n\n\n\n\n\n\nraw_top =\n{'ffdir': PosixPath('/usr/share/gromacs/top/amber99.ff'),\n'define': {'_FF_AMBER': [], '_FF_AMBER99': []},\n'defaults': {'content': [['1', '2', 'yes', '0.5', '0.8333']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'atomtypes': {'content': [\n['C', '6', '12.01', '0.0000', 'A', '3.39967e-01', '3.59824e-01'],\n['MNH3', '0', '0.0000', '0.0000', 'A', '0.00000e+00', '0.00000e+00']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'moleculetype_Urea': {'content': [['Urea', '3']],\n'else_content': [],\n'extra': [],\n'condition': None,\n'subsections': {'atoms': {'content': [['1',\n    'C',\n    '1',\n    'URE',\n    'C',\n    '1',\n    '0.880229',\n    '12.01000'],\n    ['2', 'O', '1', 'URE', 'O', '2', '-0.613359', '16.00000'],\n    ['3', 'N', '1', 'URE', 'N1', '3', '-0.923545', '14.01000'],\n    ['4', 'H', '1', 'URE', 'H11', '4', '0.395055', '1.00800'],\n    ['5', 'H', '1', 'URE', 'H12', '5', '0.395055', '1.00800'],\n    ['6', 'N', '1', 'URE', 'N2', '6', '-0.923545', '14.01000'],\n    ['7', 'H', '1', 'URE', 'H21', '7', '0.395055', '1.00800'],\n    ['8', 'H', '1', 'URE', 'H22', '8', '0.395055', '1.00800']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'bonds': {'content': [['1', '2'],\n    ['1', '3'],\n    ['1', '6'],\n    ['3', '4'],\n    ['3', '5'],\n    ['6', '7'],\n    ['6', '8']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'dihedrals': {'content': [['2', '1', '3', '4', '9'],\n    ['2', '1', '3', '5', '9'],\n    ['2', '1', '6', '7', '9'],\n    ['2', '1', '6', '8', '9'],\n    ['3', '1', '6', '7', '9'],\n    ['3', '1', '6', '8', '9'],\n    ['6', '1', '3', '4', '9'],\n    ['6', '1', '3', '5', '9'],\n    ['3', '6', '1', '2', '4'],\n    ['1', '4', '3', '5', '4'],\n    ['1', '7', '6', '8', '4']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'position_restraints': {'content': [['1', '1', '1000', '1000', '1000'],\n    ['2', '1', '1000', '0', '1000'],\n    ['3', '1', '1000', '0', '0']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'dihedral_restraints': {'content': [['3',\n    '6',\n    '1',\n    '2',\n    '1',\n    '180',\n    '0',\n    '10'],\n    ['1', '4', '3', '5', '1', '180', '0', '10']],\n    'else_content': [],\n    'extra': [],\n    'condition': None}}},\n}\n\n\n\n\nparsing.resolve_includes(path, gmx_builtin_ffs=None)\nResolve #include statements in a (top/itp) file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nFilepath to read.\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist[str]\nList of lines.\n\n\nOptional[Path]\nPath to the ff directory if one of the includes used a file from it.\n\n\n\n\n\n\n\nparsing.write_json(d, path)\nWrite dict to file according to JSON format.\n\n\n\nparsing.write_plumed(d, path)\nWrite a plumed.dat configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nd\nPlumed_dict\nDictionary containing ‘labeled_action’, ‘other’ and ‘prints’\nrequired\n\n\npath\nPath\nPath to the file. 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-    "text": "Name\nDescription\n\n\n\n\nbuild_examples\nBuild example directories for KIMMDY from integration tests.\n\n\nedgelist_to_dot_graph\nConvert a list of edges to a dot graph.\n\n\nentry_point_build_examples\nBuild examples from the command line.\n\n\nentry_point_modify_top\nModify topology file in various ways\n\n\nget_build_example_cmdline_args\nParse command line arguments.\n\n\nget_modify_top_cmdline_args\nparse cmdline args for modify_top\n\n\nmodify_top\nModify topology in various ways.\n\n\ntop_to_graph\nConvert a topology to a dot graph.\n\n\ntopology_to_edgelist\nConvert a topology to a list of edges for a dot graph.\n\n\nwrite_top_as_dot\nWrite a topology as a dot graph to a file.\n\n\n\n\n\ntools.build_examples(restore)\nBuild example directories for KIMMDY from integration tests.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nrestore\nstr\nIf True, overwrite input files in existing example directories. If “hard”, also delete output files.\nrequired\n\n\n\n\n\n\n\ntools.edgelist_to_dot_graph(ls, overlap='true')\nConvert a list of edges to a dot graph.\n\n\n\ntools.entry_point_build_examples()\nBuild examples from the command line.\n\n\n\ntools.entry_point_modify_top()\nModify topology file in various ways\n\n\n\ntools.get_build_example_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nNamespace\nparsed command line arguments\n\n\n\n\n\n\n\ntools.get_modify_top_cmdline_args()\nparse cmdline args for modify_top\n\n\n\ntools.modify_top(topology, out, parameterize=False, removeH=None, gro=None, residuetypes=None, radicals=None, search_amber_rad=True)\nModify topology in various ways.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntopology\nstr\nPath to GROMACS top file\nrequired\n\n\nout\nstr\nOutput topology file path, stem also used for gro. Can be relative to cwd.\nrequired\n\n\nparameterize\nbool\nParameterize topology with grappa after removing hydrogen\nFalse\n\n\nremoveH\nOptional[list[int]]\nRemove one or more hydrogens by atom nrs in the top file. One based.\nNone\n\n\ngro\nOptional[str]\nGROMACS gro input file. Updates structure when deleting H. Output named like top output.\nNone\n\n\nresiduetypes\nOptional[str]\nGROMACS style residuetypes file. Necessary for parameterization with non-amber atom types.\nNone\n\n\nradicals\nOptional[list[int]]\nRadicals in the system PRIOR to removing hydrogens with the removeH option. One based. Can be detected automatically in amber topologies.\nNone\n\n\nsearch_amber_rad\nbool\nAutomatic radical search only implemented for amber. If you do use another ff, set this to false, and provide a list of radicals manually, if necessary.\nTrue\n\n\n\n\n\n\n\ntools.top_to_graph(top, overlap='true')\nConvert a topology to a dot graph.\nCan be used in notebooks to write a dot file and render with quarto.\n\n\n\ntools.topology_to_edgelist(top)\nConvert a topology to a list of edges for a dot graph.\n\n\n\ntools.write_top_as_dot(top, path, overlap='true')\nWrite a topology as a dot graph to a file.\nCan be used in notebooks to write a dot file and render with quarto."
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-    "text": "coordinates\ncoordinate, topology and plumed modification functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nbreak_bond_plumed\nBreak bond in plumed configuration file.\n\n\nget_explicit_MultipleDihedrals\nTakes a valid dihedral key and returns explicit\n\n\nget_explicit_or_type\nTakes an Interaction and associated key, InteractionTypes, Topology\n\n\nis_parameterized\nParameterized topology entries have c0 and c1 attributes != None\n\n\nmerge_dihedrals\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\nmerge_top_moleculetypes_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\nmerge_top_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\n\n\nplace_atom\nPlace an atom to new coords at the last time point of the trajectory\n\n\n\n\n\ncoordinates.break_bond_plumed(files, breakpair, newplumed)\nBreak bond in plumed configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\n\nrequired\n\n\nbreakpair\ntuple[str, str]\n\nrequired\n\n\n\n\n\n\n\ncoordinates.get_explicit_MultipleDihedrals(dihedral_key, mol, dihedrals_in, ff, periodicity_max=6)\nTakes a valid dihedral key and returns explicit dihedral parameters for a given topology\n\n\n\ncoordinates.get_explicit_or_type(key, interaction, interaction_types, mol, periodicity='')\nTakes an Interaction and associated key, InteractionTypes, Topology and Periodicity (for dihedrals) and returns an object with the parameters of this Interaction\n\n\n\ncoordinates.is_parameterized(entry)\nParameterized topology entries have c0 and c1 attributes != None\n\n\n\ncoordinates.merge_dihedrals(dihedral_key, dihedral_a, dihedral_b, dihedral_types_a, dihedral_types_b, molA, molB, funct, periodicity)\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\n\ncoordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\n\ncoordinates.merge_top_slow_growth(topA, topB)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\nTODO: for now this assumes that only one moleculeype (the first, index 0) is of interest.\n\n\n\ncoordinates.place_atom(files, step, ttime=None)\nPlace an atom to new coords at the last time point of the trajectory"
+    "text": "Name\nDescription\n\n\n\n\nJSONEncoder\nEncoder that enables writing JSONs with numpy types.\n\n\nPlumed_dict\nDict representation of a plumed.dat file.\n\n\n\n\n\nparsing.JSONEncoder()\nEncoder that enables writing JSONs with numpy types.\n\n\n\nparsing.Plumed_dict()\nDict representation of a plumed.dat file.",
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-    "text": "Name\nDescription\n\n\n\n\nbreak_bond_plumed\nBreak bond in plumed configuration file.\n\n\nget_explicit_MultipleDihedrals\nTakes a valid dihedral key and returns explicit\n\n\nget_explicit_or_type\nTakes an Interaction and associated key, InteractionTypes, Topology\n\n\nis_parameterized\nParameterized topology entries have c0 and c1 attributes != None\n\n\nmerge_dihedrals\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\nmerge_top_moleculetypes_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\nmerge_top_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\n\n\nplace_atom\nPlace an atom to new coords at the last time point of the trajectory\n\n\n\n\n\ncoordinates.break_bond_plumed(files, breakpair, newplumed)\nBreak bond in plumed configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\n\nrequired\n\n\nbreakpair\ntuple[str, str]\n\nrequired\n\n\n\n\n\n\n\ncoordinates.get_explicit_MultipleDihedrals(dihedral_key, mol, dihedrals_in, ff, periodicity_max=6)\nTakes a valid dihedral key and returns explicit dihedral parameters for a given topology\n\n\n\ncoordinates.get_explicit_or_type(key, interaction, interaction_types, mol, periodicity='')\nTakes an Interaction and associated key, InteractionTypes, Topology and Periodicity (for dihedrals) and returns an object with the parameters of this Interaction\n\n\n\ncoordinates.is_parameterized(entry)\nParameterized topology entries have c0 and c1 attributes != None\n\n\n\ncoordinates.merge_dihedrals(dihedral_key, dihedral_a, dihedral_b, dihedral_types_a, dihedral_types_b, molA, molB, funct, periodicity)\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\n\ncoordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\n\ncoordinates.merge_top_slow_growth(topA, topB)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\nTODO: for now this assumes that only one moleculeype (the first, index 0) is of interest.\n\n\n\ncoordinates.place_atom(files, step, ttime=None)\nPlace an atom to new coords at the last time point of the trajectory"
+    "text": "Name\nDescription\n\n\n\n\nis_not_comment\nReturns whether a string is not a comment.\n\n\nread_distances_dat\nRead a distances.dat plumed output file.\n\n\nread_edissoc\nReads a edissoc file and turns it into a dict.\n\n\nread_json\nReturn JSON file content as dict.\n\n\nread_plumed\nRead a plumed.dat configuration file.\n\n\nread_top\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\n\n\nresolve_includes\nResolve #include statements in a (top/itp) file.\n\n\nwrite_json\nWrite dict to file according to JSON format.\n\n\nwrite_plumed\nWrite a plumed.dat configuration file.\n\n\nwrite_top\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nparsing.is_not_comment(c)\nReturns whether a string is not a comment.\nUsed for topology like files that use ‘;’ for comments.\n\n\n\nparsing.read_distances_dat(distances_dat)\nRead a distances.dat plumed output file.\n\n\n\nparsing.read_edissoc(path)\nReads a edissoc file and turns it into a dict.\nThe dissociation energy is assigned per pair of atom names. Atom names are unique to a residue, and the dict is nested by residues. The set of bond atoms make up the key, the dissociation energy E_dissoc [kJ mol-1] is the value.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. Path(“edissoc.dat”)\nrequired\n\n\n\n\n\n\n\nparsing.read_json(path)\nReturn JSON file content as dict.\n\n\n\nparsing.read_plumed(path)\nRead a plumed.dat configuration file.\nFollows the plumed naming scheme of label, keyword, action.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPlumed_dict\ndict with keys: ‘distances’ and ‘prints’ Each is a dict/list of dicts containing plumed keywords\n\n\n\n\n\n\n\nparsing.read_top(path, ffdir=None, use_gmx_dir=True)\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\nAssumptions and limitation:\n\n#include statements will be resolved\ncomments will be removed\nall lines are stripped of leading and trailing whitespace\n#undef is not supported\na section within ifdef may be a subsection of a section that was started outside of the ifdef\n#if..#endif statements only surround a full section or subsection, not individual lines within a section and a section may either be contained within if … else or it may not be, but it can not be duplicated with one part inside and one outside.\nif .. else can’t be nested\n#include s that don’t resolve to a valid file path are silently dropped\nsections that can have subsections can also exist multiple, separate times e.g. moleculetype will appear multiple times and they should not be merged\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the topology file.\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nEvery section, apart from ffdir and define,\n\n\n\ncomes with a condition that can be checked against the\n\n\n\ndefines by the helper functions to determine if the content\n\n\n\n(a list of lists) should come from content or else_content.\n\n\n\nSome sections such as moleculetype also come with subsections.\n\n\n\n\n\n\n\nraw_top =\n{'ffdir': PosixPath('/usr/share/gromacs/top/amber99.ff'),\n'define': {'_FF_AMBER': [], '_FF_AMBER99': []},\n'defaults': {'content': [['1', '2', 'yes', '0.5', '0.8333']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'atomtypes': {'content': [\n['C', '6', '12.01', '0.0000', 'A', '3.39967e-01', '3.59824e-01'],\n['MNH3', '0', '0.0000', '0.0000', 'A', '0.00000e+00', '0.00000e+00']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'moleculetype_Urea': {'content': [['Urea', '3']],\n'else_content': [],\n'extra': [],\n'condition': None,\n'subsections': {'atoms': {'content': [['1',\n    'C',\n    '1',\n    'URE',\n    'C',\n    '1',\n    '0.880229',\n    '12.01000'],\n    ['2', 'O', '1', 'URE', 'O', '2', '-0.613359', '16.00000'],\n    ['3', 'N', '1', 'URE', 'N1', '3', '-0.923545', '14.01000'],\n    ['4', 'H', '1', 'URE', 'H11', '4', '0.395055', '1.00800'],\n    ['5', 'H', '1', 'URE', 'H12', '5', '0.395055', '1.00800'],\n    ['6', 'N', '1', 'URE', 'N2', '6', '-0.923545', '14.01000'],\n    ['7', 'H', '1', 'URE', 'H21', '7', '0.395055', '1.00800'],\n    ['8', 'H', '1', 'URE', 'H22', '8', '0.395055', '1.00800']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'bonds': {'content': [['1', '2'],\n    ['1', '3'],\n    ['1', '6'],\n    ['3', '4'],\n    ['3', '5'],\n    ['6', '7'],\n    ['6', '8']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'dihedrals': {'content': [['2', '1', '3', '4', '9'],\n    ['2', '1', '3', '5', '9'],\n    ['2', '1', '6', '7', '9'],\n    ['2', '1', '6', '8', '9'],\n    ['3', '1', '6', '7', '9'],\n    ['3', '1', '6', '8', '9'],\n    ['6', '1', '3', '4', '9'],\n    ['6', '1', '3', '5', '9'],\n    ['3', '6', '1', '2', '4'],\n    ['1', '4', '3', '5', '4'],\n    ['1', '7', '6', '8', '4']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'position_restraints': {'content': [['1', '1', '1000', '1000', '1000'],\n    ['2', '1', '1000', '0', '1000'],\n    ['3', '1', '1000', '0', '0']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'dihedral_restraints': {'content': [['3',\n    '6',\n    '1',\n    '2',\n    '1',\n    '180',\n    '0',\n    '10'],\n    ['1', '4', '3', '5', '1', '180', '0', '10']],\n    'else_content': [],\n    'extra': [],\n    'condition': None}}},\n}\n\n\n\n\nparsing.resolve_includes(path, gmx_builtin_ffs=None)\nResolve #include statements in a (top/itp) file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nFilepath to read.\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist[str]\nList of lines.\n\n\nOptional[Path]\nPath to the ff directory if one of the includes used a file from it.\n\n\n\n\n\n\n\nparsing.write_json(d, path)\nWrite dict to file according to JSON format.\n\n\n\nparsing.write_plumed(d, path)\nWrite a plumed.dat configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nd\nPlumed_dict\nDictionary containing ‘labeled_action’, ‘other’ and ‘prints’\nrequired\n\n\npath\nPath\nPath to the file. 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-    "text": "utils\nUtilities for building plugins, shell convenience functions and GROMACS related functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyAtomAddress\nAddress to an atom in the topology.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nget_task_directories\ncreate list of subdirectories that match the tasks.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.get_task_directories(dir, tasks='all')\ncreate list of subdirectories that match the tasks. If tasks is “all”, all subdirectories are returned.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory to search for subdirectories\nrequired\n\n\ntasks\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\n'all'\n\n\n\n\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nfrequency_factor\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\ntemperature\nfloat\nTemperature for the Arrhenius equation in GROMACS units.\n300\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired"
+    "text": "dummyreaction.reaction.DummyReaction\nreaction.DummyReaction(self, name, runmng)\nDummy reaction, returns empty RecipeCollection\n\n\n\n\n Back to top",
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-    "text": "Name\nDescription\n\n\n\n\nTopologyAtomAddress\nAddress to an atom in the topology."
+    "text": "config\nRead and validate kimmdy.yml configuration files and package into a parsed format for internal use.\n\n\n\n\n\nName\nDescription\n\n\n\n\nConfig\nInternal representation of the configuration generated\n\n\n\n\n\nconfig.Config(self, input_file=None, recursive_dict=None, scheme=None, section='config', logfile=None, loglevel=None)\nInternal representation of the configuration generated from the input file, which enables validation before running and computationally expensive operations.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput_file\nPath | None\nPath to the config yaml file.\nNone\n\n\nrecursive_dict\ndict | None\nFor internal use only, used in reading settings in recursively.\nNone\n\n\nscheme\ndict | None\ndict containing types and defaults for casting and validating settings.\nNone\n\n\nsection\nstr\ncurrent section e.g. to determine the level of recursion in nested configs e.g. “config”, “config.mds” or “config.reactions.homolysis”\n'config'\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nattr\nGet the value of a specific attribute.\n\n\nget_attributes\nGet a list of all attributes without hidden ones (_&lt;…&gt;).\n\n\n\n\n\nconfig.Config.attr(attribute)\nGet the value of a specific attribute. Alias for self.__getattribute__\n\n\n\nconfig.Config.get_attributes()\nGet a list of all attributes without hidden ones (_&lt;…&gt;).",
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-    "text": "Name\nDescription\n\n\n\n\ncheck_gmx_version\nCheck for an existing gromacs installation.\n\n\nget_atominfo_from_atomnrs\nUse topology atoms section to convert from atomnr to atomtype\n\n\nget_atomnrs_from_plumedid\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\nget_bondprm_from_atomtypes\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\nget_edissoc_from_atomnames\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\nget_gmx_dir\nReturns the path to the gromacs installation\n\n\nget_shell_stdout\nRun command in shell and capture stdout.\n\n\nget_task_directories\ncreate list of subdirectories that match the tasks.\n\n\nmorse_transition_rate\nCalculates reaction rate constant for a bond breaking event.\n\n\nrun_gmx\nRun GROMACS command in shell.\n\n\nrun_shell_cmd\nRun command in shell.\n\n\ntruncate_sim_files\nTruncates latest trr, xtc, edr, and gro to the time to a previous\n\n\n\n\n\nutils.check_gmx_version(config)\nCheck for an existing gromacs installation.\nIf PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.\n\n\n\nutils.get_atominfo_from_atomnrs(atomnrs, top)\nUse topology atoms section to convert from atomnr to atomtype\n\n\n\nutils.get_atomnrs_from_plumedid(plumedid, plumed)\nConvert from plumedid to atomnr, information from the plumed file is used.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nplumedid\nstr\nIdentifier from a plumed input file (e.g d0).\nrequired\n\n\nplumed\nPlumed_dict\nParsed plumed input file\nrequired\n\n\n\n\n\n\n\nutils.get_bondprm_from_atomtypes(atomtypes, ffbonded)\nReturns bond parameters (b0, kb) for a set of two atomtypes.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomtypes\nlist[str]\nTwo atomtypes as defined in the respective force field\nrequired\n\n\nffbonded\ndict\nForce field ffbonded.itp file parsed through the rtp parser\nrequired\n\n\n\n\n\n\n\nutils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')\nReturns dissociation energy E_dissoc for a set of two atomnames.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\natomnames\nlist[str]\nTwo atomnames as defined in the respective force field\nrequired\n\n\nedissoc\ndict\nParsed file with dissociation energies per bond between two atomtypes or elements\nrequired\n\n\nresidue\nstr\nResidue for which the atomnames are defined\n'_'\n\n\n\n\n\n\n\nutils.get_gmx_dir(gromacs_alias='gmx')\nReturns the path to the gromacs installation\n\n\n\nutils.get_shell_stdout(s)\nRun command in shell and capture stdout.\n\n\n\nutils.get_task_directories(dir, tasks='all')\ncreate list of subdirectories that match the tasks. If tasks is “all”, all subdirectories are returned.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndir\nPath\nDirectory to search for subdirectories\nrequired\n\n\ntasks\nUnion[list[str], str]\nList of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories\n'all'\n\n\n\n\n\n\n\nutils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)\nCalculates reaction rate constant for a bond breaking event.\nUses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.\nThe calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nr_curr\nlist[float]\nBond distances for a single bond, typically from a time series.\nrequired\n\n\nr_0\nfloat\nEquilibrium bond length of the bond.\nrequired\n\n\ndissociation\n\nDissociation energy of the bond.\nrequired\n\n\nk_f\nfloat\nSpring constant of the bond.\nrequired\n\n\nfrequency_factor\nfloat\nPrefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m).\n0.288\n\n\ntemperature\nfloat\nTemperature for the Arrhenius equation in GROMACS units.\n300\n\n\n\n\n\n\n\nutils.run_gmx(s, cwd=None)\nRun GROMACS command in shell.\nAdds a ‘-quiet’ flag to the command and checks the return code.\n\n\n\nutils.run_shell_cmd(s, cwd=None)\nRun command in shell.\n\n\n\nutils.truncate_sim_files(files, time, keep_tail=True)\nTruncates latest trr, xtc, edr, and gro to the time to a previous point in time.\nThe files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntime\nOptional[float]\nTime in ps up to which the data should be truncated.\nrequired\n\n\nfiles\nTaskFiles\nTaskFiles to get the latest files.\nrequired"
+    "text": "Name\nDescription\n\n\n\n\nConfig\nInternal representation of the configuration generated\n\n\n\n\n\nconfig.Config(self, input_file=None, recursive_dict=None, scheme=None, section='config', logfile=None, loglevel=None)\nInternal representation of the configuration generated from the input file, which enables validation before running and computationally expensive operations.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput_file\nPath | None\nPath to the config yaml file.\nNone\n\n\nrecursive_dict\ndict | None\nFor internal use only, used in reading settings in recursively.\nNone\n\n\nscheme\ndict | None\ndict containing types and defaults for casting and validating settings.\nNone\n\n\nsection\nstr\ncurrent section e.g. to determine the level of recursion in nested configs e.g. “config”, “config.mds” or “config.reactions.homolysis”\n'config'\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nattr\nGet the value of a specific attribute.\n\n\nget_attributes\nGet a list of all attributes without hidden ones (_&lt;…&gt;).\n\n\n\n\n\nconfig.Config.attr(attribute)\nGet the value of a specific attribute. Alias for self.__getattribute__\n\n\n\nconfig.Config.get_attributes()\nGet a list of all attributes without hidden ones (_&lt;…&gt;).",
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-    "text": "cmd\nFunctions for starting KIMMDY either from python or the command line. Other entry points such as kimmdy-analysis also live here.\n\n\n\n\n\nName\nDescription\n\n\n\n\nconfigure_logger\nConfigure logging.\n\n\nentry_point_kimmdy\nRun KIMMDY from the command line.\n\n\nget_cmdline_args\nParse command line arguments.\n\n\nkimmdy_run\nRun KIMMDY from python.\n\n\n\n\n\ncmd.configure_logger(config)\nConfigure logging.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nconfig\nConfig\nconfiguration that contains log.level and log.file\nrequired\n\n\n\n\n\n\n\ncmd.entry_point_kimmdy()\nRun KIMMDY from the command line.\nThe configuration is gathered from the input file, which is kimmdy.yml by default. See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\ncmd.get_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\ncmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, show_plugins=False, generate_jobscript=False, debug=False, callgraph=False)\nRun KIMMDY from python.\nAlso see See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput\nPath\nkimmdy input yml file.\nPath('kimmdy.yml')\n\n\nloglevel\nOptional[str]\nLoglevel. One of [“INFO”, “WARNING”, “MESSAGE”, “DEBUG”]\nNone\n\n\nlogfile\nOptional[Path]\nFile path of the logfile.\nNone\n\n\nshow_plugins\nbool\nShow available plugins and exit.\nFalse\n\n\ngenerate_jobscript\nbool\nInstead of running KIMMDY directly, generate at jobscript.sh for slurm HPC clusters\nFalse"
+    "text": "coordinates\ncoordinate, topology and plumed modification functions\n\n\n\n\n\nName\nDescription\n\n\n\n\nbreak_bond_plumed\nBreak bond in plumed configuration file.\n\n\nget_explicit_MultipleDihedrals\nTakes a valid dihedral key and returns explicit\n\n\nget_explicit_or_type\nTakes an Interaction and associated key, InteractionTypes, Topology\n\n\nis_parameterized\nParameterized topology entries have c0 and c1 attributes != None\n\n\nmerge_dihedrals\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\nmerge_top_moleculetypes_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\nmerge_top_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\n\n\nplace_atom\nPlace an atom to new coords at the last time point of the trajectory\n\n\n\n\n\ncoordinates.break_bond_plumed(files, breakpair, newplumed)\nBreak bond in plumed configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\n\nrequired\n\n\nbreakpair\ntuple[str, str]\n\nrequired\n\n\n\n\n\n\n\ncoordinates.get_explicit_MultipleDihedrals(dihedral_key, mol, dihedrals_in, ff, periodicity_max=6)\nTakes a valid dihedral key and returns explicit dihedral parameters for a given topology\n\n\n\ncoordinates.get_explicit_or_type(key, interaction, interaction_types, mol, periodicity='')\nTakes an Interaction and associated key, InteractionTypes, Topology and Periodicity (for dihedrals) and returns an object with the parameters of this Interaction\n\n\n\ncoordinates.is_parameterized(entry)\nParameterized topology entries have c0 and c1 attributes != None\n\n\n\ncoordinates.merge_dihedrals(dihedral_key, dihedral_a, dihedral_b, dihedral_types_a, dihedral_types_b, molA, molB, funct, periodicity)\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\n\ncoordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\n\ncoordinates.merge_top_slow_growth(topA, topB)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\nTODO: for now this assumes that only one moleculeype (the first, index 0) is of interest.\n\n\n\ncoordinates.place_atom(files, step, ttime=None)\nPlace an atom to new coords at the last time point of the trajectory",
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-    "text": "Name\nDescription\n\n\n\n\nconfigure_logger\nConfigure logging.\n\n\nentry_point_kimmdy\nRun KIMMDY from the command line.\n\n\nget_cmdline_args\nParse command line arguments.\n\n\nkimmdy_run\nRun KIMMDY from python.\n\n\n\n\n\ncmd.configure_logger(config)\nConfigure logging.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nconfig\nConfig\nconfiguration that contains log.level and log.file\nrequired\n\n\n\n\n\n\n\ncmd.entry_point_kimmdy()\nRun KIMMDY from the command line.\nThe configuration is gathered from the input file, which is kimmdy.yml by default. See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\ncmd.get_cmdline_args()\nParse command line arguments.\n\n\n\n\n\nType\nDescription\n\n\n\n\nParsed command line arguments\n\n\n\n\n\n\n\n\ncmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, show_plugins=False, generate_jobscript=False, debug=False, callgraph=False)\nRun KIMMDY from python.\nAlso see See get_cmdline_args or kimmdy --help for the descriptions of the arguments.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ninput\nPath\nkimmdy input yml file.\nPath('kimmdy.yml')\n\n\nloglevel\nOptional[str]\nLoglevel. One of [“INFO”, “WARNING”, “MESSAGE”, “DEBUG”]\nNone\n\n\nlogfile\nOptional[Path]\nFile path of the logfile.\nNone\n\n\nshow_plugins\nbool\nShow available plugins and exit.\nFalse\n\n\ngenerate_jobscript\nbool\nInstead of running KIMMDY directly, generate at jobscript.sh for slurm HPC clusters\nFalse"
+    "text": "Name\nDescription\n\n\n\n\nbreak_bond_plumed\nBreak bond in plumed configuration file.\n\n\nget_explicit_MultipleDihedrals\nTakes a valid dihedral key and returns explicit\n\n\nget_explicit_or_type\nTakes an Interaction and associated key, InteractionTypes, Topology\n\n\nis_parameterized\nParameterized topology entries have c0 and c1 attributes != None\n\n\nmerge_dihedrals\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\nmerge_top_moleculetypes_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\nmerge_top_slow_growth\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\n\n\nplace_atom\nPlace an atom to new coords at the last time point of the trajectory\n\n\n\n\n\ncoordinates.break_bond_plumed(files, breakpair, newplumed)\nBreak bond in plumed configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nfiles\nTaskFiles\n\nrequired\n\n\nbreakpair\ntuple[str, str]\n\nrequired\n\n\n\n\n\n\n\ncoordinates.get_explicit_MultipleDihedrals(dihedral_key, mol, dihedrals_in, ff, periodicity_max=6)\nTakes a valid dihedral key and returns explicit dihedral parameters for a given topology\n\n\n\ncoordinates.get_explicit_or_type(key, interaction, interaction_types, mol, periodicity='')\nTakes an Interaction and associated key, InteractionTypes, Topology and Periodicity (for dihedrals) and returns an object with the parameters of this Interaction\n\n\n\ncoordinates.is_parameterized(entry)\nParameterized topology entries have c0 and c1 attributes != None\n\n\n\ncoordinates.merge_dihedrals(dihedral_key, dihedral_a, dihedral_b, dihedral_types_a, dihedral_types_b, molA, molB, funct, periodicity)\nMerge one to two Dihedrals or -Types into a Dihedral in free-energy syntax\n\n\n\ncoordinates.merge_top_moleculetypes_slow_growth(molA, molB, ff)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation\n\n\n\ncoordinates.merge_top_slow_growth(topA, topB)\nTakes two Topologies and joins them for a smooth free-energy like parameter transition simulation.\nTODO: for now this assumes that only one moleculeype (the first, index 0) is of interest.\n\n\n\ncoordinates.place_atom(files, step, ttime=None)\nPlace an atom to new coords at the last time point of the trajectory",
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-    "text": "parsing\nAll read_&lt;…&gt; and write_&lt;…&gt; functions.\n\n\n\n\n\nName\nDescription\n\n\n\n\nTopologyDict\nA raw representation of a topology file returned by read_top.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nJSONEncoder\nEncoder that enables writing JSONs with numpy types.\n\n\nPlumed_dict\nDict representation of a plumed.dat file.\n\n\n\n\n\nparsing.JSONEncoder()\nEncoder that enables writing JSONs with numpy types.\n\n\n\nparsing.Plumed_dict()\nDict representation of a plumed.dat file.\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nis_not_comment\nReturns whether a string is not a comment.\n\n\nread_distances_dat\nRead a distances.dat plumed output file.\n\n\nread_edissoc\nReads a edissoc file and turns it into a dict.\n\n\nread_json\nReturn JSON file content as dict.\n\n\nread_plumed\nRead a plumed.dat configuration file.\n\n\nread_top\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\n\n\nresolve_includes\nResolve #include statements in a (top/itp) file.\n\n\nwrite_json\nWrite dict to file according to JSON format.\n\n\nwrite_plumed\nWrite a plumed.dat configuration file.\n\n\nwrite_top\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nparsing.is_not_comment(c)\nReturns whether a string is not a comment.\nUsed for topology like files that use ‘;’ for comments.\n\n\n\nparsing.read_distances_dat(distances_dat)\nRead a distances.dat plumed output file.\n\n\n\nparsing.read_edissoc(path)\nReads a edissoc file and turns it into a dict.\nThe dissociation energy is assigned per pair of atom names. Atom names are unique to a residue, and the dict is nested by residues. The set of bond atoms make up the key, the dissociation energy E_dissoc [kJ mol-1] is the value.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. Path(“edissoc.dat”)\nrequired\n\n\n\n\n\n\n\nparsing.read_json(path)\nReturn JSON file content as dict.\n\n\n\nparsing.read_plumed(path)\nRead a plumed.dat configuration file.\nFollows the plumed naming scheme of label, keyword, action.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPlumed_dict\ndict with keys: ‘distances’ and ‘prints’ Each is a dict/list of dicts containing plumed keywords\n\n\n\n\n\n\n\nparsing.read_top(path, ffdir=None, use_gmx_dir=True)\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\nAssumptions and limitation:\n\n#include statements will be resolved\ncomments will be removed\nall lines are stripped of leading and trailing whitespace\n#undef is not supported\na section within ifdef may be a subsection of a section that was started outside of the ifdef\n#if..#endif statements only surround a full section or subsection, not individual lines within a section and a section may either be contained within if … else or it may not be, but it can not be duplicated with one part inside and one outside.\nif .. else can’t be nested\n#include s that don’t resolve to a valid file path are silently dropped\nsections that can have subsections can also exist multiple, separate times e.g. moleculetype will appear multiple times and they should not be merged\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the topology file.\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nEvery section, apart from ffdir and define,\n\n\n\ncomes with a condition that can be checked against the\n\n\n\ndefines by the helper functions to determine if the content\n\n\n\n(a list of lists) should come from content or else_content.\n\n\n\nSome sections such as moleculetype also come with subsections.\n\n\n\n\n\n\n\nraw_top =\n{'ffdir': PosixPath('/usr/share/gromacs/top/amber99.ff'),\n'define': {'_FF_AMBER': [], '_FF_AMBER99': []},\n'defaults': {'content': [['1', '2', 'yes', '0.5', '0.8333']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'atomtypes': {'content': [\n['C', '6', '12.01', '0.0000', 'A', '3.39967e-01', '3.59824e-01'],\n['MNH3', '0', '0.0000', '0.0000', 'A', '0.00000e+00', '0.00000e+00']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'moleculetype_Urea': {'content': [['Urea', '3']],\n'else_content': [],\n'extra': [],\n'condition': None,\n'subsections': {'atoms': {'content': [['1',\n    'C',\n    '1',\n    'URE',\n    'C',\n    '1',\n    '0.880229',\n    '12.01000'],\n    ['2', 'O', '1', 'URE', 'O', '2', '-0.613359', '16.00000'],\n    ['3', 'N', '1', 'URE', 'N1', '3', '-0.923545', '14.01000'],\n    ['4', 'H', '1', 'URE', 'H11', '4', '0.395055', '1.00800'],\n    ['5', 'H', '1', 'URE', 'H12', '5', '0.395055', '1.00800'],\n    ['6', 'N', '1', 'URE', 'N2', '6', '-0.923545', '14.01000'],\n    ['7', 'H', '1', 'URE', 'H21', '7', '0.395055', '1.00800'],\n    ['8', 'H', '1', 'URE', 'H22', '8', '0.395055', '1.00800']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'bonds': {'content': [['1', '2'],\n    ['1', '3'],\n    ['1', '6'],\n    ['3', '4'],\n    ['3', '5'],\n    ['6', '7'],\n    ['6', '8']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'dihedrals': {'content': [['2', '1', '3', '4', '9'],\n    ['2', '1', '3', '5', '9'],\n    ['2', '1', '6', '7', '9'],\n    ['2', '1', '6', '8', '9'],\n    ['3', '1', '6', '7', '9'],\n    ['3', '1', '6', '8', '9'],\n    ['6', '1', '3', '4', '9'],\n    ['6', '1', '3', '5', '9'],\n    ['3', '6', '1', '2', '4'],\n    ['1', '4', '3', '5', '4'],\n    ['1', '7', '6', '8', '4']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'position_restraints': {'content': [['1', '1', '1000', '1000', '1000'],\n    ['2', '1', '1000', '0', '1000'],\n    ['3', '1', '1000', '0', '0']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'dihedral_restraints': {'content': [['3',\n    '6',\n    '1',\n    '2',\n    '1',\n    '180',\n    '0',\n    '10'],\n    ['1', '4', '3', '5', '1', '180', '0', '10']],\n    'else_content': [],\n    'extra': [],\n    'condition': None}}},\n}\n\n\n\n\nparsing.resolve_includes(path, gmx_builtin_ffs=None)\nResolve #include statements in a (top/itp) file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nFilepath to read.\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist[str]\nList of lines.\n\n\nOptional[Path]\nPath to the ff directory if one of the includes used a file from it.\n\n\n\n\n\n\n\nparsing.write_json(d, path)\nWrite dict to file according to JSON format.\n\n\n\nparsing.write_plumed(d, path)\nWrite a plumed.dat configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nd\nPlumed_dict\nDictionary containing ‘labeled_action’, ‘other’ and ‘prints’\nrequired\n\n\npath\nPath\nPath to the file. 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+    "text": "schema\nHandle the schema for the config file. To be used by the config module to validate the config file and set defaults for the Config object.\nReserved keywords: - pytype - default - description - type - required\n\n\n\n\n\nName\nDescription\n\n\n\n\nSequence\nA sequence of tasks.\n\n\n\n\n\nschema.Sequence(self, tasks)\nA sequence of tasks.\nTasks can be grouped together by using a dictionary with the following keys: - mult: number of times to repeat the tasks - tasks: list of tasks to repeat\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\ntasks\n\nlist of tasks\n\n\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nconvert_schema_to_dict\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\nflatten_scheme\nRecursively get properties and their desicripions from the scheme\n\n\ngenerate_markdown_table\nGenerate markdown table from scheme\n\n\nget_combined_scheme\nReturn the schema for the config file.\n\n\nload_kimmdy_schema\nReturn the schema for the config file\n\n\nload_plugin_schemas\nReturn the schemas for the reaction plugins known to kimmdy\n\n\nprune\nRemove empty dicts from a nested dict\n\n\n\n\n\nschema.convert_schema_to_dict(dictionary)\nConvert a dictionary from a raw json schema to a nested dictionary\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndictionary\ndict\ndictionary from a raw json schema\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nnested dictionary where each leaf entry is a dictionary with the\n“pytype”, “default” and “description” keys.\n\n\n\n\n\n\n\nschema.flatten_scheme(scheme, section='')\nRecursively get properties and their desicripions from the scheme\n\n\n\nschema.generate_markdown_table(scheme, append=False)\nGenerate markdown table from scheme\nUsed in documentation generation.\n\n\n\nschema.get_combined_scheme()\nReturn the schema for the config file.\nNested scheme where each leaf entry is a dictionary with the “pytype”, “default” and “description”. Contains the schema for the main kimmdy config file and all the plugins known at runtime.\n\n\n\nschema.load_kimmdy_schema()\nReturn the schema for the config file\n\n\n\nschema.load_plugin_schemas()\nReturn the schemas for the reaction plugins known to kimmdy\n\n\n\nschema.prune(d)\nRemove empty dicts from a nested dict"
