docs: how_to page for analysis (#424)

* docs: how_to page for analysis

* chore(docs): render docs

---------

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

Author: KRiedmiller

_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_ |

docs/_reference/analysis.html

@@ -199,6 +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>
@@ -240,6 +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>
@@ -475,19 +487,19 @@ <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>
@@ -540,21 +552,21 @@ <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 +754,12 @@ <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 +796,8 @@ <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 +852,38 @@ <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">

docs/_reference/cmd.html

@@ -199,6 +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>
@@ -240,6 +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>

docs/_reference/config.html

@@ -199,6 +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>
@@ -240,6 +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>

docs/_reference/constants.html

@@ -199,6 +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>
@@ -240,6 +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>

docs/_reference/coordinates.html

@@ -199,6 +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>
@@ -240,6 +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>

docs/_reference/dummyreaction.reaction.DummyReaction.html

@@ -199,6 +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>
@@ -240,6 +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>

docs/_reference/hat_naive.reaction.NaiveHAT.html

@@ -199,6 +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>
@@ -240,6 +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>