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-    "text": "Name\nDescription\n\n\n\n\nis_not_comment\nReturns whether a string is not a comment.\n\n\nread_distances_dat\nRead a distances.dat plumed output file.\n\n\nread_edissoc\nReads a edissoc file and turns it into a dict.\n\n\nread_json\nReturn JSON file content as dict.\n\n\nread_plumed\nRead a plumed.dat configuration file.\n\n\nread_top\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\n\n\nresolve_includes\nResolve #include statements in a (top/itp) file.\n\n\nwrite_json\nWrite dict to file according to JSON format.\n\n\nwrite_plumed\nWrite a plumed.dat configuration file.\n\n\nwrite_top\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nparsing.is_not_comment(c)\nReturns whether a string is not a comment.\nUsed for topology like files that use ‘;’ for comments.\n\n\n\nparsing.read_distances_dat(distances_dat)\nRead a distances.dat plumed output file.\n\n\n\nparsing.read_edissoc(path)\nReads a edissoc file and turns it into a dict.\nThe dissociation energy is assigned per pair of atom names. Atom names are unique to a residue, and the dict is nested by residues. The set of bond atoms make up the key, the dissociation energy E_dissoc [kJ mol-1] is the value.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. Path(“edissoc.dat”)\nrequired\n\n\n\n\n\n\n\nparsing.read_json(path)\nReturn JSON file content as dict.\n\n\n\nparsing.read_plumed(path)\nRead a plumed.dat configuration file.\nFollows the plumed naming scheme of label, keyword, action.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nPlumed_dict\ndict with keys: ‘distances’ and ‘prints’ Each is a dict/list of dicts containing plumed keywords\n\n\n\n\n\n\n\nparsing.read_top(path, ffdir=None, use_gmx_dir=True)\nRead a topology file (.top,.itp,*.rtp) into a raw TopologyDict represenation.\nAssumptions and limitation:\n\n#include statements will be resolved\ncomments will be removed\nall lines are stripped of leading and trailing whitespace\n#undef is not supported\na section within ifdef may be a subsection of a section that was started outside of the ifdef\n#if..#endif statements only surround a full section or subsection, not individual lines within a section and a section may either be contained within if … else or it may not be, but it can not be duplicated with one part inside and one outside.\nif .. else can’t be nested\n#include s that don’t resolve to a valid file path are silently dropped\nsections that can have subsections can also exist multiple, separate times e.g. moleculetype will appear multiple times and they should not be merged\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nPath to the topology file.\nrequired\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nEvery section, apart from ffdir and define,\n\n\n\ncomes with a condition that can be checked against the\n\n\n\ndefines by the helper functions to determine if the content\n\n\n\n(a list of lists) should come from content or else_content.\n\n\n\nSome sections such as moleculetype also come with subsections.\n\n\n\n\n\n\n\nraw_top =\n{'ffdir': PosixPath('/usr/share/gromacs/top/amber99.ff'),\n'define': {'_FF_AMBER': [], '_FF_AMBER99': []},\n'defaults': {'content': [['1', '2', 'yes', '0.5', '0.8333']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'atomtypes': {'content': [\n['C', '6', '12.01', '0.0000', 'A', '3.39967e-01', '3.59824e-01'],\n['MNH3', '0', '0.0000', '0.0000', 'A', '0.00000e+00', '0.00000e+00']],\n'else_content': [],\n'extra': [],\n'condition': None},\n'moleculetype_Urea': {'content': [['Urea', '3']],\n'else_content': [],\n'extra': [],\n'condition': None,\n'subsections': {'atoms': {'content': [['1',\n    'C',\n    '1',\n    'URE',\n    'C',\n    '1',\n    '0.880229',\n    '12.01000'],\n    ['2', 'O', '1', 'URE', 'O', '2', '-0.613359', '16.00000'],\n    ['3', 'N', '1', 'URE', 'N1', '3', '-0.923545', '14.01000'],\n    ['4', 'H', '1', 'URE', 'H11', '4', '0.395055', '1.00800'],\n    ['5', 'H', '1', 'URE', 'H12', '5', '0.395055', '1.00800'],\n    ['6', 'N', '1', 'URE', 'N2', '6', '-0.923545', '14.01000'],\n    ['7', 'H', '1', 'URE', 'H21', '7', '0.395055', '1.00800'],\n    ['8', 'H', '1', 'URE', 'H22', '8', '0.395055', '1.00800']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'bonds': {'content': [['1', '2'],\n    ['1', '3'],\n    ['1', '6'],\n    ['3', '4'],\n    ['3', '5'],\n    ['6', '7'],\n    ['6', '8']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'dihedrals': {'content': [['2', '1', '3', '4', '9'],\n    ['2', '1', '3', '5', '9'],\n    ['2', '1', '6', '7', '9'],\n    ['2', '1', '6', '8', '9'],\n    ['3', '1', '6', '7', '9'],\n    ['3', '1', '6', '8', '9'],\n    ['6', '1', '3', '4', '9'],\n    ['6', '1', '3', '5', '9'],\n    ['3', '6', '1', '2', '4'],\n    ['1', '4', '3', '5', '4'],\n    ['1', '7', '6', '8', '4']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'position_restraints': {'content': [['1', '1', '1000', '1000', '1000'],\n    ['2', '1', '1000', '0', '1000'],\n    ['3', '1', '1000', '0', '0']],\n    'else_content': [],\n    'extra': [],\n    'condition': None},\n'dihedral_restraints': {'content': [['3',\n    '6',\n    '1',\n    '2',\n    '1',\n    '180',\n    '0',\n    '10'],\n    ['1', '4', '3', '5', '1', '180', '0', '10']],\n    'else_content': [],\n    'extra': [],\n    'condition': None}}},\n}\n\n\n\n\nparsing.resolve_includes(path, gmx_builtin_ffs=None)\nResolve #include statements in a (top/itp) file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nPath\nFilepath to read.\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist[str]\nList of lines.\n\n\nOptional[Path]\nPath to the ff directory if one of the includes used a file from it.\n\n\n\n\n\n\n\nparsing.write_json(d, path)\nWrite dict to file according to JSON format.\n\n\n\nparsing.write_plumed(d, path)\nWrite a plumed.dat configuration file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nd\nPlumed_dict\nDictionary containing ‘labeled_action’, ‘other’ and ‘prints’\nrequired\n\n\npath\nPath\nPath to the file. E.g. “plumed.dat”\nrequired\n\n\n\n\n\n\n\nparsing.write_top(top, outfile)\nWrite a TopologyDict to a topology file.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopologyDict\nRaw dictionary represenation of the topology.\nrequired\n\n\noutfile\nPath\nPath to the topology file to write to.\nrequired"
+    "text": "constants\nComstants used throughout KIMMDY\n\n\n\n\n\nName\nDescription\n\n\n\n\nATOMTYPE_BONDORDER\nTo determin if an atom is a radical.\n\n\nATOMTYPE_BONDORDER_FLAT\nTo determin if an atom is a radical.",
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-    "text": "runmanager\nThe Runmanager is the main entry point of the program.\nIt manages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nDescription\n\n\n\n\nRunManager\nThe Runmanager is the main entry point of the program.\n\n\nState\nState of the system.\n\n\n\n\n\nrunmanager.RunManager(self, config)\nThe Runmanager is the main entry point of the program.\nManages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nconfig\nConfig\nThe configuration object.\n\n\ntasks\nqueue.Queue[Task]\nTasks from config.\n\n\ncrr_tasks\nqueue.Queue[Task]\nCurrent tasks.\n\n\niteration\nint\nCurrent iteration.\n\n\nstate\nState\nCurrent state of the system.\n\n\nrecipe_collection\nRecipeCollection\nCollection of recipes.\n\n\nlatest_files\ndict[str, Path]\nDictionary of latest files.\n\n\nhistfile\nPath\nPath to history file.\n\n\ntop\n\nTopology object.\n\n\nfilehist\nlist[dict[str, TaskFiles]]\nList of dictionaries of TaskFiles.\n\n\ntask_mapping\n\nMapping of task names to runmanager methods.\n\n\nreaction_plugins\nlist[ReactionPlugin]\nList of initialized reaction plugins used in the sequence.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_latest\nReturns path to latest file of given type.\n\n\n\n\n\nrunmanager.RunManager.get_latest(suffix)\nReturns path to latest file of given type.\nFor .dat files (in general ambiguous extensions) use full file name. Errors if file is not found.\n\n\n\n\n\nrunmanager.State()\nState of the system. one of IDLE, MD, REACTION, SETUP, DONE.\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_existing_files\nInitialize latest_files with every existing file defined in config\n\n\n\n\n\nrunmanager.get_existing_files(config)\nInitialize latest_files with every existing file defined in config"
+    "text": "Name\nDescription\n\n\n\n\nATOMTYPE_BONDORDER\nTo determin if an atom is a radical.\n\n\nATOMTYPE_BONDORDER_FLAT\nTo determin if an atom is a radical.",
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-    "text": "Name\nDescription\n\n\n\n\nRunManager\nThe Runmanager is the main entry point of the program.\n\n\nState\nState of the system.\n\n\n\n\n\nrunmanager.RunManager(self, config)\nThe Runmanager is the main entry point of the program.\nManages the queue of tasks, communicates with the rest of the program and keeps track of global state.\n\n\n\n\n\nName\nType\nDescription\n\n\n\n\nconfig\nConfig\nThe configuration object.\n\n\ntasks\nqueue.Queue[Task]\nTasks from config.\n\n\ncrr_tasks\nqueue.Queue[Task]\nCurrent tasks.\n\n\niteration\nint\nCurrent iteration.\n\n\nstate\nState\nCurrent state of the system.\n\n\nrecipe_collection\nRecipeCollection\nCollection of recipes.\n\n\nlatest_files\ndict[str, Path]\nDictionary of latest files.\n\n\nhistfile\nPath\nPath to history file.\n\n\ntop\n\nTopology object.\n\n\nfilehist\nlist[dict[str, TaskFiles]]\nList of dictionaries of TaskFiles.\n\n\ntask_mapping\n\nMapping of task names to runmanager methods.\n\n\nreaction_plugins\nlist[ReactionPlugin]\nList of initialized reaction plugins used in the sequence.\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_latest\nReturns path to latest file of given type.\n\n\n\n\n\nrunmanager.RunManager.get_latest(suffix)\nReturns path to latest file of given type.\nFor .dat files (in general ambiguous extensions) use full file name. Errors if file is not found.\n\n\n\n\n\nrunmanager.State()\nState of the system. one of IDLE, MD, REACTION, SETUP, DONE."
+    "text": "topology.atomic\nAtomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc. The order of the fields comes from the gromacs topology file format. See gromacs manual\n\n\n\n\n\nName\nDescription\n\n\n\n\nAngle\nInformation about one angle\n\n\nAngleType\nInformation about one angletype\n\n\nAtom\nInformation about one atom\n\n\nAtomType\nInformation about one atom type\n\n\nBond\nInformation about one bond\n\n\nBondType\nInformation about one bondtype\n\n\nDihedral\nInformation about one proper or improper dihedral\n\n\nDihedralRestraint\nInformation about one dihedral restraint.\n\n\nDihedralType\nInformation about one dihedraltype\n\n\nExclusion\nInformation about one exclusion\n\n\nMultipleDihedralTypes\nMultiple DihedralTypess with the same ai, aj, ak, al\n\n\nMultipleDihedrals\nMultiple Dihedrals with the same ai, aj, ak, al\n\n\nPair\nInformation about one pair\n\n\nPositionRestraint\nInformation about one position restraint.\n\n\nResidueAtomSpec\nInformation about one atom in a residue\n\n\nResidueBondSpec\nInformation about one bond in a residue\n\n\nResidueImproperSpec\nInformation about one improper dihedral in a residue\n\n\nResidueProperSpec\nInformation about one proper dihedral in a residue\n\n\nResidueType\nInformation about one residuetype from aminoacids.rtp\n\n\nSettle\nInformation about one settles\n\n\n\n\n\ntopology.atomic.Angle(ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angle\nA class containing angle information as in the angles section of the topology.\nFrom gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj &lt; ai &lt; ak\n\n\n\ntopology.atomic.AngleType(i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angletype\nA class containing angle type information as in the angletypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j k func th0 cth\n\n\n\ntopology.atomic.Atom(nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=field(default_factory=list), is_radical=False)\nInformation about one atom\nA class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.\nFrom gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n\n\n\ntopology.atomic.AtomType(type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)\nInformation about one atom type\nA class containing atom type information as in the atomtypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon\n\n\n\ntopology.atomic.Bond(ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)\nInformation about one bond\nA class containing bond information as in the bonds section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai &lt; aj\n\n\n\ntopology.atomic.BondType(i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one bondtype\nA class containing bond information as in the bondtype section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes\n\n\n\ntopology.atomic.Dihedral(ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)\nInformation about one proper or improper dihedral\nA class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.\nFrom gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj &lt; ak\n\n\n\ntopology.atomic.DihedralRestraint(ai, aj, ak, al, type, phi, dphi, fc)\nInformation about one dihedral restraint.\nA class containing information as in the dihedral_restraints section of the topology.\nFrom gromacs topology: ; ai aj ak al type phi dphi fc\n\n\n\ntopology.atomic.DihedralType(i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)\nInformation about one dihedraltype\nA class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.\nFrom gromacs version of the amber* ff: ; i j k l func phase kd pn\n\n\n\ntopology.atomic.Exclusion(ai, aj, ak=None, al=None)\nInformation about one exclusion\nA class containing atom information as in the exclusions section of the topology.\nFrom gromacs topology: ; ai aj ak al\n\n\n\ntopology.atomic.MultipleDihedralTypes(ai, aj, ak, al, funct, dihedral_types)\nMultiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedral_types dict is the periodicity (c2).\n\n\n\ntopology.atomic.MultipleDihedrals(ai, aj, ak, al, funct, dihedrals)\nMultiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedrals dict is the periodicity (c2).\n\n\n\ntopology.atomic.Pair(ai, aj, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one pair\nA class containing pair information as in the pair section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3\n\n\n\ntopology.atomic.PositionRestraint(ai, funct, fc, condition=None)\nInformation about one position restraint.\nA class containing information as in the position_restraints section of the topology.\nFrom gromacs topology: ; ai funct fc(x,y,z)\n\n\n\ntopology.atomic.ResidueAtomSpec(name, type, charge, cgrp)\nInformation about one atom in a residue\n; name type charge chargegroup\n\n\n\ntopology.atomic.ResidueBondSpec(atom1, atom2, b0=None, kb=None)\nInformation about one bond in a residue\n; atom1 atom2 b0 kb\n\n\n\ntopology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one improper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)\n\n\n\ntopology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one proper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2\n\n\n\ntopology.atomic.ResidueType(residue, atoms, bonds, proper_dihedrals, improper_dihedrals)\nInformation about one residuetype from aminoacids.rtp\n\n\n\ntopology.atomic.Settle(nr, funct, doh, dhh)\nInformation about one settles\nA class containing atom information as in the settle section of the topology.\nFrom gromacs topology: ; nr funct doh dhh",
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-    "text": "Name\nDescription\n\n\n\n\nget_existing_files\nInitialize latest_files with every existing file defined in config\n\n\n\n\n\nrunmanager.get_existing_files(config)\nInitialize latest_files with every existing file defined in config"
+    "text": "Name\nDescription\n\n\n\n\nAngle\nInformation about one angle\n\n\nAngleType\nInformation about one angletype\n\n\nAtom\nInformation about one atom\n\n\nAtomType\nInformation about one atom type\n\n\nBond\nInformation about one bond\n\n\nBondType\nInformation about one bondtype\n\n\nDihedral\nInformation about one proper or improper dihedral\n\n\nDihedralRestraint\nInformation about one dihedral restraint.\n\n\nDihedralType\nInformation about one dihedraltype\n\n\nExclusion\nInformation about one exclusion\n\n\nMultipleDihedralTypes\nMultiple DihedralTypess with the same ai, aj, ak, al\n\n\nMultipleDihedrals\nMultiple Dihedrals with the same ai, aj, ak, al\n\n\nPair\nInformation about one pair\n\n\nPositionRestraint\nInformation about one position restraint.\n\n\nResidueAtomSpec\nInformation about one atom in a residue\n\n\nResidueBondSpec\nInformation about one bond in a residue\n\n\nResidueImproperSpec\nInformation about one improper dihedral in a residue\n\n\nResidueProperSpec\nInformation about one proper dihedral in a residue\n\n\nResidueType\nInformation about one residuetype from aminoacids.rtp\n\n\nSettle\nInformation about one settles\n\n\n\n\n\ntopology.atomic.Angle(ai, aj, ak, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angle\nA class containing angle information as in the angles section of the topology.\nFrom gromacs topology: ; ai aj ak funct c0 c1 c2 c3 With aj &lt; ai &lt; ak\n\n\n\ntopology.atomic.AngleType(i, j, k, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one angletype\nA class containing angle type information as in the angletypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j k func th0 cth\n\n\n\ntopology.atomic.Atom(nr, type, resnr, residue, atom, cgnr, charge, mass=None, typeB=None, chargeB=None, massB=None, bound_to_nrs=field(default_factory=list), is_radical=False)\nInformation about one atom\nA class containing atom information as in the atoms section of the topology. An atom keeps a list of which atoms it is bound to and its radical state.\nFrom gromacs topology: ; nr type resnr residue atom cgnr charge mass typeB chargeB massB\n\n\n\ntopology.atomic.AtomType(type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)\nInformation about one atom type\nA class containing atom type information as in the atomtypes section of the forcefield.\nFrom gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon\n\n\n\ntopology.atomic.Bond(ai, aj, funct, c0=None, c1=None, c2=None, c3=None, c4=None, c5=None)\nInformation about one bond\nA class containing bond information as in the bonds section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3 c4 c5 With ai &lt; aj\n\n\n\ntopology.atomic.BondType(i, j, id, id_sym, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one bondtype\nA class containing bond information as in the bondtype section of the forcefield.\nFrom gromacs version of the amber* ff: ; i j func b0 kb Where i and j are atomtypes\n\n\n\ntopology.atomic.Dihedral(ai, aj, ak, al, funct, c0=None, c1=None, periodicity='', c3=None, c4=None, c5=None)\nInformation about one proper or improper dihedral\nA class containing dihedral information as in the dihedrals section of the topology. Improper dihedrals have funct 4. Proper dihedrals have funct != 4, mostly funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity.\nFrom gromacs topology: ; ai aj ak al funct c0 c1 c2 c3 c4 c5 For proper dihedrals (funct 9): aj &lt; ak\n\n\n\ntopology.atomic.DihedralRestraint(ai, aj, ak, al, type, phi, dphi, fc)\nInformation about one dihedral restraint.\nA class containing information as in the dihedral_restraints section of the topology.\nFrom gromacs topology: ; ai aj ak al type phi dphi fc\n\n\n\ntopology.atomic.DihedralType(i, j, k, l, id, id_sym, funct, c0, c1, periodicity, c3=None, c4=None, c5=None)\nInformation about one dihedraltype\nA class containing dihedral type information as in the dihedraltypes section of the forcefield. Improper dihedrals have funct 4. Proper dihedrals have funct 9.\nNote that proper dihedrals of type 9 can be defined multiple times, for different periodicities. This is why would-be parameter c2 is called periodicity and part of the id.\nFrom gromacs version of the amber* ff: ; i j k l func phase kd pn\n\n\n\ntopology.atomic.Exclusion(ai, aj, ak=None, al=None)\nInformation about one exclusion\nA class containing atom information as in the exclusions section of the topology.\nFrom gromacs topology: ; ai aj ak al\n\n\n\ntopology.atomic.MultipleDihedralTypes(ai, aj, ak, al, funct, dihedral_types)\nMultiple DihedralTypess with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedral_types dict is the periodicity (c2).\n\n\n\ntopology.atomic.MultipleDihedrals(ai, aj, ak, al, funct, dihedrals)\nMultiple Dihedrals with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedrals dict is the periodicity (c2).\n\n\n\ntopology.atomic.Pair(ai, aj, funct, c0=None, c1=None, c2=None, c3=None)\nInformation about one pair\nA class containing pair information as in the pair section of the topology.\nFrom gromacs topology: ; ai aj funct c0 c1 c2 c3\n\n\n\ntopology.atomic.PositionRestraint(ai, funct, fc, condition=None)\nInformation about one position restraint.\nA class containing information as in the position_restraints section of the topology.\nFrom gromacs topology: ; ai funct fc(x,y,z)\n\n\n\ntopology.atomic.ResidueAtomSpec(name, type, charge, cgrp)\nInformation about one atom in a residue\n; name type charge chargegroup\n\n\n\ntopology.atomic.ResidueBondSpec(atom1, atom2, b0=None, kb=None)\nInformation about one bond in a residue\n; atom1 atom2 b0 kb\n\n\n\ntopology.atomic.ResidueImproperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one improper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cp) c2(mult)\n\n\n\ntopology.atomic.ResidueProperSpec(atom1, atom2, atom3, atom4, c0, c1, c2)\nInformation about one proper dihedral in a residue\n; atom1 atom2 atom3 atom4 c0(q0) c1(cq) c2\n\n\n\ntopology.atomic.ResidueType(residue, atoms, bonds, proper_dihedrals, improper_dihedrals)\nInformation about one residuetype from aminoacids.rtp\n\n\n\ntopology.atomic.Settle(nr, funct, doh, dhh)\nInformation about one settles\nA class containing atom information as in the settle section of the topology.\nFrom gromacs topology: ; nr funct doh dhh",
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-    "text": "topology.utils\n\n\n\n\n\nName\nDescription\n\n\n\n\nget_is_reactive_predicate_f\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\nget_moleculetype_atomics\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nget_moleculetype_header\nGet content of the header of a moleculetype from a topology dict.\n\n\nget_protein_section\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nget_reactive_section\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\nget_residue_fragments\nSplits a residue into fragments after a bond has been broken.\n\n\nget_top_section\nGet content of a section from a topology dict.\n\n\nis_not_solvent_or_ion\nReturns whether a moleculetype name is not solvent or ion.\n\n\nset_moleculetype_atomics\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nset_protein_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_reactive_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_top_section\nSet content of a section from a topology dict.\n\n\n\n\n\ntopology.utils.get_is_reactive_predicate_f(cfg)\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\n\ntopology.utils.get_moleculetype_atomics(top, moleculetype)\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_moleculetype_header(top, moleculetype)\nGet content of the header of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_protein_section(top, name)\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.get_reactive_section(top, name)\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\n\ntopology.utils.get_residue_fragments(top, residue, start1, start2, iterations=20)\nSplits a residue into fragments after a bond has been broken.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopology\nTopology\nrequired\n\n\nresidue\nlist[Atom]\nAll atoms of current residue. Ok, when it contains more atoms as long as those are not connected to broken bond.\nrequired\n\n\nstart1\nAtom\nFirst atom with broken bond\nrequired\n\n\nstart2\nAtom\nSecond atom with broken bond\nrequired\n\n\niterations\nint\nMax number of bonds from start atoms to be included when building fragmets, by default 20\n20\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nTwo fragments, or one fragment and empty set in case the\nresidue did not change its size.\n\n\n\n\n\n\n\ntopology.utils.get_top_section(top, name, moleculetype=None)\nGet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.is_not_solvent_or_ion(name)\nReturns whether a moleculetype name is not solvent or ion.\n\n\n\ntopology.utils.set_moleculetype_atomics(top, name, atomics, create=False)\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\nIf create is True, a new section is created if it does not exist.\n\n\n\ntopology.utils.set_protein_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_reactive_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_top_section(top, name, value, moleculetype=None)\nSet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result."
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-    "text": "Name\nDescription\n\n\n\n\nget_is_reactive_predicate_f\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\nget_moleculetype_atomics\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nget_moleculetype_header\nGet content of the header of a moleculetype from a topology dict.\n\n\nget_protein_section\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nget_reactive_section\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\nget_residue_fragments\nSplits a residue into fragments after a bond has been broken.\n\n\nget_top_section\nGet content of a section from a topology dict.\n\n\nis_not_solvent_or_ion\nReturns whether a moleculetype name is not solvent or ion.\n\n\nset_moleculetype_atomics\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\n\n\nset_protein_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_reactive_section\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\nset_top_section\nSet content of a section from a topology dict.\n\n\n\n\n\ntopology.utils.get_is_reactive_predicate_f(cfg)\nReturns whether a moleculetype name is configured to be recognized as reactive.\n\n\n\ntopology.utils.get_moleculetype_atomics(top, moleculetype)\nGet content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_moleculetype_header(top, moleculetype)\nGet content of the header of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.get_protein_section(top, name)\nGet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.get_reactive_section(top, name)\nGet content of a section in the Reactive moleculetype from a topology dict.\n\n\n\ntopology.utils.get_residue_fragments(top, residue, start1, start2, iterations=20)\nSplits a residue into fragments after a bond has been broken.\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ntop\nTopology\nTopology\nrequired\n\n\nresidue\nlist[Atom]\nAll atoms of current residue. Ok, when it contains more atoms as long as those are not connected to broken bond.\nrequired\n\n\nstart1\nAtom\nFirst atom with broken bond\nrequired\n\n\nstart2\nAtom\nSecond atom with broken bond\nrequired\n\n\niterations\nint\nMax number of bonds from start atoms to be included when building fragmets, by default 20\n20\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nTwo fragments, or one fragment and empty set in case the\nresidue did not change its size.\n\n\n\n\n\n\n\ntopology.utils.get_top_section(top, name, moleculetype=None)\nGet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\n\n\n\ntopology.utils.is_not_solvent_or_ion(name)\nReturns whether a moleculetype name is not solvent or ion.\n\n\n\ntopology.utils.set_moleculetype_atomics(top, name, atomics, create=False)\nSet content of the atomics (atoms/bonds/angles etc.) of a moleculetype from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.\nIf create is True, a new section is created if it does not exist.\n\n\n\ntopology.utils.set_protein_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_reactive_section(top, name, value)\nSet content of a section in the first moleculetype (protein) from a topology dict.\n\n\n\ntopology.utils.set_top_section(top, name, value, moleculetype=None)\nSet content of a section from a topology dict.\nResolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result."
+    "text": "Tutorials to help you get familiar with KIMMDY.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nGet Started\n\n\n\n\n\n\nuser\n\n\n\n\n\n\n\n\n\nJannik Buhr\n\n\n\n\n\n\n\n\n\n\n\n\nRun KIMMDY from Colbuilder fibril\n\n\n\n\n\n\nuser\n\n\n\n\n\n\n\n\n\nEric Hartmann\n\n\n\n\n\n\n\n\n\n\n\n\nWrite a Reaction Plugin\n\n\n\n\n\n\ndeveloper\n\n\n\nIn this tutorial, you will learn how to create your own reaction plugin in a GitHub repository.\n\n\n\n\n\nEric Hartmann\n\n\n\n\n\n\nNo matching items\n\n Back to top",
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-    "text": "By creating a GitHub repository, you have version control for your plugin and can share it with others. To set it up, follow these instructions."
+    "text": "By creating a GitHub repository, you have version control for your plugin and can share it with others. To set it up, follow these instructions.",
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-    "text": "By creating a GitHub repository, you have version control for your plugin and can share it with others. To set it up, follow these instructions."
+    "text": "By creating a GitHub repository, you have version control for your plugin and can share it with others. To set it up, follow these instructions.",
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     "section": "Adding the functionality of the plugin",
-    "text": "Adding the functionality of the plugin\n\nMain code\nA reaction plugin has to be a derived class from the ReactionPlugin base class. Such a class has the attributes name, runmng and config and the method get_recipe_collection, which takes a TaskFiles object as argument and returns a RecipeCollection.\nThe name is a simple string and may be useful for logging. runmng is the central RunManager of a kimmdy run and has plenty of useful attributes for your plugin, especially the system Topology, which can be accessed via self.runmg.top. config contains the reaction plugin configuration as specified in the kimmdy configuration file (typically named kimmdy.yml). A RecipeCollection contains Recipes with predefined RecipeSteps that can be used to define the modification to the system for the reaction. A Recipe also contains the rates of the specified reaction and the timespans during which the corresponding rates are valid. An example plugin can be seen below.\n\n\nPlugin main code (reaction.py)\nfrom kimmdy.recipe import (\n    Bind,\n    Recipe,\n    RecipeCollection,\n)\nfrom kimmdy.plugins import ReactionPlugin\nfrom kimmdy.tasks import TaskFiles\nfrom kimmdy.utils import (\n    get_atomnrs_from_plumedid,\n)\nfrom kimmdy.parsing import (\n    read_plumed,\n    read_distances_dat,\n)\n\n\nclass BindReaction(ReactionPlugin):\n    \"\"\"Reaction to bind two particles if they are in proximity\n    \"\"\"\n\n    def get_recipe_collection(self, files: TaskFiles):\n        logger = files.logger\n        logger.debug(\"Getting recipe for reaction: Bind\")\n\n        # get cutoff distance from config, unit is [nm]\n        cutoff = self.config.distance\n\n        # Initialization of objects from files\n        distances = read_distances_dat(files.input[\"plumed_out\"])\n        plumed = read_plumed(files.input[\"plumed\"])\n\n        recipes = []\n        # check distances file for values lower than the cutoff\n        for plumedid, dists in distances.items():\n            if plumedid == \"time\":\n                continue\n            # checks only last frame\n            if dists[-1] &lt; cutoff:\n                # get atomnrs from plumedid \n                atomnrs = get_atomnrs_from_plumedid(plumedid, plumed)\n                recipes.append(\n                    Recipe(\n                        recipe_steps=[\n                            Bind(atom_id_1=atomnrs[0], atom_id_2=atomnrs[1]),\n                        ],\n                        rates=[1],\n                        timespans=[(distances[\"time\"][0], distances[\"time\"][-1])],\n                    )\n                )\n\n        return RecipeCollection(recipes)\n\n\n\n\nConfiguration file schema\nA plugin defines which variables it needs in a schema. The schema can contain default values and types of these variables. For a Kimmdy run, reaction plugin variables are defined in the configuration file (kimmdy.yml). An example schema can be seen below.\n\n\nPlugin schema (kimmdy-yaml-schema.json)\n\n\n\nkimmdy-yaml-schema.json\n\n{\n  \"$schema\": \"https://json-schema.org/draft/2020-12/schema\",\n  \"type\": \"object\",\n  \"$id\": \"bind-config\",\n  \"description\": \"Settings for bind reactions\",\n  \"additionalProperties\": false,\n  \"properties\": {\n    \"distance\": {\n      \"description\": \"Cutoff distance for two particles to bind [nm]\",\n      \"type\": \"float\",\n      \"pytype\": \"float\"\n    },\n    \"kmc\": {\n      \"description\": \"KMC algorithm for this reaction.\",\n      \"type\": \"string\",\n      \"pytype\": \"str\",\n      \"enum\": [\"rfkmc\", \"frm\", \"extrande\"],\n      \"default\": \"rfkmc\"\n    }\n  },\n  \"required\": [\"distance\"]\n}"
+    "text": "Adding the functionality of the plugin\n\nMain code\nA reaction plugin has to be a derived class from the ReactionPlugin base class. Such a class has the attributes name, runmng and config and the method get_recipe_collection, which takes a TaskFiles object as argument and returns a RecipeCollection.\nThe name is a simple string and may be useful for logging. runmng is the central RunManager of a kimmdy run and has plenty of useful attributes for your plugin, especially the system Topology, which can be accessed via self.runmg.top. config contains the reaction plugin configuration as specified in the kimmdy configuration file (typically named kimmdy.yml). A RecipeCollection contains Recipes with predefined RecipeSteps that can be used to define the modification to the system for the reaction. A Recipe also contains the rates of the specified reaction and the timespans during which the corresponding rates are valid. An example plugin can be seen below.\n\n\nPlugin main code (reaction.py)\nfrom kimmdy.recipe import (\n    Bind,\n    Recipe,\n    RecipeCollection,\n)\nfrom kimmdy.plugins import ReactionPlugin\nfrom kimmdy.tasks import TaskFiles\nfrom kimmdy.utils import (\n    get_atomnrs_from_plumedid,\n)\nfrom kimmdy.parsing import (\n    read_plumed,\n    read_distances_dat,\n)\n\n\nclass BindReaction(ReactionPlugin):\n    \"\"\"Reaction to bind two particles if they are in proximity\n    \"\"\"\n\n    def get_recipe_collection(self, files: TaskFiles):\n        logger = files.logger\n        logger.debug(\"Getting recipe for reaction: Bind\")\n\n        # get cutoff distance from config, unit is [nm]\n        cutoff = self.config.distance\n\n        # Initialization of objects from files\n        distances = read_distances_dat(files.input[\"plumed_out\"])\n        plumed = read_plumed(files.input[\"plumed\"])\n\n        recipes = []\n        # check distances file for values lower than the cutoff\n        for plumedid, dists in distances.items():\n            if plumedid == \"time\":\n                continue\n            # checks only last frame\n            if dists[-1] &lt; cutoff:\n                # get atomnrs from plumedid \n                atomnrs = get_atomnrs_from_plumedid(plumedid, plumed)\n                recipes.append(\n                    Recipe(\n                        recipe_steps=[\n                            Bind(atom_id_1=atomnrs[0], atom_id_2=atomnrs[1]),\n                        ],\n                        rates=[1],\n                        timespans=[(distances[\"time\"][0], distances[\"time\"][-1])],\n                    )\n                )\n\n        return RecipeCollection(recipes)\n\n\n\n\nConfiguration file schema\nA plugin defines which variables it needs in a schema. The schema can contain default values and types of these variables. For a Kimmdy run, reaction plugin variables are defined in the configuration file (kimmdy.yml). An example schema can be seen below.\n\n\nPlugin schema (kimmdy-yaml-schema.json)\n\n\n\nkimmdy-yaml-schema.json\n\n{\n  \"$schema\": \"https://json-schema.org/draft/2020-12/schema\",\n  \"type\": \"object\",\n  \"$id\": \"bind-config\",\n  \"description\": \"Settings for bind reactions\",\n  \"additionalProperties\": false,\n  \"properties\": {\n    \"distance\": {\n      \"description\": \"Cutoff distance for two particles to bind [nm]\",\n      \"type\": \"float\",\n      \"pytype\": \"float\"\n    },\n    \"kmc\": {\n      \"description\": \"KMC algorithm for this reaction.\",\n      \"type\": \"string\",\n      \"pytype\": \"str\",\n      \"enum\": [\"rfkmc\", \"frm\", \"extrande\"],\n      \"default\": \"rfkmc\"\n    }\n  },\n  \"required\": [\"distance\"]\n}",
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     "section": "Making a python package",
-    "text": "Making a python package\nIt is necessary to make the plugin a python package to interface with Kimmdy. For this, package setup configuration files are necessary, for example setup.py and setup.cfg. In setup.cfg dependencies can be specified, which will be installed alongside the plugin. The interface with kimmdy is specified in the [options.entry_points] section. This section needs to refer to the class we created in the plugin main code and assign it to kimmdy.reaction_plugins, i.e. kimmdy.reaction_plugins = bind = &lt;path&gt;.&lt;to&gt;.&lt;main file&gt;:&lt;ClassName&gt;. Also, the directory containing the source code (typically src) is defined in [options.packages.find]. An example for setup.py and setup.cfg can be found below.\n\n\nsetup.py\nfrom setuptools import setup\n\nsetup()\n\n\n\n\nsetup.cfg\n\n\n\nsetup.cfg\n\n[metadata]\nname = kimmdy-reactions\nversion = 0.1\nlicense = GPL-3.0 \ndescription = Reaction template for KIMMDY\nlong_description = file: README.md\nauthor = Eric Hartmann\nauthor_email = eric.Hartmann@h-its.org\nclassifiers=\n        Programming Language :: Python :: 3\n        License :: OSI Approved :: MIT License\n        Operating System :: OS Independent\n\n[options]\npackages = find:\npackage_dir =\n    =src\ninclude_package_data = True\ninstall_requires =\n    MDAnalysis\n\npython_requires = &gt;= 3.9\n\n[options.packages.find]\nwhere=src\n\n[options.entry_points]\nkimmdy.reaction_plugins =\n    bind = bind.reaction:BindReaction\n\n\nThe main code and configuration schema file should then be moved to the specified source directory in a directory that has the name of the reaction plugin, i.e. src/&lt;plugin name&gt;/.\n\n\n\n\n\n\nTip\n\n\n\nBy adding the kimmdy tag on GitHub you can make your plugin discoverable by other users. It will show up in this list"
+    "text": "Making a python package\nIt is necessary to make the plugin a python package to interface with Kimmdy. For this, package setup configuration files are necessary, for example setup.py and setup.cfg. In setup.cfg dependencies can be specified, which will be installed alongside the plugin. The interface with kimmdy is specified in the [options.entry_points] section. This section needs to refer to the class we created in the plugin main code and assign it to kimmdy.reaction_plugins, i.e. kimmdy.reaction_plugins = bind = &lt;path&gt;.&lt;to&gt;.&lt;main file&gt;:&lt;ClassName&gt;. Also, the directory containing the source code (typically src) is defined in [options.packages.find]. An example for setup.py and setup.cfg can be found below.\n\n\nsetup.py\nfrom setuptools import setup\n\nsetup()\n\n\n\n\nsetup.cfg\n\n\n\nsetup.cfg\n\n[metadata]\nname = kimmdy-reactions\nversion = 0.1\nlicense = GPL-3.0 \ndescription = Reaction template for KIMMDY\nlong_description = file: README.md\nauthor = Eric Hartmann\nauthor_email = eric.Hartmann@h-its.org\nclassifiers=\n        Programming Language :: Python :: 3\n        License :: OSI Approved :: MIT License\n        Operating System :: OS Independent\n\n[options]\npackages = find:\npackage_dir =\n    =src\ninclude_package_data = True\ninstall_requires =\n    MDAnalysis\n\npython_requires = &gt;= 3.9\n\n[options.packages.find]\nwhere=src\n\n[options.entry_points]\nkimmdy.reaction_plugins =\n    bind = bind.reaction:BindReaction\n\n\nThe main code and configuration schema file should then be moved to the specified source directory in a directory that has the name of the reaction plugin, i.e. src/&lt;plugin name&gt;/.\n\n\n\n\n\n\nTip\n\n\n\nBy adding the kimmdy tag on GitHub you can make your plugin discoverable by other users. It will show up in this list",
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-    "text": "Improving code quality and reproducibility\nAdding tests will help in ensuring the plugin is working as expected. An example would help users to understand what your plugin does."
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-    "text": "Tutorials to help you get familiar with KIMMDY.\n\n\n\n\n\n\n\n\n  \n\n\n\n\nGet Started\n\n\n\n\n\n\n\nuser\n\n\n\n\n\n\n\n\n\n\n\nJannik Buhr\n\n\n\n\n\n\n  \n\n\n\n\nRun KIMMDY from Colbuilder fibril\n\n\n\n\n\n\n\nuser\n\n\n\n\n\n\n\n\n\n\n\nEric Hartmann\n\n\n\n\n\n\n  \n\n\n\n\nWrite a Reaction Plugin\n\n\n\n\n\n\n\ndeveloper\n\n\n\n\nIn this tutorial, you will learn how to create your own reaction plugin in a GitHub repository.\n\n\n\n\n\n\nEric Hartmann\n\n\n\n\n\n\nNo matching items\n\n Back to top"
+    "text": "Improving code quality and reproducibility\nAdding tests will help in ensuring the plugin is working as expected. An example would help users to understand what your plugin does.",
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-    "text": "The prefered method of starting a KIMMDY run is via the command line, though Python entry points are supported as well."
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-    "text": "KIMMDY\n\n!kimmdy --help\n\nusage: kimmdy [-h] [--input INPUT] [--checkpoint CHECKPOINT]\n              [--loglevel LOGLEVEL] [--logfile LOGFILE] [--show-plugins]\n              [--generate-jobscript] [--version] [--debug] [--callgraph]\n\nWelcome to KIMMDY. `kimmdy` runs KIMMDY, further tools are available as\n`kimmdy-...` commands. These are `-analysis`, `-modify-top` and `-build-\nexamples`. Access their help with `kimmdy-... -h.`\n\noptions:\n  -h, --help            show this help message and exit\n  --input INPUT, -i INPUT\n                        Kimmdy input file. Default `kimmdy.yml`\n  --checkpoint CHECKPOINT, -c CHECKPOINT\n                        File path of a kimmdy.cpt file to restart KIMMDY from\n                        a checkpoint. If a directory is given, the file\n                        kimmdy.cpt in that directory is used.\n  --loglevel LOGLEVEL, -l LOGLEVEL\n                        logging level (CRITICAL, ERROR, WARNING, INFO, DEBUG)\n  --logfile LOGFILE, -f LOGFILE\n                        logfile\n  --show-plugins        List available plugins\n  --generate-jobscript  Instead of running KIMMDY directly, generate at\n                        jobscript.sh for slurm HPC clusters.You can then run\n                        this jobscript with sbatch jobscript.sh\n  --version             show program's version number and exit\n  --debug               on error, drop into debugger\n  --callgraph           Generate visualization of function calls. Mostly\n                        useful for debugging and documentation."
+    "text": "KIMMDY\n\n!kimmdy --help\n\nusage: kimmdy [-h] [--input INPUT] [--checkpoint CHECKPOINT]\n              [--loglevel LOGLEVEL] [--logfile LOGFILE] [--show-plugins]\n              [--generate-jobscript] [--version] [--debug] [--callgraph]\n\nWelcome to KIMMDY. `kimmdy` runs KIMMDY, further tools are available as\n`kimmdy-...` commands. These are `-analysis`, `-modify-top` and `-build-\nexamples`. Access their help with `kimmdy-... -h.`\n\noptions:\n  -h, --help            show this help message and exit\n  --input INPUT, -i INPUT\n                        Kimmdy input file. Default `kimmdy.yml`\n  --checkpoint CHECKPOINT, -c CHECKPOINT\n                        File path of a kimmdy.cpt file to restart KIMMDY from\n                        a checkpoint. If a directory is given, the file\n                        kimmdy.cpt in that directory is used.\n  --loglevel LOGLEVEL, -l LOGLEVEL\n                        logging level (CRITICAL, ERROR, WARNING, INFO, DEBUG)\n  --logfile LOGFILE, -f LOGFILE\n                        logfile\n  --show-plugins        List available plugins\n  --generate-jobscript  Instead of running KIMMDY directly, generate at\n                        jobscript.sh for slurm HPC clusters.You can then run\n                        this jobscript with sbatch jobscript.sh\n  --version             show program's version number and exit\n  --debug               on error, drop into debugger\n  --callgraph           Generate visualization of function calls. Mostly\n                        useful for debugging and documentation.",
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-    "text": "Analysis\n\n!kimmdy-analysis --help\n\nusage: kimmdy-analysis [-h] module ...\n\nWelcome to the KIMMDY analysis module. Use this module to analyse existing\nKIMMDY runs.\n\npositional arguments:\n  module\n    trjcat            Concatenate trajectories of a KIMMDY run\n    energy            Plot GROMACS energy for a KIMMDY run\n    radical_population\n                      Plot population of radicals for one or multiple KIMMDY\n                      run(s)\n    rates             Plot rates of all possible reactions after a MD run.\n                      Rates must have been saved!\n    runtime           Plot runtime of the tasks of a kimmdy run.\n\noptions:\n  -h, --help          show this help message and exit"
+    "text": "Analysis\n\n!kimmdy-analysis --help\n\nusage: kimmdy-analysis [-h] module ...\n\nWelcome to the KIMMDY analysis module. Use this module to analyse existing\nKIMMDY runs.\n\npositional arguments:\n  module\n    trjcat            Concatenate trajectories of a KIMMDY run\n    energy            Plot GROMACS energy for a KIMMDY run\n    radical_population\n                      Plot population of radicals for one or multiple KIMMDY\n                      run(s)\n    rates             Plot rates of all possible reactions after a MD run.\n                      Rates must have been saved!\n    runtime           Plot runtime of the tasks of a kimmdy run.\n\noptions:\n  -h, --help          show this help message and exit",
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-    "text": "Remove Hydrogen\nThis module builds or restores the example directory in the package.\n\n!kimmdy-modify-top --help\n\nusage: kimmdy-modify-top [-h] [-p] [-r REMOVEH [REMOVEH ...]] [-c GROFILE]\n                         [-t RESIDUETYPES] [-x RADICALS]\n                         top out\n\nWelcome to the KIMMDY modify top module\n\npositional arguments:\n  top                   GROMACS top file\n  out                   Output top file name\n\noptions:\n  -h, --help            show this help message and exit\n  -p, --parameterize    Parameterize topology with grappa. (default: False)\n  -r REMOVEH [REMOVEH ...], --removeH REMOVEH [REMOVEH ...]\n                        Remove one or more hydrogens by atom nrs in the top\n                        file. (default: None)\n  -c GROFILE, --grofile GROFILE\n                        If necessary, also apply actions on gro file to create\n                        a compatible gro/top file pair. (default: None)\n  -t RESIDUETYPES, --residuetypes RESIDUETYPES\n                        GROMACS style residuetypes file. Necessary for\n                        parameterization with non-amber atom types. (default:\n                        None)\n  -x RADICALS, --radicals RADICALS\n                        Radicals in the system PRIOR to removing hydrogens\n                        with the removeH option. (default: )"
+    "text": "Remove Hydrogen\nThis module builds or restores the example directory in the package.\n\n!kimmdy-modify-top --help\n\nusage: kimmdy-modify-top [-h] [-p] [-r REMOVEH [REMOVEH ...]] [-c GROFILE]\n                         [-t RESIDUETYPES] [-x RADICALS]\n                         top out\n\nWelcome to the KIMMDY modify top module\n\npositional arguments:\n  top                   GROMACS top file\n  out                   Output top file name\n\noptions:\n  -h, --help            show this help message and exit\n  -p, --parameterize    Parameterize topology with grappa. (default: False)\n  -r REMOVEH [REMOVEH ...], --removeH REMOVEH [REMOVEH ...]\n                        Remove one or more hydrogens by atom nrs in the top\n                        file. (default: None)\n  -c GROFILE, --grofile GROFILE\n                        If necessary, also apply actions on gro file to create\n                        a compatible gro/top file pair. (default: None)\n  -t RESIDUETYPES, --residuetypes RESIDUETYPES\n                        GROMACS style residuetypes file. Necessary for\n                        parameterization with non-amber atom types. (default:\n                        None)\n  -x RADICALS, --radicals RADICALS\n                        Radicals in the system PRIOR to removing hydrogens\n                        with the removeH option. (default: )",
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-    "text": "Examples\nThis module builds or restores the example directory in the package.\n\n!kimmdy-build-examples --help\n\nusage: kimmdy-build-examples [-h] [-r [RESTORE]]\n\nBuild examples for KIMMDY.\n\noptions:\n  -h, --help            show this help message and exit\n  -r [RESTORE], --restore [RESTORE]\n                        Overwrite input files in existing example directories,\n                        use keyword 'hard' to also delete output files."
+    "text": "Examples\nThis module builds or restores the example directory in the package.\n\n!kimmdy-build-examples --help\n\nusage: kimmdy-build-examples [-h] [-r [RESTORE]]\n\nBuild examples for KIMMDY.\n\noptions:\n  -h, --help            show this help message and exit\n  -r [RESTORE], --restore [RESTORE]\n                        Overwrite input files in existing example directories,\n                        use keyword 'hard' to also delete output files.",
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+    "text": "How-To Guides\n\n\n\n\n\n\n   \n     \n     \n       Order By\n       Default\n         \n          Title\n        \n         \n          Author\n        \n     \n  \n    \n      \n      \n    \n\n\n\n\n\nTitle\n\n\nAuthor\n\n\n\n\n\n\nAnalyze a KIMMDY run\n\n\nKai Riedmiller\n\n\n\n\nContribute\n\n\n \n\n\n\n\nExamples\n\n\n \n\n\n\n\nHigh Performance Computing\n\n\n \n\n\n\n\nInstall Machine Learning Plugins\n\n\n \n\n\n\n\nReaction only\n\n\nKai Riedmiller\n\n\n\n\n\nNo matching items\n\n Back to top",
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-    "text": "Warning\n\n\n\nThe following plugins are not yet publicly available. As such, this guide is only for internal use and will be updated once the plugins are ready."
+    "text": "Warning\n\n\n\nThe following plugins are not yet publicly available. As such, this guide is only for internal use and will be updated once the plugins are ready.",
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     "section": "Complete Installation with ML Plugins",
-    "text": "Complete Installation with ML Plugins\nconda is required for this installation to access the tensorflow and openmm packages. Solving the dependencies of the environment can overflow memory on the original conda solver. So we change the solver to the new libmamba. We also add the conda-forge channel to access the openmm package.\nconda install -n base conda-libmamba-solver\nconda config --set solver libmamba\nconda config --append channels conda-forge\nCreate a new environment.\nconda create -n kimmdy_full python=3.10 tensorflow==2.10 openmm\nconda activate kimmdy_full\nClone all repositories and install them in editable mode for development.\ngit clone git@github.com:hits-mbm-dev/kimmdy.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-reactions.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-grappa.git\ngit clone git@github.com:hits-mbm-dev/HAT_reaction_plugin.git\ngit clone git@github.com:hits-mbm-dev/grappa.git\n\npushd kimmdy\n# installs kimmdy, kimmdy-reactions and kimmdy-grappa\npip install -r requirements.txt\npopd\n\npushd HAT_reaction_plugin\npip install -r requirements.txt\npopd\n\npushd grappa\npip install -e .\npopd\n\nPotential problems when running\n\nopenmm can’t find the correct libstdc++.so.6\n\nsymlink system libstdc++.so.6 to the conda libstdc++.so.6\n\n\npushd $CONDA_PREFIX/lib\nmv libstdc++.so.6 libstdc++.so.6.old\nln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 libstdc++.so.6\npopd"
+    "text": "Complete Installation with ML Plugins\nconda is required for this installation to access the tensorflow and openmm packages. Solving the dependencies of the environment can overflow memory on the original conda solver. So we change the solver to the new libmamba. We also add the conda-forge channel to access the openmm package.\nconda install -n base conda-libmamba-solver\nconda config --set solver libmamba\nconda config --append channels conda-forge\nCreate a new environment.\nconda create -n kimmdy_full python=3.10 tensorflow==2.10 openmm\nconda activate kimmdy_full\nClone all repositories and install them in editable mode for development.\ngit clone git@github.com:hits-mbm-dev/kimmdy.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-reactions.git\ngit clone git@github.com:hits-mbm-dev/kimmdy-grappa.git\ngit clone git@github.com:hits-mbm-dev/HAT_reaction_plugin.git\ngit clone git@github.com:hits-mbm-dev/grappa.git\n\npushd kimmdy\n# installs kimmdy, kimmdy-reactions and kimmdy-grappa\npip install -r requirements.txt\npopd\n\npushd HAT_reaction_plugin\npip install -r requirements.txt\npopd\n\npushd grappa\npip install -e .\npopd\n\nPotential problems when running\n\nopenmm can’t find the correct libstdc++.so.6\n\nsymlink system libstdc++.so.6 to the conda libstdc++.so.6\n\n\npushd $CONDA_PREFIX/lib\nmv libstdc++.so.6 libstdc++.so.6.old\nln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 libstdc++.so.6\npopd",
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+    "text": "Through kimmdy-analysis, several tools are provided to analyze various aspects of KIMMDY runs.",
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+    "text": "Energy\nkimmdy-analysis energy sets the usual energy analysis by gmx energy into the context of KIMMDY, by showing the KIMMDY MD steps next to the energy plot. An example KIMMDY run of three HAT reactions is shown below.\nAll energy terms supported in the GROMACS tool gmx energy can be plotted. The lowest plot shows which KIMMDY MD run is running at a given time. Here, three HAT reactions are performed, each in between two equilibrium MD simulations.",
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+    "section": "Radical Occupancy",
+    "text": "Radical Occupancy\nkimmdy-analysis radical_population analyzes where, and for how long radi- cals are in the system. The resulting statistic can be visualized in two ways. First, as values on a three-dimensional snapshot of the system, as shown in below. For this, a pdb file of the structure is generated, containing the calculated radical occupancy as its beta value for visualization with established software, like vmd. And second, as a bar plot of the fractional radical occupancy per atom. Depending on the number of involved atoms, the structure, or the bar plot might be more useful.",
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+    "section": "Radical Migrations",
+    "text": "Radical Migrations\nThe kimmdy-analysis radical_migration tool can generate visualizations. Depicting between which atoms HAT reactions occur. The arrows can be colored according to the number of HAT reactions, or the maximum rate for the respective transition.",
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+    "section": "Reaction Rates",
+    "text": "Reaction Rates\nkimmdy-analysis rates can generate plots of all available rates entering a kMC step. By default, KIMMDY generates in the kMC step of every reaction a plot, showing calculated rates over the course of the latest simulation. This can be turned off in the input yaml. If in the kMC step a reaction is chosen, the corresponding rates are highlighted bold and dashed. Each reaction recipe has a string representation, consisting of the involved atom numbers and symbols for the actions. Bonds breaking are depicted as bolt. A new bond, and a movement are both represented with an arrow.",
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+    "section": "Runtimes",
+    "text": "Runtimes\nkimmdy-analysis runtime analyzes the runtime of kimmdy. Besides showing the runtime of all tasks performed it can group tasks, and types of tasks together. The example analyzes the runtime of KIMMDY performing 20 consecutive HAT reactions after an initial homolysis reaction. As the simulated system is quite small (the charged_peptide example is used), the MD simulations are comparatively fast. For bigger systems, the MD runtime will increase, while the time required for HAT reaction barrier predictions will not, as it only atoms close to a radical are taken into account. Therefore, the computational overhead of KIMMDY should be negligible in most use cases.",
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-    "text": "KIMMDY uses conventional commits and semantic versioning, automated via release please.\nIf a PR adds multiple commits, we use the squash and merge option to keep the commit history clean. If a PR unavoidably contains changes the message can be edited before merging to ensure release please picks up all changes.\nThe following example message (first line is the title in the GitHub UI, the rest is the body in the window below):\nGenerates the following changelog:"
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-    "text": "Local testing\nFor developoment, we provide a docker image containing gromacs and multiple python versions to test against.\nTo run the test locally, you must:\n\ninstall docker\ninstall act, easiest option is with github cli\n\ninstall github cli (gh)\ngh extension install https://github.com/nektos/gh-act\n\nrun tests with gh extension exec act -j test --artifact-server-path ./artifacts\n\ncustomize which python versions to test in tox.ini\nhtml coverage report is exported into artifacts"
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-    "text": "You might want to apply a KIMMDY reaction to an already existing simulation. Here are some important points for doing so."
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-    "text": "KIMMDY yaml\nIf you want to start your sequence of tasks with a reaction, you have to give KIMMDY a trajectory. This, you do with the trr key in the kimmdy.yml file."
+    "text": "You need an installation of python (&gt;= 3.10) and (possibly PLUMED patched) GROMACS in your HPC environment.\nExample setup:\nsrun -t 1400:00 --mem=16000 -n20 --pty /bin/bash\nml EasyBuild\neb ./assets/Python-3.10.8.eb\nPrepare a bash script _modules.sh that loads the required modules and activates the python environment in which KIMMDY is installed.\nRun\nkimmdy --generate-jobscript\nto generate a file jobscript.sh that can be submitted to the HPC cluster.\nThis commands generates a kimmdy checkpoint and prepares the output folder. KIMMDY can then be started and re-started from the checkpoint via the jobscript, which uses\n# -c = continue, same  as --from-latest-checkpoint\nkimmdy -c",
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-    "section": "Pre-averaged plumed input",
-    "text": "Pre-averaged plumed input\nSometimes it is handy to pre-compute the averages of the distances plumed recordes. Usually, the plumed output (distances.dat) contains one line per timestep, each line starting with the time.\nIf you calculate the averages yourself, you end up having only one line, but need to tell KIMMDY how long the timeframe was, which was averaged. To do this, make sure to write the duration of your averaged simulation in the time field like this for a 10ps simulation:\n#! FIELDS time d0 d1 d2 d3 d4\n10.000000 0.142401 0.151588 0.143725 0.156734 0.152581\nYou still need the plumed config file, even if KIMMDY does not execute plumed in the current example, as KIMMDY reads the filename of the plumed output from the plumed config."
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-    "href": "guide/explanation/topology.html",
-    "title": "Visualize Topologies",
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+    "href": "guide/how-to/hcp.html#setup",
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     "section": "",
-    "text": "from kimmdy.parsing import read_top\nfrom kimmdy.topology.topology import Topology\nfrom pathlib import Path\nfrom kimmdy.tools import write_top_as_dot\n\n\nala_top = read_top(Path('../../tests/test_files/test_topology/Ala_R_prm.top'), use_gmx_dir=False)\ntop = Topology(ala_top)\n\nwrite_top_as_dot(top, \"ala-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n  \n\n1 CT\n\n 1 CT   \n\n2 HC\n\n 2 HC   \n\n1 CT–2 HC\n\n   \n\n3 HC\n\n 3 HC   \n\n1 CT–3 HC\n\n   \n\n4 HC\n\n 4 HC   \n\n1 CT–4 HC\n\n   \n\n5 C\n\n 5 C   \n\n1 CT–5 C\n\n   \n\n6 O\n\n 6 O   \n\n5 C–6 O\n\n   \n\n7 N\n\n 7 N   \n\n5 C–7 N\n\n   \n\n8 H\n\n 8 H   \n\n7 N–8 H\n\n   \n\n9 CT\n\n 9 CT   \n\n7 N–9 CT\n\n   \n\n10 CT\n\n 10 CT   \n\n9 CT–10 CT\n\n   \n\n14 C\n\n 14 C   \n\n9 CT–14 C\n\n   \n\n11 HC\n\n 11 HC   \n\n10 CT–11 HC\n\n   \n\n12 HC\n\n 12 HC   \n\n10 CT–12 HC\n\n   \n\n13 HC\n\n 13 HC   \n\n10 CT–13 HC\n\n   \n\n15 O\n\n 15 O   \n\n14 C–15 O\n\n   \n\n16 N\n\n 16 N   \n\n14 C–16 N\n\n   \n\n17 H\n\n 17 H   \n\n16 N–17 H\n\n   \n\n18 CT\n\n 18 CT   \n\n16 N–18 CT\n\n   \n\n19 H1\n\n 19 H1   \n\n18 CT–19 H1\n\n   \n\n20 H1\n\n 20 H1   \n\n18 CT–20 H1\n\n   \n\n21 H1\n\n 21 H1   \n\n18 CT–21 H1\n\n  \n\n\nFigure 1: A diagram of the Ala topology"
+    "text": "You need an installation of python (&gt;= 3.10) and (possibly PLUMED patched) GROMACS in your HPC environment.\nExample setup:\nsrun -t 1400:00 --mem=16000 -n20 --pty /bin/bash\nml EasyBuild\neb ./assets/Python-3.10.8.eb\nPrepare a bash script _modules.sh that loads the required modules and activates the python environment in which KIMMDY is installed.\nRun\nkimmdy --generate-jobscript\nto generate a file jobscript.sh that can be submitted to the HPC cluster.\nThis commands generates a kimmdy checkpoint and prepares the output folder. KIMMDY can then be started and re-started from the checkpoint via the jobscript, which uses\n# -c = continue, same  as --from-latest-checkpoint\nkimmdy -c",
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-    "title": "Visualize Topologies",
+    "objectID": "guide/explanation/index.html",
+    "href": "guide/explanation/index.html",
+    "title": "Explanations",
     "section": "",
-    "text": "from kimmdy.parsing import read_top\nfrom kimmdy.topology.topology import Topology\nfrom pathlib import Path\nfrom kimmdy.tools import write_top_as_dot\n\n\nala_top = read_top(Path('../../tests/test_files/test_topology/Ala_R_prm.top'), use_gmx_dir=False)\ntop = Topology(ala_top)\n\nwrite_top_as_dot(top, \"ala-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n  \n\n1 CT\n\n 1 CT   \n\n2 HC\n\n 2 HC   \n\n1 CT–2 HC\n\n   \n\n3 HC\n\n 3 HC   \n\n1 CT–3 HC\n\n   \n\n4 HC\n\n 4 HC   \n\n1 CT–4 HC\n\n   \n\n5 C\n\n 5 C   \n\n1 CT–5 C\n\n   \n\n6 O\n\n 6 O   \n\n5 C–6 O\n\n   \n\n7 N\n\n 7 N   \n\n5 C–7 N\n\n   \n\n8 H\n\n 8 H   \n\n7 N–8 H\n\n   \n\n9 CT\n\n 9 CT   \n\n7 N–9 CT\n\n   \n\n10 CT\n\n 10 CT   \n\n9 CT–10 CT\n\n   \n\n14 C\n\n 14 C   \n\n9 CT–14 C\n\n   \n\n11 HC\n\n 11 HC   \n\n10 CT–11 HC\n\n   \n\n12 HC\n\n 12 HC   \n\n10 CT–12 HC\n\n   \n\n13 HC\n\n 13 HC   \n\n10 CT–13 HC\n\n   \n\n15 O\n\n 15 O   \n\n14 C–15 O\n\n   \n\n16 N\n\n 16 N   \n\n14 C–16 N\n\n   \n\n17 H\n\n 17 H   \n\n16 N–17 H\n\n   \n\n18 CT\n\n 18 CT   \n\n16 N–18 CT\n\n   \n\n19 H1\n\n 19 H1   \n\n18 CT–19 H1\n\n   \n\n20 H1\n\n 20 H1   \n\n18 CT–20 H1\n\n   \n\n21 H1\n\n 21 H1   \n\n18 CT–21 H1\n\n  \n\n\nFigure 1: A diagram of the Ala topology"
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-    "href": "guide/explanation/topology.html#multiple-molecules",
-    "title": "Visualize Topologies",
-    "section": "Multiple molecules",
-    "text": "Multiple molecules\n\nurea_dict = read_top(Path('../../tests/test_files/test_topology/urea.top'), use_gmx_dir=False)\nurea = Topology(urea_dict)\nwrite_top_as_dot(urea, \"urea-top.dot\")\n\n\n\n\n\n\n\n\n\nG\n\n  \n\n1 C\n\n 1 C   \n\n2 O\n\n 2 O   \n\n1 C–2 O\n\n   \n\n3 N\n\n 3 N   \n\n1 C–3 N\n\n   \n\n6 N\n\n 6 N   \n\n1 C–6 N\n\n   \n\n4 H\n\n 4 H   \n\n3 N–4 H\n\n   \n\n5 H\n\n 5 H   \n\n3 N–5 H\n\n   \n\n7 H\n\n 7 H   \n\n6 N–7 H\n\n   \n\n8 H\n\n 8 H   \n\n6 N–8 H\n\n  \n\n\nFigure 2: Topology of one molecule of urea\n\n\n\n\nWhen we want to run reactions within molecules that are either separate moleculetypes or multiples of the same moleculetype, KIMMDY can combine those into a single moleculetype and make multiples explicit.\ni.e. if we have a topology with two molecules of urea defined as:\n[ system ]\nUrea in Water\n\n[ molecules ]\n;molecule name   nr.\nUrea             2\nSOL              1000\n\nurea_dict = read_top(Path('../../tests/test_files/test_topology/urea-times-2.top'), use_gmx_dir=False)\nurea = Topology(urea_dict)\nwrite_top_as_dot(urea, \"urea-2-top.dot\")\n\nWe end up with\n\n\n\n\n\n\n\n\nG\n\n  \n\n1 C\n\n 1 C   \n\n2 O\n\n 2 O   \n\n1 C–2 O\n\n   \n\n3 N\n\n 3 N   \n\n1 C–3 N\n\n   \n\n6 N\n\n 6 N   \n\n1 C–6 N\n\n   \n\n4 H\n\n 4 H   \n\n3 N–4 H\n\n   \n\n5 H\n\n 5 H   \n\n3 N–5 H\n\n   \n\n7 H\n\n 7 H   \n\n6 N–7 H\n\n   \n\n8 H\n\n 8 H   \n\n6 N–8 H\n\n   \n\n9 C\n\n 9 C   \n\n10 O\n\n 10 O   \n\n9 C–10 O\n\n   \n\n11 N\n\n 11 N   \n\n9 C–11 N\n\n   \n\n14 N\n\n 14 N   \n\n9 C–14 N\n\n   \n\n12 H\n\n 12 H   \n\n11 N–12 H\n\n   \n\n13 H\n\n 13 H   \n\n11 N–13 H\n\n   \n\n15 H\n\n 15 H   \n\n14 N–15 H\n\n   \n\n16 H\n\n 16 H   \n\n14 N–16 H\n\n  \n\n\nFigure 3: A diagram of the two urea molecules topology\n\n\n\n\nThis way, explicit atom numbers match up with the atom numbers in the coordinate file (or rather, line numbers - 2, since the numbers in the actual atomnr column can overflow due to the fixed-width file format)."
+    "text": "Pages that help you understand the inner workings of KIMMDY\n\n\n\n\n\n\n   \n     \n     \n       Order By\n       Default\n         \n          Title\n        \n         \n          Author\n        \n     \n  \n    \n      \n      \n    \n\n\n\n\n\nTitle\n\n\nAuthor\n\n\n\n\n\n\nComponents of KIMMDY\n\n\nKai Riedmiller\n\n\n\n\nVisualize Topologies\n\n\n \n\n\n\n\n\nNo matching items\n\n Back to top",
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diff --git a/docs/site_libs/bootstrap/bootstrap-dark.min.css b/docs/site_libs/bootstrap/bootstrap-dark.min.css
index 5858fd96..81032aa1 100644
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.input-group{width:auto}.btn-group{border-radius:.25rem}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(1px*-1)}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n+3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(1px*-1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: 0.5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: #75AADB;--bs-nav-link-hover-color: #5e88af;--bs-nav-link-disabled-color: rgba(255, 255, 255, 0.75);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out}@media(prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem 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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:rgba(0,0,0,0) !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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30'%3e%3cpath stroke='%2398989f' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme=dark] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='%2398989f' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: 0.5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width: 1px;--bs-card-border-color: rgba(0, 0, 0, 0.175);--bs-card-border-radius: 0.25rem;--bs-card-box-shadow: ;--bs-card-inner-border-radius: calc(0.25rem - 1px);--bs-card-cap-padding-y: 0.5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: #adb5bd;--bs-card-cap-color: ;--bs-card-height: ;--bs-card-color: ;--bs-card-bg: #050725;--bs-card-img-overlay-padding: 1rem;--bs-card-group-margin: 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var(--bs-card-spacer-x);color:var(--bs-card-color)}.card-title{margin-bottom:var(--bs-card-title-spacer-y);color:var(--bs-card-title-color)}.card-subtitle{margin-top:calc(-0.5*var(--bs-card-title-spacer-y));margin-bottom:0;color:var(--bs-card-subtitle-color)}.card-text:last-child{margin-bottom:0}.card-link+.card-link{margin-left:var(--bs-card-spacer-x)}.card-header{padding:var(--bs-card-cap-padding-y) var(--bs-card-cap-padding-x);margin-bottom:0;color:var(--bs-card-cap-color);background-color:var(--bs-card-cap-bg);border-bottom:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card-header:first-child{border-radius:var(--bs-card-inner-border-radius) var(--bs-card-inner-border-radius) 0 0}.card-footer{padding:var(--bs-card-cap-padding-y) var(--bs-card-cap-padding-x);color:var(--bs-card-cap-color);background-color:var(--bs-card-cap-bg);border-top:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card-footer:last-child{border-radius:0 0 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reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme=dark] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23788eb7'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23788eb7'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: rgba(255, 255, 255, 0.75);--bs-breadcrumb-item-padding-x: 0.5rem;--bs-breadcrumb-item-active-color: rgba(255, 255, 255, 0.75);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, ">") /* rtl: var(--bs-breadcrumb-divider, ">") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: 0.75rem;--bs-pagination-padding-y: 0.375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: #75AADB;--bs-pagination-bg: #050725;--bs-pagination-border-width: 1px;--bs-pagination-border-color: #dee2e6;--bs-pagination-border-radius: 0.25rem;--bs-pagination-hover-color: #5e88af;--bs-pagination-hover-bg: #f8f9fa;--bs-pagination-hover-border-color: #dee2e6;--bs-pagination-focus-color: #5e88af;--bs-pagination-focus-bg: #e9ecef;--bs-pagination-focus-box-shadow: 0 0 0 0.25rem rgba(30, 66, 135, 0.25);--bs-pagination-active-color: #ffffff;--bs-pagination-active-bg: #1E4287;--bs-pagination-active-border-color: #1E4287;--bs-pagination-disabled-color: rgba(255, 255, 255, 0.75);--bs-pagination-disabled-bg: #e9ecef;--bs-pagination-disabled-border-color: #dee2e6;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out,box-shadow .15s ease-in-out}@media(prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(1px*-1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: 0.75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: 0.5rem}.pagination-sm{--bs-pagination-padding-x: 0.5rem;--bs-pagination-padding-y: 0.25rem;--bs-pagination-font-size:0.875rem;--bs-pagination-border-radius: 0.2em}.badge{--bs-badge-padding-x: 0.65em;--bs-badge-padding-y: 0.35em;--bs-badge-font-size:0.75em;--bs-badge-font-weight: 700;--bs-badge-color: #ffffff;--bs-badge-border-radius: 0.25rem;display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 1px solid var(--bs-alert-border-color);--bs-alert-border-radius: 0.25rem;--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:0.75rem;--bs-progress-bg: #e9ecef;--bs-progress-border-radius: 0.25rem;--bs-progress-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.075);--bs-progress-bar-color: #ffffff;--bs-progress-bar-bg: #1E4287;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media(prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media(prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: rgba(255, 255, 255, 0.8705882353);--bs-list-group-bg: #050725;--bs-list-group-border-color: #dee2e6;--bs-list-group-border-width: 1px;--bs-list-group-border-radius: 0.25rem;--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: 0.5rem;--bs-list-group-action-color: rgba(255, 255, 255, 0.75);--bs-list-group-action-hover-color: #000;--bs-list-group-action-hover-bg: #f8f9fa;--bs-list-group-action-active-color: rgba(255, 255, 255, 0.8705882353);--bs-list-group-action-active-bg: #e9ecef;--bs-list-group-disabled-color: rgba(255, 255, 255, 0.75);--bs-list-group-disabled-bg: #050725;--bs-list-group-active-color: #ffffff;--bs-list-group-active-bg: #1E4287;--bs-list-group-active-border-color: #1E4287;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1*var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media(min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: 0.5;--bs-btn-close-hover-opacity: 0.75;--bs-btn-close-focus-shadow: 0 0 0 0.25rem rgba(30, 66, 135, 0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: 0.25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:rgba(0,0,0,0) var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.25rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme=dark] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: 0.75rem;--bs-toast-padding-y: 0.5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:0.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(5, 7, 37, 0.85);--bs-toast-border-width: 1px;--bs-toast-border-color: rgba(0, 0, 0, 0.175);--bs-toast-border-radius: 0.25rem;--bs-toast-box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15);--bs-toast-header-color: rgba(255, 255, 255, 0.75);--bs-toast-header-bg: rgba(5, 7, 37, 0.85);--bs-toast-header-border-color: rgba(0, 0, 0, 0.175);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-0.5*var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: 0.5rem;--bs-modal-color: ;--bs-modal-bg: #050725;--bs-modal-border-color: rgba(0, 0, 0, 0.175);--bs-modal-border-width: 1px;--bs-modal-border-radius: 0.5rem;--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075);--bs-modal-inner-border-radius: calc(0.5rem - 1px);--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: #dee2e6;--bs-modal-header-border-width: 1px;--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: 0.5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: #dee2e6;--bs-modal-footer-border-width: 1px;position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform .3s ease-out;transform:translate(0, -50px)}@media(prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin)*2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin)*2)}.modal-content{position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #000;--bs-backdrop-opacity: 0.5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid var(--bs-modal-header-border-color);border-top-left-radius:var(--bs-modal-inner-border-radius);border-top-right-radius:var(--bs-modal-inner-border-radius)}.modal-header .btn-close{padding:calc(var(--bs-modal-header-padding-y)*.5) calc(var(--bs-modal-header-padding-x)*.5);margin:calc(-0.5*var(--bs-modal-header-padding-y)) calc(-0.5*var(--bs-modal-header-padding-x)) calc(-0.5*var(--bs-modal-header-padding-y)) auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:flex-end;-webkit-justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap)*.5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid 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[screen-end]}body:not(.floating):not(.docked) .page-columns.toc-left .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset] 5fr [page-start] 35px [page-start-inset] minmax(0px, 145px) [body-start-outset] 35px [body-start] 1.5em [body-content-start] minmax(450px, calc(800px - 3em)) [body-content-end] 1.5em [body-end body-end-outset page-end-inset page-end] 5fr [screen-end-inset] 1.5em [screen-end]}body.floating .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset] 5fr [page-start page-start-inset body-start-outset body-start] 1.5em [body-content-start] minmax(500px, calc(750px - 3em)) [body-content-end] 1.5em [body-end] 50px [body-end-outset] minmax(75px, 150px) [page-end-inset] 25px [page-end] 5fr [screen-end-inset] 1.5em [screen-end]}body.docked .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset page-start page-start-inset body-start-outset body-start body-content-start] minmax(500px, calc(750px - 3em)) [body-content-end] 1.5em [body-end] 50px [body-end-outset] minmax(25px, 50px) [page-end-inset] 50px [page-end] 5fr [screen-end-inset] 1.5em [screen-end]}body.docked.fullcontent .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset page-start page-start-inset body-start-outset body-start body-content-start] minmax(500px, calc(1000px - 3em)) [body-content-end] 1.5em [body-end body-end-outset page-end-inset page-end] 5fr [screen-end-inset] 1.5em [screen-end]}body.floating.fullcontent .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset] 5fr [page-start page-start-inset body-start-outset body-start] 1em [body-content-start] minmax(500px, calc(800px - 3em)) [body-content-end] 1.5em [body-end body-end-outset page-end-inset page-end] 4fr [screen-end-inset] 1.5em [screen-end]}body.docked.slimcontent .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset page-start page-start-inset body-start-outset body-start body-content-start] minmax(500px, calc(750px - 3em)) [body-content-end] 1.5em [body-end] 50px [body-end-outset] minmax(25px, 50px) [page-end-inset] 50px [page-end] 5fr [screen-end-inset] 1.5em [screen-end]}body.docked.listing .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset page-start page-start-inset body-start-outset body-start body-content-start] minmax(500px, calc(750px - 3em)) [body-content-end] 1.5em [body-end] 50px [body-end-outset] minmax(25px, 50px) [page-end-inset] 50px [page-end] 5fr [screen-end-inset] 1.5em [screen-end]}body.floating.slimcontent .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset] 5fr [page-start page-start-inset body-start-outset body-start] 1em [body-content-start] minmax(500px, calc(750px - 3em)) [body-content-end] 1.5em [body-end] 35px [body-end-outset] minmax(75px, 145px) [page-end-inset] 35px [page-end] 4fr [screen-end-inset] 1.5em [screen-end]}body.floating.listing .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset] 5fr [page-start page-start-inset body-start-outset body-start] 1em [body-content-start] minmax(500px, calc(750px - 3em)) [body-content-end] 1.5em [body-end] 50px [body-end-outset] minmax(75px, 150px) [page-end-inset] 25px [page-end] 4fr [screen-end-inset] 1.5em [screen-end]}}@media(max-width: 767.98px){body .page-columns,body.fullcontent:not(.floating):not(.docked) .page-columns,body.slimcontent:not(.floating):not(.docked) .page-columns,body.docked .page-columns,body.docked.slimcontent .page-columns,body.docked.fullcontent .page-columns,body.floating .page-columns,body.floating.slimcontent .page-columns,body.floating.fullcontent .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset page-start page-start-inset body-start-outset body-start body-content-start] minmax(0px, 1fr) [body-content-end body-end body-end-outset page-end-inset page-end screen-end-inset] 1.5em [screen-end]}body:not(.floating):not(.docked) .page-columns.toc-left{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset page-start page-start-inset body-start-outset body-start body-content-start] minmax(0px, 1fr) [body-content-end body-end body-end-outset page-end-inset page-end screen-end-inset] 1.5em [screen-end]}body:not(.floating):not(.docked) .page-columns.toc-left .page-columns{display:grid;gap:0;grid-template-columns:[screen-start] 1.5em [screen-start-inset page-start page-start-inset body-start-outset body-start body-content-start] minmax(0px, 1fr) [body-content-end body-end body-end-outset page-end-inset page-end screen-end-inset] 1.5em [screen-end]}nav[role=doc-toc]{display:none}}body,.page-row-navigation{grid-template-rows:[page-top] max-content [contents-top] max-content [contents-bottom] max-content [page-bottom]}.page-rows-contents{grid-template-rows:[content-top] minmax(max-content, 1fr) [content-bottom] minmax(60px, max-content) [page-bottom]}.page-full{grid-column:screen-start/screen-end !important}.page-columns>*{grid-column:body-content-start/body-content-end}.page-columns.column-page>*{grid-column:page-start/page-end}.page-columns.column-page-left>*{grid-column:page-start/body-content-end}.page-columns.column-page-right>*{grid-column:body-content-start/page-end}.page-rows{grid-auto-rows:auto}.header{grid-column:screen-start/screen-end;grid-row:page-top/contents-top}#quarto-content{padding:0;grid-column:screen-start/screen-end;grid-row:contents-top/contents-bottom}body.floating .sidebar.sidebar-navigation{grid-column:page-start/body-start;grid-row:content-top/page-bottom}body.docked 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.column-page-inset-right{grid-column:body-content-start/page-end-inset;z-index:998;transform:translate3d(0, 0, 0)}.page-columns .column-page-inset-right figcaption table{background:#050725}.page-columns .column-page-left{grid-column:page-start/body-content-end;z-index:998;transform:translate3d(0, 0, 0)}.page-columns .column-page-left table{background:#050725}.page-columns .column-page-right{grid-column:body-content-start/page-end;z-index:998;transform:translate3d(0, 0, 0)}.page-columns .column-page-right figcaption table{background:#050725}#quarto-content.page-columns #quarto-margin-sidebar,#quarto-content.page-columns #quarto-sidebar{z-index:1}@media(max-width: 991.98px){#quarto-content.page-columns #quarto-margin-sidebar.collapse,#quarto-content.page-columns #quarto-sidebar.collapse,#quarto-content.page-columns #quarto-margin-sidebar.collapsing,#quarto-content.page-columns #quarto-sidebar.collapsing{z-index:1055}}#quarto-content.page-columns 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diff --git a/docs/site_libs/bootstrap/bootstrap-icons.css b/docs/site_libs/bootstrap/bootstrap-icons.css
index c3bfba65..285e4448 100644
--- a/docs/site_libs/bootstrap/bootstrap-icons.css
+++ b/docs/site_libs/bootstrap/bootstrap-icons.css
@@ -1,5 +1,5 @@
 /*!
- * Bootstrap Icons v1.10.5 (https://icons.getbootstrap.com/)
+ * Bootstrap Icons v1.11.1 (https://icons.getbootstrap.com/)
  * Copyright 2019-2023 The Bootstrap Authors
  * Licensed under MIT (https://github.com/twbs/icons/blob/main/LICENSE)
  */
@@ -8,7 +8,7 @@
   font-display: block;
   font-family: "bootstrap-icons";
   src: 
-url("./bootstrap-icons.woff?1fa40e8900654d2863d011707b9fb6f2") format("woff");
+url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff");
 }
 
 .bi::before,
@@ -1979,3 +1979,100 @@ url("./bootstrap-icons.woff?1fa40e8900654d2863d011707b9fb6f2") format("woff");
 .bi-sina-weibo::before { content: "\f8ca"; }
 .bi-tencent-qq::before { content: "\f8cb"; }
 .bi-wikipedia::before { content: "\f8cc"; }
+.bi-alphabet-uppercase::before { content: "\f2a5"; }
+.bi-alphabet::before { content: "\f68a"; }
+.bi-amazon::before { content: "\f68d"; }
+.bi-arrows-collapse-vertical::before { content: "\f690"; }
+.bi-arrows-expand-vertical::before { content: "\f695"; }
+.bi-arrows-vertical::before { content: "\f698"; }
+.bi-arrows::before { content: "\f6a2"; }
+.bi-ban-fill::before { content: "\f6a3"; }
+.bi-ban::before { content: "\f6b6"; }
+.bi-bing::before { content: "\f6c2"; }
+.bi-cake::before { content: "\f6e0"; }
+.bi-cake2::before { content: "\f6ed"; }
+.bi-cookie::before { content: "\f6ee"; }
+.bi-copy::before { content: "\f759"; }
+.bi-crosshair::before { content: "\f769"; }
+.bi-crosshair2::before { content: "\f794"; }
+.bi-emoji-astonished-fill::before { content: "\f795"; }
+.bi-emoji-astonished::before { content: "\f79a"; }
+.bi-emoji-grimace-fill::before { content: "\f79b"; }
+.bi-emoji-grimace::before { content: "\f7a0"; }
+.bi-emoji-grin-fill::before { content: "\f7a1"; }
+.bi-emoji-grin::before { content: "\f7a6"; }
+.bi-emoji-surprise-fill::before { content: "\f7a7"; }
+.bi-emoji-surprise::before { content: "\f7ac"; }
+.bi-emoji-tear-fill::before { content: "\f7ad"; }
+.bi-emoji-tear::before { content: "\f7b2"; }
+.bi-envelope-arrow-down-fill::before { content: "\f7b3"; }
+.bi-envelope-arrow-down::before { content: "\f7b8"; }
+.bi-envelope-arrow-up-fill::before { content: "\f7b9"; }
+.bi-envelope-arrow-up::before { content: "\f7be"; }
+.bi-feather::before { content: "\f7bf"; }
+.bi-feather2::before { content: "\f7c4"; }
+.bi-floppy-fill::before { content: "\f7c5"; }
+.bi-floppy::before { content: "\f7d8"; }
+.bi-floppy2-fill::before { content: "\f7d9"; }
+.bi-floppy2::before { content: "\f7e4"; }
+.bi-gitlab::before { content: "\f7e5"; }
+.bi-highlighter::before { content: "\f7f8"; }
+.bi-marker-tip::before { content: "\f802"; }
+.bi-nvme-fill::before { content: "\f803"; }
+.bi-nvme::before { content: "\f80c"; }
+.bi-opencollective::before { content: "\f80d"; }
+.bi-pci-card-network::before { content: "\f8cd"; }
+.bi-pci-card-sound::before { content: "\f8ce"; }
+.bi-radar::before { content: "\f8cf"; }
+.bi-send-arrow-down-fill::before { content: "\f8d0"; }
+.bi-send-arrow-down::before { content: "\f8d1"; }
+.bi-send-arrow-up-fill::before { content: "\f8d2"; }
+.bi-send-arrow-up::before { content: "\f8d3"; }
+.bi-sim-slash-fill::before { content: "\f8d4"; }
+.bi-sim-slash::before { content: "\f8d5"; }
+.bi-sourceforge::before { content: "\f8d6"; }
+.bi-substack::before { content: "\f8d7"; }
+.bi-threads-fill::before { content: "\f8d8"; }
+.bi-threads::before { content: "\f8d9"; }
+.bi-transparency::before { content: "\f8da"; }
+.bi-twitter-x::before { content: "\f8db"; }
+.bi-type-h4::before { content: "\f8dc"; }
+.bi-type-h5::before { content: "\f8dd"; }
+.bi-type-h6::before { content: "\f8de"; }
+.bi-backpack-fill::before { content: "\f8df"; }
+.bi-backpack::before { content: "\f8e0"; }
+.bi-backpack2-fill::before { content: "\f8e1"; }
+.bi-backpack2::before { content: "\f8e2"; }
+.bi-backpack3-fill::before { content: "\f8e3"; }
+.bi-backpack3::before { content: "\f8e4"; }
+.bi-backpack4-fill::before { content: "\f8e5"; }
+.bi-backpack4::before { content: "\f8e6"; }
+.bi-brilliance::before { content: "\f8e7"; }
+.bi-cake-fill::before { content: "\f8e8"; }
+.bi-cake2-fill::before { content: "\f8e9"; }
+.bi-duffle-fill::before { content: "\f8ea"; }
+.bi-duffle::before { content: "\f8eb"; }
+.bi-exposure::before { content: "\f8ec"; }
+.bi-gender-neuter::before { content: "\f8ed"; }
+.bi-highlights::before { content: "\f8ee"; }
+.bi-luggage-fill::before { content: "\f8ef"; }
+.bi-luggage::before { content: "\f8f0"; }
+.bi-mailbox-flag::before { content: "\f8f1"; }
+.bi-mailbox2-flag::before { content: "\f8f2"; }
+.bi-noise-reduction::before { content: "\f8f3"; }
+.bi-passport-fill::before { content: "\f8f4"; }
+.bi-passport::before { content: "\f8f5"; }
+.bi-person-arms-up::before { content: "\f8f6"; }
+.bi-person-raised-hand::before { content: "\f8f7"; }
+.bi-person-standing-dress::before { content: "\f8f8"; }
+.bi-person-standing::before { content: "\f8f9"; }
+.bi-person-walking::before { content: "\f8fa"; }
+.bi-person-wheelchair::before { content: "\f8fb"; }
+.bi-shadows::before { content: "\f8fc"; }
+.bi-suitcase-fill::before { content: "\f8fd"; }
+.bi-suitcase-lg-fill::before { content: "\f8fe"; }
+.bi-suitcase-lg::before { content: "\f8ff"; }
+.bi-suitcase::before { content: "\f900"; }
+.bi-suitcase2-fill::before { content: "\f901"; }
+.bi-suitcase2::before { content: "\f902"; }
+.bi-vignette::before { content: "\f903"; }
diff --git a/docs/site_libs/bootstrap/bootstrap-icons.woff b/docs/site_libs/bootstrap/bootstrap-icons.woff
index 6e72a590..dbeeb055 100644
Binary files a/docs/site_libs/bootstrap/bootstrap-icons.woff and b/docs/site_libs/bootstrap/bootstrap-icons.woff differ
diff --git a/docs/site_libs/bootstrap/bootstrap.min.css b/docs/site_libs/bootstrap/bootstrap.min.css
index f5baf17c..878b1c26 100644
--- a/docs/site_libs/bootstrap/bootstrap.min.css
+++ b/docs/site_libs/bootstrap/bootstrap.min.css
@@ -1,10 +1,9 @@
 @import"https://fonts.googleapis.com/css2?family=Miriam+Libre&family=Roboto&display=swap";/*!
- * Bootstrap v5.1.3 (https://getbootstrap.com/)
- * Copyright 2011-2021 The Bootstrap Authors
- * Copyright 2011-2021 Twitter, Inc.
+ * Bootstrap  v5.3.1 (https://getbootstrap.com/)
+ * Copyright 2011-2023 The Bootstrap Authors
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
- */:root{--bs-blue: #0d6efd;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-pink: #d63384;--bs-red: #dc3545;--bs-orange: #fd7e14;--bs-yellow: #ffc107;--bs-green: #198754;--bs-teal: #20c997;--bs-cyan: #0dcaf0;--bs-white: #ffffff;--bs-gray: #6c757d;--bs-gray-dark: #343a40;--bs-gray-100: #f8f9fa;--bs-gray-200: #e9ecef;--bs-gray-300: #dee2e6;--bs-gray-400: #ced4da;--bs-gray-500: #adb5bd;--bs-gray-600: #6c757d;--bs-gray-700: #495057;--bs-gray-800: #343a40;--bs-gray-900: #212529;--bs-default: #dee2e6;--bs-primary: #1E4287;--bs-secondary: #6c757d;--bs-success: #198754;--bs-info: #0dcaf0;--bs-warning: #ffc107;--bs-danger: #dc3545;--bs-light: #f8f9fa;--bs-dark: #212529;--bs-default-rgb: 222, 226, 230;--bs-primary-rgb: 30, 66, 135;--bs-secondary-rgb: 108, 117, 125;--bs-success-rgb: 25, 135, 84;--bs-info-rgb: 13, 202, 240;--bs-warning-rgb: 255, 193, 7;--bs-danger-rgb: 220, 53, 69;--bs-light-rgb: 248, 249, 250;--bs-dark-rgb: 33, 37, 41;--bs-white-rgb: 255, 255, 255;--bs-black-rgb: 0, 0, 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.dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(1px*-1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: 0.5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: #1E4287;--bs-nav-link-hover-color: #18356c;--bs-nav-link-disabled-color: rgba(33, 37, 41, 0.75);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out}@media(prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem 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#1e4287;--bs-navbar-nav-link-padding-x: 0.5rem;--bs-navbar-toggler-padding-y: 0.25;--bs-navbar-toggler-padding-x: 0;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='%23545555' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(84, 85, 85, 0);--bs-navbar-toggler-border-radius: 0.25rem;--bs-navbar-toggler-focus-width: 0.25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:rgba(0,0,0,0) !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:rgba(0,0,0,0) !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme=dark] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23788eb7'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23788eb7'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: rgba(33, 37, 41, 0.75);--bs-breadcrumb-item-padding-x: 0.5rem;--bs-breadcrumb-item-active-color: rgba(33, 37, 41, 0.75);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, ">") /* rtl: var(--bs-breadcrumb-divider, ">") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: 0.75rem;--bs-pagination-padding-y: 0.375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: #1E4287;--bs-pagination-bg: #ffffff;--bs-pagination-border-width: 1px;--bs-pagination-border-color: #dee2e6;--bs-pagination-border-radius: 0.25rem;--bs-pagination-hover-color: #18356c;--bs-pagination-hover-bg: #f8f9fa;--bs-pagination-hover-border-color: #dee2e6;--bs-pagination-focus-color: #18356c;--bs-pagination-focus-bg: #e9ecef;--bs-pagination-focus-box-shadow: 0 0 0 0.25rem rgba(30, 66, 135, 0.25);--bs-pagination-active-color: #ffffff;--bs-pagination-active-bg: #1E4287;--bs-pagination-active-border-color: #1E4287;--bs-pagination-disabled-color: rgba(33, 37, 41, 0.75);--bs-pagination-disabled-bg: #e9ecef;--bs-pagination-disabled-border-color: #dee2e6;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out,box-shadow .15s ease-in-out}@media(prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(1px*-1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: 0.75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: 0.5rem}.pagination-sm{--bs-pagination-padding-x: 0.5rem;--bs-pagination-padding-y: 0.25rem;--bs-pagination-font-size:0.875rem;--bs-pagination-border-radius: 0.2em}.badge{--bs-badge-padding-x: 0.65em;--bs-badge-padding-y: 0.35em;--bs-badge-font-size:0.75em;--bs-badge-font-weight: 700;--bs-badge-color: #ffffff;--bs-badge-border-radius: 0.25rem;display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 1px solid var(--bs-alert-border-color);--bs-alert-border-radius: 0.25rem;--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:0.75rem;--bs-progress-bg: #e9ecef;--bs-progress-border-radius: 0.25rem;--bs-progress-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.075);--bs-progress-bar-color: #ffffff;--bs-progress-bar-bg: #1E4287;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media(prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media(prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: #212529;--bs-list-group-bg: #ffffff;--bs-list-group-border-color: #dee2e6;--bs-list-group-border-width: 1px;--bs-list-group-border-radius: 0.25rem;--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: 0.5rem;--bs-list-group-action-color: rgba(33, 37, 41, 0.75);--bs-list-group-action-hover-color: #000;--bs-list-group-action-hover-bg: #f8f9fa;--bs-list-group-action-active-color: #212529;--bs-list-group-action-active-bg: #e9ecef;--bs-list-group-disabled-color: rgba(33, 37, 41, 0.75);--bs-list-group-disabled-bg: #ffffff;--bs-list-group-active-color: #ffffff;--bs-list-group-active-bg: #1E4287;--bs-list-group-active-border-color: #1E4287;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1*var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media(min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: 0.5;--bs-btn-close-hover-opacity: 0.75;--bs-btn-close-focus-shadow: 0 0 0 0.25rem rgba(30, 66, 135, 0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: 0.25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:rgba(0,0,0,0) var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.25rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme=dark] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: 0.75rem;--bs-toast-padding-y: 0.5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:0.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(255, 255, 255, 0.85);--bs-toast-border-width: 1px;--bs-toast-border-color: rgba(0, 0, 0, 0.175);--bs-toast-border-radius: 0.25rem;--bs-toast-box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15);--bs-toast-header-color: rgba(33, 37, 41, 0.75);--bs-toast-header-bg: rgba(255, 255, 255, 0.85);--bs-toast-header-border-color: rgba(0, 0, 0, 0.175);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-0.5*var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: 0.5rem;--bs-modal-color: ;--bs-modal-bg: #ffffff;--bs-modal-border-color: rgba(0, 0, 0, 0.175);--bs-modal-border-width: 1px;--bs-modal-border-radius: 0.5rem;--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075);--bs-modal-inner-border-radius: calc(0.5rem - 1px);--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: #dee2e6;--bs-modal-header-border-width: 1px;--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: 0.5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: #dee2e6;--bs-modal-footer-border-width: 1px;position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform .3s ease-out;transform:translate(0, -50px)}@media(prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin)*2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin)*2)}.modal-content{position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #000;--bs-backdrop-opacity: 0.5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid var(--bs-modal-header-border-color);border-top-left-radius:var(--bs-modal-inner-border-radius);border-top-right-radius:var(--bs-modal-inner-border-radius)}.modal-header .btn-close{padding:calc(var(--bs-modal-header-padding-y)*.5) calc(var(--bs-modal-header-padding-x)*.5);margin:calc(-0.5*var(--bs-modal-header-padding-y)) calc(-0.5*var(--bs-modal-header-padding-x)) calc(-0.5*var(--bs-modal-header-padding-y)) auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:flex-end;-webkit-justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap)*.5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid var(--bs-modal-footer-border-color);border-bottom-right-radius:var(--bs-modal-inner-border-radius);border-bottom-left-radius:var(--bs-modal-inner-border-radius)}.modal-footer>*{margin:calc(var(--bs-modal-footer-gap)*.5)}@media(min-width: 576px){.modal{--bs-modal-margin: 1.75rem;--bs-modal-box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15)}.modal-dialog{max-width:var(--bs-modal-width);margin-right:auto;margin-left:auto}.modal-sm{--bs-modal-width: 300px}}@media(min-width: 992px){.modal-lg,.modal-xl{--bs-modal-width: 800px}}@media(min-width: 1200px){.modal-xl{--bs-modal-width: 1140px}}.modal-fullscreen{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen .modal-header,.modal-fullscreen .modal-footer{border-radius:0}.modal-fullscreen .modal-body{overflow-y:auto}@media(max-width: 575.98px){.modal-fullscreen-sm-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-sm-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-sm-down .modal-header,.modal-fullscreen-sm-down .modal-footer{border-radius:0}.modal-fullscreen-sm-down .modal-body{overflow-y:auto}}@media(max-width: 767.98px){.modal-fullscreen-md-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-md-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-md-down .modal-header,.modal-fullscreen-md-down .modal-footer{border-radius:0}.modal-fullscreen-md-down .modal-body{overflow-y:auto}}@media(max-width: 991.98px){.modal-fullscreen-lg-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-lg-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-lg-down .modal-header,.modal-fullscreen-lg-down .modal-footer{border-radius:0}.modal-fullscreen-lg-down .modal-body{overflow-y:auto}}@media(max-width: 1199.98px){.modal-fullscreen-xl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xl-down .modal-header,.modal-fullscreen-xl-down .modal-footer{border-radius:0}.modal-fullscreen-xl-down .modal-body{overflow-y:auto}}@media(max-width: 1399.98px){.modal-fullscreen-xxl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xxl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xxl-down .modal-header,.modal-fullscreen-xxl-down .modal-footer{border-radius:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex: 1080;--bs-tooltip-max-width: 200px;--bs-tooltip-padding-x: 0.5rem;--bs-tooltip-padding-y: 0.25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:0.875rem;--bs-tooltip-color: #ffffff;--bs-tooltip-bg: #000;--bs-tooltip-border-radius: 0.25rem;--bs-tooltip-opacity: 0.9;--bs-tooltip-arrow-width: 0.8rem;--bs-tooltip-arrow-height: 0.4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:Roboto;font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-tooltip-font-size);word-wrap:break-word;opacity:0}.tooltip.show{opacity:var(--bs-tooltip-opacity)}.tooltip .tooltip-arrow{display:block;width:var(--bs-tooltip-arrow-width);height:var(--bs-tooltip-arrow-height)}.tooltip .tooltip-arrow::before{position:absolute;content:"";border-color:rgba(0,0,0,0);border-style:solid}.bs-tooltip-top .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^=top] .tooltip-arrow{bottom:calc(-1*var(--bs-tooltip-arrow-height))}.bs-tooltip-top .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^=top] .tooltip-arrow::before{top:-1px;border-width:var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width)*.5) 0;border-top-color:var(--bs-tooltip-bg)}.bs-tooltip-end .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^=right] .tooltip-arrow{left:calc(-1*var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-end .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^=right] .tooltip-arrow::before{right:-1px;border-width:calc(var(--bs-tooltip-arrow-width)*.5) var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width)*.5) 0;border-right-color:var(--bs-tooltip-bg)}.bs-tooltip-bottom .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^=bottom] .tooltip-arrow{top:calc(-1*var(--bs-tooltip-arrow-height))}.bs-tooltip-bottom .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^=bottom] .tooltip-arrow::before{bottom:-1px;border-width:0 calc(var(--bs-tooltip-arrow-width)*.5) var(--bs-tooltip-arrow-height);border-bottom-color:var(--bs-tooltip-bg)}.bs-tooltip-start .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^=left] .tooltip-arrow{right:calc(-1*var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-start .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^=left] .tooltip-arrow::before{left:-1px;border-width:calc(var(--bs-tooltip-arrow-width)*.5) 0 calc(var(--bs-tooltip-arrow-width)*.5) var(--bs-tooltip-arrow-height);border-left-color:var(--bs-tooltip-bg)}.tooltip-inner{max-width:var(--bs-tooltip-max-width);padding:var(--bs-tooltip-padding-y) var(--bs-tooltip-padding-x);color:var(--bs-tooltip-color);text-align:center;background-color:var(--bs-tooltip-bg);border-radius:var(--bs-tooltip-border-radius)}.popover{--bs-popover-zindex: 1070;--bs-popover-max-width: 276px;--bs-popover-font-size:0.875rem;--bs-popover-bg: #ffffff;--bs-popover-border-width: 1px;--bs-popover-border-color: rgba(0, 0, 0, 0.175);--bs-popover-border-radius: 0.5rem;--bs-popover-inner-border-radius: calc(0.5rem - 1px);--bs-popover-box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15);--bs-popover-header-padding-x: 1rem;--bs-popover-header-padding-y: 0.5rem;--bs-popover-header-font-size:1rem;--bs-popover-header-color: inherit;--bs-popover-header-bg: #e9ecef;--bs-popover-body-padding-x: 1rem;--bs-popover-body-padding-y: 1rem;--bs-popover-body-color: #212529;--bs-popover-arrow-width: 1rem;--bs-popover-arrow-height: 0.5rem;--bs-popover-arrow-border: var(--bs-popover-border-color);z-index:var(--bs-popover-zindex);display:block;max-width:var(--bs-popover-max-width);font-family:Roboto;font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-popover-font-size);word-wrap:break-word;background-color:var(--bs-popover-bg);background-clip:padding-box;border:var(--bs-popover-border-width) solid 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diff --git a/docs/site_libs/bootstrap/bootstrap.min.js b/docs/site_libs/bootstrap/bootstrap.min.js
index cc0a2556..e8f21f70 100644
--- a/docs/site_libs/bootstrap/bootstrap.min.js
+++ b/docs/site_libs/bootstrap/bootstrap.min.js
@@ -1,7 +1,7 @@
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+  * Bootstrap v5.3.1 (https://getbootstrap.com/)
+  * Copyright 2011-2023 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors)
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img",this._element).forEach((t=>{j.on(t,"dragstart.bs.carousel",(t=>t.preventDefault()))})),this._pointerEvent?(j.on(this._element,"pointerdown.bs.carousel",(t=>e(t))),j.on(this._element,"pointerup.bs.carousel",(t=>n(t))),this._element.classList.add("pointer-event")):(j.on(this._element,"touchstart.bs.carousel",(t=>e(t))),j.on(this._element,"touchmove.bs.carousel",(t=>i(t))),j.on(this._element,"touchend.bs.carousel",(t=>n(t))))}_keydown(t){if(/input|textarea/i.test(t.target.tagName))return;const e=tt[t.key];e&&(t.preventDefault(),this._slide(e))}_getItemIndex(t){return this._items=t&&t.parentNode?V.find(".carousel-item",t.parentNode):[],this._items.indexOf(t)}_getItemByOrder(t,e){const i=t===Q;return v(this._items,e,i,this._config.wrap)}_triggerSlideEvent(t,e){const i=this._getItemIndex(t),n=this._getItemIndex(V.findOne(nt,this._element));return j.trigger(this._element,"slide.bs.carousel",{relatedTarget:t,direction:e,from:n,to:i})}_setActiveIndicatorElement(t){if(this._indicatorsElement){const e=V.findOne(".active",this._indicatorsElement);e.classList.remove(it),e.removeAttribute("aria-current");const i=V.find("[data-bs-target]",this._indicatorsElement);for(let e=0;e<i.length;e++)if(Number.parseInt(i[e].getAttribute("data-bs-slide-to"),10)===this._getItemIndex(t)){i[e].classList.add(it),i[e].setAttribute("aria-current","true");break}}}_updateInterval(){const t=this._activeElement||V.findOne(nt,this._element);if(!t)return;const e=Number.parseInt(t.getAttribute("data-bs-interval"),10);e?(this._config.defaultInterval=this._config.defaultInterval||this._config.interval,this._config.interval=e):this._config.interval=this._config.defaultInterval||this._config.interval}_slide(t,e){const i=this._directionToOrder(t),n=V.findOne(nt,this._element),s=this._getItemIndex(n),o=e||this._getItemByOrder(i,n),r=this._getItemIndex(o),a=Boolean(this._interval),l=i===Q,c=l?"carousel-item-start":"carousel-item-end",h=l?"carousel-item-next":"carousel-item-prev",d=this._orderToDirection(i);if(o&&o.classList.contains(it))return void(this._isSliding=!1);if(this._isSliding)return;if(this._triggerSlideEvent(o,d).defaultPrevented)return;if(!n||!o)return;this._isSliding=!0,a&&this.pause(),this._setActiveIndicatorElement(o),this._activeElement=o;const f=()=>{j.trigger(this._element,et,{relatedTarget:o,direction:d,from:s,to:r})};if(this._element.classList.contains("slide")){o.classList.add(h),u(o),n.classList.add(c),o.classList.add(c);const t=()=>{o.classList.remove(c,h),o.classList.add(it),n.classList.remove(it,h,c),this._isSliding=!1,setTimeout(f,0)};this._queueCallback(t,n,!0)}else n.classList.remove(it),o.classList.add(it),this._isSliding=!1,f();a&&this.cycle()}_directionToOrder(t){return[J,Z].includes(t)?m()?t===Z?G:Q:t===Z?Q:G:t}_orderToDirection(t){return[Q,G].includes(t)?m()?t===G?Z:J:t===G?J:Z:t}static carouselInterface(t,e){const i=st.getOrCreateInstance(t,e);let{_config:n}=i;"object"==typeof e&&(n={...n,...e});const s="string"==typeof e?e:n.slide;if("number"==typeof e)i.to(e);else if("string"==typeof s){if(void 0===i[s])throw new TypeError(`No method named "${s}"`);i[s]()}else n.interval&&n.ride&&(i.pause(),i.cycle())}static jQueryInterface(t){return this.each((function(){st.carouselInterface(this,t)}))}static dataApiClickHandler(t){const e=n(this);if(!e||!e.classList.contains("carousel"))return;const i={...U.getDataAttributes(e),...U.getDataAttributes(this)},s=this.getAttribute("data-bs-slide-to");s&&(i.interval=!1),st.carouselInterface(e,i),s&&st.getInstance(e).to(s),t.preventDefault()}}j.on(document,"click.bs.carousel.data-api","[data-bs-slide], [data-bs-slide-to]",st.dataApiClickHandler),j.on(window,"load.bs.carousel.data-api",(()=>{const t=V.find('[data-bs-ride="carousel"]');for(let e=0,i=t.length;e<i;e++)st.carouselInterface(t[e],st.getInstance(t[e]))})),g(st);const ot="collapse",rt={toggle:!0,parent:null},at={toggle:"boolean",parent:"(null|element)"},lt="show",ct="collapse",ht="collapsing",dt="collapsed",ut=":scope .collapse .collapse",ft='[data-bs-toggle="collapse"]';class pt extends B{constructor(t,e){super(t),this._isTransitioning=!1,this._config=this._getConfig(e),this._triggerArray=[];const n=V.find(ft);for(let t=0,e=n.length;t<e;t++){const e=n[t],s=i(e),o=V.find(s).filter((t=>t===this._element));null!==s&&o.length&&(this._selector=s,this._triggerArray.push(e))}this._initializeChildren(),this._config.parent||this._addAriaAndCollapsedClass(this._triggerArray,this._isShown()),this._config.toggle&&this.toggle()}static get Default(){return rt}static get NAME(){return ot}toggle(){this._isShown()?this.hide():this.show()}show(){if(this._isTransitioning||this._isShown())return;let t,e=[];if(this._config.parent){const t=V.find(ut,this._config.parent);e=V.find(".collapse.show, .collapse.collapsing",this._config.parent).filter((e=>!t.includes(e)))}const i=V.findOne(this._selector);if(e.length){const n=e.find((t=>i!==t));if(t=n?pt.getInstance(n):null,t&&t._isTransitioning)return}if(j.trigger(this._element,"show.bs.collapse").defaultPrevented)return;e.forEach((e=>{i!==e&&pt.getOrCreateInstance(e,{toggle:!1}).hide(),t||H.set(e,"bs.collapse",null)}));const n=this._getDimension();this._element.classList.remove(ct),this._element.classList.add(ht),this._element.style[n]=0,this._addAriaAndCollapsedClass(this._triggerArray,!0),this._isTransitioning=!0;const s=`scroll${n[0].toUpperCase()+n.slice(1)}`;this._queueCallback((()=>{this._isTransitioning=!1,this._element.classList.remove(ht),this._element.classList.add(ct,lt),this._element.style[n]="",j.trigger(this._element,"shown.bs.collapse")}),this._element,!0),this._element.style[n]=`${this._element[s]}px`}hide(){if(this._isTransitioning||!this._isShown())return;if(j.trigger(this._element,"hide.bs.collapse").defaultPrevented)return;const t=this._getDimension();this._element.style[t]=`${this._element.getBoundingClientRect()[t]}px`,u(this._element),this._element.classList.add(ht),this._element.classList.remove(ct,lt);const e=this._triggerArray.length;for(let t=0;t<e;t++){const e=this._triggerArray[t],i=n(e);i&&!this._isShown(i)&&this._addAriaAndCollapsedClass([e],!1)}this._isTransitioning=!0,this._element.style[t]="",this._queueCallback((()=>{this._isTransitioning=!1,this._element.classList.remove(ht),this._element.classList.add(ct),j.trigger(this._element,"hidden.bs.collapse")}),this._element,!0)}_isShown(t=this._element){return t.classList.contains(lt)}_getConfig(t){return(t={...rt,...U.getDataAttributes(this._element),...t}).toggle=Boolean(t.toggle),t.parent=r(t.parent),a(ot,t,at),t}_getDimension(){return this._element.classList.contains("collapse-horizontal")?"width":"height"}_initializeChildren(){if(!this._config.parent)return;const t=V.find(ut,this._config.parent);V.find(ft,this._config.parent).filter((e=>!t.includes(e))).forEach((t=>{const e=n(t);e&&this._addAriaAndCollapsedClass([t],this._isShown(e))}))}_addAriaAndCollapsedClass(t,e){t.length&&t.forEach((t=>{e?t.classList.remove(dt):t.classList.add(dt),t.setAttribute("aria-expanded",e)}))}static jQueryInterface(t){return this.each((function(){const e={};"string"==typeof t&&/show|hide/.test(t)&&(e.toggle=!1);const i=pt.getOrCreateInstance(this,e);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t]()}}))}}j.on(document,"click.bs.collapse.data-api",ft,(function(t){("A"===t.target.tagName||t.delegateTarget&&"A"===t.delegateTarget.tagName)&&t.preventDefault();const e=i(this);V.find(e).forEach((t=>{pt.getOrCreateInstance(t,{toggle:!1}).toggle()}))})),g(pt);var mt="top",gt="bottom",_t="right",bt="left",vt="auto",yt=[mt,gt,_t,bt],wt="start",Et="end",At="clippingParents",Tt="viewport",Ot="popper",Ct="reference",kt=yt.reduce((function(t,e){return t.concat([e+"-"+wt,e+"-"+Et])}),[]),Lt=[].concat(yt,[vt]).reduce((function(t,e){return t.concat([e,e+"-"+wt,e+"-"+Et])}),[]),xt="beforeRead",Dt="read",St="afterRead",Nt="beforeMain",It="main",Pt="afterMain",jt="beforeWrite",Mt="write",Ht="afterWrite",Bt=[xt,Dt,St,Nt,It,Pt,jt,Mt,Ht];function Rt(t){return t?(t.nodeName||"").toLowerCase():null}function Wt(t){if(null==t)return window;if("[object Window]"!==t.toString()){var e=t.ownerDocument;return e&&e.defaultView||window}return t}function $t(t){return t instanceof Wt(t).Element||t instanceof Element}function zt(t){return t instanceof Wt(t).HTMLElement||t instanceof HTMLElement}function qt(t){return"undefined"!=typeof ShadowRoot&&(t instanceof Wt(t).ShadowRoot||t instanceof ShadowRoot)}const Ft={name:"applyStyles",enabled:!0,phase:"write",fn:function(t){var e=t.state;Object.keys(e.elements).forEach((function(t){var i=e.styles[t]||{},n=e.attributes[t]||{},s=e.elements[t];zt(s)&&Rt(s)&&(Object.assign(s.style,i),Object.keys(n).forEach((function(t){var e=n[t];!1===e?s.removeAttribute(t):s.setAttribute(t,!0===e?"":e)})))}))},effect:function(t){var e=t.state,i={popper:{position:e.options.strategy,left:"0",top:"0",margin:"0"},arrow:{position:"absolute"},reference:{}};return 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n=Yt(i);if("none"!==n.transform||"none"!==n.perspective||"paint"===n.contain||-1!==["transform","perspective"].indexOf(n.willChange)||e&&"filter"===n.willChange||e&&n.filter&&"none"!==n.filter)return i;i=i.parentNode}return null}(t)||e}function ee(t){return["top","bottom"].indexOf(t)>=0?"x":"y"}var ie=Math.max,ne=Math.min,se=Math.round;function oe(t,e,i){return ie(t,ne(e,i))}function re(t){return Object.assign({},{top:0,right:0,bottom:0,left:0},t)}function ae(t,e){return e.reduce((function(e,i){return e[i]=t,e}),{})}const le={name:"arrow",enabled:!0,phase:"main",fn:function(t){var e,i=t.state,n=t.name,s=t.options,o=i.elements.arrow,r=i.modifiersData.popperOffsets,a=Ut(i.placement),l=ee(a),c=[bt,_t].indexOf(a)>=0?"height":"width";if(o&&r){var h=function(t,e){return re("number"!=typeof(t="function"==typeof 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e=t.x,i=t.y,n=window.devicePixelRatio||1;return{x:se(se(e*n)/n)||0,y:se(se(i*n)/n)||0}}(r):"function"==typeof h?h(r):r,u=d.x,f=void 0===u?0:u,p=d.y,m=void 0===p?0:p,g=r.hasOwnProperty("x"),_=r.hasOwnProperty("y"),b=bt,v=mt,y=window;if(c){var w=te(i),E="clientHeight",A="clientWidth";w===Wt(i)&&"static"!==Yt(w=Gt(i)).position&&"absolute"===a&&(E="scrollHeight",A="scrollWidth"),w=w,s!==mt&&(s!==bt&&s!==_t||o!==Et)||(v=gt,m-=w[E]-n.height,m*=l?1:-1),s!==bt&&(s!==mt&&s!==gt||o!==Et)||(b=_t,f-=w[A]-n.width,f*=l?1:-1)}var T,O=Object.assign({position:a},c&&he);return l?Object.assign({},O,((T={})[v]=_?"0":"",T[b]=g?"0":"",T.transform=(y.devicePixelRatio||1)<=1?"translate("+f+"px, "+m+"px)":"translate3d("+f+"px, "+m+"px, 0)",T)):Object.assign({},O,((e={})[v]=_?m+"px":"",e[b]=g?f+"px":"",e.transform="",e))}const ue={name:"computeStyles",enabled:!0,phase:"beforeWrite",fn:function(t){var e=t.state,i=t.options,n=i.gpuAcceleration,s=void 0===n||n,o=i.adaptive,r=void 0===o||o,a=i.roundOffsets,l=void 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C=O[s];Object.keys(T).forEach((function(t){var e=[_t,gt].indexOf(t)>=0?1:-1,i=[mt,gt].indexOf(t)>=0?"y":"x";T[t]+=C[i]*e}))}return T}function Le(t,e){void 0===e&&(e={});var i=e,n=i.placement,s=i.boundary,o=i.rootBoundary,r=i.padding,a=i.flipVariations,l=i.allowedAutoPlacements,c=void 0===l?Lt:l,h=ce(n),d=h?a?kt:kt.filter((function(t){return ce(t)===h})):yt,u=d.filter((function(t){return c.indexOf(t)>=0}));0===u.length&&(u=d);var f=u.reduce((function(e,i){return e[i]=ke(t,{placement:i,boundary:s,rootBoundary:o,padding:r})[Ut(i)],e}),{});return Object.keys(f).sort((function(t,e){return f[t]-f[e]}))}const xe={name:"flip",enabled:!0,phase:"main",fn:function(t){var e=t.state,i=t.options,n=t.name;if(!e.modifiersData[n]._skip){for(var s=i.mainAxis,o=void 0===s||s,r=i.altAxis,a=void 0===r||r,l=i.fallbackPlacements,c=i.padding,h=i.boundary,d=i.rootBoundary,u=i.altBoundary,f=i.flipVariations,p=void 0===f||f,m=i.allowedAutoPlacements,g=e.options.placement,_=Ut(g),b=l||(_!==g&&p?function(t){if(Ut(t)===vt)return[];var e=ge(t);return[be(t),e,be(e)]}(g):[ge(g)]),v=[g].concat(b).reduce((function(t,i){return t.concat(Ut(i)===vt?Le(e,{placement:i,boundary:h,rootBoundary:d,padding:c,flipVariations:p,allowedAutoPlacements:m}):i)}),[]),y=e.rects.reference,w=e.rects.popper,E=new Map,A=!0,T=v[0],O=0;O<v.length;O++){var C=v[O],k=Ut(C),L=ce(C)===wt,x=[mt,gt].indexOf(k)>=0,D=x?"width":"height",S=ke(e,{placement:C,boundary:h,rootBoundary:d,altBoundary:u,padding:c}),N=x?L?_t:bt:L?gt:mt;y[D]>w[D]&&(N=ge(N));var I=ge(N),P=[];if(o&&P.push(S[k]<=0),a&&P.push(S[N]<=0,S[I]<=0),P.every((function(t){return t}))){T=C,A=!1;break}E.set(C,P)}if(A)for(var j=function(t){var e=v.find((function(e){var i=E.get(e);if(i)return i.slice(0,t).every((function(t){return t}))}));if(e)return 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e=t.state,i=t.options,n=t.name,s=i.offset,o=void 0===s?[0,0]:s,r=Lt.reduce((function(t,i){return t[i]=function(t,e,i){var n=Ut(t),s=[bt,mt].indexOf(n)>=0?-1:1,o="function"==typeof i?i(Object.assign({},e,{placement:t})):i,r=o[0],a=o[1];return r=r||0,a=(a||0)*s,[bt,_t].indexOf(n)>=0?{x:a,y:r}:{x:r,y:a}}(i,e.rects,o),t}),{}),a=r[e.placement],l=a.x,c=a.y;null!=e.modifiersData.popperOffsets&&(e.modifiersData.popperOffsets.x+=l,e.modifiersData.popperOffsets.y+=c),e.modifiersData[n]=r}},Pe={name:"popperOffsets",enabled:!0,phase:"read",fn:function(t){var e=t.state,i=t.name;e.modifiersData[i]=Ce({reference:e.rects.reference,element:e.rects.popper,strategy:"absolute",placement:e.placement})},data:{}},je={name:"preventOverflow",enabled:!0,phase:"main",fn:function(t){var e=t.state,i=t.options,n=t.name,s=i.mainAxis,o=void 0===s||s,r=i.altAxis,a=void 0!==r&&r,l=i.boundary,c=i.rootBoundary,h=i.altBoundary,d=i.padding,u=i.tether,f=void 0===u||u,p=i.tetherOffset,m=void 0===p?0:p,g=ke(e,{boundary:l,rootBoundary:c,padding:d,altBoundary:h}),_=Ut(e.placement),b=ce(e.placement),v=!b,y=ee(_),w="x"===y?"y":"x",E=e.modifiersData.popperOffsets,A=e.rects.reference,T=e.rects.popper,O="function"==typeof m?m(Object.assign({},e.rects,{placement:e.placement})):m,C={x:0,y:0};if(E){if(o||a){var k="y"===y?mt:bt,L="y"===y?gt:_t,x="y"===y?"height":"width",D=E[y],S=E[y]+g[k],N=E[y]-g[L],I=f?-T[x]/2:0,P=b===wt?A[x]:T[x],j=b===wt?-T[x]:-A[x],M=e.elements.arrow,H=f&&M?Kt(M):{width:0,height:0},B=e.modifiersData["arrow#persistent"]?e.modifiersData["arrow#persistent"].padding:{top:0,right:0,bottom:0,left:0},R=B[k],W=B[L],$=oe(0,A[x],H[x]),z=v?A[x]/2-I-$-R-O:P-$-R-O,q=v?-A[x]/2+I+$+W+O:j+$+W+O,F=e.elements.arrow&&te(e.elements.arrow),U=F?"y"===y?F.clientTop||0:F.clientLeft||0:0,V=e.modifiersData.offset?e.modifiersData.offset[e.placement][y]:0,K=E[y]+z-V-U,X=E[y]+q-V;if(o){var Y=oe(f?ne(S,K):S,D,f?ie(N,X):N);E[y]=Y,C[y]=Y-D}if(a){var Q="x"===y?mt:bt,G="x"===y?gt:_t,Z=E[w],J=Z+g[Q],tt=Z-g[G],et=oe(f?ne(J,K):J,Z,f?ie(tt,X):tt);E[w]=et,C[w]=et-Z}}e.modifiersData[n]=C}},requiresIfExists:["offset"]};function Me(t,e,i){void 0===i&&(i=!1);var n=zt(e);zt(e)&&function(t){var e=t.getBoundingClientRect();e.width,t.offsetWidth,e.height,t.offsetHeight}(e);var s,o,r=Gt(e),a=Vt(t),l={scrollLeft:0,scrollTop:0},c={x:0,y:0};return(n||!n&&!i)&&(("body"!==Rt(e)||we(r))&&(l=(s=e)!==Wt(s)&&zt(s)?{scrollLeft:(o=s).scrollLeft,scrollTop:o.scrollTop}:ve(s)),zt(e)?((c=Vt(e)).x+=e.clientLeft,c.y+=e.clientTop):r&&(c.x=ye(r))),{x:a.left+l.scrollLeft-c.x,y:a.top+l.scrollTop-c.y,width:a.width,height:a.height}}function He(t){var e=new Map,i=new Set,n=[];function s(t){i.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!i.has(t)){var n=e.get(t);n&&s(n)}})),n.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){i.has(t.name)||s(t)})),n}var Be={placement:"bottom",modifiers:[],strategy:"absolute"};function Re(){for(var t=arguments.length,e=new Array(t),i=0;i<t;i++)e[i]=arguments[i];return!e.some((function(t){return!(t&&"function"==typeof t.getBoundingClientRect)}))}function We(t){void 0===t&&(t={});var e=t,i=e.defaultModifiers,n=void 0===i?[]:i,s=e.defaultOptions,o=void 0===s?Be:s;return function(t,e,i){void 0===i&&(i=o);var s,r,a={placement:"bottom",orderedModifiers:[],options:Object.assign({},Be,o),modifiersData:{},elements:{reference:t,popper:e},attributes:{},styles:{}},l=[],c=!1,h={state:a,setOptions:function(i){var s="function"==typeof i?i(a.options):i;d(),a.options=Object.assign({},o,a.options,s),a.scrollParents={reference:$t(t)?Ae(t):t.contextElement?Ae(t.contextElement):[],popper:Ae(e)};var r,c,u=function(t){var e=He(t);return Bt.reduce((function(t,i){return t.concat(e.filter((function(t){return t.phase===i})))}),[])}((r=[].concat(n,a.options.modifiers),c=r.reduce((function(t,e){var i=t[e.name];return t[e.name]=i?Object.assign({},i,e,{options:Object.assign({},i.options,e.options),data:Object.assign({},i.data,e.data)}):e,t}),{}),Object.keys(c).map((function(t){return c[t]}))));return a.orderedModifiers=u.filter((function(t){return t.enabled})),a.orderedModifiers.forEach((function(t){var e=t.name,i=t.options,n=void 0===i?{}:i,s=t.effect;if("function"==typeof s){var o=s({state:a,name:e,instance:h,options:n});l.push(o||function(){})}})),h.update()},forceUpdate:function(){if(!c){var t=a.elements,e=t.reference,i=t.popper;if(Re(e,i)){a.rects={reference:Me(e,te(i),"fixed"===a.options.strategy),popper:Kt(i)},a.reset=!1,a.placement=a.options.placement,a.orderedModifiers.forEach((function(t){return a.modifiersData[t.name]=Object.assign({},t.data)}));for(var n=0;n<a.orderedModifiers.length;n++)if(!0!==a.reset){var s=a.orderedModifiers[n],o=s.fn,r=s.options,l=void 0===r?{}:r,d=s.name;"function"==typeof o&&(a=o({state:a,options:l,name:d,instance:h})||a)}else a.reset=!1,n=-1}}},update:(s=function(){return new Promise((function(t){h.forceUpdate(),t(a)}))},function(){return r||(r=new Promise((function(t){Promise.resolve().then((function(){r=void 0,t(s())}))}))),r}),destroy:function(){d(),c=!0}};if(!Re(t,e))return h;function d(){l.forEach((function(t){return t()})),l=[]}return h.setOptions(i).then((function(t){!c&&i.onFirstUpdate&&i.onFirstUpdate(t)})),h}}var $e=We(),ze=We({defaultModifiers:[pe,Pe,ue,Ft]}),qe=We({defaultModifiers:[pe,Pe,ue,Ft,Ie,xe,je,le,Ne]});const Fe=Object.freeze({__proto__:null,popperGenerator:We,detectOverflow:ke,createPopperBase:$e,createPopper:qe,createPopperLite:ze,top:mt,bottom:gt,right:_t,left:bt,auto:vt,basePlacements:yt,start:wt,end:Et,clippingParents:At,viewport:Tt,popper:Ot,reference:Ct,variationPlacements:kt,placements:Lt,beforeRead:xt,read:Dt,afterRead:St,beforeMain:Nt,main:It,afterMain:Pt,beforeWrite:jt,write:Mt,afterWrite:Ht,modifierPhases:Bt,applyStyles:Ft,arrow:le,computeStyles:ue,eventListeners:pe,flip:xe,hide:Ne,offset:Ie,popperOffsets:Pe,preventOverflow:je}),Ue="dropdown",Ve="Escape",Ke="Space",Xe="ArrowUp",Ye="ArrowDown",Qe=new 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this._isShown()?this.hide():this.show()}show(){if(c(this._element)||this._isShown(this._menu))return;const t={relatedTarget:this._element};if(j.trigger(this._element,"show.bs.dropdown",t).defaultPrevented)return;const e=hi.getParentFromElement(this._element);this._inNavbar?U.setDataAttribute(this._menu,"popper","none"):this._createPopper(e),"ontouchstart"in document.documentElement&&!e.closest(".navbar-nav")&&[].concat(...document.body.children).forEach((t=>j.on(t,"mouseover",d))),this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add(Je),this._element.classList.add(Je),j.trigger(this._element,"shown.bs.dropdown",t)}hide(){if(c(this._element)||!this._isShown(this._menu))return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){j.trigger(this._element,"hide.bs.dropdown",t).defaultPrevented||("ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._popper&&this._popper.destroy(),this._menu.classList.remove(Je),this._element.classList.remove(Je),this._element.setAttribute("aria-expanded","false"),U.removeDataAttribute(this._menu,"popper"),j.trigger(this._element,"hidden.bs.dropdown",t))}_getConfig(t){if(t={...this.constructor.Default,...U.getDataAttributes(this._element),...t},a(Ue,t,this.constructor.DefaultType),"object"==typeof t.reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${Ue.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" 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null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return"static"===this._config.display&&(t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,..."function"==typeof this._config.popperConfig?this._config.popperConfig(t):this._config.popperConfig}}_selectMenuItem({key:t,target:e}){const i=V.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter(l);i.length&&v(i,e,t===Ye,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(t&&(2===t.button||"keyup"===t.type&&"Tab"!==t.key))return;const e=V.find(ti);for(let i=0,n=e.length;i<n;i++){const n=hi.getInstance(e[i]);if(!n||!1===n._config.autoClose)continue;if(!n._isShown())continue;const s={relatedTarget:n._element};if(t){const e=t.composedPath(),i=e.includes(n._menu);if(e.includes(n._element)||"inside"===n._config.autoClose&&!i||"outside"===n._config.autoClose&&i)continue;if(n._menu.contains(t.target)&&("keyup"===t.type&&"Tab"===t.key||/input|select|option|textarea|form/i.test(t.target.tagName)))continue;"click"===t.type&&(s.clickEvent=t)}n._completeHide(s)}}static getParentFromElement(t){return n(t)||t.parentNode}static dataApiKeydownHandler(t){if(/input|textarea/i.test(t.target.tagName)?t.key===Ke||t.key!==Ve&&(t.key!==Ye&&t.key!==Xe||t.target.closest(ei)):!Qe.test(t.key))return;const e=this.classList.contains(Je);if(!e&&t.key===Ve)return;if(t.preventDefault(),t.stopPropagation(),c(this))return;const i=this.matches(ti)?this:V.prev(this,ti)[0],n=hi.getOrCreateInstance(i);if(t.key!==Ve)return t.key===Xe||t.key===Ye?(e||n.show(),void n._selectMenuItem(t)):void(e&&t.key!==Ke||hi.clearMenus());n.hide()}}j.on(document,Ze,ti,hi.dataApiKeydownHandler),j.on(document,Ze,ei,hi.dataApiKeydownHandler),j.on(document,Ge,hi.clearMenus),j.on(document,"keyup.bs.dropdown.data-api",hi.clearMenus),j.on(document,Ge,ti,(function(t){t.preventDefault(),hi.getOrCreateInstance(this).toggle()})),g(hi);const di=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",ui=".sticky-top";class fi{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,"paddingRight",(e=>e+t)),this._setElementAttributes(di,"paddingRight",(e=>e+t)),this._setElementAttributes(ui,"marginRight",(e=>e-t))}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t)[e];t.style[e]=`${i(Number.parseFloat(s))}px`}))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,"paddingRight"),this._resetElementAttributes(di,"paddingRight"),this._resetElementAttributes(ui,"marginRight")}_saveInitialAttribute(t,e){const i=t.style[e];i&&U.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=U.getDataAttribute(t,e);void 0===i?t.style.removeProperty(e):(U.removeDataAttribute(t,e),t.style[e]=i)}))}_applyManipulationCallback(t,e){o(t)?e(t):V.find(t,this._element).forEach(e)}isOverflowing(){return this.getWidth()>0}}const pi={className:"modal-backdrop",isVisible:!0,isAnimated:!1,rootElement:"body",clickCallback:null},mi={className:"string",isVisible:"boolean",isAnimated:"boolean",rootElement:"(element|string)",clickCallback:"(function|null)"},gi="show",_i="mousedown.bs.backdrop";class bi{constructor(t){this._config=this._getConfig(t),this._isAppended=!1,this._element=null}show(t){this._config.isVisible?(this._append(),this._config.isAnimated&&u(this._getElement()),this._getElement().classList.add(gi),this._emulateAnimation((()=>{_(t)}))):_(t)}hide(t){this._config.isVisible?(this._getElement().classList.remove(gi),this._emulateAnimation((()=>{this.dispose(),_(t)}))):_(t)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_getConfig(t){return(t={...pi,..."object"==typeof t?t:{}}).rootElement=r(t.rootElement),a("backdrop",t,mi),t}_append(){this._isAppended||(this._config.rootElement.append(this._getElement()),j.on(this._getElement(),_i,(()=>{_(this._config.clickCallback)})),this._isAppended=!0)}dispose(){this._isAppended&&(j.off(this._element,_i),this._element.remove(),this._isAppended=!1)}_emulateAnimation(t){b(t,this._getElement(),this._config.isAnimated)}}const vi={trapElement:null,autofocus:!0},yi={trapElement:"element",autofocus:"boolean"},wi=".bs.focustrap",Ei="backward";class Ai{constructor(t){this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}activate(){const{trapElement:t,autofocus:e}=this._config;this._isActive||(e&&t.focus(),j.off(document,wi),j.on(document,"focusin.bs.focustrap",(t=>this._handleFocusin(t))),j.on(document,"keydown.tab.bs.focustrap",(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,j.off(document,wi))}_handleFocusin(t){const{target:e}=t,{trapElement:i}=this._config;if(e===document||e===i||i.contains(e))return;const n=V.focusableChildren(i);0===n.length?i.focus():this._lastTabNavDirection===Ei?n[n.length-1].focus():n[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?Ei:"forward")}_getConfig(t){return t={...vi,..."object"==typeof t?t:{}},a("focustrap",t,yi),t}}const Ti="modal",Oi="Escape",Ci={backdrop:!0,keyboard:!0,focus:!0},ki={backdrop:"(boolean|string)",keyboard:"boolean",focus:"boolean"},Li="hidden.bs.modal",xi="show.bs.modal",Di="resize.bs.modal",Si="click.dismiss.bs.modal",Ni="keydown.dismiss.bs.modal",Ii="mousedown.dismiss.bs.modal",Pi="modal-open",ji="show",Mi="modal-static";class Hi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._dialog=V.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._ignoreBackdropClick=!1,this._isTransitioning=!1,this._scrollBar=new fi}static get Default(){return Ci}static get NAME(){return Ti}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||j.trigger(this._element,xi,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isAnimated()&&(this._isTransitioning=!0),this._scrollBar.hide(),document.body.classList.add(Pi),this._adjustDialog(),this._setEscapeEvent(),this._setResizeEvent(),j.on(this._dialog,Ii,(()=>{j.one(this._element,"mouseup.dismiss.bs.modal",(t=>{t.target===this._element&&(this._ignoreBackdropClick=!0)}))})),this._showBackdrop((()=>this._showElement(t))))}hide(){if(!this._isShown||this._isTransitioning)return;if(j.trigger(this._element,"hide.bs.modal").defaultPrevented)return;this._isShown=!1;const t=this._isAnimated();t&&(this._isTransitioning=!0),this._setEscapeEvent(),this._setResizeEvent(),this._focustrap.deactivate(),this._element.classList.remove(ji),j.off(this._element,Si),j.off(this._dialog,Ii),this._queueCallback((()=>this._hideModal()),this._element,t)}dispose(){[window,this._dialog].forEach((t=>j.off(t,".bs.modal"))),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new bi({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_getConfig(t){return t={...Ci,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Ti,t,ki),t}_showElement(t){const e=this._isAnimated(),i=V.findOne(".modal-body",this._dialog);this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0,i&&(i.scrollTop=0),e&&u(this._element),this._element.classList.add(ji),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,j.trigger(this._element,"shown.bs.modal",{relatedTarget:t})}),this._dialog,e)}_setEscapeEvent(){this._isShown?j.on(this._element,Ni,(t=>{this._config.keyboard&&t.key===Oi?(t.preventDefault(),this.hide()):this._config.keyboard||t.key!==Oi||this._triggerBackdropTransition()})):j.off(this._element,Ni)}_setResizeEvent(){this._isShown?j.on(window,Di,(()=>this._adjustDialog())):j.off(window,Di)}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(Pi),this._resetAdjustments(),this._scrollBar.reset(),j.trigger(this._element,Li)}))}_showBackdrop(t){j.on(this._element,Si,(t=>{this._ignoreBackdropClick?this._ignoreBackdropClick=!1:t.target===t.currentTarget&&(!0===this._config.backdrop?this.hide():"static"===this._config.backdrop&&this._triggerBackdropTransition())})),this._backdrop.show(t)}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(j.trigger(this._element,"hidePrevented.bs.modal").defaultPrevented)return;const{classList:t,scrollHeight:e,style:i}=this._element,n=e>document.documentElement.clientHeight;!n&&"hidden"===i.overflowY||t.contains(Mi)||(n||(i.overflowY="hidden"),t.add(Mi),this._queueCallback((()=>{t.remove(Mi),n||this._queueCallback((()=>{i.overflowY=""}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;(!i&&t&&!m()||i&&!t&&m())&&(this._element.style.paddingLeft=`${e}px`),(i&&!t&&!m()||!i&&t&&m())&&(this._element.style.paddingRight=`${e}px`)}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=Hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}j.on(document,"click.bs.modal.data-api",'[data-bs-toggle="modal"]',(function(t){const e=n(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),j.one(e,xi,(t=>{t.defaultPrevented||j.one(e,Li,(()=>{l(this)&&this.focus()}))}));const i=V.findOne(".modal.show");i&&Hi.getInstance(i).hide(),Hi.getOrCreateInstance(e).toggle(this)})),R(Hi),g(Hi);const Bi="offcanvas",Ri={backdrop:!0,keyboard:!0,scroll:!1},Wi={backdrop:"boolean",keyboard:"boolean",scroll:"boolean"},$i="show",zi=".offcanvas.show",qi="hidden.bs.offcanvas";class Fi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get NAME(){return Bi}static get Default(){return Ri}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||j.trigger(this._element,"show.bs.offcanvas",{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._element.style.visibility="visible",this._backdrop.show(),this._config.scroll||(new fi).hide(),this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add($i),this._queueCallback((()=>{this._config.scroll||this._focustrap.activate(),j.trigger(this._element,"shown.bs.offcanvas",{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(j.trigger(this._element,"hide.bs.offcanvas").defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.remove($i),this._backdrop.hide(),this._queueCallback((()=>{this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._element.style.visibility="hidden",this._config.scroll||(new fi).reset(),j.trigger(this._element,qi)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_getConfig(t){return t={...Ri,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Bi,t,Wi),t}_initializeBackDrop(){return new bi({className:"offcanvas-backdrop",isVisible:this._config.backdrop,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:()=>this.hide()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_addEventListeners(){j.on(this._element,"keydown.dismiss.bs.offcanvas",(t=>{this._config.keyboard&&"Escape"===t.key&&this.hide()}))}static jQueryInterface(t){return this.each((function(){const e=Fi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}j.on(document,"click.bs.offcanvas.data-api",'[data-bs-toggle="offcanvas"]',(function(t){const e=n(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this))return;j.one(e,qi,(()=>{l(this)&&this.focus()}));const i=V.findOne(zi);i&&i!==e&&Fi.getInstance(i).hide(),Fi.getOrCreateInstance(e).toggle(this)})),j.on(window,"load.bs.offcanvas.data-api",(()=>V.find(zi).forEach((t=>Fi.getOrCreateInstance(t).show())))),R(Fi),g(Fi);const Ui=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Vi=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,Ki=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,Xi=(t,e)=>{const i=t.nodeName.toLowerCase();if(e.includes(i))return!Ui.has(i)||Boolean(Vi.test(t.nodeValue)||Ki.test(t.nodeValue));const n=e.filter((t=>t instanceof RegExp));for(let t=0,e=n.length;t<e;t++)if(n[t].test(i))return!0;return!1};function Yi(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(let t=0,i=s.length;t<i;t++){const i=s[t],n=i.nodeName.toLowerCase();if(!Object.keys(e).includes(n)){i.remove();continue}const o=[].concat(...i.attributes),r=[].concat(e["*"]||[],e[n]||[]);o.forEach((t=>{Xi(t,r)||i.removeAttribute(t.nodeName)}))}return n.body.innerHTML}const Qi="tooltip",Gi=new Set(["sanitize","allowList","sanitizeFn"]),Zi={animation:"boolean",template:"string",title:"(string|element|function)",trigger:"string",delay:"(number|object)",html:"boolean",selector:"(string|boolean)",placement:"(string|function)",offset:"(array|string|function)",container:"(string|element|boolean)",fallbackPlacements:"array",boundary:"(string|element)",customClass:"(string|function)",sanitize:"boolean",sanitizeFn:"(null|function)",allowList:"object",popperConfig:"(null|object|function)"},Ji={AUTO:"auto",TOP:"top",RIGHT:m()?"left":"right",BOTTOM:"bottom",LEFT:m()?"right":"left"},tn={animation:!0,template:'<div class="tooltip" role="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',trigger:"hover focus",title:"",delay:0,html:!1,selector:!1,placement:"top",offset:[0,0],container:!1,fallbackPlacements:["top","right","bottom","left"],boundary:"clippingParents",customClass:"",sanitize:!0,sanitizeFn:null,allowList:{"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},popperConfig:null},en={HIDE:"hide.bs.tooltip",HIDDEN:"hidden.bs.tooltip",SHOW:"show.bs.tooltip",SHOWN:"shown.bs.tooltip",INSERTED:"inserted.bs.tooltip",CLICK:"click.bs.tooltip",FOCUSIN:"focusin.bs.tooltip",FOCUSOUT:"focusout.bs.tooltip",MOUSEENTER:"mouseenter.bs.tooltip",MOUSELEAVE:"mouseleave.bs.tooltip"},nn="fade",sn="show",on="show",rn="out",an=".tooltip-inner",ln=".modal",cn="hide.bs.modal",hn="hover",dn="focus";class un extends B{constructor(t,e){if(void 0===Fe)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t),this._isEnabled=!0,this._timeout=0,this._hoverState="",this._activeTrigger={},this._popper=null,this._config=this._getConfig(e),this.tip=null,this._setListeners()}static get Default(){return tn}static get NAME(){return Qi}static get Event(){return en}static get DefaultType(){return Zi}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(t){if(this._isEnabled)if(t){const e=this._initializeOnDelegatedTarget(t);e._activeTrigger.click=!e._activeTrigger.click,e._isWithActiveTrigger()?e._enter(null,e):e._leave(null,e)}else{if(this.getTipElement().classList.contains(sn))return void this._leave(null,this);this._enter(null,this)}}dispose(){clearTimeout(this._timeout),j.off(this._element.closest(ln),cn,this._hideModalHandler),this.tip&&this.tip.remove(),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this.isWithContent()||!this._isEnabled)return;const t=j.trigger(this._element,this.constructor.Event.SHOW),e=h(this._element),i=null===e?this._element.ownerDocument.documentElement.contains(this._element):e.contains(this._element);if(t.defaultPrevented||!i)return;"tooltip"===this.constructor.NAME&&this.tip&&this.getTitle()!==this.tip.querySelector(an).innerHTML&&(this._disposePopper(),this.tip.remove(),this.tip=null);const n=this.getTipElement(),s=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME);n.setAttribute("id",s),this._element.setAttribute("aria-describedby",s),this._config.animation&&n.classList.add(nn);const o="function"==typeof this._config.placement?this._config.placement.call(this,n,this._element):this._config.placement,r=this._getAttachment(o);this._addAttachmentClass(r);const{container:a}=this._config;H.set(n,this.constructor.DATA_KEY,this),this._element.ownerDocument.documentElement.contains(this.tip)||(a.append(n),j.trigger(this._element,this.constructor.Event.INSERTED)),this._popper?this._popper.update():this._popper=qe(this._element,n,this._getPopperConfig(r)),n.classList.add(sn);const l=this._resolvePossibleFunction(this._config.customClass);l&&n.classList.add(...l.split(" ")),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>{j.on(t,"mouseover",d)}));const c=this.tip.classList.contains(nn);this._queueCallback((()=>{const t=this._hoverState;this._hoverState=null,j.trigger(this._element,this.constructor.Event.SHOWN),t===rn&&this._leave(null,this)}),this.tip,c)}hide(){if(!this._popper)return;const t=this.getTipElement();if(j.trigger(this._element,this.constructor.Event.HIDE).defaultPrevented)return;t.classList.remove(sn),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._activeTrigger.click=!1,this._activeTrigger.focus=!1,this._activeTrigger.hover=!1;const e=this.tip.classList.contains(nn);this._queueCallback((()=>{this._isWithActiveTrigger()||(this._hoverState!==on&&t.remove(),this._cleanTipClass(),this._element.removeAttribute("aria-describedby"),j.trigger(this._element,this.constructor.Event.HIDDEN),this._disposePopper())}),this.tip,e),this._hoverState=""}update(){null!==this._popper&&this._popper.update()}isWithContent(){return Boolean(this.getTitle())}getTipElement(){if(this.tip)return this.tip;const t=document.createElement("div");t.innerHTML=this._config.template;const e=t.children[0];return this.setContent(e),e.classList.remove(nn,sn),this.tip=e,this.tip}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),an)}_sanitizeAndSetContent(t,e,i){const n=V.findOne(i,t);e||!n?this.setElementContent(n,e):n.remove()}setElementContent(t,e){if(null!==t)return o(e)?(e=r(e),void(this._config.html?e.parentNode!==t&&(t.innerHTML="",t.append(e)):t.textContent=e.textContent)):void(this._config.html?(this._config.sanitize&&(e=Yi(e,this._config.allowList,this._config.sanitizeFn)),t.innerHTML=e):t.textContent=e)}getTitle(){const t=this._element.getAttribute("data-bs-original-title")||this._config.title;return this._resolvePossibleFunction(t)}updateAttachment(t){return"right"===t?"end":"left"===t?"start":t}_initializeOnDelegatedTarget(t,e){return e||this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return"function"==typeof t?t.call(this._element):t}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"onChange",enabled:!0,phase:"afterWrite",fn:t=>this._handlePopperPlacementChange(t)}],onFirstUpdate:t=>{t.options.placement!==t.placement&&this._handlePopperPlacementChange(t)}};return{...e,..."function"==typeof this._config.popperConfig?this._config.popperConfig(e):this._config.popperConfig}}_addAttachmentClass(t){this.getTipElement().classList.add(`${this._getBasicClassPrefix()}-${this.updateAttachment(t)}`)}_getAttachment(t){return Ji[t.toUpperCase()]}_setListeners(){this._config.trigger.split(" ").forEach((t=>{if("click"===t)j.on(this._element,this.constructor.Event.CLICK,this._config.selector,(t=>this.toggle(t)));else if("manual"!==t){const e=t===hn?this.constructor.Event.MOUSEENTER:this.constructor.Event.FOCUSIN,i=t===hn?this.constructor.Event.MOUSELEAVE:this.constructor.Event.FOCUSOUT;j.on(this._element,e,this._config.selector,(t=>this._enter(t))),j.on(this._element,i,this._config.selector,(t=>this._leave(t)))}})),this._hideModalHandler=()=>{this._element&&this.hide()},j.on(this._element.closest(ln),cn,this._hideModalHandler),this._config.selector?this._config={...this._config,trigger:"manual",selector:""}:this._fixTitle()}_fixTitle(){const t=this._element.getAttribute("title"),e=typeof this._element.getAttribute("data-bs-original-title");(t||"string"!==e)&&(this._element.setAttribute("data-bs-original-title",t||""),!t||this._element.getAttribute("aria-label")||this._element.textContent||this._element.setAttribute("aria-label",t),this._element.setAttribute("title",""))}_enter(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusin"===t.type?dn:hn]=!0),e.getTipElement().classList.contains(sn)||e._hoverState===on?e._hoverState=on:(clearTimeout(e._timeout),e._hoverState=on,e._config.delay&&e._config.delay.show?e._timeout=setTimeout((()=>{e._hoverState===on&&e.show()}),e._config.delay.show):e.show())}_leave(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusout"===t.type?dn:hn]=e._element.contains(t.relatedTarget)),e._isWithActiveTrigger()||(clearTimeout(e._timeout),e._hoverState=rn,e._config.delay&&e._config.delay.hide?e._timeout=setTimeout((()=>{e._hoverState===rn&&e.hide()}),e._config.delay.hide):e.hide())}_isWithActiveTrigger(){for(const t in this._activeTrigger)if(this._activeTrigger[t])return!0;return!1}_getConfig(t){const e=U.getDataAttributes(this._element);return Object.keys(e).forEach((t=>{Gi.has(t)&&delete e[t]})),(t={...this.constructor.Default,...e,..."object"==typeof t&&t?t:{}}).container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),a(Qi,t,this.constructor.DefaultType),t.sanitize&&(t.template=Yi(t.template,t.allowList,t.sanitizeFn)),t}_getDelegateConfig(){const t={};for(const e in this._config)this.constructor.Default[e]!==this._config[e]&&(t[e]=this._config[e]);return t}_cleanTipClass(){const t=this.getTipElement(),e=new RegExp(`(^|\\s)${this._getBasicClassPrefix()}\\S+`,"g"),i=t.getAttribute("class").match(e);null!==i&&i.length>0&&i.map((t=>t.trim())).forEach((e=>t.classList.remove(e)))}_getBasicClassPrefix(){return"bs-tooltip"}_handlePopperPlacementChange(t){const{state:e}=t;e&&(this.tip=e.elements.popper,this._cleanTipClass(),this._addAttachmentClass(this._getAttachment(e.placement)))}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null)}static jQueryInterface(t){return this.each((function(){const e=un.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(un);const fn={...un.Default,placement:"right",offset:[0,8],trigger:"click",content:"",template:'<div class="popover" role="tooltip"><div class="popover-arrow"></div><h3 class="popover-header"></h3><div 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i=`scroll${e[0].toUpperCase()+e.slice(1)}`;this._queueCallback((()=>{this._isTransitioning=!1,this._element.classList.remove(Mt),this._element.classList.add(Pt,Nt),this._element.style[e]="",N.trigger(this._element,St)}),this._element,!0),this._element.style[e]=`${this._element[i]}px`}hide(){if(this._isTransitioning||!this._isShown())return;if(N.trigger(this._element,Dt).defaultPrevented)return;const t=this._getDimension();this._element.style[t]=`${this._element.getBoundingClientRect()[t]}px`,d(this._element),this._element.classList.add(Mt),this._element.classList.remove(Pt,Nt);for(const t of this._triggerArray){const e=z.getElementFromSelector(t);e&&!this._isShown(e)&&this._addAriaAndCollapsedClass([t],!1)}this._isTransitioning=!0,this._element.style[t]="",this._queueCallback((()=>{this._isTransitioning=!1,this._element.classList.remove(Mt),this._element.classList.add(Pt),N.trigger(this._element,$t)}),this._element,!0)}_isShown(t=this._element){return 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s(t){i.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!i.has(t)){var n=e.get(t);n&&s(n)}})),n.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){i.has(t.name)||s(t)})),n}var fi={placement:"bottom",modifiers:[],strategy:"absolute"};function pi(){for(var t=arguments.length,e=new Array(t),i=0;i<t;i++)e[i]=arguments[i];return!e.some((function(t){return!(t&&"function"==typeof t.getBoundingClientRect)}))}function mi(t){void 0===t&&(t={});var e=t,i=e.defaultModifiers,n=void 0===i?[]:i,s=e.defaultOptions,o=void 0===s?fi:s;return function(t,e,i){void 0===i&&(i=o);var s,r,a={placement:"bottom",orderedModifiers:[],options:Object.assign({},fi,o),modifiersData:{},elements:{reference:t,popper:e},attributes:{},styles:{}},l=[],c=!1,h={state:a,setOptions:function(i){var s="function"==typeof 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vi=Object.freeze(Object.defineProperty({__proto__:null,afterMain:ae,afterRead:se,afterWrite:he,applyStyles:_e,arrow:je,auto:Kt,basePlacements:Qt,beforeMain:oe,beforeRead:ie,beforeWrite:le,bottom:Rt,clippingParents:Ut,computeStyles:Be,createPopper:bi,createPopperBase:gi,createPopperLite:_i,detectOverflow:ii,end:Yt,eventListeners:Re,flip:si,hide:ai,left:Vt,main:re,modifierPhases:de,offset:li,placements:ee,popper:Jt,popperGenerator:mi,popperOffsets:ci,preventOverflow:hi,read:ne,reference:Zt,right:qt,start:Xt,top:zt,variationPlacements:te,viewport:Gt,write:ce},Symbol.toStringTag,{value:"Module"})),yi="dropdown",wi=".bs.dropdown",Ai=".data-api",Ei="ArrowUp",Ti="ArrowDown",Ci=`hide${wi}`,Oi=`hidden${wi}`,xi=`show${wi}`,ki=`shown${wi}`,Li=`click${wi}${Ai}`,Si=`keydown${wi}${Ai}`,Di=`keyup${wi}${Ai}`,$i="show",Ii='[data-bs-toggle="dropdown"]:not(.disabled):not(:disabled)',Ni=`${Ii}.${$i}`,Pi=".dropdown-menu",Mi=p()?"top-end":"top-start",ji=p()?"top-start":"top-end",Fi=p()?"bottom-end":"bottom-start",Hi=p()?"bottom-start":"bottom-end",Wi=p()?"left-start":"right-start",Bi=p()?"right-start":"left-start",zi={autoClose:!0,boundary:"clippingParents",display:"dynamic",offset:[0,2],popperConfig:null,reference:"toggle"},Ri={autoClose:"(boolean|string)",boundary:"(string|element)",display:"string",offset:"(array|string|function)",popperConfig:"(null|object|function)",reference:"(string|element|object)"};class qi extends W{constructor(t,e){super(t,e),this._popper=null,this._parent=this._element.parentNode,this._menu=z.next(this._element,Pi)[0]||z.prev(this._element,Pi)[0]||z.findOne(Pi,this._parent),this._inNavbar=this._detectNavbar()}static get Default(){return zi}static get DefaultType(){return Ri}static get NAME(){return yi}toggle(){return this._isShown()?this.hide():this.show()}show(){if(l(this._element)||this._isShown())return;const t={relatedTarget:this._element};if(!N.trigger(this._element,xi,t).defaultPrevented){if(this._createPopper(),"ontouchstart"in document.documentElement&&!this._parent.closest(".navbar-nav"))for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add($i),this._element.classList.add($i),N.trigger(this._element,ki,t)}}hide(){if(l(this._element)||!this._isShown())return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){if(!N.trigger(this._element,Ci,t).defaultPrevented){if("ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.off(t,"mouseover",h);this._popper&&this._popper.destroy(),this._menu.classList.remove($i),this._element.classList.remove($i),this._element.setAttribute("aria-expanded","false"),F.removeDataAttribute(this._menu,"popper"),N.trigger(this._element,Oi,t)}}_getConfig(t){if("object"==typeof(t=super._getConfig(t)).reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${yi.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" method.`);return t}_createPopper(){if(void 0===vi)throw new TypeError("Bootstrap's dropdowns require Popper (https://popper.js.org)");let t=this._element;"parent"===this._config.reference?t=this._parent:o(this._config.reference)?t=r(this._config.reference):"object"==typeof this._config.reference&&(t=this._config.reference);const e=this._getPopperConfig();this._popper=bi(t,this._menu,e)}_isShown(){return this._menu.classList.contains($i)}_getPlacement(){const t=this._parent;if(t.classList.contains("dropend"))return Wi;if(t.classList.contains("dropstart"))return Bi;if(t.classList.contains("dropup-center"))return"top";if(t.classList.contains("dropdown-center"))return"bottom";const e="end"===getComputedStyle(this._menu).getPropertyValue("--bs-position").trim();return t.classList.contains("dropup")?e?ji:Mi:e?Hi:Fi}_detectNavbar(){return null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return(this._inNavbar||"static"===this._config.display)&&(F.setDataAttribute(this._menu,"popper","static"),t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,...g(this._config.popperConfig,[t])}}_selectMenuItem({key:t,target:e}){const i=z.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter((t=>a(t)));i.length&&b(i,e,t===Ti,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=qi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(2===t.button||"keyup"===t.type&&"Tab"!==t.key)return;const e=z.find(Ni);for(const i of e){const e=qi.getInstance(i);if(!e||!1===e._config.autoClose)continue;const n=t.composedPath(),s=n.includes(e._menu);if(n.includes(e._element)||"inside"===e._config.autoClose&&!s||"outside"===e._config.autoClose&&s)continue;if(e._menu.contains(t.target)&&("keyup"===t.type&&"Tab"===t.key||/input|select|option|textarea|form/i.test(t.target.tagName)))continue;const o={relatedTarget:e._element};"click"===t.type&&(o.clickEvent=t),e._completeHide(o)}}static dataApiKeydownHandler(t){const e=/input|textarea/i.test(t.target.tagName),i="Escape"===t.key,n=[Ei,Ti].includes(t.key);if(!n&&!i)return;if(e&&!i)return;t.preventDefault();const s=this.matches(Ii)?this:z.prev(this,Ii)[0]||z.next(this,Ii)[0]||z.findOne(Ii,t.delegateTarget.parentNode),o=qi.getOrCreateInstance(s);if(n)return t.stopPropagation(),o.show(),void o._selectMenuItem(t);o._isShown()&&(t.stopPropagation(),o.hide(),s.focus())}}N.on(document,Si,Ii,qi.dataApiKeydownHandler),N.on(document,Si,Pi,qi.dataApiKeydownHandler),N.on(document,Li,qi.clearMenus),N.on(document,Di,qi.clearMenus),N.on(document,Li,Ii,(function(t){t.preventDefault(),qi.getOrCreateInstance(this).toggle()})),m(qi);const Vi="backdrop",Ki="show",Qi=`mousedown.bs.${Vi}`,Xi={className:"modal-backdrop",clickCallback:null,isAnimated:!1,isVisible:!0,rootElement:"body"},Yi={className:"string",clickCallback:"(function|null)",isAnimated:"boolean",isVisible:"boolean",rootElement:"(element|string)"};class Ui extends H{constructor(t){super(),this._config=this._getConfig(t),this._isAppended=!1,this._element=null}static get Default(){return Xi}static get DefaultType(){return Yi}static get NAME(){return Vi}show(t){if(!this._config.isVisible)return void g(t);this._append();const e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(Ki),this._emulateAnimation((()=>{g(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(Ki),this._emulateAnimation((()=>{this.dispose(),g(t)}))):g(t)}dispose(){this._isAppended&&(N.off(this._element,Qi),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=r(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),N.on(t,Qi,(()=>{g(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){_(t,this._getElement(),this._config.isAnimated)}}const Gi=".bs.focustrap",Ji=`focusin${Gi}`,Zi=`keydown.tab${Gi}`,tn="backward",en={autofocus:!0,trapElement:null},nn={autofocus:"boolean",trapElement:"element"};class sn extends H{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return en}static get DefaultType(){return nn}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),N.off(document,Gi),N.on(document,Ji,(t=>this._handleFocusin(t))),N.on(document,Zi,(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,N.off(document,Gi))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const i=z.focusableChildren(e);0===i.length?e.focus():this._lastTabNavDirection===tn?i[i.length-1].focus():i[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?tn:"forward")}}const on=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",rn=".sticky-top",an="padding-right",ln="margin-right";class cn{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,an,(e=>e+t)),this._setElementAttributes(on,an,(e=>e+t)),this._setElementAttributes(rn,ln,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,an),this._resetElementAttributes(on,an),this._resetElementAttributes(rn,ln)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${i(Number.parseFloat(s))}px`)}))}_saveInitialAttribute(t,e){const i=t.style.getPropertyValue(e);i&&F.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=F.getDataAttribute(t,e);null!==i?(F.removeDataAttribute(t,e),t.style.setProperty(e,i)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const i of z.find(t,this._element))e(i)}}const hn=".bs.modal",dn=`hide${hn}`,un=`hidePrevented${hn}`,fn=`hidden${hn}`,pn=`show${hn}`,mn=`shown${hn}`,gn=`resize${hn}`,_n=`click.dismiss${hn}`,bn=`mousedown.dismiss${hn}`,vn=`keydown.dismiss${hn}`,yn=`click${hn}.data-api`,wn="modal-open",An="show",En="modal-static",Tn={backdrop:!0,focus:!0,keyboard:!0},Cn={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class On extends W{constructor(t,e){super(t,e),this._dialog=z.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new cn,this._addEventListeners()}static get Default(){return Tn}static get DefaultType(){return Cn}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||N.trigger(this._element,pn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(wn),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(N.trigger(this._element,dn).defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(An),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){N.off(window,hn),N.off(this._dialog,hn),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Ui({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=z.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(An),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,N.trigger(this._element,mn,{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){N.on(this._element,vn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():this._triggerBackdropTransition())})),N.on(window,gn,(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),N.on(this._element,bn,(t=>{N.one(this._element,_n,(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(wn),this._resetAdjustments(),this._scrollBar.reset(),N.trigger(this._element,fn)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(N.trigger(this._element,un).defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(En)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(En),this._queueCallback((()=>{this._element.classList.remove(En),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;if(i&&!t){const t=p()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!i&&t){const t=p()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=On.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}N.on(document,yn,'[data-bs-toggle="modal"]',(function(t){const e=z.getElementFromSelector(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),N.one(e,pn,(t=>{t.defaultPrevented||N.one(e,fn,(()=>{a(this)&&this.focus()}))}));const i=z.findOne(".modal.show");i&&On.getInstance(i).hide(),On.getOrCreateInstance(e).toggle(this)})),R(On),m(On);const xn=".bs.offcanvas",kn=".data-api",Ln=`load${xn}${kn}`,Sn="show",Dn="showing",$n="hiding",In=".offcanvas.show",Nn=`show${xn}`,Pn=`shown${xn}`,Mn=`hide${xn}`,jn=`hidePrevented${xn}`,Fn=`hidden${xn}`,Hn=`resize${xn}`,Wn=`click${xn}${kn}`,Bn=`keydown.dismiss${xn}`,zn={backdrop:!0,keyboard:!0,scroll:!1},Rn={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class qn extends W{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return zn}static get DefaultType(){return Rn}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||N.trigger(this._element,Nn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new cn).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Dn),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Sn),this._element.classList.remove(Dn),N.trigger(this._element,Pn,{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(N.trigger(this._element,Mn).defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add($n),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Sn,$n),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new cn).reset(),N.trigger(this._element,Fn)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new Ui({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():N.trigger(this._element,jn)}:null})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_addEventListeners(){N.on(this._element,Bn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():N.trigger(this._element,jn))}))}static jQueryInterface(t){return this.each((function(){const e=qn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}N.on(document,Wn,'[data-bs-toggle="offcanvas"]',(function(t){const e=z.getElementFromSelector(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;N.one(e,Fn,(()=>{a(this)&&this.focus()}));const i=z.findOne(In);i&&i!==e&&qn.getInstance(i).hide(),qn.getOrCreateInstance(e).toggle(this)})),N.on(window,Ln,(()=>{for(const t of z.find(In))qn.getOrCreateInstance(t).show()})),N.on(window,Hn,(()=>{for(const t of z.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&qn.getOrCreateInstance(t).hide()})),R(qn),m(qn);const Vn={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Kn=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Qn=/^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i,Xn=(t,e)=>{const i=t.nodeName.toLowerCase();return e.includes(i)?!Kn.has(i)||Boolean(Qn.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(i)))},Yn={allowList:Vn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"<div></div>"},Un={allowList:"object",content:"object",extraClass:"(string|function)",html:"boolean",sanitize:"boolean",sanitizeFn:"(null|function)",template:"string"},Gn={entry:"(string|element|function|null)",selector:"(string|element)"};class Jn extends H{constructor(t){super(),this._config=this._getConfig(t)}static get Default(){return Yn}static get DefaultType(){return Un}static get NAME(){return"TemplateFactory"}getContent(){return Object.values(this._config.content).map((t=>this._resolvePossibleFunction(t))).filter(Boolean)}hasContent(){return this.getContent().length>0}changeContent(t){return this._checkContent(t),this._config.content={...this._config.content,...t},this}toHtml(){const t=document.createElement("div");t.innerHTML=this._maybeSanitize(this._config.template);for(const[e,i]of Object.entries(this._config.content))this._setContent(t,i,e);const e=t.children[0],i=this._resolvePossibleFunction(this._config.extraClass);return i&&e.classList.add(...i.split(" ")),e}_typeCheckConfig(t){super._typeCheckConfig(t),this._checkContent(t.content)}_checkContent(t){for(const[e,i]of Object.entries(t))super._typeCheckConfig({selector:e,entry:i},Gn)}_setContent(t,e,i){const n=z.findOne(i,t);n&&((e=this._resolvePossibleFunction(e))?o(e)?this._putElementInTemplate(r(e),n):this._config.html?n.innerHTML=this._maybeSanitize(e):n.textContent=e:n.remove())}_maybeSanitize(t){return this._config.sanitize?function(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(const t of s){const i=t.nodeName.toLowerCase();if(!Object.keys(e).includes(i)){t.remove();continue}const n=[].concat(...t.attributes),s=[].concat(e["*"]||[],e[i]||[]);for(const e of n)Xn(e,s)||t.removeAttribute(e.nodeName)}return n.body.innerHTML}(t,this._config.allowList,this._config.sanitizeFn):t}_resolvePossibleFunction(t){return g(t,[this])}_putElementInTemplate(t,e){if(this._config.html)return e.innerHTML="",void e.append(t);e.textContent=t.textContent}}const Zn=new Set(["sanitize","allowList","sanitizeFn"]),ts="fade",es="show",is=".modal",ns="hide.bs.modal",ss="hover",os="focus",rs={AUTO:"auto",TOP:"top",RIGHT:p()?"left":"right",BOTTOM:"bottom",LEFT:p()?"right":"left"},as={allowList:Vn,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,6],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'<div class="tooltip" role="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',title:"",trigger:"hover focus"},ls={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class cs extends W{constructor(t,e){if(void 0===vi)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t,e),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return as}static get DefaultType(){return ls}static get NAME(){return"tooltip"}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){this._isEnabled&&(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()?this._leave():this._enter())}dispose(){clearTimeout(this._timeout),N.off(this._element.closest(is),ns,this._hideModalHandler),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const t=N.trigger(this._element,this.constructor.eventName("show")),e=(c(this._element)||this._element.ownerDocument.documentElement).contains(this._element);if(t.defaultPrevented||!e)return;this._disposePopper();const i=this._getTipElement();this._element.setAttribute("aria-describedby",i.getAttribute("id"));const{container:n}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(n.append(i),N.trigger(this._element,this.constructor.eventName("inserted"))),this._popper=this._createPopper(i),i.classList.add(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._queueCallback((()=>{N.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(this._isShown()&&!N.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented){if(this._getTipElement().classList.remove(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.off(t,"mouseover",h);this._activeTrigger.click=!1,this._activeTrigger[os]=!1,this._activeTrigger[ss]=!1,this._isHovered=null,this._queueCallback((()=>{this._isWithActiveTrigger()||(this._isHovered||this._disposePopper(),this._element.removeAttribute("aria-describedby"),N.trigger(this._element,this.constructor.eventName("hidden")))}),this.tip,this._isAnimated())}}update(){this._popper&&this._popper.update()}_isWithContent(){return Boolean(this._getTitle())}_getTipElement(){return this.tip||(this.tip=this._createTipElement(this._newContent||this._getContentForTemplate())),this.tip}_createTipElement(t){const e=this._getTemplateFactory(t).toHtml();if(!e)return null;e.classList.remove(ts,es),e.classList.add(`bs-${this.constructor.NAME}-auto`);const i=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME).toString();return e.setAttribute("id",i),this._isAnimated()&&e.classList.add(ts),e}setContent(t){this._newContent=t,this._isShown()&&(this._disposePopper(),this.show())}_getTemplateFactory(t){return this._templateFactory?this._templateFactory.changeContent(t):this._templateFactory=new Jn({...this._config,content:t,extraClass:this._resolvePossibleFunction(this._config.customClass)}),this._templateFactory}_getContentForTemplate(){return{".tooltip-inner":this._getTitle()}}_getTitle(){return this._resolvePossibleFunction(this._config.title)||this._element.getAttribute("data-bs-original-title")}_initializeOnDelegatedTarget(t){return this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_isAnimated(){return this._config.animation||this.tip&&this.tip.classList.contains(ts)}_isShown(){return this.tip&&this.tip.classList.contains(es)}_createPopper(t){const e=g(this._config.placement,[this,t,this._element]),i=rs[e.toUpperCase()];return bi(this._element,t,this._getPopperConfig(i))}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return g(t,[this._element])}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"preSetPlacement",enabled:!0,phase:"beforeMain",fn:t=>{this._getTipElement().setAttribute("data-popper-placement",t.state.placement)}}]};return{...e,...g(this._config.popperConfig,[e])}}_setListeners(){const t=this._config.trigger.split(" ");for(const e of t)if("click"===e)N.on(this._element,this.constructor.eventName("click"),this._config.selector,(t=>{this._initializeOnDelegatedTarget(t).toggle()}));else 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diff --git a/docs/site_libs/quarto-contrib/glightbox/glightbox.min.css b/docs/site_libs/quarto-contrib/glightbox/glightbox.min.css
new file mode 100644
index 00000000..3c9ff877
--- /dev/null
+++ b/docs/site_libs/quarto-contrib/glightbox/glightbox.min.css
@@ -0,0 +1 @@
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diff --git a/docs/site_libs/quarto-contrib/glightbox/glightbox.min.js b/docs/site_libs/quarto-contrib/glightbox/glightbox.min.js
new file mode 100644
index 00000000..997908b5
--- /dev/null
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Math.abs(e-t)>=Math.abs(i-n)?e-t>0?"Left":"Right":i-n>0?"Up":"Down"}},{key:"on",value:function(e,t){this[e]&&this[e].add(t)}},{key:"off",value:function(e,t){this[e]&&this[e].del(t)}},{key:"destroy",value:function(){return this.singleTapTimeout&&clearTimeout(this.singleTapTimeout),this.tapTimeout&&clearTimeout(this.tapTimeout),this.longTapTimeout&&clearTimeout(this.longTapTimeout),this.swipeTimeout&&clearTimeout(this.swipeTimeout),this.element.removeEventListener("touchstart",this.start),this.element.removeEventListener("touchmove",this.move),this.element.removeEventListener("touchend",this.end),this.element.removeEventListener("touchcancel",this.cancel),this.rotate.del(),this.touchStart.del(),this.multipointStart.del(),this.multipointEnd.del(),this.pinch.del(),this.swipe.del(),this.tap.del(),this.doubleTap.del(),this.longTap.del(),this.singleTap.del(),this.pressMove.del(),this.twoFingerPressMove.del(),this.touchMove.del(),this.touchEnd.del(),this.touchCancel.del(),this.preV=this.pinchStartLen=this.zoom=this.isDoubleTap=this.delta=this.last=this.now=this.tapTimeout=this.singleTapTimeout=this.longTapTimeout=this.swipeTimeout=this.x1=this.x2=this.y1=this.y2=this.preTapPosition=this.rotate=this.touchStart=this.multipointStart=this.multipointEnd=this.pinch=this.swipe=this.tap=this.doubleTap=this.longTap=this.singleTap=this.pressMove=this.touchMove=this.touchEnd=this.touchCancel=this.twoFingerPressMove=null,window.removeEventListener("scroll",this._cancelAllHandler),null}}]),e}();function W(e){var t=function(){var e,t=document.createElement("fakeelement"),i={transition:"transitionend",OTransition:"oTransitionEnd",MozTransition:"transitionend",WebkitTransition:"webkitTransitionEnd"};for(e in i)if(void 0!==t.style[e])return i[e]}(),i=window.innerWidth||document.documentElement.clientWidth||document.body.clientWidth,n=c(e,"gslide-media")?e:e.querySelector(".gslide-media"),s=u(n,".ginner-container"),l=e.querySelector(".gslide-description");i>769&&(n=s),h(n,"greset"),v(n,"translate3d(0, 0, 0)"),a(t,{onElement:n,once:!0,withCallback:function(e,t){d(n,"greset")}}),n.style.opacity="",l&&(l.style.opacity="")}function B(e){if(e.events.hasOwnProperty("touch"))return!1;var t,i,n,s=y(),l=s.width,o=s.height,r=!1,a=null,g=null,f=null,p=!1,m=1,x=1,b=!1,S=!1,w=null,T=null,C=null,k=null,E=0,A=0,L=!1,I=!1,O={},P={},M=0,z=0,X=document.getElementById("glightbox-slider"),Y=document.querySelector(".goverlay"),q=new 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h,d=s.targetTouches[0].clientX,c=s.targetTouches[0].clientY,u=M-d,m=z-c;if(Math.abs(u)>Math.abs(m)?(L=!1,I=!0):(I=!1,L=!0),t=P.pageX-O.pageX,E=100*t/l,i=P.pageY-O.pageY,A=100*i/o,L&&f&&(h=1-Math.abs(i)/o,Y.style.opacity=h,e.settings.touchFollowAxis&&(E=0)),I&&(h=1-Math.abs(t)/l,g.style.opacity=h,e.settings.touchFollowAxis&&(A=0)),!f)return v(g,"translate3d(".concat(E,"%, 0, 0)"));v(g,"translate3d(".concat(E,"%, ").concat(A,"%, 0)"))}},touchEnd:function(){if(r){if(p=!1,S||b)return C=w,void(k=T);var t=Math.abs(parseInt(A)),i=Math.abs(parseInt(E));if(!(t>29&&f))return t<29&&i<25?(h(Y,"greset"),Y.style.opacity=1,W(g)):void 0;e.close()}},multipointEnd:function(){setTimeout((function(){b=!1}),50)},multipointStart:function(){b=!0,m=x||1},pinch:function(e){if(!f||p)return!1;b=!0,f.scaleX=f.scaleY=m*e.zoom;var t=m*e.zoom;if(S=!0,t<=1)return S=!1,t=1,k=null,C=null,w=null,T=null,void f.setAttribute("style","");t>4.5&&(t=4.5),f.style.transform="scale3d(".concat(t,", ").concat(t,", 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s.drag(e)}),!1),this.img.addEventListener("click",(function(e){return s.slide.classList.contains("dragging-nav")?(s.zoomOut(),!1):s.zoomedIn?void(s.zoomedIn&&!s.dragging&&s.zoomOut()):s.zoomIn()}),!1),this.img.setZoomEvents=!0}return n(e,[{key:"zoomIn",value:function(){var e=this.widowWidth();if(!(this.zoomedIn||e<=768)){var t=this.img;if(t.setAttribute("data-style",t.getAttribute("style")),t.style.maxWidth=t.naturalWidth+"px",t.style.maxHeight=t.naturalHeight+"px",t.naturalWidth>e){var i=e/2-t.naturalWidth/2;this.setTranslate(this.img.parentNode,i,0)}this.slide.classList.add("zoomed"),this.zoomedIn=!0}}},{key:"zoomOut",value:function(){this.img.parentNode.setAttribute("style",""),this.img.setAttribute("style",this.img.getAttribute("data-style")),this.slide.classList.remove("zoomed"),this.zoomedIn=!1,this.currentX=null,this.currentY=null,this.initialX=null,this.initialY=null,this.xOffset=0,this.yOffset=0,this.onclose&&"function"==typeof this.onclose&&this.onclose()}},{key:"dragStart",value:function(e){e.preventDefault(),this.zoomedIn?("touchstart"===e.type?(this.initialX=e.touches[0].clientX-this.xOffset,this.initialY=e.touches[0].clientY-this.yOffset):(this.initialX=e.clientX-this.xOffset,this.initialY=e.clientY-this.yOffset),e.target===this.img&&(this.active=!0,this.img.classList.add("dragging"))):this.active=!1}},{key:"dragEnd",value:function(e){var t=this;e.preventDefault(),this.initialX=this.currentX,this.initialY=this.currentY,this.active=!1,setTimeout((function(){t.dragging=!1,t.img.isDragging=!1,t.img.classList.remove("dragging")}),100)}},{key:"drag",value:function(e){this.active&&(e.preventDefault(),"touchmove"===e.type?(this.currentX=e.touches[0].clientX-this.initialX,this.currentY=e.touches[0].clientY-this.initialY):(this.currentX=e.clientX-this.initialX,this.currentY=e.clientY-this.initialY),this.xOffset=this.currentX,this.yOffset=this.currentY,this.img.isDragging=!0,this.dragging=!0,this.setTranslate(this.img,this.currentX,this.currentY))}},{key:"onMove",value:function(e){if(this.zoomedIn){var t=e.clientX-this.img.naturalWidth/2,i=e.clientY-this.img.naturalHeight/2;this.setTranslate(this.img,t,i)}}},{key:"setTranslate",value:function(e,t,i){e.style.transform="translate3d("+t+"px, "+i+"px, 0)"}},{key:"widowWidth",value:function(){return window.innerWidth||document.documentElement.clientWidth||document.body.clientWidth}}]),e}(),V=function(){function e(){var i=this,n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{};t(this,e);var s=n.dragEl,l=n.toleranceX,o=void 0===l?40:l,r=n.toleranceY,a=void 0===r?65:r,h=n.slide,d=void 0===h?null:h,c=n.instance,u=void 0===c?null:c;this.el=s,this.active=!1,this.dragging=!1,this.currentX=null,this.currentY=null,this.initialX=null,this.initialY=null,this.xOffset=0,this.yOffset=0,this.direction=null,this.lastDirection=null,this.toleranceX=o,this.toleranceY=a,this.toleranceReached=!1,this.dragContainer=this.el,this.slide=d,this.instance=u,this.el.addEventListener("mousedown",(function(e){return i.dragStart(e)}),!1),this.el.addEventListener("mouseup",(function(e){return i.dragEnd(e)}),!1),this.el.addEventListener("mousemove",(function(e){return i.drag(e)}),!1)}return n(e,[{key:"dragStart",value:function(e){if(this.slide.classList.contains("zoomed"))this.active=!1;else{"touchstart"===e.type?(this.initialX=e.touches[0].clientX-this.xOffset,this.initialY=e.touches[0].clientY-this.yOffset):(this.initialX=e.clientX-this.xOffset,this.initialY=e.clientY-this.yOffset);var t=e.target.nodeName.toLowerCase();e.target.classList.contains("nodrag")||u(e.target,".nodrag")||-1!==["input","select","textarea","button","a"].indexOf(t)?this.active=!1:(e.preventDefault(),(e.target===this.el||"img"!==t&&u(e.target,".gslide-inline"))&&(this.active=!0,this.el.classList.add("dragging"),this.dragContainer=u(e.target,".ginner-container")))}}},{key:"dragEnd",value:function(e){var t=this;e&&e.preventDefault(),this.initialX=0,this.initialY=0,this.currentX=null,this.currentY=null,this.initialX=null,this.initialY=null,this.xOffset=0,this.yOffset=0,this.active=!1,this.doSlideChange&&(this.instance.preventOutsideClick=!0,"right"==this.doSlideChange&&this.instance.prevSlide(),"left"==this.doSlideChange&&this.instance.nextSlide()),this.doSlideClose&&this.instance.close(),this.toleranceReached||this.setTranslate(this.dragContainer,0,0,!0),setTimeout((function(){t.instance.preventOutsideClick=!1,t.toleranceReached=!1,t.lastDirection=null,t.dragging=!1,t.el.isDragging=!1,t.el.classList.remove("dragging"),t.slide.classList.remove("dragging-nav"),t.dragContainer.style.transform="",t.dragContainer.style.transition=""}),100)}},{key:"drag",value:function(e){if(this.active){e.preventDefault(),this.slide.classList.add("dragging-nav"),"touchmove"===e.type?(this.currentX=e.touches[0].clientX-this.initialX,this.currentY=e.touches[0].clientY-this.initialY):(this.currentX=e.clientX-this.initialX,this.currentY=e.clientY-this.initialY),this.xOffset=this.currentX,this.yOffset=this.currentY,this.el.isDragging=!0,this.dragging=!0,this.doSlideChange=!1,this.doSlideClose=!1;var t=Math.abs(this.currentX),i=Math.abs(this.currentY);if(t>0&&t>=Math.abs(this.currentY)&&(!this.lastDirection||"x"==this.lastDirection)){this.yOffset=0,this.lastDirection="x",this.setTranslate(this.dragContainer,this.currentX,0);var n=this.shouldChange();if(!this.instance.settings.dragAutoSnap&&n&&(this.doSlideChange=n),this.instance.settings.dragAutoSnap&&n)return this.instance.preventOutsideClick=!0,this.toleranceReached=!0,this.active=!1,this.instance.preventOutsideClick=!0,this.dragEnd(null),"right"==n&&this.instance.prevSlide(),void("left"==n&&this.instance.nextSlide())}if(this.toleranceY>0&&i>0&&i>=t&&(!this.lastDirection||"y"==this.lastDirection)){this.xOffset=0,this.lastDirection="y",this.setTranslate(this.dragContainer,0,this.currentY);var s=this.shouldClose();return!this.instance.settings.dragAutoSnap&&s&&(this.doSlideClose=!0),void(this.instance.settings.dragAutoSnap&&s&&this.instance.close())}}}},{key:"shouldChange",value:function(){var e=!1;if(Math.abs(this.currentX)>=this.toleranceX){var t=this.currentX>0?"right":"left";("left"==t&&this.slide!==this.slide.parentNode.lastChild||"right"==t&&this.slide!==this.slide.parentNode.firstChild)&&(e=t)}return e}},{key:"shouldClose",value:function(){var e=!1;return Math.abs(this.currentY)>=this.toleranceY&&(e=!0),e}},{key:"setTranslate",value:function(e,t,i){var n=arguments.length>3&&void 0!==arguments[3]&&arguments[3];e.style.transition=n?"all .2s ease":"",e.style.transform="translate3d(".concat(t,"px, ").concat(i,"px, 0)")}}]),e}();function j(e,t,i,n){var s=e.querySelector(".gslide-media"),l=new 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0!==arguments[0]?arguments[0]:{};t(this,e),this.defaults={href:"",sizes:"",srcset:"",title:"",type:"",videoProvider:"",description:"",alt:"",descPosition:"bottom",effect:"",width:"",height:"",content:!1,zoomable:!0,draggable:!0},L(i)&&(this.defaults=l(this.defaults,i))}return n(e,[{key:"sourceType",value:function(e){var t=e;if(null!==(e=e.toLowerCase()).match(/\.(jpeg|jpg|jpe|gif|png|apn|webp|avif|svg)/))return"image";if(e.match(/(youtube\.com|youtube-nocookie\.com)\/watch\?v=([a-zA-Z0-9\-_]+)/)||e.match(/youtu\.be\/([a-zA-Z0-9\-_]+)/)||e.match(/(youtube\.com|youtube-nocookie\.com)\/embed\/([a-zA-Z0-9\-_]+)/))return"video";if(e.match(/vimeo\.com\/([0-9]*)/))return"video";if(null!==e.match(/\.(mp4|ogg|webm|mov)/))return"video";if(null!==e.match(/\.(mp3|wav|wma|aac|ogg)/))return"audio";if(e.indexOf("#")>-1&&""!==t.split("#").pop().trim())return"inline";return e.indexOf("goajax=true")>-1?"ajax":"external"}},{key:"parseConfig",value:function(e,t){var i=this,n=l({descPosition:t.descPosition},this.defaults);if(L(e)&&!k(e)){O(e,"type")||(O(e,"content")&&e.content?e.type="inline":O(e,"href")&&(e.type=this.sourceType(e.href)));var s=l(n,e);return this.setSize(s,t),s}var r="",a=e.getAttribute("data-glightbox"),h=e.nodeName.toLowerCase();if("a"===h&&(r=e.href),"img"===h&&(r=e.src,n.alt=e.alt),n.href=r,o(n,(function(s,l){O(t,l)&&"width"!==l&&(n[l]=t[l]);var o=e.dataset[l];I(o)||(n[l]=i.sanitizeValue(o))})),n.content&&(n.type="inline"),!n.type&&r&&(n.type=this.sourceType(r)),I(a)){if(!n.title&&"a"==h){var d=e.title;I(d)||""===d||(n.title=d)}if(!n.title&&"img"==h){var c=e.alt;I(c)||""===c||(n.title=c)}}else{var u=[];o(n,(function(e,t){u.push(";\\s?"+t)})),u=u.join("\\s?:|"),""!==a.trim()&&o(n,(function(e,t){var s=a,l=new RegExp("s?"+t+"s?:s?(.*?)("+u+"s?:|$)"),o=s.match(l);if(o&&o.length&&o[1]){var r=o[1].trim().replace(/;\s*$/,"");n[t]=i.sanitizeValue(r)}}))}if(n.description&&"."===n.description.substring(0,1)){var g;try{g=document.querySelector(n.description).innerHTML}catch(e){if(!(e instanceof DOMException))throw e}g&&(n.description=g)}if(!n.description){var v=e.querySelector(".glightbox-desc");v&&(n.description=v.innerHTML)}return this.setSize(n,t,e),this.slideConfig=n,n}},{key:"setSize",value:function(e,t){var i=arguments.length>2&&void 0!==arguments[2]?arguments[2]:null,n="video"==e.type?this.checkSize(t.videosWidth):this.checkSize(t.width),s=this.checkSize(t.height);return e.width=O(e,"width")&&""!==e.width?this.checkSize(e.width):n,e.height=O(e,"height")&&""!==e.height?this.checkSize(e.height):s,i&&"image"==e.type&&(e._hasCustomWidth=!!i.dataset.width,e._hasCustomHeight=!!i.dataset.height),e}},{key:"checkSize",value:function(e){return M(e)?"".concat(e,"px"):e}},{key:"sanitizeValue",value:function(e){return"true"!==e&&"false"!==e?e:"true"===e}}]),e}(),$=function(){function e(i,n,s){t(this,e),this.element=i,this.instance=n,this.index=s}return n(e,[{key:"setContent",value:function(){var e=this,t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:null,i=arguments.length>1&&void 0!==arguments[1]&&arguments[1];if(c(t,"loaded"))return!1;var n=this.instance.settings,s=this.slideConfig,l=w();T(n.beforeSlideLoad)&&n.beforeSlideLoad({index:this.index,slide:t,player:!1});var o=s.type,r=s.descPosition,a=t.querySelector(".gslide-media"),d=t.querySelector(".gslide-title"),u=t.querySelector(".gslide-desc"),g=t.querySelector(".gdesc-inner"),v=i,f="gSlideTitle_"+this.index,p="gSlideDesc_"+this.index;if(T(n.afterSlideLoad)&&(v=function(){T(i)&&i(),n.afterSlideLoad({index:e.index,slide:t,player:e.instance.getSlidePlayerInstance(e.index)})}),""==s.title&&""==s.description?g&&g.parentNode.parentNode.removeChild(g.parentNode):(d&&""!==s.title?(d.id=f,d.innerHTML=s.title):d.parentNode.removeChild(d),u&&""!==s.description?(u.id=p,l&&n.moreLength>0?(s.smallDescription=this.slideShortDesc(s.description,n.moreLength,n.moreText),u.innerHTML=s.smallDescription,this.descriptionEvents(u,s)):u.innerHTML=s.description):u.parentNode.removeChild(u),h(a.parentNode,"desc-".concat(r)),h(g.parentNode,"description-".concat(r))),h(a,"gslide-".concat(o)),h(t,"loaded"),"video"!==o){if("external"!==o)return"inline"===o?(G.apply(this.instance,[t,s,this.index,v]),void(s.draggable&&new V({dragEl:t.querySelector(".gslide-inline"),toleranceX:n.dragToleranceX,toleranceY:n.dragToleranceY,slide:t,instance:this.instance}))):void("image"!==o?T(v)&&v():j(t,s,this.index,(function(){var i=t.querySelector("img");s.draggable&&new V({dragEl:i,toleranceX:n.dragToleranceX,toleranceY:n.dragToleranceY,slide:t,instance:e.instance}),s.zoomable&&i.naturalWidth>i.offsetWidth&&(h(i,"zoomable"),new H(i,t,(function(){e.instance.resize()}))),T(v)&&v()})));Z.apply(this,[t,s,this.index,v])}else F.apply(this.instance,[t,s,this.index,v])}},{key:"slideShortDesc",value:function(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:50,i=arguments.length>2&&void 0!==arguments[2]&&arguments[2],n=document.createElement("div");n.innerHTML=e;var s=n.innerText,l=i;if((e=s.trim()).length<=t)return e;var o=e.substr(0,t-1);return l?(n=null,o+'... <a href="#" class="desc-more">'+i+"</a>"):o}},{key:"descriptionEvents",value:function(e,t){var i=this,n=e.querySelector(".desc-more");if(!n)return!1;a("click",{onElement:n,withCallback:function(e,n){e.preventDefault();var s=document.body,l=u(n,".gslide-desc");if(!l)return!1;l.innerHTML=t.description,h(s,"gdesc-open");var o=a("click",{onElement:[s,u(l,".gslide-description")],withCallback:function(e,n){"a"!==e.target.nodeName.toLowerCase()&&(d(s,"gdesc-open"),h(s,"gdesc-closed"),l.innerHTML=t.smallDescription,i.descriptionEvents(l,t),setTimeout((function(){d(s,"gdesc-closed")}),400),o.destroy())}})}})}},{key:"create",value:function(){return m(this.instance.settings.slideHTML)}},{key:"getConfig",value:function(){k(this.element)||this.element.hasOwnProperty("draggable")||(this.element.draggable=this.instance.settings.draggable);var e=new U(this.instance.settings.slideExtraAttributes);return this.slideConfig=e.parseConfig(this.element,this.instance.settings),this.slideConfig}}]),e}(),J=w(),K=null!==w()||void 0!==document.createTouch||"ontouchstart"in window||"onmsgesturechange"in window||navigator.msMaxTouchPoints,Q=document.getElementsByTagName("html")[0],ee={selector:".glightbox",elements:null,skin:"clean",theme:"clean",closeButton:!0,startAt:null,autoplayVideos:!0,autofocusVideos:!0,descPosition:"bottom",width:"900px",height:"506px",videosWidth:"960px",beforeSlideChange:null,afterSlideChange:null,beforeSlideLoad:null,afterSlideLoad:null,slideInserted:null,slideRemoved:null,slideExtraAttributes:null,onOpen:null,onClose:null,loop:!1,zoomable:!0,draggable:!0,dragAutoSnap:!1,dragToleranceX:40,dragToleranceY:65,preload:!0,oneSlidePerOpen:!1,touchNavigation:!0,touchFollowAxis:!0,keyboardNavigation:!0,closeOnOutsideClick:!0,plugins:!1,plyr:{css:"https://cdn.plyr.io/3.6.12/plyr.css",js:"https://cdn.plyr.io/3.6.12/plyr.js",config:{ratio:"16:9",fullscreen:{enabled:!0,iosNative:!0},youtube:{noCookie:!0,rel:0,showinfo:0,iv_load_policy:3},vimeo:{byline:!1,portrait:!1,title:!1,transparent:!1}}},openEffect:"zoom",closeEffect:"zoom",slideEffect:"slide",moreText:"See more",moreLength:60,cssEfects:{fade:{in:"fadeIn",out:"fadeOut"},zoom:{in:"zoomIn",out:"zoomOut"},slide:{in:"slideInRight",out:"slideOutLeft"},slideBack:{in:"slideInLeft",out:"slideOutRight"},none:{in:"none",out:"none"}},svg:{close:'<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 512 512" xml:space="preserve"><g><g><path d="M505.943,6.058c-8.077-8.077-21.172-8.077-29.249,0L6.058,476.693c-8.077,8.077-8.077,21.172,0,29.249C10.096,509.982,15.39,512,20.683,512c5.293,0,10.586-2.019,14.625-6.059L505.943,35.306C514.019,27.23,514.019,14.135,505.943,6.058z"/></g></g><g><g><path d="M505.942,476.694L35.306,6.059c-8.076-8.077-21.172-8.077-29.248,0c-8.077,8.076-8.077,21.171,0,29.248l470.636,470.636c4.038,4.039,9.332,6.058,14.625,6.058c5.293,0,10.587-2.019,14.624-6.057C514.018,497.866,514.018,484.771,505.942,476.694z"/></g></g></svg>',next:'<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 477.175 477.175" xml:space="preserve"> <g><path d="M360.731,229.075l-225.1-225.1c-5.3-5.3-13.8-5.3-19.1,0s-5.3,13.8,0,19.1l215.5,215.5l-215.5,215.5c-5.3,5.3-5.3,13.8,0,19.1c2.6,2.6,6.1,4,9.5,4c3.4,0,6.9-1.3,9.5-4l225.1-225.1C365.931,242.875,365.931,234.275,360.731,229.075z"/></g></svg>',prev:'<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 477.175 477.175" xml:space="preserve"><g><path d="M145.188,238.575l215.5-215.5c5.3-5.3,5.3-13.8,0-19.1s-13.8-5.3-19.1,0l-225.1,225.1c-5.3,5.3-5.3,13.8,0,19.1l225.1,225c2.6,2.6,6.1,4,9.5,4s6.9-1.3,9.5-4c5.3-5.3,5.3-13.8,0-19.1L145.188,238.575z"/></g></svg>'},slideHTML:'<div class="gslide">\n    <div class="gslide-inner-content">\n        <div class="ginner-container">\n            <div class="gslide-media">\n            </div>\n            <div class="gslide-description">\n                <div class="gdesc-inner">\n                    <h4 class="gslide-title"></h4>\n                    <div class="gslide-desc"></div>\n                </div>\n            </div>\n        </div>\n    </div>\n</div>',lightboxHTML:'<div id="glightbox-body" class="glightbox-container" tabindex="-1" role="dialog" aria-hidden="false">\n    <div class="gloader visible"></div>\n    <div class="goverlay"></div>\n    <div class="gcontainer">\n    <div id="glightbox-slider" class="gslider"></div>\n    <button class="gclose gbtn" aria-label="Close" data-taborder="3">{closeSVG}</button>\n    <button class="gprev gbtn" aria-label="Previous" data-taborder="2">{prevSVG}</button>\n    <button class="gnext gbtn" aria-label="Next" data-taborder="1">{nextSVG}</button>\n</div>\n</div>'},te=function(){function e(){var i=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{};t(this,e),this.customOptions=i,this.settings=l(ee,i),this.effectsClasses=this.getAnimationClasses(),this.videoPlayers={},this.apiEvents=[],this.fullElementsList=!1}return n(e,[{key:"init",value:function(){var e=this,t=this.getSelector();t&&(this.baseEvents=a("click",{onElement:t,withCallback:function(t,i){t.preventDefault(),e.open(i)}})),this.elements=this.getElements()}},{key:"open",value:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:null,t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:null;if(0===this.elements.length)return!1;this.activeSlide=null,this.prevActiveSlideIndex=null,this.prevActiveSlide=null;var i=M(t)?t:this.settings.startAt;if(k(e)){var n=e.getAttribute("data-gallery");n&&(this.fullElementsList=this.elements,this.elements=this.getGalleryElements(this.elements,n)),I(i)&&(i=this.getElementIndex(e))<0&&(i=0)}M(i)||(i=0),this.build(),g(this.overlay,"none"===this.settings.openEffect?"none":this.settings.cssEfects.fade.in);var s=document.body,l=window.innerWidth-document.documentElement.clientWidth;if(l>0){var o=document.createElement("style");o.type="text/css",o.className="gcss-styles",o.innerText=".gscrollbar-fixer {margin-right: ".concat(l,"px}"),document.head.appendChild(o),h(s,"gscrollbar-fixer")}h(s,"glightbox-open"),h(Q,"glightbox-open"),J&&(h(document.body,"glightbox-mobile"),this.settings.slideEffect="slide"),this.showSlide(i,!0),1===this.elements.length?(h(this.prevButton,"glightbox-button-hidden"),h(this.nextButton,"glightbox-button-hidden")):(d(this.prevButton,"glightbox-button-hidden"),d(this.nextButton,"glightbox-button-hidden")),this.lightboxOpen=!0,this.trigger("open"),T(this.settings.onOpen)&&this.settings.onOpen(),K&&this.settings.touchNavigation&&B(this),this.settings.keyboardNavigation&&X(this)}},{key:"openAt",value:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:0;this.open(null,e)}},{key:"showSlide",value:function(){var e=this,t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:0,i=arguments.length>1&&void 0!==arguments[1]&&arguments[1];f(this.loader),this.index=parseInt(t);var n=this.slidesContainer.querySelector(".current");n&&d(n,"current"),this.slideAnimateOut();var s=this.slidesContainer.querySelectorAll(".gslide")[t];if(c(s,"loaded"))this.slideAnimateIn(s,i),p(this.loader);else{f(this.loader);var l=this.elements[t],o={index:this.index,slide:s,slideNode:s,slideConfig:l.slideConfig,slideIndex:this.index,trigger:l.node,player:null};this.trigger("slide_before_load",o),l.instance.setContent(s,(function(){p(e.loader),e.resize(),e.slideAnimateIn(s,i),e.trigger("slide_after_load",o)}))}this.slideDescription=s.querySelector(".gslide-description"),this.slideDescriptionContained=this.slideDescription&&c(this.slideDescription.parentNode,"gslide-media"),this.settings.preload&&(this.preloadSlide(t+1),this.preloadSlide(t-1)),this.updateNavigationClasses(),this.activeSlide=s}},{key:"preloadSlide",value:function(e){var t=this;if(e<0||e>this.elements.length-1)return!1;if(I(this.elements[e]))return!1;var i=this.slidesContainer.querySelectorAll(".gslide")[e];if(c(i,"loaded"))return!1;var n=this.elements[e],s=n.type,l={index:e,slide:i,slideNode:i,slideConfig:n.slideConfig,slideIndex:e,trigger:n.node,player:null};this.trigger("slide_before_load",l),"video"===s||"external"===s?setTimeout((function(){n.instance.setContent(i,(function(){t.trigger("slide_after_load",l)}))}),200):n.instance.setContent(i,(function(){t.trigger("slide_after_load",l)}))}},{key:"prevSlide",value:function(){this.goToSlide(this.index-1)}},{key:"nextSlide",value:function(){this.goToSlide(this.index+1)}},{key:"goToSlide",value:function(){var e=arguments.length>0&&void 0!==arguments[0]&&arguments[0];if(this.prevActiveSlide=this.activeSlide,this.prevActiveSlideIndex=this.index,!this.loop()&&(e<0||e>this.elements.length-1))return!1;e<0?e=this.elements.length-1:e>=this.elements.length&&(e=0),this.showSlide(e)}},{key:"insertSlide",value:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:-1;t<0&&(t=this.elements.length);var i=new $(e,this,t),n=i.getConfig(),s=l({},n),o=i.create(),r=this.elements.length-1;s.index=t,s.node=!1,s.instance=i,s.slideConfig=n,this.elements.splice(t,0,s);var a=null,h=null;if(this.slidesContainer){if(t>r)this.slidesContainer.appendChild(o);else{var d=this.slidesContainer.querySelectorAll(".gslide")[t];this.slidesContainer.insertBefore(o,d)}(this.settings.preload&&0==this.index&&0==t||this.index-1==t||this.index+1==t)&&this.preloadSlide(t),0===this.index&&0===t&&(this.index=1),this.updateNavigationClasses(),a=this.slidesContainer.querySelectorAll(".gslide")[t],h=this.getSlidePlayerInstance(t),s.slideNode=a}this.trigger("slide_inserted",{index:t,slide:a,slideNode:a,slideConfig:n,slideIndex:t,trigger:null,player:h}),T(this.settings.slideInserted)&&this.settings.slideInserted({index:t,slide:a,player:h})}},{key:"removeSlide",value:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:-1;if(e<0||e>this.elements.length-1)return!1;var t=this.slidesContainer&&this.slidesContainer.querySelectorAll(".gslide")[e];t&&(this.getActiveSlideIndex()==e&&(e==this.elements.length-1?this.prevSlide():this.nextSlide()),t.parentNode.removeChild(t)),this.elements.splice(e,1),this.trigger("slide_removed",e),T(this.settings.slideRemoved)&&this.settings.slideRemoved(e)}},{key:"slideAnimateIn",value:function(e,t){var i=this,n=e.querySelector(".gslide-media"),s=e.querySelector(".gslide-description"),l={index:this.prevActiveSlideIndex,slide:this.prevActiveSlide,slideNode:this.prevActiveSlide,slideIndex:this.prevActiveSlide,slideConfig:I(this.prevActiveSlideIndex)?null:this.elements[this.prevActiveSlideIndex].slideConfig,trigger:I(this.prevActiveSlideIndex)?null:this.elements[this.prevActiveSlideIndex].node,player:this.getSlidePlayerInstance(this.prevActiveSlideIndex)},o={index:this.index,slide:this.activeSlide,slideNode:this.activeSlide,slideConfig:this.elements[this.index].slideConfig,slideIndex:this.index,trigger:this.elements[this.index].node,player:this.getSlidePlayerInstance(this.index)};if(n.offsetWidth>0&&s&&(p(s),s.style.display=""),d(e,this.effectsClasses),t)g(e,this.settings.cssEfects[this.settings.openEffect].in,(function(){i.settings.autoplayVideos&&i.slidePlayerPlay(e),i.trigger("slide_changed",{prev:l,current:o}),T(i.settings.afterSlideChange)&&i.settings.afterSlideChange.apply(i,[l,o])}));else{var r=this.settings.slideEffect,a="none"!==r?this.settings.cssEfects[r].in:r;this.prevActiveSlideIndex>this.index&&"slide"==this.settings.slideEffect&&(a=this.settings.cssEfects.slideBack.in),g(e,a,(function(){i.settings.autoplayVideos&&i.slidePlayerPlay(e),i.trigger("slide_changed",{prev:l,current:o}),T(i.settings.afterSlideChange)&&i.settings.afterSlideChange.apply(i,[l,o])}))}setTimeout((function(){i.resize(e)}),100),h(e,"current")}},{key:"slideAnimateOut",value:function(){if(!this.prevActiveSlide)return!1;var e=this.prevActiveSlide;d(e,this.effectsClasses),h(e,"prev");var t=this.settings.slideEffect,i="none"!==t?this.settings.cssEfects[t].out:t;this.slidePlayerPause(e),this.trigger("slide_before_change",{prev:{index:this.prevActiveSlideIndex,slide:this.prevActiveSlide,slideNode:this.prevActiveSlide,slideIndex:this.prevActiveSlideIndex,slideConfig:I(this.prevActiveSlideIndex)?null:this.elements[this.prevActiveSlideIndex].slideConfig,trigger:I(this.prevActiveSlideIndex)?null:this.elements[this.prevActiveSlideIndex].node,player:this.getSlidePlayerInstance(this.prevActiveSlideIndex)},current:{index:this.index,slide:this.activeSlide,slideNode:this.activeSlide,slideIndex:this.index,slideConfig:this.elements[this.index].slideConfig,trigger:this.elements[this.index].node,player:this.getSlidePlayerInstance(this.index)}}),T(this.settings.beforeSlideChange)&&this.settings.beforeSlideChange.apply(this,[{index:this.prevActiveSlideIndex,slide:this.prevActiveSlide,player:this.getSlidePlayerInstance(this.prevActiveSlideIndex)},{index:this.index,slide:this.activeSlide,player:this.getSlidePlayerInstance(this.index)}]),this.prevActiveSlideIndex>this.index&&"slide"==this.settings.slideEffect&&(i=this.settings.cssEfects.slideBack.out),g(e,i,(function(){var t=e.querySelector(".ginner-container"),i=e.querySelector(".gslide-media"),n=e.querySelector(".gslide-description");t.style.transform="",i.style.transform="",d(i,"greset"),i.style.opacity="",n&&(n.style.opacity=""),d(e,"prev")}))}},{key:"getAllPlayers",value:function(){return this.videoPlayers}},{key:"getSlidePlayerInstance",value:function(e){var t="gvideo"+e,i=this.getAllPlayers();return!(!O(i,t)||!i[t])&&i[t]}},{key:"stopSlideVideo",value:function(e){if(k(e)){var t=e.querySelector(".gvideo-wrapper");t&&(e=t.getAttribute("data-index"))}console.log("stopSlideVideo is deprecated, use slidePlayerPause");var i=this.getSlidePlayerInstance(e);i&&i.playing&&i.pause()}},{key:"slidePlayerPause",value:function(e){if(k(e)){var t=e.querySelector(".gvideo-wrapper");t&&(e=t.getAttribute("data-index"))}var i=this.getSlidePlayerInstance(e);i&&i.playing&&i.pause()}},{key:"playSlideVideo",value:function(e){if(k(e)){var t=e.querySelector(".gvideo-wrapper");t&&(e=t.getAttribute("data-index"))}console.log("playSlideVideo is deprecated, use slidePlayerPlay");var i=this.getSlidePlayerInstance(e);i&&!i.playing&&i.play()}},{key:"slidePlayerPlay",value:function(e){var t;if(!J||null!==(t=this.settings.plyr.config)&&void 0!==t&&t.muted){if(k(e)){var i=e.querySelector(".gvideo-wrapper");i&&(e=i.getAttribute("data-index"))}var n=this.getSlidePlayerInstance(e);n&&!n.playing&&(n.play(),this.settings.autofocusVideos&&n.elements.container.focus())}}},{key:"setElements",value:function(e){var t=this;this.settings.elements=!1;var i=[];e&&e.length&&o(e,(function(e,n){var s=new $(e,t,n),o=s.getConfig(),r=l({},o);r.slideConfig=o,r.instance=s,r.index=n,i.push(r)})),this.elements=i,this.lightboxOpen&&(this.slidesContainer.innerHTML="",this.elements.length&&(o(this.elements,(function(){var e=m(t.settings.slideHTML);t.slidesContainer.appendChild(e)})),this.showSlide(0,!0)))}},{key:"getElementIndex",value:function(e){var t=!1;return o(this.elements,(function(i,n){if(O(i,"node")&&i.node==e)return t=n,!0})),t}},{key:"getElements",value:function(){var e=this,t=[];this.elements=this.elements?this.elements:[],!I(this.settings.elements)&&E(this.settings.elements)&&this.settings.elements.length&&o(this.settings.elements,(function(i,n){var s=new $(i,e,n),o=s.getConfig(),r=l({},o);r.node=!1,r.index=n,r.instance=s,r.slideConfig=o,t.push(r)}));var i=!1;return this.getSelector()&&(i=document.querySelectorAll(this.getSelector())),i?(o(i,(function(i,n){var s=new $(i,e,n),o=s.getConfig(),r=l({},o);r.node=i,r.index=n,r.instance=s,r.slideConfig=o,r.gallery=i.getAttribute("data-gallery"),t.push(r)})),t):t}},{key:"getGalleryElements",value:function(e,t){return e.filter((function(e){return 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n=O(this.settings.svg,"next")?this.settings.svg.next:"",s=O(this.settings.svg,"prev")?this.settings.svg.prev:"",l=O(this.settings.svg,"close")?this.settings.svg.close:"",r=this.settings.lightboxHTML;r=m(r=(r=(r=r.replace(/{nextSVG}/g,n)).replace(/{prevSVG}/g,s)).replace(/{closeSVG}/g,l)),document.body.appendChild(r);var d=document.getElementById("glightbox-body");this.modal=d;var g=d.querySelector(".gclose");this.prevButton=d.querySelector(".gprev"),this.nextButton=d.querySelector(".gnext"),this.overlay=d.querySelector(".goverlay"),this.loader=d.querySelector(".gloader"),this.slidesContainer=document.getElementById("glightbox-slider"),this.bodyHiddenChildElms=i,this.events={},h(this.modal,"glightbox-"+this.settings.skin),this.settings.closeButton&&g&&(this.events.close=a("click",{onElement:g,withCallback:function(t,i){t.preventDefault(),e.close()}})),g&&!this.settings.closeButton&&g.parentNode.removeChild(g),this.nextButton&&(this.events.next=a("click",{onElement:this.nextButton,withCallback:function(t,i){t.preventDefault(),e.nextSlide()}})),this.prevButton&&(this.events.prev=a("click",{onElement:this.prevButton,withCallback:function(t,i){t.preventDefault(),e.prevSlide()}})),this.settings.closeOnOutsideClick&&(this.events.outClose=a("click",{onElement:d,withCallback:function(t,i){e.preventOutsideClick||c(document.body,"glightbox-mobile")||u(t.target,".ginner-container")||u(t.target,".gbtn")||c(t.target,"gnext")||c(t.target,"gprev")||e.close()}})),o(this.elements,(function(t,i){e.slidesContainer.appendChild(t.instance.create()),t.slideNode=e.slidesContainer.querySelectorAll(".gslide")[i]})),K&&h(document.body,"glightbox-touch"),this.events.resize=a("resize",{onElement:window,withCallback:function(){e.resize()}}),this.built=!0}},{key:"resize",value:function(){var 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e=this.loop();d(this.nextButton,"disabled"),d(this.prevButton,"disabled"),0==this.index&&this.elements.length-1==0?(h(this.prevButton,"disabled"),h(this.nextButton,"disabled")):0!==this.index||e?this.index!==this.elements.length-1||e||h(this.nextButton,"disabled"):h(this.prevButton,"disabled")}},{key:"loop",value:function(){var e=O(this.settings,"loopAtEnd")?this.settings.loopAtEnd:null;return e=O(this.settings,"loop")?this.settings.loop:e,e}},{key:"close",value:function(){var e=this;if(!this.lightboxOpen){if(this.events){for(var t in this.events)this.events.hasOwnProperty(t)&&this.events[t].destroy();this.events=null}return!1}if(this.closing)return!1;this.closing=!0,this.slidePlayerPause(this.activeSlide),this.fullElementsList&&(this.elements=this.fullElementsList),this.bodyHiddenChildElms.length&&o(this.bodyHiddenChildElms,(function(e){e.removeAttribute("aria-hidden")})),h(this.modal,"glightbox-closing"),g(this.overlay,"none"==this.settings.openEffect?"none":this.settings.cssEfects.fade.out),g(this.activeSlide,this.settings.cssEfects[this.settings.closeEffect].out,(function(){if(e.activeSlide=null,e.prevActiveSlideIndex=null,e.prevActiveSlide=null,e.built=!1,e.events){for(var t in e.events)e.events.hasOwnProperty(t)&&e.events[t].destroy();e.events=null}var i=document.body;d(Q,"glightbox-open"),d(i,"glightbox-open touching gdesc-open glightbox-touch glightbox-mobile gscrollbar-fixer"),e.modal.parentNode.removeChild(e.modal),e.trigger("close"),T(e.settings.onClose)&&e.settings.onClose();var n=document.querySelector(".gcss-styles");n&&n.parentNode.removeChild(n),e.lightboxOpen=!1,e.closing=null}))}},{key:"destroy",value:function(){this.close(),this.clearAllEvents(),this.baseEvents&&this.baseEvents.destroy()}},{key:"on",value:function(e,t){var i=arguments.length>2&&void 0!==arguments[2]&&arguments[2];if(!e||!T(t))throw new TypeError("Event name and callback must be defined");this.apiEvents.push({evt:e,once:i,callback:t})}},{key:"once",value:function(e,t){this.on(e,t,!0)}},{key:"trigger",value:function(e){var t=this,i=arguments.length>1&&void 0!==arguments[1]?arguments[1]:null,n=[];o(this.apiEvents,(function(t,s){var l=t.evt,o=t.once,r=t.callback;l==e&&(r(i),o&&n.push(s))})),n.length&&o(n,(function(e){return t.apiEvents.splice(e,1)}))}},{key:"clearAllEvents",value:function(){this.apiEvents.splice(0,this.apiEvents.length)}},{key:"version",value:function(){return"3.1.0"}}]),e}();return function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},t=new te(e);return t.init(),t}}));
\ No newline at end of file
diff --git a/docs/site_libs/quarto-contrib/glightbox/lightbox.css b/docs/site_libs/quarto-contrib/glightbox/lightbox.css
new file mode 100644
index 00000000..2c29fe1b
--- /dev/null
+++ b/docs/site_libs/quarto-contrib/glightbox/lightbox.css
@@ -0,0 +1,22 @@
+body:not(.glightbox-mobile) div.gslide div.gslide-description,
+body:not(.glightbox-mobile) div.gslide-description .gslide-title,
+body:not(.glightbox-mobile) div.gslide-description .gslide-desc {
+  color: var(--quarto-body-color);
+  background-color: var(--quarto-body-bg);
+}
+
+.goverlay {
+  background: rgba(0, 0, 0, 0.7);
+}
+
+div.gslide-description .gslide-title {
+  margin-top: 0.25em;
+  margin-bottom: 0.25em;
+  font-weight: 500;
+  font-family: inherit;
+}
+
+div.gslide-description .gslide-desc {
+  padding-bottom: 0.5em;
+  font-family: inherit;
+}
diff --git a/docs/site_libs/quarto-html/quarto.js b/docs/site_libs/quarto-html/quarto.js
index c3935c7e..91be5220 100644
--- a/docs/site_libs/quarto-html/quarto.js
+++ b/docs/site_libs/quarto-html/quarto.js
@@ -18,25 +18,12 @@ const layoutMarginEls = () => {
       // clear the top margin so we recompute it
       marginChild.style.marginTop = null;
       const top = marginChild.getBoundingClientRect().top + window.scrollY;
-      console.log({
-        childtop: marginChild.getBoundingClientRect().top,
-        scroll: window.scrollY,
-        top,
-        lastBottom,
-      });
       if (top < lastBottom) {
         const margin = lastBottom - top;
         marginChild.style.marginTop = `${margin}px`;
       }
       const styles = window.getComputedStyle(marginChild);
       const marginTop = parseFloat(styles["marginTop"]);
-
-      console.log({
-        top,
-        height: marginChild.getBoundingClientRect().height,
-        marginTop,
-        total: top + marginChild.getBoundingClientRect().height + marginTop,
-      });
       lastBottom = top + marginChild.getBoundingClientRect().height + marginTop;
     }
   }
diff --git a/docs/site_libs/quarto-nav/quarto-nav.js b/docs/site_libs/quarto-nav/quarto-nav.js
index 6221d4b5..ebfc262e 100644
--- a/docs/site_libs/quarto-nav/quarto-nav.js
+++ b/docs/site_libs/quarto-nav/quarto-nav.js
@@ -85,6 +85,17 @@ window.document.addEventListener("DOMContentLoaded", function () {
     }
   }
 
+  function dashboardOffset() {
+    const dashboardNavEl = window.document.getElementById(
+      "quarto-dashboard-header"
+    );
+    if (dashboardNavEl !== null) {
+      return dashboardNavEl.clientHeight;
+    } else {
+      return 0;
+    }
+  }
+
   function updateDocumentOffsetWithoutAnimation() {
     updateDocumentOffset(false);
   }
@@ -92,7 +103,7 @@ window.document.addEventListener("DOMContentLoaded", function () {
   function updateDocumentOffset(animated) {
     // set body offset
     const topOffset = headerOffset();
-    const bodyOffset = topOffset + footerOffset();
+    const bodyOffset = topOffset + footerOffset() + dashboardOffset();
     const bodyEl = window.document.body;
     bodyEl.setAttribute("data-bs-offset", topOffset);
     bodyEl.style.paddingTop = topOffset + "px";
diff --git a/docs/site_libs/quarto-search/autocomplete.umd.js b/docs/site_libs/quarto-search/autocomplete.umd.js
index 2cb1a857..ae0063aa 100644
--- a/docs/site_libs/quarto-search/autocomplete.umd.js
+++ b/docs/site_libs/quarto-search/autocomplete.umd.js
@@ -1,3 +1,3 @@
-/*! @algolia/autocomplete-js 1.9.2 | MIT License | © Algolia, Inc. and contributors | https://github.com/algolia/autocomplete */
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t=O.value.renderer,n=t.components,r=u(t,gr);g.current=qt(r,O.value.core,{components:Bt(n,(function(e){return!e.value.hasOwnProperty("__autocomplete_componentName")})),initialState:j.current},e),v(),c(),S.value.refresh().then((function(){D(j.current)}))}function k(e){requestAnimationFrame((function(){var t=O.value.core.environment.document.body.contains(A.value.detachedOverlay);e!==t&&(e?(O.value.core.environment.document.body.appendChild(A.value.detachedOverlay),O.value.core.environment.document.body.classList.add("aa-Detached"),A.value.input.focus()):(O.value.core.environment.document.body.removeChild(A.value.detachedOverlay),O.value.core.environment.document.body.classList.remove("aa-Detached")))}))}return a((function(){var e=S.value.getEnvironmentProps({formElement:A.value.form,panelElement:A.value.panel,inputElement:A.value.input});return Ht(O.value.core.environment,e),function(){Ht(O.value.core.environment,Object.keys(e).reduce((function(e,t){return n(n({},e),{},o({},t,void 0))}),{}))}})),a((function(){var e=_.value?O.value.core.environment.document.body:O.value.renderer.panelContainer,t=_.value?A.value.detachedOverlay:A.value.panel;return _.value&&j.current.isOpen&&k(!0),D(j.current),function(){e.contains(t)&&e.removeChild(t)}})),a((function(){var e=O.value.renderer.container;return e.appendChild(A.value.root),function(){e.removeChild(A.value.root)}})),a((function(){var e=p((function(e){D(e.state)}),0);return h.current=function(t){var n=t.state,r=t.prevState;(_.value&&r.isOpen!==n.isOpen&&k(n.isOpen),_.value||!n.isOpen||r.isOpen||E(),n.query!==r.query)&&O.value.core.environment.document.querySelectorAll(".aa-Panel--scrollable").forEach((function(e){0!==e.scrollTop&&(e.scrollTop=0)}));e({state:n})},function(){h.current=void 0}})),a((function(){var e=p((function(){var e=_.value;_.value=O.value.core.environment.matchMedia(O.value.renderer.detachedMediaQuery).matches,e!==_.value?C({}):requestAnimationFrame(E)}),20);return O.value.core.environment.addEventListener("resize",e),function(){O.value.core.environment.removeEventListener("resize",e)}})),a((function(){if(!_.value)return function(){};function e(e){A.value.detachedContainer.classList.toggle("aa-DetachedContainer--modal",e)}function t(t){e(t.matches)}var n=O.value.core.environment.matchMedia(getComputedStyle(O.value.core.environment.document.documentElement).getPropertyValue("--aa-detached-modal-media-query"));e(n.matches);var r=Boolean(n.addEventListener);return r?n.addEventListener("change",t):n.addListener(t),function(){r?n.removeEventListener("change",t):n.removeListener(t)}})),a((function(){return requestAnimationFrame(E),function(){}})),n(n({},w),{},{update:C,destroy:function(){l()}})},e.getAlgoliaFacets=function(e){var t=hr({transformResponse:function(e){return e.facetHits}}),r=e.queries.map((function(e){return n(n({},e),{},{type:"facet"})}));return t(n(n({},e),{},{queries:r}))},e.getAlgoliaResults=Or,Object.defineProperty(e,"__esModule",{value:!0})}));
 
diff --git a/docs/site_libs/quarto-search/quarto-search.js b/docs/site_libs/quarto-search/quarto-search.js
index 96dd7e24..4a6f7e29 100644
--- a/docs/site_libs/quarto-search/quarto-search.js
+++ b/docs/site_libs/quarto-search/quarto-search.js
@@ -361,7 +361,8 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
                 state,
                 setActiveItemId,
                 setContext,
-                refresh
+                refresh,
+                quartoSearchOptions
               );
             },
           },
@@ -379,7 +380,19 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
   document.addEventListener("keyup", (event) => {
     const { key } = event;
     const kbds = quartoSearchOptions["keyboard-shortcut"];
-    if (kbds && kbds.includes(key)) {
+    const focusedEl = document.activeElement;
+
+    const isFormElFocused = [
+      "input",
+      "select",
+      "textarea",
+      "button",
+      "option",
+    ].find((tag) => {
+      return focusedEl.tagName.toLowerCase() === tag;
+    });
+
+    if (kbds && kbds.includes(key) && !isFormElFocused) {
       event.preventDefault();
       window.quartoOpenSearch();
     }
@@ -396,11 +409,30 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
     }
   }
 
+  function throttle(func, wait) {
+    let waiting = false;
+    return function () {
+      if (!waiting) {
+        func.apply(this, arguments);
+        waiting = true;
+        setTimeout(function () {
+          waiting = false;
+        }, wait);
+      }
+    };
+  }
+
   // If the main document scrolls dismiss the search results
   // (otherwise, since they're floating in the document they can scroll with the document)
-  window.document.body.onscroll = () => {
-    setIsOpen(false);
-  };
+  window.document.body.onscroll = throttle(() => {
+    // Only do this if we're not detached
+    // Bug #7117
+    // This will happen when the keyboard is shown on ios (resulting in a scroll)
+    // which then closed the search UI
+    if (!window.matchMedia(detachedMediaQuery).matches) {
+      setIsOpen(false);
+    }
+  }, 50);
 
   if (showSearchResults) {
     setIsOpen(true);
@@ -440,15 +472,27 @@ function configurePlugins(quartoSearchOptions) {
         const algoliaInsightsPlugin = createAlgoliaInsightsPlugin({
           insightsClient: window.aa,
           onItemsChange({ insights, insightsEvents }) {
-            const events = insightsEvents.map((event) => {
-              const maxEvents = event.objectIDs.slice(0, 20);
-              return {
-                ...event,
-                objectIDs: maxEvents,
-              };
+            const events = insightsEvents.flatMap((event) => {
+              // This API limits the number of items per event to 20
+              const chunkSize = 20;
+              const itemChunks = [];
+              const eventItems = event.items;
+              for (let i = 0; i < eventItems.length; i += chunkSize) {
+                itemChunks.push(eventItems.slice(i, i + chunkSize));
+              }
+              // Split the items into multiple events that can be sent
+              const events = itemChunks.map((items) => {
+                return {
+                  ...event,
+                  items,
+                };
+              });
+              return events;
             });
 
-            insights.viewedObjectIDs(...events);
+            for (const event of events) {
+              insights.viewedObjectIDs(event);
+            }
           },
         });
         return algoliaInsightsPlugin;
@@ -665,6 +709,7 @@ async function readSearchData() {
       );
     }
   }
+
   return fuseIndex;
 }
 
@@ -693,7 +738,8 @@ function renderItem(
   state,
   setActiveItemId,
   setContext,
-  refresh
+  refresh,
+  quartoSearchOptions
 ) {
   switch (item.type) {
     case kItemTypeDoc:
@@ -703,7 +749,9 @@ function renderItem(
         item.title,
         item.section,
         item.text,
-        item.href
+        item.href,
+        item.crumbs,
+        quartoSearchOptions
       );
     case kItemTypeMore:
       return createMoreCard(
@@ -728,15 +776,46 @@ function renderItem(
   }
 }
 
-function createDocumentCard(createElement, icon, title, section, text, href) {
+function createDocumentCard(
+  createElement,
+  icon,
+  title,
+  section,
+  text,
+  href,
+  crumbs,
+  quartoSearchOptions
+) {
   const iconEl = createElement("i", {
     class: `bi bi-${icon} search-result-icon`,
   });
   const titleEl = createElement("p", { class: "search-result-title" }, title);
+  const titleContents = [iconEl, titleEl];
+  const showParent = quartoSearchOptions["show-item-context"];
+  if (crumbs && showParent) {
+    let crumbsOut = undefined;
+    const crumbClz = ["search-result-crumbs"];
+    if (showParent === "root") {
+      crumbsOut = crumbs.length > 1 ? crumbs[0] : undefined;
+    } else if (showParent === "parent") {
+      crumbsOut = crumbs.length > 1 ? crumbs[crumbs.length - 2] : undefined;
+    } else {
+      crumbsOut = crumbs.length > 1 ? crumbs.join(" > ") : undefined;
+      crumbClz.push("search-result-crumbs-wrap");
+    }
+
+    const crumbEl = createElement(
+      "p",
+      { class: crumbClz.join(" ") },
+      crumbsOut
+    );
+    titleContents.push(crumbEl);
+  }
+
   const titleContainerEl = createElement(
     "div",
     { class: "search-result-title-container" },
-    [iconEl, titleEl]
+    titleContents
   );
 
   const textEls = [];
@@ -1118,17 +1197,19 @@ function algoliaSearch(query, limit, algoliaOptions) {
         const remappedHits = response.hits.map((hit) => {
           return hit.map((item) => {
             const newItem = { ...item };
-            ["href", "section", "title", "text"].forEach((keyName) => {
-              const mappedName = indexFields[keyName];
-              if (
-                mappedName &&
-                item[mappedName] !== undefined &&
-                mappedName !== keyName
-              ) {
-                newItem[keyName] = item[mappedName];
-                delete newItem[mappedName];
+            ["href", "section", "title", "text", "crumbs"].forEach(
+              (keyName) => {
+                const mappedName = indexFields[keyName];
+                if (
+                  mappedName &&
+                  item[mappedName] !== undefined &&
+                  mappedName !== keyName
+                ) {
+                  newItem[keyName] = item[mappedName];
+                  delete newItem[mappedName];
+                }
               }
-            });
+            );
             newItem.text = highlightMatch(query, newItem.text);
             return newItem;
           });
@@ -1154,6 +1235,7 @@ function fuseSearch(query, fuse, fuseOptions) {
       section: result.item.section,
       href: addParam(result.item.href, kQueryArg, query),
       text: highlightMatch(query, result.item.text),
+      crumbs: result.item.crumbs,
     };
   });
 }
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 8d3f55ac..99d32811 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -1,155 +1,163 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/explanation/index.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/explanation/components.html</loc>
+    <lastmod>2024-04-12T15:05:28.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/index.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/explanation/topology.html</loc>
+    <lastmod>2023-12-06T13:12:40.000Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/examples.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <lastmod>2023-12-06T13:12:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/hcp.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/reaction_only.html</loc>
+    <lastmod>2024-02-22T10:21:34.000Z</lastmod>
+  </url>
+  <url>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/contribute.html</loc>
+    <lastmod>2023-12-06T13:12:40.000Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/references/input.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <lastmod>2024-02-15T14:00:55.000Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/getting-started.html</loc>
-    <lastmod>2024-03-25T16:56:42.337Z</lastmod>
+    <lastmod>2024-04-12T07:54:29.000Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/colbuilder.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <lastmod>2024-04-12T07:53:48.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.TopologyDict.html</loc>
-    <lastmod>2024-03-25T16:57:45.621Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/recipe.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.ff.html</loc>
-    <lastmod>2024-03-25T16:57:45.529Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/tasks.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/index.html</loc>
-    <lastmod>2024-03-25T16:57:45.477Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/plugins.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/config.html</loc>
-    <lastmod>2024-03-25T16:57:45.673Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/kmc.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/kmc.html</loc>
-    <lastmod>2024-03-25T16:57:45.717Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.utils.html</loc>
+    <lastmod>2024-04-12T15:07:36.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.topology.html</loc>
-    <lastmod>2024-03-25T16:57:45.529Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.ff.html</loc>
+    <lastmod>2024-04-12T15:07:36.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/schema.html</loc>
-    <lastmod>2024-03-25T16:57:45.825Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/runmanager.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/homolysis.reaction.Homolysis.html</loc>
-    <lastmod>2024-03-25T16:57:45.897Z</lastmod>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/recipe.html</loc>
-    <lastmod>2024-03-25T16:57:45.801Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/utils.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/analysis.html</loc>
-    <lastmod>2024-03-25T16:57:45.653Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/index.html</loc>
+    <lastmod>2024-04-12T15:07:36.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/hat_naive.reaction.NaiveHAT.html</loc>
-    <lastmod>2024-03-25T16:57:45.897Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/cmd.html</loc>
+    <lastmod>2024-04-12T15:07:36.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.atomic.html</loc>
-    <lastmod>2024-03-25T16:57:45.621Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.topology.html</loc>
+    <lastmod>2024-04-12T15:07:36.000Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/index.html</loc>
-    <lastmod>2024-03-25T16:56:42.341Z</lastmod>
+    <lastmod>2023-12-14T13:21:07.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/dummyreaction.reaction.DummyReaction.html</loc>
-    <lastmod>2024-03-25T16:57:45.901Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/tools.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/constants.html</loc>
-    <lastmod>2024-03-25T16:57:45.677Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/analysis.html</loc>
+    <lastmod>2024-04-12T15:07:39.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/tasks.html</loc>
-    <lastmod>2024-03-25T16:57:45.841Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/hat_naive.reaction.NaiveHAT.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/plugins.html</loc>
-    <lastmod>2024-03-25T16:57:45.753Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/tools.html</loc>
-    <lastmod>2024-03-25T16:57:45.865Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/dummyreaction.reaction.DummyReaction.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
+  </url>
+  <url>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/config.html</loc>
+    <lastmod>2024-04-12T15:07:39.000Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/coordinates.html</loc>
-    <lastmod>2024-03-25T16:57:45.697Z</lastmod>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/utils.html</loc>
-    <lastmod>2024-03-25T16:57:45.893Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/schema.html</loc>
+    <lastmod>2024-04-12T15:07:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/cmd.html</loc>
-    <lastmod>2024-03-25T16:57:45.501Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/constants.html</loc>
+    <lastmod>2024-04-12T15:07:39.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.html</loc>
-    <lastmod>2024-03-25T16:57:45.745Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.atomic.html</loc>
+    <lastmod>2024-04-12T15:07:39.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/runmanager.html</loc>
-    <lastmod>2024-03-25T16:57:45.813Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.TopologyDict.html</loc>
+    <lastmod>2024-04-12T15:07:39.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.utils.html</loc>
-    <lastmod>2024-03-25T16:57:45.557Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/index.html</loc>
+    <lastmod>2023-12-06T13:12:40.000Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/write-plugin.html</loc>
-    <lastmod>2024-03-25T16:56:42.341Z</lastmod>
+    <lastmod>2023-12-06T13:12:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/index.html</loc>
-    <lastmod>2024-03-25T16:56:42.341Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/references/cmd_ref.html</loc>
+    <lastmod>2024-02-15T14:00:55.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/references/cmd_ref.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/index.html</loc>
+    <lastmod>2023-12-06T13:12:40.000Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/install-ml-plugins.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <lastmod>2023-12-08T10:02:39.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/contribute.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/analyze.html</loc>
+    <lastmod>2024-04-12T15:05:28.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/reaction_only.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/hcp.html</loc>
+    <lastmod>2023-12-06T13:12:40.000Z</lastmod>
   </url>
   <url>
-    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/explanation/topology.html</loc>
-    <lastmod>2024-03-25T16:56:42.333Z</lastmod>
+    <loc>http://hits-mbm-dev.github.io/kimmdy/guide/explanation/index.html</loc>
+    <lastmod>2023-12-06T13:12:40.000Z</lastmod>
   </url>
 </urlset>
diff --git a/guide/explanation/components.qmd b/guide/explanation/components.qmd
new file mode 100644
index 00000000..5d3dc20a
--- /dev/null
+++ b/guide/explanation/components.qmd
@@ -0,0 +1,29 @@
+---
+title: Components of KIMMDY
+author: Kai Riedmiller
+---
+
+Here is an overview of the most important components of KIMMDY, and how they interact with each other:
+
+<div class="mxgraph" style="max-width:100%;border:1px solid transparent;" data-mxgraph="{&quot;highlight&quot;:&quot;#0000ff&quot;,&quot;nav&quot;:true,&quot;resize&quot;:true,&quot;toolbar&quot;:&quot;zoom layers tags lightbox&quot;,&quot;edit&quot;:&quot;_blank&quot;,&quot;xml&quot;:&quot;&lt;mxfile host=\&quot;embed.diagrams.net\&quot; modified=\&quot;2024-04-12T13:01:39.162Z\&quot; agent=\&quot;Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:125.0) Gecko/20100101 Firefox/125.0\&quot; etag=\&quot;2LzvXIML8sgRkzA7WiYD\&quot; version=\&quot;24.0.7\&quot; type=\&quot;embed\&quot;&gt;\n  &lt;diagram id=\&quot;C5RBs43oDa-KdzZeNtuy\&quot; name=\&quot;Page-1\&quot;&gt;\n    &lt;mxGraphModel dx=\&quot;1088\&quot; dy=\&quot;769\&quot; grid=\&quot;1\&quot; gridSize=\&quot;10\&quot; guides=\&quot;1\&quot; tooltips=\&quot;1\&quot; connect=\&quot;1\&quot; arrows=\&quot;1\&quot; fold=\&quot;1\&quot; page=\&quot;1\&quot; pageScale=\&quot;1\&quot; pageWidth=\&quot;827\&quot; pageHeight=\&quot;1169\&quot; math=\&quot;0\&quot; shadow=\&quot;0\&quot;&gt;\n      &lt;root&gt;\n        &lt;mxCell id=\&quot;WIyWlLk6GJQsqaUBKTNV-0\&quot; /&gt;\n        &lt;mxCell id=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-0\&quot; /&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-1\&quot; value=\&quot;\&quot; style=\&quot;ellipse;whiteSpace=wrap;html=1;align=center;aspect=fixed;fillColor=none;strokeColor=none;resizable=0;perimeter=centerPerimeter;rotatable=0;allowArrows=0;points=[];outlineConnect=1;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;620\&quot; y=\&quot;20\&quot; width=\&quot;10\&quot; height=\&quot;10\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; value=\&quot;RunManager\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=26;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;320\&quot; y=\&quot;20\&quot; width=\&quot;160\&quot; height=\&quot;340\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;mxRectangle x=\&quot;340\&quot; y=\&quot;130\&quot; width=\&quot;110\&quot; height=\&quot;30\&quot; as=\&quot;alternateBounds\&quot; /&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-58\&quot; value=\&quot;+ config\&quot; style=\&quot;html=1;whiteSpace=wrap;align=left;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;26\&quot; width=\&quot;160\&quot; height=\&quot;24\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-73\&quot; value=\&quot;&amp;lt;div&amp;gt;+ tasks: task queue&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;+ crr_tasks: priority queue\&quot; style=\&quot;html=1;whiteSpace=wrap;align=left;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;50\&quot; width=\&quot;160\&quot; height=\&quot;40\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-74\&quot; value=\&quot;&amp;lt;div align=&amp;quot;left&amp;quot;&amp;gt;+ reaction plugins&amp;lt;/div&amp;gt;\&quot; style=\&quot;html=1;whiteSpace=wrap;align=left;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;90\&quot; width=\&quot;160\&quot; height=\&quot;20\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-95\&quot; value=\&quot;&amp;lt;div align=&amp;quot;left&amp;quot;&amp;gt;&amp;lt;i&amp;gt;+ parametrizer plugin&amp;lt;/i&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;html=1;whiteSpace=wrap;align=left;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;110\&quot; width=\&quot;160\&quot; height=\&quot;20\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;ZZ1oNmMWEcc1Qex5SiT5-0\&quot; value=\&quot;&amp;lt;div align=&amp;quot;left&amp;quot;&amp;gt;&amp;lt;i&amp;gt;+ top&amp;lt;br&amp;gt;&amp;lt;/i&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;html=1;whiteSpace=wrap;align=left;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;130\&quot; width=\&quot;160\&quot; height=\&quot;20\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-4\&quot; value=\&quot;&amp;lt;div&amp;gt;+ state&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ time&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ latest files&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;150\&quot; width=\&quot;160\&quot; height=\&quot;60\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-5\&quot; value=\&quot;\&quot; style=\&quot;line;strokeWidth=1;fillColor=none;align=left;verticalAlign=middle;spacingTop=-1;spacingLeft=3;spacingRight=3;rotatable=0;labelPosition=right;points=[];portConstraint=eastwest;strokeColor=inherit;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;210\&quot; width=\&quot;160\&quot; height=\&quot;8\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-6\&quot; value=\&quot;&amp;lt;div&amp;gt;+ __next__&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ run md&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ query reaction&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;strokeColor=none;fillColor=none;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;218\&quot; width=\&quot;160\&quot; height=\&quot;52\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-23\&quot; value=\&quot;\&quot; style=\&quot;line;strokeWidth=1;fillColor=none;align=left;verticalAlign=middle;spacingTop=-1;spacingLeft=3;spacingRight=3;rotatable=0;labelPosition=right;points=[];portConstraint=eastwest;strokeColor=inherit;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;270\&quot; width=\&quot;160\&quot; height=\&quot;8\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-22\&quot; value=\&quot;+ decide recipe&amp;lt;div&amp;gt;&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;strokeColor=none;fillColor=none;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;278\&quot; width=\&quot;160\&quot; height=\&quot;22\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-25\&quot; value=\&quot;\&quot; style=\&quot;line;strokeWidth=1;fillColor=none;align=left;verticalAlign=middle;spacingTop=-1;spacingLeft=3;spacingRight=3;rotatable=0;labelPosition=right;points=[];portConstraint=eastwest;strokeColor=inherit;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;300\&quot; width=\&quot;160\&quot; height=\&quot;8\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-24\&quot; value=\&quot;+ apply recipe&amp;lt;div&amp;gt;&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;strokeColor=none;fillColor=none;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-3\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;308\&quot; width=\&quot;160\&quot; height=\&quot;32\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-84\&quot; style=\&quot;edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;enuX_6VsqPwF3hcZr7AK-12\&quot; target=\&quot;enuX_6VsqPwF3hcZr7AK-58\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;mxPoint x=\&quot;250\&quot; y=\&quot;58\&quot; as=\&quot;targetPoint\&quot; /&gt;\n            &lt;Array as=\&quot;points\&quot;&gt;\n              &lt;mxPoint x=\&quot;179\&quot; y=\&quot;58\&quot; /&gt;\n            &lt;/Array&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-12\&quot; value=\&quot;Config\&quot; style=\&quot;html=1;whiteSpace=wrap;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;128\&quot; y=\&quot;90\&quot; width=\&quot;157\&quot; height=\&quot;50\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-18\&quot; value=\&quot;kimmdy.yml\&quot; style=\&quot;shape=note2;boundedLbl=1;whiteSpace=wrap;html=1;size=25;verticalAlign=top;align=center;fillColor=#ffe6cc;strokeColor=#d79b00;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;218\&quot; y=\&quot;170\&quot; width=\&quot;67\&quot; height=\&quot;70\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-20\&quot; value=\&quot;scheme definition\&quot; style=\&quot;shape=note2;boundedLbl=1;whiteSpace=wrap;html=1;size=27;verticalAlign=top;align=center;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;128\&quot; y=\&quot;265\&quot; width=\&quot;67\&quot; height=\&quot;80\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-23\&quot; value=\&quot;&amp;lt;div&amp;gt;Task&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;&amp;lt;span style=&amp;quot;font-weight: normal;&amp;quot;&amp;gt;Container for tasks to put&amp;lt;br&amp;gt;&amp;lt;/span&amp;gt;&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;&amp;lt;span style=&amp;quot;font-weight: normal;&amp;quot;&amp;gt;into queue&amp;lt;/span&amp;gt;&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=50;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;576\&quot; y=\&quot;20\&quot; width=\&quot;207\&quot; height=\&quot;150\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-24\&quot; value=\&quot;&amp;lt;div&amp;gt;+ Callable: function to execute later&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ kwargs: arguments for the callable&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ name&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ out dir&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-23\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;50\&quot; width=\&quot;207\&quot; height=\&quot;70\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-25\&quot; value=\&quot;\&quot; style=\&quot;line;strokeWidth=1;fillColor=none;align=left;verticalAlign=middle;spacingTop=-1;spacingLeft=3;spacingRight=3;rotatable=0;labelPosition=right;points=[];portConstraint=eastwest;strokeColor=inherit;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-23\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;120\&quot; width=\&quot;207\&quot; height=\&quot;8\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-26\&quot; value=\&quot;+ call: execute task\&quot; style=\&quot;text;strokeColor=none;fillColor=none;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-23\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;128\&quot; width=\&quot;207\&quot; height=\&quot;22\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-29\&quot; value=\&quot;RecipeCollection\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=26;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;113\&quot; y=\&quot;380\&quot; width=\&quot;187\&quot; height=\&quot;160\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-30\&quot; value=\&quot;+ recipes: list of recipes\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-29\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;26\&quot; width=\&quot;187\&quot; height=\&quot;26\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-31\&quot; value=\&quot;\&quot; style=\&quot;line;strokeWidth=1;fillColor=none;align=left;verticalAlign=middle;spacingTop=-1;spacingLeft=3;spacingRight=3;rotatable=0;labelPosition=right;points=[];portConstraint=eastwest;strokeColor=inherit;\&quot; 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as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-33\&quot; value=\&quot;Recipe\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=26;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;320\&quot; y=\&quot;380\&quot; width=\&quot;160\&quot; height=\&quot;160\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-34\&quot; value=\&quot;&amp;lt;div&amp;gt;+ recipe_steps&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ rates&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ timespans&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; 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parent=\&quot;enuX_6VsqPwF3hcZr7AK-44\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;26\&quot; width=\&quot;80\&quot; height=\&quot;44\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-48\&quot; value=\&quot;Bind\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=26;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-42\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;100\&quot; y=\&quot;40\&quot; width=\&quot;80\&quot; height=\&quot;70\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-49\&quot; value=\&quot;&amp;lt;div&amp;gt;+ atom 1&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ atom 2&amp;amp;nbsp; &amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-48\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;26\&quot; width=\&quot;80\&quot; height=\&quot;44\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-50\&quot; value=\&quot;Place\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=26;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-42\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;100\&quot; y=\&quot;120\&quot; width=\&quot;80\&quot; height=\&quot;70\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-51\&quot; value=\&quot;&amp;lt;div&amp;gt;+ atom 1&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+coordinates&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; 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width=\&quot;80\&quot; height=\&quot;44\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-54\&quot; value=\&quot;Modify top\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=26;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-42\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;10\&quot; y=\&quot;200\&quot; width=\&quot;170\&quot; height=\&quot;70\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-55\&quot; value=\&quot;+ callable(top) -&amp;amp;gt; top&amp;amp;nbsp; \&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;fontColor=#333333;strokeColor=#666666;\&quot; 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width=\&quot;207\&quot; height=\&quot;124\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-93\&quot; value=\&quot;\&quot; style=\&quot;line;strokeWidth=1;fillColor=none;align=left;verticalAlign=middle;spacingTop=-1;spacingLeft=3;spacingRight=3;rotatable=0;labelPosition=right;points=[];portConstraint=eastwest;strokeColor=inherit;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-91\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;150\&quot; width=\&quot;207\&quot; height=\&quot;8\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-94\&quot; value=\&quot;&amp;lt;div&amp;gt;+ break_bond&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ bind_bond&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ del_atom&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ reindex_atomnrs&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;+ parametrize&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;strokeColor=none;fillColor=none;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-91\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;158\&quot; width=\&quot;207\&quot; height=\&quot;82\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-96\&quot; style=\&quot;edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;exitX=1;exitY=0.5;exitDx=0;exitDy=0;entryX=-0.001;entryY=0.045;entryDx=0;entryDy=0;entryPerimeter=0;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;ZZ1oNmMWEcc1Qex5SiT5-0\&quot; target=\&quot;enuX_6VsqPwF3hcZr7AK-91\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;Array as=\&quot;points\&quot;&gt;\n              &lt;mxPoint x=\&quot;520\&quot; y=\&quot;160\&quot; /&gt;\n              &lt;mxPoint x=\&quot;520\&quot; y=\&quot;471\&quot; /&gt;\n            &lt;/Array&gt;\n            &lt;mxPoint x=\&quot;520\&quot; y=\&quot;471\&quot; as=\&quot;targetPoint\&quot; /&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-112\&quot; value=\&quot;&amp;lt;i&amp;gt;&amp;amp;lt;&amp;amp;lt;Reaction&amp;amp;gt;&amp;amp;gt;&amp;lt;/i&amp;gt;&amp;lt;br&amp;gt;&amp;lt;b&amp;gt;Interface for plugins&amp;lt;/b&amp;gt;\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=40;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;576\&quot; y=\&quot;180\&quot; width=\&quot;207\&quot; height=\&quot;150\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-113\&quot; value=\&quot;&amp;lt;p style=&amp;quot;margin:0px;margin-left:4px;&amp;quot;&amp;gt;&amp;lt;i&amp;gt;+ name&amp;lt;br&amp;gt;+ runmanager&amp;lt;/i&amp;gt;&amp;lt;/p&amp;gt;&amp;lt;p style=&amp;quot;margin:0px;margin-left:4px;&amp;quot;&amp;gt;&amp;lt;i&amp;gt;+ config: sub-config of this step&amp;lt;/i&amp;gt;&amp;lt;/p&amp;gt;\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=2;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;fillColor=#E3E3E3;strokeColor=#666666;fontColor=#333333;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-112\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;40\&quot; width=\&quot;207\&quot; height=\&quot;60\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-114\&quot; value=\&quot;\&quot; style=\&quot;line;strokeWidth=1;fillColor=none;align=left;verticalAlign=middle;spacingTop=-1;spacingLeft=3;spacingRight=3;rotatable=0;labelPosition=right;points=[];portConstraint=eastwest;strokeColor=inherit;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-112\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;100\&quot; width=\&quot;207\&quot; height=\&quot;8\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-115\&quot; value=\&quot;&amp;lt;p style=&amp;quot;margin:0px;margin-left:4px;&amp;quot;&amp;gt;+ get_recipe_collection(TaskFiles)&amp;lt;/p&amp;gt;&amp;amp;nbsp;→ RecipeCollection\&quot; style=\&quot;text;strokeColor=none;fillColor=none;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;\&quot; parent=\&quot;enuX_6VsqPwF3hcZr7AK-112\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;108\&quot; width=\&quot;207\&quot; height=\&quot;42\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-116\&quot; value=\&quot;&amp;lt;div&amp;gt;plugin&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;scheme definition&amp;lt;/div&amp;gt;\&quot; style=\&quot;shape=note2;boundedLbl=1;whiteSpace=wrap;html=1;size=25;verticalAlign=top;align=center;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;218\&quot; y=\&quot;265\&quot; width=\&quot;67\&quot; height=\&quot;80\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-117\&quot; style=\&quot;edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;enuX_6VsqPwF3hcZr7AK-116\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;mxPoint x=\&quot;200\&quot; y=\&quot;140\&quot; as=\&quot;targetPoint\&quot; /&gt;\n            &lt;Array as=\&quot;points\&quot;&gt;\n              &lt;mxPoint x=\&quot;200\&quot; y=\&quot;270\&quot; /&gt;\n            &lt;/Array&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-119\&quot; style=\&quot;edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;exitX=0.476;exitY=0;exitDx=0;exitDy=0;exitPerimeter=0;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;enuX_6VsqPwF3hcZr7AK-20\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;mxPoint x=\&quot;160\&quot; y=\&quot;260\&quot; as=\&quot;sourcePoint\&quot; /&gt;\n            &lt;mxPoint x=\&quot;160\&quot; y=\&quot;140\&quot; as=\&quot;targetPoint\&quot; /&gt;\n            &lt;Array as=\&quot;points\&quot;&gt;\n              &lt;mxPoint x=\&quot;160\&quot; y=\&quot;203\&quot; /&gt;\n              &lt;mxPoint x=\&quot;160\&quot; y=\&quot;203\&quot; /&gt;\n            &lt;/Array&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;enuX_6VsqPwF3hcZr7AK-120\&quot; style=\&quot;edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=-0.004;entryY=0.224;entryDx=0;entryDy=0;entryPerimeter=0;exitX=1;exitY=0.5;exitDx=0;exitDy=0;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;enuX_6VsqPwF3hcZr7AK-73\&quot; target=\&quot;enuX_6VsqPwF3hcZr7AK-23\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;Array as=\&quot;points\&quot;&gt;\n              &lt;mxPoint x=\&quot;540\&quot; y=\&quot;90\&quot; /&gt;\n              &lt;mxPoint x=\&quot;540\&quot; y=\&quot;54\&quot; /&gt;\n            &lt;/Array&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;ZZ1oNmMWEcc1Qex5SiT5-1\&quot; value=\&quot;\&quot; style=\&quot;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;endArrow=halfCircle;endFill=0;sketch=0;sourcePerimeterSpacing=0;targetPerimeterSpacing=0;endSize=6;exitX=1;exitY=0.5;exitDx=0;exitDy=0;strokeColor=default;strokeWidth=1;align=center;verticalAlign=middle;fontFamily=Helvetica;fontSize=11;fontColor=default;labelBackgroundColor=default;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;enuX_6VsqPwF3hcZr7AK-95\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;mxPoint x=\&quot;463\&quot; y=\&quot;130\&quot; as=\&quot;sourcePoint\&quot; /&gt;\n            &lt;mxPoint x=\&quot;540\&quot; y=\&quot;260\&quot; as=\&quot;targetPoint\&quot; /&gt;\n            &lt;Array as=\&quot;points\&quot;&gt;\n              &lt;mxPoint x=\&quot;540\&quot; y=\&quot;140\&quot; /&gt;\n            &lt;/Array&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;ZZ1oNmMWEcc1Qex5SiT5-2\&quot; value=\&quot;&amp;lt;i&amp;gt;&amp;amp;lt;&amp;amp;lt;Parametrizer&amp;amp;gt;&amp;amp;gt;&amp;lt;/i&amp;gt;&amp;lt;br&amp;gt;&amp;lt;b&amp;gt;Interface for plugins&amp;lt;/b&amp;gt;\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=40;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;576\&quot; y=\&quot;350\&quot; width=\&quot;207\&quot; height=\&quot;90\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;ZZ1oNmMWEcc1Qex5SiT5-4\&quot; value=\&quot;\&quot; style=\&quot;line;strokeWidth=1;fillColor=none;align=left;verticalAlign=middle;spacingTop=-1;spacingLeft=3;spacingRight=3;rotatable=0;labelPosition=right;points=[];portConstraint=eastwest;strokeColor=inherit;\&quot; parent=\&quot;ZZ1oNmMWEcc1Qex5SiT5-2\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;40\&quot; width=\&quot;207\&quot; height=\&quot;8\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;ZZ1oNmMWEcc1Qex5SiT5-5\&quot; value=\&quot;&amp;lt;p style=&amp;quot;margin:0px;margin-left:4px;&amp;quot;&amp;gt;+&amp;amp;nbsp;&amp;lt;span class=&amp;quot;t&amp;quot;&amp;gt;&amp;lt;span class=&amp;quot;nam&amp;quot;&amp;gt;parameterize_topology&amp;lt;/span&amp;gt;&amp;lt;span class=&amp;quot;op&amp;quot;&amp;gt;&amp;lt;/span&amp;gt;&amp;lt;/span&amp;gt;(top)&amp;lt;/p&amp;gt;&amp;amp;nbsp;→ top\&quot; style=\&quot;text;strokeColor=none;fillColor=none;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;\&quot; parent=\&quot;ZZ1oNmMWEcc1Qex5SiT5-2\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;48\&quot; width=\&quot;207\&quot; height=\&quot;42\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;ZZ1oNmMWEcc1Qex5SiT5-6\&quot; value=\&quot;\&quot; style=\&quot;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;endArrow=oval;endFill=0;endSize=10;strokeWidth=1;sketch=0;exitX=-0.001;exitY=0.219;exitDx=0;exitDy=0;exitPerimeter=0;strokeColor=default;align=center;verticalAlign=middle;fontFamily=Helvetica;fontSize=11;fontColor=default;labelBackgroundColor=default;sourcePerimeterSpacing=0;targetPerimeterSpacing=0;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;ZZ1oNmMWEcc1Qex5SiT5-2\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;mxPoint x=\&quot;573\&quot; y=\&quot;370\&quot; as=\&quot;sourcePoint\&quot; /&gt;\n            &lt;mxPoint x=\&quot;540\&quot; y=\&quot;260\&quot; as=\&quot;targetPoint\&quot; /&gt;\n            &lt;Array as=\&quot;points\&quot;&gt;\n              &lt;mxPoint x=\&quot;540\&quot; y=\&quot;370\&quot; /&gt;\n            &lt;/Array&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-5\&quot; value=\&quot;KMC\&quot; style=\&quot;shape=folder;fontStyle=1;tabWidth=110;tabHeight=30;tabPosition=left;html=1;boundedLbl=1;labelInHeader=1;container=1;collapsible=0;recursiveResize=0;whiteSpace=wrap;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;320\&quot; y=\&quot;560\&quot; width=\&quot;187\&quot; height=\&quot;280\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-16\&quot; value=\&quot;rfKMC\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=26;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;AoEu70FCAJxQCigTwmNW-5\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;9\&quot; y=\&quot;40\&quot; width=\&quot;170\&quot; height=\&quot;70\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-17\&quot; value=\&quot;&amp;lt;div&amp;gt;+ rfKMC(recipeCollection)&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;→ KMCResult(recipe, time)&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=0;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;\&quot; parent=\&quot;AoEu70FCAJxQCigTwmNW-16\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;26\&quot; width=\&quot;170\&quot; height=\&quot;44\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-18\&quot; value=\&quot;Extrande[_mod]\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=26;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;AoEu70FCAJxQCigTwmNW-5\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;9\&quot; y=\&quot;120\&quot; width=\&quot;170\&quot; height=\&quot;70\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-19\&quot; value=\&quot;&amp;lt;div&amp;gt;+ Extrande(recipeCollection)&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;→ KMCResult(recipe, time)&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=0;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;\&quot; parent=\&quot;AoEu70FCAJxQCigTwmNW-18\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;26\&quot; width=\&quot;170\&quot; height=\&quot;44\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-20\&quot; value=\&quot;first_reaction_method\&quot; style=\&quot;swimlane;fontStyle=1;align=center;verticalAlign=top;childLayout=stackLayout;horizontal=1;startSize=26;horizontalStack=0;resizeParent=1;resizeParentMax=0;resizeLast=0;collapsible=1;marginBottom=0;whiteSpace=wrap;html=1;\&quot; parent=\&quot;AoEu70FCAJxQCigTwmNW-5\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry x=\&quot;9\&quot; y=\&quot;200\&quot; width=\&quot;170\&quot; height=\&quot;70\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-21\&quot; value=\&quot;&amp;lt;div&amp;gt;+ frm(recipeCollection)&amp;lt;/div&amp;gt;&amp;lt;div&amp;gt;→ KMCResult(recipe, time)&amp;lt;br&amp;gt;&amp;lt;/div&amp;gt;\&quot; style=\&quot;text;align=left;verticalAlign=top;spacingLeft=4;spacingRight=4;overflow=hidden;rotatable=0;points=[[0,0.5],[1,0.5]];portConstraint=eastwest;whiteSpace=wrap;html=1;fontStyle=0;labelBackgroundColor=none;labelBorderColor=none;textShadow=0;fillStyle=auto;\&quot; parent=\&quot;AoEu70FCAJxQCigTwmNW-20\&quot; vertex=\&quot;1\&quot;&gt;\n          &lt;mxGeometry y=\&quot;26\&quot; width=\&quot;170\&quot; height=\&quot;44\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-26\&quot; style=\&quot;edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=0.583;entryY=0.046;entryDx=0;entryDy=0;entryPerimeter=0;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;AoEu70FCAJxQCigTwmNW-22\&quot; target=\&quot;AoEu70FCAJxQCigTwmNW-5\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;Array as=\&quot;points\&quot;&gt;\n              &lt;mxPoint x=\&quot;500\&quot; y=\&quot;309\&quot; /&gt;\n              &lt;mxPoint x=\&quot;500\&quot; y=\&quot;573\&quot; /&gt;\n            &lt;/Array&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-27\&quot; style=\&quot;edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=0.786;entryY=0.996;entryDx=0;entryDy=0;entryPerimeter=0;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;enuX_6VsqPwF3hcZr7AK-18\&quot; target=\&quot;enuX_6VsqPwF3hcZr7AK-12\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot; /&gt;\n        &lt;/mxCell&gt;\n        &lt;mxCell id=\&quot;AoEu70FCAJxQCigTwmNW-29\&quot; style=\&quot;edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=-0.003;entryY=0.133;entryDx=0;entryDy=0;entryPerimeter=0;\&quot; parent=\&quot;WIyWlLk6GJQsqaUBKTNV-1\&quot; source=\&quot;enuX_6VsqPwF3hcZr7AK-58\&quot; target=\&quot;enuX_6VsqPwF3hcZr7AK-23\&quot; edge=\&quot;1\&quot;&gt;\n          &lt;mxGeometry relative=\&quot;1\&quot; as=\&quot;geometry\&quot;&gt;\n            &lt;mxPoint x=\&quot;570\&quot; y=\&quot;58\&quot; as=\&quot;targetPoint\&quot; /&gt;\n          &lt;/mxGeometry&gt;\n        &lt;/mxCell&gt;\n      &lt;/root&gt;\n    &lt;/mxGraphModel&gt;\n  &lt;/diagram&gt;\n&lt;/mxfile&gt;\n&quot;}"></div>
+<script type="text/javascript" src="https://viewer.diagrams.net/js/viewer-static.min.js"></script>
+
+Attributes have a gray, the user-supplied input an orange backdrop.
+
+
+A KIMMDY run is orchestrated from a central class called [`RunManager`](/_reference/runmanager.html).
+After the user input from the command line interface is handled in the [`cmd`](/_reference/cmd.html) module, a
+[`RunManager`](/_reference/runmanager.html) is instantiated with a [`config`](/_reference/config.html)
+built from the input yaml file. During the
+initialization, the [`topology`](/_reference/topology.topology.html#kimmdy.topology.topology.Topology)
+is loaded, and the plugins for reactions and
+parametrizing are instantiated. The run then starts with a call to [`RunManager`](/_reference/runmanager.html).`run`.
+This triggers building of the initial task queue, which then gets processed.
+In addition to this main task queue, there is also a priority queue available, for tasks to
+submit other tasks to. These get executed as soon as the current task has finished,
+but before any eventual other tasks in the main queue.
+During the task queue building process, reactions are expanded into three tasks.
+The first one calls the plugin itself to obtain reaction recipes. Then, one recipe must
+be chosen from all possible ones in a kMC step. Finally, the recipe must be applied
+at the correct time of the last simulation.
+
diff --git a/guide/explanation/kimmdy_flow.pdf b/guide/explanation/kimmdy_flow.pdf
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diff --git a/guide/how-to/analysis_figures/hat_ch_pep_occ.png b/guide/how-to/analysis_figures/hat_ch_pep_occ.png
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diff --git a/guide/how-to/analysis_figures/hat_radical_population_fingerprint.png b/guide/how-to/analysis_figures/hat_radical_population_fingerprint.png
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diff --git a/guide/how-to/analyze.qmd b/guide/how-to/analyze.qmd
new file mode 100644
index 00000000..cac051b8
--- /dev/null
+++ b/guide/how-to/analyze.qmd
@@ -0,0 +1,85 @@
+---
+title: Analyze a KIMMDY run
+author: Kai Riedmiller
+lightbox: true
+---
+
+Through [`kimmdy-analysis`](/guide/references/cmd_ref.html#analysis), several tools are provided to analyze various aspects of
+KIMMDY runs.
+
+
+## Energy
+
+`kimmdy-analysis energy` sets the usual energy analysis by gmx energy into
+the context of KIMMDY, by showing the KIMMDY MD steps next to the energy
+plot. An example KIMMDY run of three HAT reactions is shown below.
+
+All energy terms
+supported in the GROMACS tool `gmx energy` can be plotted. The lowest plot shows
+which KIMMDY MD run is running at a given time. Here, three HAT reactions are
+performed, each in between two equilibrium MD simulations.
+
+![](/guide/how-to/analysis_figures/ala_3hat_energy.png){.lightbox width=60%}
+
+
+## Radical Occupancy
+
+`kimmdy-analysis radical_population` analyzes where, and for how long radi-
+cals are in the system. The resulting statistic can be visualized in two ways. First,
+as values on a three-dimensional snapshot of the system, as shown in below.
+For this, a pdb file of the structure is generated, containing the calculated radical
+occupancy as its beta value for visualization with established software, like vmd. And
+second, as a bar plot of the fractional radical occupancy per atom.
+Depending on the number of involved atoms, the structure, or the bar plot might
+be more useful.
+
+:::{layout-ncol=2}
+
+![](/guide/how-to/analysis_figures/hat_ch_pep_occ.png)
+
+![](/guide/how-to/analysis_figures/hat_radical_population_fingerprint.png)
+
+:::
+
+## Radical Migrations
+
+The `kimmdy-analysis radical_migration` tool can generate visualizations.
+Depicting between which atoms HAT reactions occur. The arrows
+can be colored according to the number of HAT reactions, or the maximum rate for
+the respective transition.
+
+![](/guide/how-to/analysis_figures/hat_ch_pep_arr.png){width=60%}
+
+## Reaction Rates
+
+`kimmdy-analysis rates` can generate plots of all available rates entering a kMC step.
+By default, KIMMDY generates in the kMC step of every reaction a plot, showing
+calculated rates over the course of the latest simulation. This can be turned off in the input yaml.
+If in the kMC step a reaction is chosen, the corresponding rates
+are highlighted bold and dashed. Each reaction recipe has a string representation,
+consisting of the involved atom numbers and symbols for the actions. Bonds breaking
+are depicted as bolt. A new bond, and a movement are both represented with an arrow.
+
+![](/guide/how-to/analysis_figures/reaction_rates.svg){.lightbox width=60%}
+
+
+## Runtimes
+
+`kimmdy-analysis runtime` analyzes the runtime of kimmdy. Besides showing
+the runtime of all tasks performed it can group tasks, and types of tasks together.
+The example analyzes the runtime of KIMMDY performing
+20 consecutive HAT reactions after an initial homolysis reaction.
+As the simulated system is
+quite small (the charged_peptide example is used), the MD simulations are comparatively fast.
+For bigger systems, the MD runtime will increase, while the time required for HAT
+reaction barrier predictions will not, as it only atoms close to a radical are taken into
+account. Therefore, the computational overhead of KIMMDY should be negligible
+in most use cases.
+
+:::{layout-ncol=2}
+
+![](/guide/how-to/analysis_figures/runtime_per_stage.svg){.lightbox}
+
+![](/guide/how-to/analysis_figures/runtime_per_task.svg){.lightbox}
+
+:::
\ No newline at end of file
diff --git a/objects.json b/objects.json
index 0bb36fe1..228b5f31 100644
--- a/objects.json
+++ b/objects.json
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